Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold41
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2798036
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 10448 characters in sequence are not A, C, G, or T
File 12 of 21
Found at i:1225294 original size:15 final size:15
Alignment explanation
Indices: 1225274--1225341 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 15
1225264 CTGAATTTAT
1225274 TTTAAATTTAAATTA
1 TTTAAATTTAAATTA
*
1225289 TTTAAA-TAATAATT-
1 TTTAAATTTA-AATTA
*
1225303 TTT-AATTTAAAATA
1 TTTAAATTTAAATTA
* *
1225317 TTTAAAATATAAATAA
1 TTT-AAATTTAAATTA
*
1225333 TTTTAATTT
1 TTTAAATTT
1225342 TTTATTAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
13 5 0.12
14 10 0.25
15 14 0.35
16 11 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTAAATTTAAATTA
Found at i:1225631 original size:17 final size:18
Alignment explanation
Indices: 1225609--1225650 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1225599 AAATTAAAAG
*
1225609 TTTATTATGTATTTA-TT
1 TTTATTATGTAATTATTT
*
1225626 TTTATT-TTTAATTATTT
1 TTTATTATGTAATTATTT
1225643 TTTATTAT
1 TTTATTAT
1225651 ATTTAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 6 0.29
17 14 0.67
18 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTATTATGTAATTATTT
Found at i:1225650 original size:20 final size:20
Alignment explanation
Indices: 1225618--1225656 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1225608 GTTTATTATG
*
1225618 TATTTATTTTTATTTTTAAT
1 TATTTATTTTTATATTTAAT
1225638 TATTT-TTTATTATATTTAA
1 TATTTATTT-TTATATTTAA
1225657 AAGGGCATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATATTTAAT
Found at i:1226029 original size:31 final size:31
Alignment explanation
Indices: 1225968--1226032 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
1225958 TTTCTCACCT
* * *
1225968 TTAATTTTGGTTGAAACTTTAAATTAATATA
1 TTAATATTGGTTGAAAATTTAAAATAATATA
1225999 TTAATATT-GTTGAAAATTTAAAAT-ATATA
1 TTAATATTGGTTGAAAATTTAAAATAATATA
1226028 -TAATA
1 TTAATA
1226033 AATATATGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 5 0.16
29 5 0.16
30 14 0.45
31 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.46
Consensus pattern (31 bp):
TTAATATTGGTTGAAAATTTAAAATAATATA
Found at i:1230747 original size:21 final size:21
Alignment explanation
Indices: 1230723--1230769 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1230713 TATTAAAAGT
* *
1230723 TACATTTTTTTATCCAAAAAA
1 TACATTGTTTCATCCAAAAAA
* *
1230744 TACATTGTTTCATTCAACAAA
1 TACATTGTTTCATCCAAAAAA
1230765 TACAT
1 TACAT
1230770 CACTTCATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (21 bp):
TACATTGTTTCATCCAAAAAA
Found at i:1231500 original size:53 final size:53
Alignment explanation
Indices: 1231420--1231580 Score: 304
Period size: 53 Copynumber: 3.0 Consensus size: 53
1231410 GCAGCGATAT
* *
1231420 CTTTTATCATATCCCTTGATAGACCTTTTGTAAATAAGTCTGCTAAATTGTTA
1 CTTTTATCATATCCCTTGATAGACCTTTTGTCAATAGGTCTGCTAAATTGTTA
1231473 CTTTTATCATATCCCTTGATAGACCTTTTGTCAATAGGTCTGCTAAATTGTTA
1 CTTTTATCATATCCCTTGATAGACCTTTTGTCAATAGGTCTGCTAAATTGTTA
1231526 CTTTTATCATATCCCTTGATAGACCTTTTGTCAATAGGTCTGCTAAATTGTTA
1 CTTTTATCATATCCCTTGATAGACCTTTTGTCAATAGGTCTGCTAAATTGTTA
1231579 CT
1 CT
1231581 GGACTTAACA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 106 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.43
Consensus pattern (53 bp):
CTTTTATCATATCCCTTGATAGACCTTTTGTCAATAGGTCTGCTAAATTGTTA
Found at i:1234548 original size:2 final size:2
Alignment explanation
Indices: 1234541--1234575 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1234531 TCTTTTGTCT
1234541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1234576 GACTCATGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1234897 original size:27 final size:28
Alignment explanation
Indices: 1234867--1234955 Score: 74
Period size: 27 Copynumber: 3.2 Consensus size: 28
1234857 AAATATATGT
* *
1234867 AATATTTTAAATTTAATAT-GATATAAA
1 AATATTTTAAATATAATATAAATATAAA
* * *
1234894 AATAATATAAATATAATATAAATATATA
1 AATATTTTAAATATAATATAAATATAAA
* * *
1234922 AAT-TTTTATATAATAATTTTATATATAAA
1 AATATTTTAAAT-ATAA-TATAAATATAAA
1234951 AATAT
1 AATAT
1234956 AAAACCAATT
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
27 21 0.45
28 13 0.28
29 12 0.26
30 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
AATATTTTAAATATAATATAAATATAAA
Found at i:1234916 original size:11 final size:11
Alignment explanation
Indices: 1234881--1234919 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
1234871 TTTTAAATTT
*
1234881 AATATGATATA
1 AATATAATATA
*
1234892 AAAATAATATA
1 AATATAATATA
1234903 AATATAATATA
1 AATATAATATA
1234914 AATATA
1 AATATA
1234920 TAAATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
AATATAATATA
Found at i:1240949 original size:6 final size:6
Alignment explanation
Indices: 1240938--1240962 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1240928 TCAAATTTTA
1240938 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
1240963 GATACTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:1245739 original size:2 final size:2
Alignment explanation
Indices: 1245732--1245760 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1245722 TACGCATACT
1245732 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1245761 TTATTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1248670 original size:19 final size:21
Alignment explanation
Indices: 1248648--1248687 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1248638 AATAAATATG
*
1248648 TTTA-ATATTTTAAA-ATTTT
1 TTTATATATTTGAAAGATTTT
1248667 TTTATATATTTGAAAGATTTT
1 TTTATATATTTGAAAGATTTT
1248688 AAAAAAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTATATATTTGAAAGATTTT
Found at i:1249078 original size:44 final size:45
Alignment explanation
Indices: 1249023--1249131 Score: 118
Period size: 44 Copynumber: 2.4 Consensus size: 45
1249013 AATTGATTTA
*
1249023 ATTAAAAATTAAAAATTAAATATATGATTATAA-TAT-TAA-ATAT
1 ATTAAAAATTAAAAATTAAATATATGATT-TAATTATATAATATAA
* ** *
1249066 ATTAAATGATTAATAAA-TATTTATTTGATTTAATTATATAATATAA
1 ATTAAA-AATTAA-AAATTAAATATATGATTTAATTATATAATATAA
1249112 ATTAAAAATTAAAAATTAAA
1 ATTAAAAATTAAAAATTAAA
1249132 AATTTATTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
43 9 0.17
44 21 0.40
45 13 0.25
46 9 0.17
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (45 bp):
ATTAAAAATTAAAAATTAAATATATGATTTAATTATATAATATAA
Found at i:1249132 original size:6 final size:7
Alignment explanation
Indices: 1249110--1249135 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1249100 TATATAATAT
1249110 AAATTAA
1 AAATTAA
1249117 AAATTAA
1 AAATTAA
1249124 AAATTAA
1 AAATTAA
1249131 AAATT
1 AAATT
1249136 TATTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AAATTAA
Found at i:1249171 original size:14 final size:15
Alignment explanation
Indices: 1249108--1249147 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
1249098 ATTATATAAT
1249108 ATAAATTAAAAATTA
1 ATAAATTAAAAATTA
*
1249123 A-AAATTAAAAATTT
1 ATAAATTAAAAATTA
*
1249137 ATTAATTAAAA
1 ATAAATTAAAA
1249148 CAATTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAAATTAAAAATTA
Found at i:1252427 original size:12 final size:12
Alignment explanation
Indices: 1252407--1252440 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1252397 GATCGTATTG
*
1252407 AATCATAAAATT
1 AATCCTAAAATT
1252419 AATCCTAAAATT
1 AATCCTAAAATT
*
1252431 GATCCTAAAA
1 AATCCTAAAA
1252441 AATTATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (12 bp):
AATCCTAAAATT
Found at i:1253893 original size:28 final size:28
Alignment explanation
Indices: 1253857--1253925 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
1253847 TCATGAGTTT
1253857 ATTATTTTTTATATAATACTATATTTTA
1 ATTATTTTTTATATAATACTATATTTTA
** ** *
1253885 ATTATTTTTTATATCTTGTTTTATTTTA
1 ATTATTTTTTATATAATACTATATTTTA
1253913 ATTA-TTTTTATAT
1 ATTATTTTTTATAT
1253926 TATATTCATA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 9 0.25
28 27 0.75
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (28 bp):
ATTATTTTTTATATAATACTATATTTTA
Found at i:1254308 original size:20 final size:20
Alignment explanation
Indices: 1254265--1254326 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 20
1254255 GTTTATCATA
* *
1254265 ATAATTTA-ATTTTAATTTT
1 ATAATTTATATTTTTATATT
1254284 A-AATTTATATTTTTATATT
1 ATAATTTATATTTTTATATT
*
1254303 ATAA-TTATATTTAATATATT
1 ATAATTTATATTT-TTATATT
1254323 ATAA
1 ATAA
1254327 ATAATAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.16
19 19 0.51
20 12 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATAATTTATATTTTTATATT
Found at i:1254334 original size:17 final size:17
Alignment explanation
Indices: 1254314--1254375 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
1254304 TAATTATATT
*
1254314 TAATATATTATAAATAA
1 TAATAAATTATAAATAA
1254331 TAATAAAATTA-AAATAA
1 TAAT-AAATTATAAATAA
* *
1254348 TATAAAAATT-TAAATAC
1 TA-ATAAATTATAAATAA
1254365 TAATATAATTA
1 TAATA-AATTA
1254376 AAAAATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
16 2 0.06
17 28 0.78
18 6 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
TAATAAATTATAAATAA
Found at i:1254369 original size:34 final size:32
Alignment explanation
Indices: 1254324--1254392 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 32
1254314 TAATATATTA
1254324 TAAATAATAATAAAATTAAAATAATATAAAAATT
1 TAAATAATAATAAAATTAAAA-AAT-TAAAAATT
* * *
1254358 TAAATACTAATATAATTAAAAAATTTAAAATT
1 TAAATAATAATAAAATTAAAAAATTAAAAATT
1254390 TAA
1 TAA
1254393 CAATTGATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 10 0.31
33 3 0.09
34 19 0.59
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (32 bp):
TAAATAATAATAAAATTAAAAAATTAAAAATT
Found at i:1254738 original size:15 final size:15
Alignment explanation
Indices: 1254718--1254751 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1254708 ATTTGTAATT
1254718 TTTAAA-TTATTTAAA
1 TTTAAATTTATTT-AA
1254733 TTTAAATTTATTTAA
1 TTTAAATTTATTTAA
1254748 TTTA
1 TTTA
1254752 TATAATACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAAATTTATTTAA
Found at i:1259713 original size:22 final size:23
Alignment explanation
Indices: 1259686--1259737 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
1259676 TTAAAATAAT
1259686 ATATTTTTAAAA-ATAGATTTTAA
1 ATATTTTTAAAATATA-ATTTTAA
1259709 A-ATTTTTAAAATATAATTTTAA
1 ATATTTTTAAAATATAATTTTAA
1259731 ATATTTT
1 ATATTTT
1259738 ATTATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATTTTTAAAATATAATTTTAA
Found at i:1260111 original size:13 final size:12
Alignment explanation
Indices: 1260092--1260126 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1260082 TTTATTTTCC
1260092 AAATATATTTTT
1 AAATATATTTTT
*
1260104 AAATTATAATTTT
1 AAA-TATATTTTT
1260117 AAATATATTT
1 AAATATATTT
1260127 ATTTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AAATATATTTTT
Found at i:1260134 original size:16 final size:16
Alignment explanation
Indices: 1260097--1260146 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1260087 TTTCCAAATA
1260097 TATTTTTAAAT-TA--
1 TATTTTTAAATATATT
*
1260110 TAATTTTAAATATATT
1 TATTTTTAAATATATT
1260126 TATTTTTAAA-ATAATT
1 TATTTTTAAATAT-ATT
1260142 TATTT
1 TATTT
1260147 ATTTGTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 10 0.32
14 2 0.06
15 2 0.06
16 17 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTTAAATATATT
Found at i:1260138 original size:42 final size:42
Alignment explanation
Indices: 1260056--1260142 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
1260046 AAATATTAAT
* * *
1260056 TTTTTAGATATATAATTTTAAAATTTTTTATTTTCCAAATATA
1 TTTTTAAATATATAATTTTAAAATTATTTATTTTCAAAATA-A
*
1260099 TTTTTAAAT-TATAATTTT-AAATATATTTATTTTTAAAATAA
1 TTTTTAAATATATAATTTTAAAAT-TATTTATTTTCAAAATAA
1260140 TTT
1 TTT
1260143 ATTTATTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 8 0.21
42 23 0.59
43 8 0.21
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (42 bp):
TTTTTAAATATATAATTTTAAAATTATTTATTTTCAAAATAA
Found at i:1260172 original size:23 final size:23
Alignment explanation
Indices: 1260129--1260172 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1260119 ATATATTTAT
* **
1260129 TTTTAAAATAATTTATTTATTTG
1 TTTTAAAAAAATTTAAATATTTG
1260152 TTTTAAAAAAATTTAAATATT
1 TTTTAAAAAAATTTAAATATT
1260173 AATTTATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTTAAAAAAATTTAAATATTTG
Found at i:1260183 original size:23 final size:21
Alignment explanation
Indices: 1260153--1260195 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1260143 ATTTATTTGT
1260153 TTTAAAAAAATTTAAATATTAA
1 TTTAAAAAAA-TTAAATATTAA
*
1260175 TTTATAAAAAATTAAGTATTA
1 TTTA-AAAAAATTAAATATTA
1260196 CGTGCATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTAAAAAAATTAAATATTAA
Found at i:1262410 original size:24 final size:24
Alignment explanation
Indices: 1262374--1262419 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1262364 TAGGTTATTT
1262374 TTGTTTGTAAAAAATGGTGGCTTG
1 TTGTTTGTAAAAAATGGTGGCTTG
* *
1262398 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTAAAAAATGGTGGCT
1262420 AATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.43
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGGTGGCTTG
Found at i:1263292 original size:20 final size:21
Alignment explanation
Indices: 1263269--1263325 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
1263259 ACAATTCAAA
**
1263269 GTATCGATACATGTTGCA-AT
1 GTATCGATACATGTTAAAGAT
**
1263289 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTAAAGAT
1263310 GTATCGATACATGTTA
1 GTATCGATACATGTTA
1263326 TTGGGATTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (21 bp):
GTATCGATACATGTTAAAGAT
Found at i:1263389 original size:13 final size:13
Alignment explanation
Indices: 1263371--1263396 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1263361 TACACCAAGT
1263371 ATGTATCGATACA
1 ATGTATCGATACA
1263384 ATGTATCGATACA
1 ATGTATCGATACA
1263397 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1263393 original size:32 final size:33
Alignment explanation
Indices: 1263352--1263416 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1263342 GTAGCCAAAC
* **
1263352 ATGTATCGATACACCAAGTA-TGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1263384 ATGTATCGATACACAAAAAATTGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1263417 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACACAAAAAATTGTATCGATACA
Found at i:1267481 original size:15 final size:15
Alignment explanation
Indices: 1267461--1267491 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1267451 TAAAAATGTC
*
1267461 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1267476 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1267491 C
1 C
1267492 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1269577 original size:20 final size:21
Alignment explanation
Indices: 1269506--1269583 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
1269496 AATGTCCAAA
*
1269506 ATGTATCGATACA-TGTTTCT
1 ATGTATCGATACATTGATTCT
* *
1269526 GTGTATCGATACATCTGGAAATTCA
1 ATGTATCGATACAT-T-G--ATTCT
1269551 ATGTATCGATACATTG-TTCT
1 ATGTATCGATACATTGATTCT
*
1269571 TTGTATCGATACA
1 ATGTATCGATACA
1269584 GGGTGATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 27 0.57
22 1 0.02
23 2 0.04
24 1 0.02
25 16 0.34
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATTGATTCT
Found at i:1270067 original size:21 final size:20
Alignment explanation
Indices: 1270025--1270067 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1270015 GGCAGCACCA
* * *
1270025 CCAGGTCGCGACCGGCACTC
1 CCAGGTCACAACCGGCAATC
1270045 CCAGGTCACAACCGGGCAATC
1 CCAGGTCACAACC-GGCAATC
1270066 CC
1 CC
1270068 CACACTAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.21, C:0.44, G:0.26, T:0.09
Consensus pattern (20 bp):
CCAGGTCACAACCGGCAATC
Found at i:1272156 original size:13 final size:13
Alignment explanation
Indices: 1272138--1272163 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1272128 TACACCAAGT
1272138 ATGTATCGATACA
1 ATGTATCGATACA
1272151 ATGTATCGATACA
1 ATGTATCGATACA
1272164 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1272160 original size:32 final size:33
Alignment explanation
Indices: 1272119--1272183 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1272109 GTAGCCAAAC
* **
1272119 ATGTATCGATACACCAAGTA-TGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1272151 ATGTATCGATACACAAAAAATTGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1272184 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACACAAAAAATTGTATCGATACA
Found at i:1276858 original size:25 final size:24
Alignment explanation
Indices: 1276802--1276887 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 24
1276792 ACCCTTTGTA
1276802 TTTGTCAAATATGGTGGTTTCTTTTG
1 TTTGTCAAATATGGTGG-TT-TTTTG
1276828 TATTTGTCAAATATGGTGGTTATTTTG
1 --TTTGTCAAATATGGTGGTT-TTTTG
* * * * *
1276855 TTTGTAAAAAATGATGGCTTGTTG
1 TTTGTCAAATATGGTGGTTTTTTG
1276879 TTTGTCAAA
1 TTTGTCAAA
1276888 ATTGTTGGCT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
24 12 0.24
25 15 0.29
27 7 0.14
28 17 0.33
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.49
Consensus pattern (24 bp):
TTTGTCAAATATGGTGGTTTTTTG
Found at i:1276882 original size:24 final size:24
Alignment explanation
Indices: 1276852--1276897 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1276842 GGTGGTTATT
1276852 TTGTTTGTAAAAAATGATGGCTTG
1 TTGTTTGTAAAAAATGATGGCTTG
* * *
1276876 TTGTTTGTCAAAATTGTTGGCT
1 TTGTTTGTAAAAAATGATGGCT
1276898 AATTTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.46
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGATGGCTTG
Found at i:1279342 original size:15 final size:14
Alignment explanation
Indices: 1279316--1279368 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 14
1279306 ATAAATTAAA
1279316 AAATAACACAAAAT
1 AAATAACACAAAAT
1279330 AAATAATCACAAAAAAATT
1 AAATAA-CAC---AAAA-T
1279349 AAATAAACACAAAAT
1 AAAT-AACACAAAAT
1279364 AAATA
1 AAATA
1279369 TATAAACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 7 0.21
15 8 0.24
16 4 0.12
18 4 0.12
19 8 0.24
20 2 0.06
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (14 bp):
AAATAACACAAAAT
Found at i:1279353 original size:19 final size:19
Alignment explanation
Indices: 1279325--1279376 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1279315 AAAATAACAC
*
1279325 AAAA-TAAATAATCACAAA
1 AAAATTAAATAAACACAAA
1279343 AAAATTAAATAAACACAAA
1 AAAATTAAATAAACACAAA
*
1279362 ATAAA-TATATAAACA
1 A-AAATTAAATAAACA
1279377 TATCAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 4 0.13
19 23 0.77
20 3 0.10
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAATTAAATAAACACAAA
Found at i:1280645 original size:114 final size:113
Alignment explanation
Indices: 1280384--1280725 Score: 339
Period size: 114 Copynumber: 3.0 Consensus size: 113
1280374 ATAAAGTCAT
** * * *
1280384 AAATTATTTAATTTAAAATCAAGTCTTATAAAAAAATATATATTAAAAAAATAAGTCTAACATAC
1 AAATTATTTAATTCGAGATCAAAT-TTAT-AAAAAATATATATTAAAAAAATAAGTCTAACGTAC
* * * * * * *
1280449 TTATTTAACTAATATATTT-GTGTCTATTCTATTTAATTTTACTT-GATCAT
64 TTATTTAACTAATTTATTTAAT-TTTATTTTATTTAATTATA-TTAGATAAA
* *
1280499 AAATTATTTAATTTGAGATCAAATTTAGTAAAAAATATATATTAAAAAAATACGTCTAACGTACT
1 AAATTATTTAATTCGAGATCAAATTTA-TAAAAAATATATATTAAAAAAATAAGTCTAACGTACT
*
1280564 TATTTAACTAATTTATTTACTTTTATTTTATTTAATTATATTAGATAAA
65 TATTTAACTAATTTATTTAATTTTATTTTATTTAATTATATTAGATAAA
* ** * * ** *
1280613 AAATTATTTAATTCGAGATTGAGCTTTATAAAAAATATACATTAGACAAAATAAAACTTAA-GTG
1 AAATTATTTAATTCGAGA-TCAAATTTATAAAAAATATATATTA-AAAAAATAAGTC-TAACGTA
* * *
1280677 CATATTTAATTAATTTATTTAAAATTTATTTTATTTAATTATGATTAGA
63 CTTATTTAACTAATTTATTT-AATTTTATTTTATTTAATTAT-ATTAGA
1280726 CTAATATTTT
Statistics
Matches: 193, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
113 2 0.01
114 106 0.55
115 57 0.30
116 22 0.11
117 6 0.03
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.44
Consensus pattern (113 bp):
AAATTATTTAATTCGAGATCAAATTTATAAAAAATATATATTAAAAAAATAAGTCTAACGTACTT
ATTTAACTAATTTATTTAATTTTATTTTATTTAATTATATTAGATAAA
Found at i:1296011 original size:14 final size:14
Alignment explanation
Indices: 1295992--1296022 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1295982 AAACAGCCAT
1295992 TAAGGGTAATGTAA
1 TAAGGGTAATGTAA
1296006 TAAGGGTAATGTAA
1 TAAGGGTAATGTAA
1296020 TAA
1 TAA
1296023 CCATCTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (14 bp):
TAAGGGTAATGTAA
Found at i:1297019 original size:10 final size:10
Alignment explanation
Indices: 1297006--1297038 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1296996 TTGAATAGGG
*
1297006 CATTATAGAT
1 CATTATGGAT
1297016 CATTATGGAT
1 CATTATGGAT
1297026 CATTATGGAT
1 CATTATGGAT
1297036 CAT
1 CAT
1297039 GCCCGAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (10 bp):
CATTATGGAT
Found at i:1299032 original size:46 final size:47
Alignment explanation
Indices: 1298950--1299041 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 47
1298940 TTAACAATAT
*
1298950 TCTAGGTACAGACTCTTGAACCCAAAAGTCCAAAACTCAAAAAGAAC
1 TCTAGGTACAAACTCTTGAACCCAAAAGTCCAAAACTCAAAAAGAAC
* * *
1298997 TCTAGGTACAAACT-TTTAACTCAAAAGTCTC-AAACTTAAAAAGAA
1 TCTAGGTACAAACTCTTGAACCCAAAAGTC-CAAAACTCAAAAAGAA
1299042 TGTCAAGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 26 0.65
47 14 0.35
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (47 bp):
TCTAGGTACAAACTCTTGAACCCAAAAGTCCAAAACTCAAAAAGAAC
Found at i:1303465 original size:12 final size:12
Alignment explanation
Indices: 1303448--1303472 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1303438 TTGTTATATA
1303448 AAATAATTTATT
1 AAATAATTTATT
1303460 AAATAATTTATT
1 AAATAATTTATT
1303472 A
1 A
1303473 TAAAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATTTATT
Found at i:1319249 original size:14 final size:16
Alignment explanation
Indices: 1319218--1319264 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1319208 AAAAAAAGTC
1319218 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAGCA-AA
1319234 AAAATG-AAAAG-AAA
1 AAAATGCAAAAGCAAA
*
1319248 AAAGTGCAAAAGCAAA
1 AAAATGCAAAAGCAAA
1319264 A
1 A
1319265 TAAAAAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 13 0.48
17 1 0.04
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAATGCAAAAGCAAA
Found at i:1319286 original size:37 final size:36
Alignment explanation
Indices: 1319209--1319286 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 36
1319199 CAAAATGACA
* *
1319209 AAAAAAGTCAAAAGCAAAAGCACAAAAAATGAAAAG
1 AAAAAAGTCAAAAGCAAAAGCACAAAAAAGGAAAAC
*
1319245 AAAAAAGTGCAAAAGCAAAA-TA-AAAAAAGGGAACAAC
1 AAAAAAGT-CAAAAGCAAAAGCACAAAAAA-GGAA-AAC
1319282 AAAAA
1 AAAAA
1319287 TAAAAAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 6 0.17
36 12 0.33
37 18 0.50
ACGTcount: A:0.71, C:0.10, G:0.14, T:0.05
Consensus pattern (36 bp):
AAAAAAGTCAAAAGCAAAAGCACAAAAAAGGAAAAC
Found at i:1323290 original size:52 final size:52
Alignment explanation
Indices: 1323220--1323340 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
1323210 GAAAATTTAT
*
1323220 CTGCATGTATCAATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCAATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1323272 CTGCATGTATCAATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCAATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1323324 CTGCATGTATCGATACA
1 CTGCATGTATCAATACA
1323341 AAGATCAATG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCAATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1323351 original size:52 final size:52
Alignment explanation
Indices: 1323220--1323360 Score: 196
Period size: 52 Copynumber: 2.7 Consensus size: 52
1323210 GAAAATTTAT
* *
1323220 CTGCATGTATCAATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCAATACA-TAAGATAATGTATCGATACATCTGGGCAAATTTGC
***
1323272 CTGCATGTATCAATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCAATACATAAGATAATGTATCGATACATCTGGGCAAATTTGC
*
1323324 CTGCATGTATCGATACA-AAGATCAATGTATCGATACA
1 CTGCATGTATCAATACATAAGAT-AATGTATCGATACA
1323361 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 4 0.05
52 77 0.95
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCAATACATAAGATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1323364 original size:13 final size:13
Alignment explanation
Indices: 1323346--1323373 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1323336 ATACAAAGAT
1323346 CAATGTATCGATA
1 CAATGTATCGATA
1323359 CAATGTATCGATA
1 CAATGTATCGATA
1323372 CA
1 CA
1323374 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1323441 original size:20 final size:20
Alignment explanation
Indices: 1323416--1323469 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1323406 TAGCTTAAAT
1323416 TGTATCGATACAAAAAACTA
1 TGTATCGATACAAAAAACTA
* ***
1323436 TGTATCGATACAACATTTTA
1 TGTATCGATACAAAAAACTA
1323456 TGTATCGATACAAA
1 TGTATCGATACAAA
1323470 TCGTTGAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (20 bp):
TGTATCGATACAAAAAACTA
Found at i:1324277 original size:82 final size:82
Alignment explanation
Indices: 1324135--1325193 Score: 1540
Period size: 82 Copynumber: 12.8 Consensus size: 82
1324125 AGTACTGTGA
* * * *
1324135 CCTTTTAAAGTCCACAACTCCGTGGTATCCTTTTAAAGTCCACAACTCCATGGTACCCTTTTAAA
1 CCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AA
*
1324200 GTCCACAACTCCATGGCA-C
63 GTCCACAACTCCGTGGCATC
* * *
1324219 CCTTTAAAATCCACAACTCCGTGGCACCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGT
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
1324284 CCACAACTCCGTGGCA-C
65 CCACAACTCCGTGGCATC
* * *
1324301 CCTTTTAAAGTCCATAACTTCATGGCACCCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTTAA
1 CCTTTT-AAGTCCACAACTCCGTGGCACCC-TTTTAAGTCCACAACTCCGTGGCACCC-TTTTAA
1324366 GTCCACAACTCCGTGGCA-C
63 GTCCACAACTCCGTGGCATC
* * *
1324385 CCTTTTAAGGTCCATAACTCCATGGCACCCTTTTAAGTCCATAACTCCGTGGCACCCTTTTAAGT
1 CCTTTTAA-GTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
*
1324450 CCACAACTACGT-GCA-C
65 CCACAACTCCGTGGCATC
*
1324466 CCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
**
1324531 CACAACTTGGTGGCATC
66 CACAACTCCGTGGCATC
*
1324548 CCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1324613 CACAACTCCGTGGCATC
66 CACAACTCCGTGGCATC
* * * *
1324630 CCTTTTAAGTTCACGACTCCGCGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAATC
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1324695 CACAACTCCGTGGCATC
66 CACAACTCCGTGGCATC
* *
1324712 CCTTTTAAGTCCGCAACTCCGTGGCACCCTTTTAAGTCCGCAACTCCGTGGCACCCTTTTAAGTC
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* *
1324777 CATAACTCTGTGGCATC
66 CACAACTCCGTGGCATC
* * * *
1324794 TCTTTTAAGTCCATAACTTTC-TGGCACCCTTTTAAAGTCCACAACTTCGTGGCACCCTTTTAAA
1 CCTTTTAAGTCCACAAC-TCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AA
*
1324858 GTCCACAACTTCGTGGCA-C
63 GTCCACAACTCCGTGGCATC
*
1324877 CCTTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
1 CC-TTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AA
1324942 GTCCACAACTCCGTGGCA-C
63 GTCCACAACTCCGTGGCATC
* *
1324961 CCTTTTAAGTCTACAAGTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
1325026 CACAACTTCGTGGCATC
66 CACAACTCCGTGGCATC
1325043 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
1325108 CATAACTCCGTGGCATC
66 CACAACTCCGTGGCATC
* * * * *
1325125 TCTTTTAAAGTCCATAACTCTGTGGCACCCTTTTAAGTTCACAACTTCGTGGCACCCTTTTTAAG
1 CCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCC-TTTTAAG
1325190 TCCA
64 TCCA
1325194 TAAGATGGTG
Statistics
Matches: 897, Mismatches: 64, Indels: 28
0.91 0.06 0.03
Matches are distributed among these distances:
80 62 0.07
81 34 0.04
82 439 0.49
83 175 0.20
84 183 0.20
85 4 0.00
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (82 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
CACAACTCCGTGGCATC
Found at i:1325206 original size:28 final size:27
Alignment explanation
Indices: 1324135--1325193 Score: 1528
Period size: 27 Copynumber: 38.5 Consensus size: 27
1324125 AGTACTGTGA
* *
1324135 CCTTTTAAAGTCCACAACTCCGTGGTAT
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* *
1324163 CCTTTTAAAGTCCACAACTCCATGGTAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
*
1324191 CCTTTTAAAGTCCACAACTCCATGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* *
1324219 CCTTTAAAATCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1324246 CTTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1324273 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* * *
1324301 CCTTTTAAAGTCCATAACTTCATGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
1324329 CCTTTTTAAGTCCACAACTCCGTGGCAC
1 CC-TTTTAAGTCCACAACTCCGTGGCAC
1324357 CCTTTTTAAGTCCACAACTCCGTGGCAC
1 CC-TTTTAAGTCCACAACTCCGTGGCAC
* *
1324385 CCTTTTAAGGTCCATAACTCCATGGCAC
1 CCTTTTAA-GTCCACAACTCCGTGGCAC
*
1324413 CCTTTTAAGTCCATAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1324440 CCTTTTAAGTCCACAACTACGT-GCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1324466 CCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1324493 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
**
1324520 CCTTTTAAGTCCACAACTTGGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
*
1324548 CCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1324575 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1324602 CCTTTTAAGTCCACAACTCCGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
* * *
1324630 CCTTTTAAGTTCACGACTCCGCGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1324657 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1324684 CCTTTTAAATCCACAACTCCGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
*
1324712 CCTTTTAAGTCCGCAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1324739 CCTTTTAAGTCCGCAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* *
1324766 CCTTTTAAGTCCATAACTCTGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
* * *
1324794 TCTTTTAAGTCCATAACTTTC-TGGCAC
1 CCTTTTAAGTCCACAAC-TCCGTGGCAC
*
1324821 CCTTTTAAAGTCCACAACTTCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
*
1324849 CCTTTTAAAGTCCACAACTTCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
*
1324877 CCTTTTTAAGTCCACAACTTCGTGGCAC
1 CC-TTTTAAGTCCACAACTCCGTGGCAC
1324905 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
1324933 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* *
1324961 CCTTTTAAGTCTACAAGTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1324988 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1325015 CCTTTTAAGTCCACAACTTCGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
1325043 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1325070 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1325097 CCTTTTAAGTCCATAACTCCGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
* * *
1325125 TCTTTTAAAGTCCATAACTCTGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* *
1325153 CCTTTTAAGTTCACAACTTCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1325180 CCTTTTTAAGTCCA
1 CC-TTTTAAGTCCA
1325194 TAAGATGGTG
Statistics
Matches: 952, Mismatches: 62, Indels: 34
0.91 0.06 0.03
Matches are distributed among these distances:
26 24 0.03
27 454 0.48
28 446 0.47
29 28 0.03
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:1325241 original size:58 final size:58
Alignment explanation
Indices: 1325164--1325485 Score: 225
Period size: 58 Copynumber: 5.6 Consensus size: 58
1325154 CTTTTAAGTT
* * * * * *
1325164 CACAACTTCGTGGCACCCTTTT-TAAGTCCATAAGATGGTGGCATTCCCTTCT-AAAGCC
1 CACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGATAGTGGCA--CCCTTCTCAAAGCC
* *
1325222 CACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCC
1 CACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGATAGTGGCACCCTTCTCAAAGCC
* * * * *
1325280 CACAAGTTAATGGCA-TCTTTTCAAAGCCTACAAG-TCAGTGGCA-TCTTTTCAAAGTCC
1 CACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGAT-AGTGGCACCCTTCTCAAAG-CC
* * * * *
1325337 ACACAAGTTGGTGGCATCC-TTTCAAAACCCACAAG-TCAGTGGCATCCTT-TCATAGCC
1 -CACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGAT-AGTGGCACCCTTCTCAAAGCC
* * * * * * *
1325394 CACAAGTCAATGACA-CCATTTCAAAACCCACAAG-TCAGTGACACCATT-TCAAAGCCC
1 CACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGAT-AGTGGCACCCTTCTCAAAG-CC
** *
1325451 ACACAAGTCGGTGGCAACCCATTTCAAAGCCCACA
1 -CACAAGTTAGTGGC-ACCCTTTTCAAAGCCCACA
1325486 CAAGTCGGTA
Statistics
Matches: 221, Mismatches: 31, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
55 2 0.01
56 54 0.24
57 36 0.16
58 92 0.42
59 21 0.10
60 16 0.07
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (58 bp):
CACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGATAGTGGCACCCTTCTCAAAGCC
Found at i:1325312 original size:28 final size:28
Alignment explanation
Indices: 1325216--1325453 Score: 251
Period size: 28 Copynumber: 8.4 Consensus size: 28
1325206 ATTCCCTTCT
*
1325216 AAAGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTTAGTGGCA-TCTTTTC
*
1325245 AAAGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTTAGTGGCA-TCTTTTC
*
1325274 AAAGCCCACAAGTTAATGGCATCTTTTC
1 AAAGCCCACAAGTTAGTGGCATCTTTTC
* *
1325302 AAAGCCTACAAGTCAGTGGCATCTTTTC
1 AAAGCCCACAAGTTAGTGGCATCTTTTC
* *
1325330 AAAGTCCACACAAGTTGGTGGCATCCTTTC
1 AAAG-CC-CACAAGTTAGTGGCATCTTTTC
* * *
1325360 AAAACCCACAAGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTTAGTGGCATCTTTTC
* * * * * *
1325388 ATAGCCCACAAGTCAATGACACCATTTC
1 AAAGCCCACAAGTTAGTGGCATCTTTTC
* * * * *
1325416 AAAACCCACAAGTCAGTGACACCATTTC
1 AAAGCCCACAAGTTAGTGGCATCTTTTC
1325444 AAAGCCCACA
1 AAAGCCCACA
1325454 CAAGTCGGTG
Statistics
Matches: 185, Mismatches: 22, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
28 111 0.60
29 53 0.29
30 21 0.11
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (28 bp):
AAAGCCCACAAGTTAGTGGCATCTTTTC
Found at i:1325476 original size:32 final size:32
Alignment explanation
Indices: 1325326--1325736 Score: 377
Period size: 32 Copynumber: 13.2 Consensus size: 32
1325316 AGTGGCATCT
* * *
1325326 TTTCAAAGTCCACACAAGTTGGTGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
1325356 TTTCAAA-ACC-CACAAGTCAGTGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* ** *
1325384 TTTCATAG-CC-CACAAGTCAATGAC-A-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
1325412 TTTCAAA-ACC-CACAAGTCAGTGAC-A-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1325440 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1325472 TTTCAAAGCCCACACAAGTCGGTAGCAACCCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAA-CCCA
* * *
1325505 TTTCAAAGCCTACACAAGTCGATGGCAACCTA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1325537 TTTCAAAGCCCACACAAGTCGGTGGCAATCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1325569 TTTCAAAGCCCACACAAGTCGGTGGCAATCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1325601 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
1325633 TTTCAAAGCCCACACAAGTTGATGGGAACCTC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACC-CA
* ** *
1325665 TTTCAAAAGTCCACAC-TTTCGGTGGCAACCCTT
1 TTTC-AAAGCCCACACAAGTCGGTGGCAACCC-A
* * * *
1325698 TTTAAAAGCCCACGCAAGTCAGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1325730 TTTCAAA
1 TTTCAAA
1325737 TCACCATTTT
Statistics
Matches: 328, Mismatches: 40, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
27 2 0.01
28 69 0.21
29 4 0.01
30 19 0.06
31 2 0.01
32 178 0.54
33 54 0.16
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.21
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:1325553 original size:97 final size:97
Alignment explanation
Indices: 1325440--1325736 Score: 397
Period size: 97 Copynumber: 3.1 Consensus size: 97
1325430 AGTGACACCA
*
1325440 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTAGCAACCCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCCT
*
1325505 TTTCAAAGCCTACACAAGTCGATGGCAA-CCT
66 TTTCAAAGCCCACACAAGTCGATGGCAACCCT
* *
1325536 ATTTCAAAGCCCACACAAGTCGGTGGCAATCCATTTCAAAGCCCACACAAGTCGGTGGCAA-TCC
1 -TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCC
*
1325600 TTTTCAAAGCCCACACAAGTCGGTGGCAACCCT
65 TTTTCAAAGCCCACACAAGTCGATGGCAACCCT
* * * * **
1325633 TTTCAAAGCCCACACAAGTTGATGGGAACCTC-TTTCAAAAGTCCACAC-TTTCGGTGGCAACCC
1 TTTCAAAGCCCACACAAGTCGGTGGCAACC-CATTTC-AAAGCCCACACAAGTCGGTGGCAACCC
* * *
1325696 TTTTTAAAAGCCCACGCAAGTC-AGTGGCAACCCT
64 CTTTTCAAAGCCCACACAAGTCGA-TGGCAACCCT
1325730 TTTCAAA
1 TTTCAAA
1325737 TCACCATTTT
Statistics
Matches: 178, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
96 69 0.39
97 109 0.61
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.21
Consensus pattern (97 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCCT
TTTCAAAGCCCACACAAGTCGATGGCAACCCT
Found at i:1325579 original size:129 final size:122
Alignment explanation
Indices: 1325222--1325736 Score: 482
Period size: 129 Copynumber: 4.2 Consensus size: 122
1325212 TTCTAAAGCC
** **
1325222 CACAAGTTAGTGGC-ACCCTTTTCAAAG-CC-CACAAGTTAGTGGC-ACCCTTTTCAAAGCCCAC
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCAC
* * * * *
1325283 AAGTTAATGGCATCT-TTTCAAAGCCTACAAGTCAGTGGCAT-CTTTTCAAAGTCCA
66 AAGTCAATGGCACCTATTTCAAAGCCCACAAGTCAGTGGCATCCATTTCAAAGCCCA
* * * * * *
1325338 CACAAGTTGGTGGC-ATCC-TTTCAAA-ACC-CACAAGTCAGTGGC-ATCC-TTTCATAGCCCAC
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCAC
* * *
1325397 AAGTCAATGACACC-ATTTCAAAACCCACAAGTCAGTGACA-CCATTTCAAAGCCCA
66 AAGTCAATGGCACCTATTTCAAAGCCCACAAGTCAGTGGCATCCATTTCAAAGCCCA
* *
1325452 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTAGCAACCCCTTTTCAAAGCCTA
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAA-CCCTTTTCAAAGCC--
* *
1325517 CACAAGTCGATGGCAACCTATTTCAAAGCCCACACAAGTCGGTGGCAATCCATTTCAAAGCCCA
63 CACAAGTCAATGGC-ACCTATTTCAAAG-CC-CACAAGTCAGTGGC-ATCCATTTCAAAGCCCA
*
1325581 CACAAGTCGGTGGCAATCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCAC
1 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAG-CC-C
** * * * ** * * * *
1325646 ACAAGTTGATGGGAACCTCTTTCAAAAGTCCACACTTTCGGTGGCAACCCTTTTTAAAAGCCCA
64 ACAAGTCAAT-GGCACCTATTTC-AAAGCCCACA-AGTCAGTGGC-ATCC-ATTTCAAAGCCCA
* *
1325710 CGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCTTTTCAAA
1325737 TCACCATTTT
Statistics
Matches: 336, Mismatches: 40, Indels: 33
0.82 0.10 0.08
Matches are distributed among these distances:
114 70 0.21
115 28 0.08
116 23 0.07
117 2 0.01
118 12 0.04
119 1 0.00
120 2 0.01
121 9 0.03
123 12 0.04
124 3 0.01
125 8 0.02
126 2 0.01
127 16 0.05
128 45 0.13
129 103 0.31
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (122 bp):
CACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCAC
AAGTCAATGGCACCTATTTCAAAGCCCACAAGTCAGTGGCATCCATTTCAAAGCCCA
Found at i:1326994 original size:17 final size:15
Alignment explanation
Indices: 1326974--1327022 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
1326964 TTAGATAAGA
1326974 AAGAAAGAAAGAAGATG
1 AAGAAAGAAAGAA-A-G
1326991 AAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAG
1327005 AA-AAAGAAA-AAA-
1 AAGAAAGAAAGAAAG
1327017 AAGAAA
1 AAGAAA
1327023 AAATATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.07
13 6 0.20
14 9 0.30
15 1 0.03
16 9 0.30
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:1327021 original size:15 final size:17
Alignment explanation
Indices: 1326974--1327024 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 17
1326964 TTAGATAAGA
1326974 AAGAAAGAAAGAAGATGAAG
1 AAGAAAGAAAGAA-A--AAG
1326994 AAGAAAGAAAGAAAAAG
1 AAGAAAGAAAGAAAAAG
1327011 AA-AAA-AAAGAAAAA
1 AAGAAAGAAAGAAAAA
1327025 ATATGAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.29
16 3 0.10
17 5 0.16
19 1 0.03
20 13 0.42
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (17 bp):
AAGAAAGAAAGAAAAAG
Found at i:1333444 original size:23 final size:23
Alignment explanation
Indices: 1333418--1333461 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1333408 GAAAAATGCA
1333418 TATTATCATAAGAAAAAAATATG
1 TATTATCATAAGAAAAAAATATG
*
1333441 TATTATCATAAGGAAAAAATA
1 TATTATCATAAGAAAAAAATA
1333462 AAATTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (23 bp):
TATTATCATAAGAAAAAAATATG
Found at i:1335156 original size:55 final size:56
Alignment explanation
Indices: 1335097--1335203 Score: 137
Period size: 55 Copynumber: 1.9 Consensus size: 56
1335087 GGAGTAGCTA
* * * *
1335097 GTAAGTTTAGCTCCAGTTGAAA-TTGACACCTA-ATATAATAGCCTAAGAGTAATTG
1 GTAAGTTTAGCTCCAGTTAAAATTTG-CACCTAGATAAAAAAACCTAAGAGTAATTG
* *
1335152 GTAAGTTTATCTCTAGTTAAAATTTGCACCTAGATAAAAAAACCTAAGAGTA
1 GTAAGTTTAGCTCCAGTTAAAATTTGCACCTAGATAAAAAAACCTAAGAGTA
1335204 GCAAATAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
55 25 0.57
56 19 0.43
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (56 bp):
GTAAGTTTAGCTCCAGTTAAAATTTGCACCTAGATAAAAAAACCTAAGAGTAATTG
Found at i:1335286 original size:111 final size:112
Alignment explanation
Indices: 1335156--1335367 Score: 252
Period size: 111 Copynumber: 1.9 Consensus size: 112
1335146 TAATTGGTAA
* * * *
1335156 GTTTATCTCTAGTTAAAATT-TGCACCTAGATAAAAAAACCT-AAGAGTAGCAAATAAGTTTT-G
1 GTTTAGCTCAAGTTAAAATTGT-CACCTAAAT-AAAAAACCTCAAAAGTAGCAAAT-AGTTTTAG
* * *
1335218 CCCTAGTTGAAATT-GCATCTAAATAAGAGAGCCCAAGAACAACTTGTAG
63 CCCAAGTTGAAATTGGCACCTAAATAAGAAAGCCCAAGAACAACTTGTAG
* * * * *
1335267 GTTTAGCTCAAGTTGAAATTGTCACCTAAATGAGAAAGCTCAAAAGTAGCAAATAGTTTTAGCTC
1 GTTTAGCTCAAGTTAAAATTGTCACCTAAATAAAAAACCTCAAAAGTAGCAAATAGTTTTAGCCC
*
1335332 AAGTTGAAATTGGCACCTAGATAAGAAAGCCCAAGA
66 AAGTTGAAATTGGCACCTAAATAAGAAAGCCCAAGA
1335368 GTAACTAATA
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
110 12 0.14
111 50 0.60
112 22 0.26
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (112 bp):
GTTTAGCTCAAGTTAAAATTGTCACCTAAATAAAAAACCTCAAAAGTAGCAAATAGTTTTAGCCC
AAGTTGAAATTGGCACCTAAATAAGAAAGCCCAAGAACAACTTGTAG
Found at i:1335626 original size:111 final size:112
Alignment explanation
Indices: 1335459--1335740 Score: 272
Period size: 111 Copynumber: 2.5 Consensus size: 112
1335449 AAAATTGGCC
* * * *
1335459 CCCATATGAGAAAACCC-AAAAGTAGCTAGTATGTTTAGC-TCTAGTTGAAATTGGCACCATAAG
1 CCCAAATGA-AAAACCCTAAGAGTAGCTGGTAGGTTTAGCTTC-AGTTGAAATTGGCACCAT-AG
* * *
1335522 -GAGAAAGCCAAAGAGTAGCTAGTAAGTTTAGATC-AAGTTAAAA-TATGCA
63 TGAAAAAGCCAAAGAGTAGCTACTAAGTTTAGATCTAA-TTAAAATTA-ACA
** * *
1335571 -CCAGTTGAAAAACCCTAAGAGTAGCTGGTAGGTTTAACTTCAGTTAAAATTGGCACC-TAGTTG
1 CCCAAATGAAAAACCCTAAGAGTAGCTGGTAGGTTTAGCTTCAGTTGAAATTGGCACCATAG-TG
* * * * *
1335634 AAAAAGTCTAAGAGTAGCTACTAGGTTTAGCTCTAATTGAAATTAACA
65 AAAAAGCCAAAGAGTAGCTACTAAGTTTAGATCTAATTAAAATTAACA
* * * * *
1335682 CCCAAATGAAAAATCCTAAGAATAGTTGATAGGTTTAGCTTTAGTTGAAATTGGCACCA
1 CCCAAATGAAAAACCCTAAGAGTAGCTGGTAGGTTTAGCTTCAGTTGAAATTGGCACCA
1335741 AAATGATTAA
Statistics
Matches: 138, Mismatches: 24, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
109 2 0.01
110 8 0.06
111 74 0.54
112 54 0.39
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (112 bp):
CCCAAATGAAAAACCCTAAGAGTAGCTGGTAGGTTTAGCTTCAGTTGAAATTGGCACCATAGTGA
AAAAGCCAAAGAGTAGCTACTAAGTTTAGATCTAATTAAAATTAACA
Found at i:1335651 original size:56 final size:55
Alignment explanation
Indices: 1335532--1335663 Score: 162
Period size: 55 Copynumber: 2.4 Consensus size: 55
1335522 GAGAAAGCCA
*
1335532 AAGAGTAGCTAGTAAGTTTAGATCAAGTTAAAATATGCACCAGTTGAAAAACCCT
1 AAGAGTAGCTAGTAGGTTTAGATCAAGTTAAAATATGCACCAGTTGAAAAACCCT
* **
1335587 AAGAGTAGCTGGTAGGTTTA-ACTTC-AGTTAAAAT-TGGCACCTAGTTGAAAAAGTCT
1 AAGAGTAGCTAGTAGGTTTAGA--TCAAGTTAAAATAT-GCACC-AGTTGAAAAACCCT
*
1335643 AAGAGTAGCTACTAGGTTTAG
1 AAGAGTAGCTAGTAGGTTTAG
1335664 CTCTAATTGA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
54 2 0.03
55 32 0.48
56 32 0.48
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (55 bp):
AAGAGTAGCTAGTAGGTTTAGATCAAGTTAAAATATGCACCAGTTGAAAAACCCT
Found at i:1335677 original size:56 final size:56
Alignment explanation
Indices: 1335079--1335739 Score: 298
Period size: 56 Copynumber: 11.9 Consensus size: 56
1335069 CCTAAATAAG
** * * * *
1335079 AAAGCCTTGGAGTAGCTAGTAAGTTTAGCTCCAGTTGAAATTGACACCTA-AT-ATA
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGA-A
* ** * * * * * * *
1335134 ATAGCCTAAGAGTAATTGGTAAGTTTATCTCTAGTTAAAATTTGCACCTAGATAAA
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGAA
* * * * * * * **
1335190 AAAACCTAAGAGTAGCAAATAAGTTTTGCCCTAGTTGAAATT-GCATCTAAAT-AA
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGAA
* * ** * * * * ** *
1335244 GAGAGCCCAAGAACAACTTGTAGGTTTAGCTCAAGTTGAAATTGTCACCTAAATGAG
1 -AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGAA
* * * * * *
1335301 AAAG-CTCAAAAGTAGCAAATAGTTTTAGCTCAAGTTGAAATTGGCACCTAGAT-AA
1 AAAGCCT-AAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGAA
* * * * * * **
1335356 GAAAGCCCAAGAGTAACTAATATGTTTCA-CCCTAATTGAAATTGGCATCC-AAATGAA
1 -AAAGCCTAAGAGTAGCTAGTAGGTTT-AGCTCTAGTTGAAATTGGCA-CCTAGTTGAA
* * ** * * * *
1335413 AGAA-CCTAAAATTATTTAGTAAGTTTCA-C-CTGAGTTAAAATTGGCCCCCA-TATGAGA
1 A-AAGCCTAAGAGTAGCTAGTAGGTTT-AGCTCT-AGTTGAAATTGGCACCTAGT-TGA-A
* * * *
1335470 AAA-CCCAAAAGTAGCTAGTATGTTTAGCTCTAGTTGAAATTGGCACCATAAG--GAG
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACC-T-AGTTGAA
* * * * *
1335525 AAAGCCAAAGAGTAGCTAGTAAGTTTAGATCAAGTTAAAATAT-GCACC-AGTTGAA
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAAT-TGGCACCTAGTTGAA
* * * *
1335580 AAACCCTAAGAGTAGCTGGTAGGTTTAACT-TCAGTTAAAATTGGCACCTAGTTGAA
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCT-AGTTGAAATTGGCACCTAGTTGAA
* * * ** * **
1335636 AAAGTCTAAGAGTAGCTACTAGGTTTAGCTCTAATTGAAATTAACACCCAAATGAA
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGAA
* * * *
1335692 AAATCCTAAGAATAG-TTGATAGGTTTAGCTTTAGTTGAAATTGGCACC
1 AAAGCCTAAGAGTAGCTAG-TAGGTTTAGCTCTAGTTGAAATTGGCACC
1335740 AAAATGATTA
Statistics
Matches: 458, Mismatches: 118, Indels: 59
0.72 0.19 0.09
Matches are distributed among these distances:
53 2 0.00
54 3 0.01
55 127 0.28
56 309 0.67
57 16 0.03
58 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (56 bp):
AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGAA
Found at i:1336988 original size:22 final size:22
Alignment explanation
Indices: 1336962--1337006 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1336952 TAGAGAAACC
1336962 AAAAA-AGAAAAAGAAAAACAGAG
1 AAAAATAGAAAAA-AAAAA-AGAG
1336985 AAAAATAGAAAAAAAAAAAGAG
1 AAAAATAGAAAAAAAAAAAGAG
1337007 TTCTTCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 10 0.48
24 7 0.33
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (22 bp):
AAAAATAGAAAAAAAAAAAGAG
Found at i:1338093 original size:76 final size:75
Alignment explanation
Indices: 1337956--1338134 Score: 180
Period size: 76 Copynumber: 2.3 Consensus size: 75
1337946 ATCGAGTCTA
* * * * * * *
1337956 AGGTCATGAAAGAATTTTCATTTAGATATATGTCCGTTAAGGTCATTTAAGTAATATTACATCAA
1 AGGTCATGTAA-AACTTTCATGTCGATACATGTCCGTTAAGGTCATTTAAGCAATAGTACATCAA
1338021 AAACAAG-TCT
65 AAACAAGCTCT
* * * * *
1338031 ACGGTCATGTGAAAACTTTCTTGTCGATACATGTCTGTTAAGGTCATTTAGGCAATGGTACATTA
1 A-GGTCATGT-AAAACTTTCATGTCGATACATGTCCGTTAAGGTCATTTAAGCAATAGTACATCA
*
1338096 AAACCAAGCTTCT
64 AAAACAAGC-TCT
**
1338109 AGGTTTTGTAAAACTTTCATGTCGAT
1 AGGTCATGTAAAACTTTCATGTCGAT
1338135 GGATGTCTTT
Statistics
Matches: 84, Mismatches: 16, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
75 1 0.01
76 71 0.85
77 8 0.10
78 4 0.05
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (75 bp):
AGGTCATGTAAAACTTTCATGTCGATACATGTCCGTTAAGGTCATTTAAGCAATAGTACATCAAA
AACAAGCTCT
Found at i:1339665 original size:13 final size:13
Alignment explanation
Indices: 1339647--1339671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1339637 ATTACTCACA
1339647 TGTATCGATACAT
1 TGTATCGATACAT
1339660 TGTATCGATACA
1 TGTATCGATACA
1339672 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1339736 original size:52 final size:52
Alignment explanation
Indices: 1339680--1339800 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1339670 CACTGATCTT
*
1339680 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1339732 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1339784 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1339801 TAACTTTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1348092 original size:31 final size:30
Alignment explanation
Indices: 1348057--1348199 Score: 164
Period size: 31 Copynumber: 4.6 Consensus size: 30
1348047 AAAAATAAAA
1348057 AAAGTCCACGACTCAGTGGAAATCTCTTCTC
1 AAAGTCCACGACTCAGTGG-AATCTCTTCTC
*
1348088 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGG-AATCTCTTCTC
* *
1348119 AAAGTCCACGACGCAGTGGCATC-CTTCTC
1 AAAGTCCACGACTCAGTGGAATCTCTTCTC
* *
1348148 TTTAAAGTCCACGACTCAGTGGCAT-TTTGTCTC
1 ---AAAGTCCACGACTCAGTGGAATCTCT-TCTC
*
1348181 AAAGTCCACGACTCTGTGG
1 AAAGTCCACGACTCAGTGG
1348200 CACTTTTTTC
Statistics
Matches: 99, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
29 5 0.05
30 21 0.21
31 47 0.47
32 22 0.22
33 4 0.04
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGAATCTCTTCTC
Found at i:1348201 original size:62 final size:61
Alignment explanation
Indices: 1348057--1348201 Score: 188
Period size: 62 Copynumber: 2.3 Consensus size: 61
1348047 AAAAATAAAA
*
1348057 AAAGTCCACGACTCAGTGGAAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGG-CATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
* *
1348119 AAAGTCCACGACGCAGTGGCATC-CTTCTCTTTAAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCTCTTCTC---AAAGTCCACGACTCAGTGGCAATCTCTG-CTC
*
1348181 AAAGTCCACGACTCTGTGGCA
1 AAAGTCCACGACTCAGTGGCA
1348202 CTTTTTTCAT
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
60 6 0.08
61 6 0.08
62 42 0.57
63 20 0.27
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (61 bp):
AAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
Found at i:1348234 original size:34 final size:32
Alignment explanation
Indices: 1348186--1349025 Score: 557
Period size: 34 Copynumber: 25.8 Consensus size: 32
1348176 GTCTCAAAGT
* * *
1348186 CCACGACTCTGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTC-T-TTTAAGC
* *
1348220 CCACAACTCCGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* *
1348254 CCACAACTCCGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
1348288 CCACAACTCCGTGGCACTCTTTTTTCCTTTTCAAAGC
1 CCACAACTCCGTGGCA--CTTTTTT-CTTTT--AAGC
*
1348325 CCACAACTCCGTGGCACCTTTTTCTTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT-AAGC
* * ****
1348358 CCACAACTCTGTGGCACCTACAACTTTGT--G-
1 CCACAACTCCGTGGCACTTTTTTCTTT-TAAGC
* * ** * *
1348388 GCAC-TCT-C-TTTC-C---CTT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
*
1348412 CCACAACTCCGTGGCACCTTTTTCTGTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCT-TTT-AAGC
1348446 CCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGC
1 CCACAACTCCGTGGCACT-TTTTT--CTTTT--AAGC
1348483 CCACAACTCCGTGGCACTTTTTTCTTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT-AAGC
*
1348516 CCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGT
1 CCACAACTCCGTGGCACT-TTTTT--CTTTTAAGC
* * *
1348551 CTACAACTCCGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* * *
1348585 CCACAACTCCGTGGCACCTTCTTCATTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTC-TTT-TAAGC
* * *
1348619 CCACGACTCCGTGGCAC--TCTT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
* *
1348648 CCACAACTCCGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* *
1348682 CCACAACTCCGTGGCAC--TCTT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
* *
1348711 CCACAACTCTGTGGCACTCTTTTTCCTTCTAAGC
1 CCACAACTCCGTGGCACT-TTTTT-CTTTTAAGC
* * * *
1348745 CCACAACTCTGTGGCATTCTTTTTCCGTTTAAGT
1 CCACAACTCCGTGGCA--CTTTTTTCTTTTAAGC
* ** **
1348779 CCACAACGCCGTGGCAC--CCTTC--CAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
* *
1348807 CCACAACTCCGTGGCACCTTCTTT-TTTAAAGC
1 CCACAACTCCGTGGCA-CTTTTTTCTTTTAAGC
* *
1348839 CCACAACTCCGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* * *
1348873 CCACAACTCCGTGGCACCTTCTTCATTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTC-TTT-TAAGC
* * *
1348907 CCACGACTCCGTGGCAC--TCTT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
* *
1348936 CCACAACTCCGTGGCACCTTCTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT--AAGC
* *
1348970 CCACAACTCCGTGGCAC--TCTT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
*
1348999 CCACAACTCTGTGGCACTCTTTTTCTT
1 CCACAACTCCGTGGCACT-TTTTTCTT
1349026 CCAAAGCCCA
Statistics
Matches: 676, Mismatches: 69, Indels: 123
0.78 0.08 0.14
Matches are distributed among these distances:
22 3 0.00
23 2 0.00
24 3 0.00
25 2 0.00
26 2 0.00
27 4 0.01
28 19 0.03
29 85 0.13
30 11 0.02
31 24 0.04
32 62 0.09
33 55 0.08
34 292 0.43
35 40 0.06
36 20 0.03
37 52 0.08
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (32 bp):
CCACAACTCCGTGGCACTTTTTTCTTTTAAGC
Found at i:1348436 original size:87 final size:88
Alignment explanation
Indices: 1348298--1348462 Score: 287
Period size: 87 Copynumber: 1.9 Consensus size: 88
1348288 CCACAACTCC
* *
1348298 GTGGCACTCTTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCAC
1 GTGGCACTCTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCAC
*
1348362 AACTCTGTGGCACCTACAACTTT
66 AACTCCGTGGCACCTACAACTTT
*
1348385 GTGGCACTCTCTTTCCCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCAC
1 GTGGCACTCTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCAC
1348450 AACTCCGTGGCAC
66 AACTCCGTGGCAC
1348463 TCTTTTTCCC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
87 49 0.67
88 24 0.33
ACGTcount: A:0.20, C:0.33, G:0.14, T:0.33
Consensus pattern (88 bp):
GTGGCACTCTCTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCAC
AACTCCGTGGCACCTACAACTTT
Found at i:1348531 original size:158 final size:158
Alignment explanation
Indices: 1348243--1348698 Score: 554
Period size: 158 Copynumber: 2.8 Consensus size: 158
1348233 GCACCTTCTT
1348243 CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCT
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCT
* *
1348308 TTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGC
66 TTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGC
1348373 ACCTACAACTTTGTGGCACTCTCTTTCC
131 ACCTACAACTTTGTGGCACTCTCTTTCC
* *
1348401 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTT-AAAGCCCACAACTCCGTGGCACTC
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCT-TTTCAAAGCCCACAACTCCGTGGCACTC
*
1348465 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGG
65 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGG
* * ** * *
1348530 CACTCTTTTTC-CCTTTTAAGTCTACAACTCCGTGGCACCTTCTT
130 CAC-C---TACAAC-TTT--GT-GGC-ACT-C-T----CTTTC-C
* *
1348574 CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCATTTCAAAGCCCACGACTCCGTGGCACTC-
1 CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCT
*
1348638 ---T---TTTT-AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGG
66 TTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTT-AAAGCCCACAACTCCGTGG
1348696 CAC
130 CAC
1348699 TCTTTTTAAA
Statistics
Matches: 262, Mismatches: 17, Indels: 30
0.85 0.06 0.10
Matches are distributed among these distances:
158 123 0.47
159 4 0.02
161 1 0.00
162 5 0.02
164 2 0.01
165 32 0.12
166 29 0.11
167 1 0.00
168 1 0.00
169 1 0.00
172 7 0.03
173 56 0.21
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.32
Consensus pattern (158 bp):
CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCT
TTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGC
ACCTACAACTTTGTGGCACTCTCTTTCC
Found at i:1348660 original size:63 final size:64
Alignment explanation
Indices: 1348407--1349060 Score: 637
Period size: 63 Copynumber: 10.0 Consensus size: 64
1348397 TTCCCTTTTT
* *
1348407 AAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACC---TTCTTTTTAAAGCCCACAACTCCGTGGCAC-CTTCTT--
1348472 CTTTTC
60 C-TTTC
* * *
1348478 AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 AAAGCCCACAACTCCGTGGCAC-CTTCT-TTTTAAAGCCCACAACTCCGTGGCAC-CTTCTT--C
1348543 TTT-
61 TTTC
* * *
1348546 TAAGTCTACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCAT
1 AAAGCCCACAACTCCGTGGCACCTTC-T-TTTT-AAAGCCCACAACTCCGTGGCACCTTCTTC-T
1348611 TTC
62 TTC
*
1348614 AAAGCCCACGACTCCGTGGCA-C-TCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTC-TTTC
* * *
1348677 AAAGCCCACAACTCCGTGGCA-C-TCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTC
1 AAAGCCCACAACTCCGTGGCACCTTCTTTTTAAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTC
* * * * * *
1348740 TAAGCCCACAACTCTGTGGCATTCTT-TTTCCGTTTAAGTCCACAACGCCGTGGCACC--CTTC-
1 AAAGCCCACAACTCCGTGGCA-CCTTCTTT---TTAAAGCCCACAACTCCGTGGCACCTTCTTCT
1348801 --C
62 TTC
1348802 AAAGCCCACAACTCCGTGGCACCTTCTTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
1 AAAGCCCACAACTCCGTGGCACCTTC-TTTTTAAAGCCCACAACTCCGTGGCACCTTCTTC-TTT
1348867 C
64 C
*
1348868 AAAGCCCACAACTCCGTGGCACCTTCTTCATTTCAAAGCCCACGACTCCGTGGCA-C-TCTT-TT
1 AAAGCCCACAACTCCGTGGCACCTTCTT--TTT-AAAGCCCACAACTCCGTGGCACCTTCTTCTT
1348930 T-
63 TC
1348931 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCA-C-TCTT-TT
1 AAAGCCCACAACTCCGTGGCACCTTC-T-TTTT-AAAGCCCACAACTCCGTGGCACCTTCTTCTT
1348993 T-
63 TC
* * *
1348994 AAAGCCCACAACTCTGTGGCACTCTT-TTTCTTCCAAAGCCCACACAAGTCGGTGGCAACCTTCT
1 AAAGCCCACAACTCCGTGGCAC-CTTCTTT-TT--AAAG-CC-CACAACTCCGTGGC-ACCTTCT
1349058 TCT
59 TCT
1349061 AAAGCCCACA
Statistics
Matches: 512, Mismatches: 36, Indels: 72
0.83 0.06 0.12
Matches are distributed among these distances:
60 22 0.04
61 5 0.01
62 27 0.05
63 191 0.37
64 19 0.04
65 23 0.04
66 36 0.07
67 12 0.02
68 91 0.18
69 29 0.06
70 35 0.07
71 22 0.04
ACGTcount: A:0.21, C:0.35, G:0.13, T:0.30
Consensus pattern (64 bp):
AAAGCCCACAACTCCGTGGCACCTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTC
Found at i:1348889 original size:288 final size:291
Alignment explanation
Indices: 1348401--1349037 Score: 998
Period size: 288 Copynumber: 2.2 Consensus size: 291
1348391 CTCTCTTTCC
* *
1348401 CTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTC
1 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCT-TCT-AAGCCCACAACTCCGTGGCACTC
* * * **
1348465 TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGG
64 TTTTTCCCGTTT-AAAGCCCACAACGCCGTGGCAC----TCCTTCCAAAGCCCACAACTCCGTGG
* * *
1348530 CACTCTTTTTCCCTTTTAAGTCTACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCC
124 CACTCTTTTT--CTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCC
1348595 GTGGCACCTTCTTCATTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGT
187 GTGGCACCTTCTTCATTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGT
1348660 GGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACT
252 GGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACT
* *
1348700 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCTGTGGCATTCT
1 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT-CTTCTAAGCCCACAACTCCGTGGCACTCT
*
1348765 TTTT-CCGTTT-AAGTCCACAACGCCGTGGCAC-CCTTCCAAAGCCCACAACTCCGTGGCAC-CT
65 TTTTCCCGTTTAAAGCCCACAACGCCGTGGCACTCCTTCCAAAGCCCACAACTCCGTGGCACTCT
1348826 TCTTT-TTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCAC
130 T-TTTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCAC
1348890 CTTCTTCATTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCT
194 CTTCTTCATTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCT
1348955 TCTTCTTTTCAAAGCCCACAACTCCGTGGCACT
259 TCTTCTTTTCAAAGCCCACAACTCCGTGGCACT
*
1348988 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCTTCCAAAGCCCACA
1 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCTT-CTAAGCCCACA
1349038 CAAGTCGGTG
Statistics
Matches: 320, Mismatches: 14, Indels: 19
0.91 0.04 0.05
Matches are distributed among these distances:
287 3 0.01
288 199 0.62
290 3 0.01
291 28 0.09
296 19 0.06
298 5 0.02
299 53 0.17
300 8 0.03
301 2 0.01
ACGTcount: A:0.21, C:0.35, G:0.13, T:0.30
Consensus pattern (291 bp):
CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCTTCTAAGCCCACAACTCCGTGGCACTCTT
TTTCCCGTTTAAAGCCCACAACGCCGTGGCACTCCTTCCAAAGCCCACAACTCCGTGGCACTCTT
TTTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCT
TCTTCATTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTC
TTCTTTTCAAAGCCCACAACTCCGTGGCACT
Found at i:1349037 original size:34 final size:34
Alignment explanation
Indices: 1348407--1349037 Score: 640
Period size: 34 Copynumber: 19.3 Consensus size: 34
1348397 TTCCCTTTTT
*
1348407 AAAGCCCACAACTCCGTGGCAC-CTTTTTCTGTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCT-TTC
1348441 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTT--C-TTTC
*
1348478 AAAGCCCACAACTCCGTGGCACT-TTTTTCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTC
1348511 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT-
1 AAAGCCCACAACTCCGTGGCACTCTTTTT--CTTTC
* * * *
1348546 TAAGTCTACAACTCCGTGGCAC-CTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC-TTTC
*
1348580 AAAGCCCACAACTCCGTGGCAC-CTTCTTCATTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC-TTTC
*
1348614 AAAGCCCACGACTCCGTGGCACTC---TT-TTT-
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTC
*
1348643 AAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC-TTTC
1348677 AAAGCCCACAACTCCGTGGCACTC---TT-TTT-
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTC
* *
1348706 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTC
* * *
1348740 TAAGCCCACAACTCTGTGGCATTCTTTTTCCGTTT-
1 AAAGCCCACAACTCCGTGGCACTCTTTTT-C-TTTC
* * *
1348775 -AAGTCCACAACGCCGTGGCAC-C-----CTTCC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTC
1348802 AAAGCCCACAACTCCGTGGCAC-CTTCTTT-TTT-
1 AAAGCCCACAACTCCGTGGCACTCTT-TTTCTTTC
*
1348834 AAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC-TTTC
*
1348868 AAAGCCCACAACTCCGTGGCAC-CTTCTTCATTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC-TTTC
*
1348902 AAAGCCCACGACTCCGTGGCACTC---TT-TTT-
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTC
*
1348931 AAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC-TTTC
1348965 AAAGCCCACAACTCCGTGGCACTC---TT-TTT-
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTC
* *
1348994 AAAGCCCACAACTCTGTGGCACTCTTTTTCTTCC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTC
1349028 AAAGCCCACA
1 AAAGCCCACA
1349038 CAAGTCGGTG
Statistics
Matches: 518, Mismatches: 31, Indels: 96
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.00
27 1 0.00
28 22 0.04
29 88 0.17
30 12 0.02
31 6 0.01
32 38 0.07
33 45 0.09
34 236 0.46
35 30 0.06
36 11 0.02
37 26 0.05
38 1 0.00
ACGTcount: A:0.21, C:0.36, G:0.13, T:0.30
Consensus pattern (34 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTC
Found at i:1349096 original size:65 final size:64
Alignment explanation
Indices: 1349023--1349163 Score: 232
Period size: 65 Copynumber: 2.2 Consensus size: 64
1349013 CACTCTTTTT
* *
1349023 CTTCCAAAGCCCACACAAGTCGGTGGCAACC-TTCTTCTAAAGCCCACACAAGTCGGTGGCAACC
1 CTTCCAAAGCCCACACAAGTCGGTGGCAACCATTC-TCTAAAGCCCACACAAATCGATGGCAACC
1349087 CTTCTCAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAATCGATGGCAACC
1 CTTC-CAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAATCGATGGCAACC
1349152 CTTCC-AAGCCCA
1 CTTCCAAAGCCCA
1349164 ATATAGCTGG
Statistics
Matches: 73, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
63 7 0.10
64 5 0.07
65 58 0.79
66 3 0.04
ACGTcount: A:0.30, C:0.37, G:0.16, T:0.17
Consensus pattern (64 bp):
CTTCCAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAATCGATGGCAACC
Found at i:1349102 original size:32 final size:32
Alignment explanation
Indices: 1349023--1349163 Score: 200
Period size: 33 Copynumber: 4.4 Consensus size: 32
1349013 CACTCTTTTT
1349023 CTTC-CAAAGCCCACACAAGTCGGTGGCAA-C
1 CTTCTCAAAGCCCACACAAGTCGGTGGCAACC
1349053 CTTCTTCTAAAGCCCACACAAGTCGGTGGCAACC
1 CTTC-TC-AAAGCCCACACAAGTCGGTGGCAACC
1349087 CTTCTCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTCTCAAAGCCCACACAAGTCGGTGGCAACC
* * *
1349119 ATTCTCTAAAGCCCACACAAATCGATGGCAACC
1 CTTCTC-AAAGCCCACACAAGTCGGTGGCAACC
1349152 CTTC-C-AAGCCCA
1 CTTCTCAAAGCCCA
1349164 ATATAGCTGG
Statistics
Matches: 102, Mismatches: 4, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
30 11 0.11
32 33 0.32
33 53 0.52
34 5 0.05
ACGTcount: A:0.30, C:0.37, G:0.16, T:0.17
Consensus pattern (32 bp):
CTTCTCAAAGCCCACACAAGTCGGTGGCAACC
Found at i:1349163 original size:288 final size:281
Alignment explanation
Indices: 1348401--1349135 Score: 816
Period size: 288 Copynumber: 2.5 Consensus size: 281
1348391 CTCTCTTTCC
* * * *
1348401 CTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTGTTTAAAGCCCACAACTCCGTGGC-ACT
1 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTC-CTTCAAAGCCCACAACTCGGTGGCAAC-
* * ** * **
1348464 CTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTG
64 CTTCTT-CC--GT-AAAGCCCACAAAGCCGTGGCAC-----CCTTCCAAAGCCCACAACTCCGTG
* * * * *
1348529 GCACTCTTTTTCCCTTTTAAGTCTACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTC
120 GCAC-CTTCTT--C--TAAAGCCCACAAATCCGTGGCACC-TCTTC---TCAAAGCCCACAACTC
1348594 CGTGGCACCTTCTTCATTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCG
176 CGTGGCACCTTCTTCATTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCG
1348659 TGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACT
241 TGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACT
* * **
1348700 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCTGTGGCATTCT
1 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCGGTGGCAACCT
* * * *
1348765 TTTTCCGTTTAAGTCCACAACGCCGTGGCACCCTTCCAAAGCCCACAACTCCGTGGCACCTTCTT
66 TCTTCCG-TAAAGCCCACAAAGCCGTGGCACCCTTCCAAAGCCCACAACTCCGTGGCACCTTC--
* *
1348830 TTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCT
128 TTCTAAAGCCCACAAATCCGTGGCACC-TCTTC---TCAAAGCCCACAACTCCGTGGCACCTTCT
1348895 TCATTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTC
189 TCATTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTC
1348960 TTTTCAAAGCCCACAACTCCGTGGCACT
254 TTTTCAAAGCCCACAACTCCGTGGCACT
*
1348988 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT-CTTCCAAAGCCCACACAAGTCGGTGGCAA
1 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTT-CAAAG-CC-CACAACTCGGTGGCAA
* * *
1349052 CCTTCTT-C-TAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGC
63 CCTTCTTCCGTAAAGCCCACA-AAG-CCGTGGC-ACCCTTC-CAAAG-CC-CACAACTCCGTGGC
1349115 AACCATTC-TCTAAAGCCCACA
122 -ACC-TTCTTCTAAAGCCCACA
1349136 CAAATCGATG
Statistics
Matches: 388, Mismatches: 32, Indels: 39
0.85 0.07 0.08
Matches are distributed among these distances:
287 12 0.03
288 193 0.50
289 9 0.02
290 28 0.07
291 30 0.08
292 16 0.04
293 12 0.03
294 3 0.01
295 3 0.01
296 19 0.05
297 1 0.00
298 2 0.01
299 53 0.14
300 7 0.02
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.29
Consensus pattern (281 bp):
CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCGGTGGCAACCT
TCTTCCGTAAAGCCCACAAAGCCGTGGCACCCTTCCAAAGCCCACAACTCCGTGGCACCTTCTTC
TAAAGCCCACAAATCCGTGGCACCTCTTCTCAAAGCCCACAACTCCGTGGCACCTTCTTCATTTC
AAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAA
AGCCCACAACTCCGTGGCACT
Found at i:1349314 original size:43 final size:43
Alignment explanation
Indices: 1349248--1349442 Score: 192
Period size: 43 Copynumber: 4.2 Consensus size: 43
1349238 TTGGCACCTT
* *
1349248 CACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
*
1349291 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT-G-G
* * *
1349336 CCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGG
1 -------CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
*
1349386 CACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
1 CACC-T-----TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
1349435 CACCTTTA
1 CACCTTTA
1349443 TCTTTAAGCC
Statistics
Matches: 126, Mismatches: 11, Indels: 30
0.75 0.07 0.18
Matches are distributed among these distances:
43 44 0.35
44 2 0.02
45 1 0.01
48 1 0.01
49 39 0.31
50 1 0.01
51 1 0.01
52 37 0.29
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.29
Consensus pattern (43 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
Found at i:1349493 original size:49 final size:49
Alignment explanation
Indices: 1349161--1349485 Score: 419
Period size: 49 Copynumber: 6.7 Consensus size: 49
1349151 CCTTCCAAGC
*
1349161 CCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
* * * *
1349210 CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAGC
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
*
1349259 CCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
*
1349302 CCAATATAGCTGGCCTTGAATCAGCATATTGGCGCCTTTTCCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGT
* * * * *
1349354 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
* *
1349403 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGC
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
* * * *
1349452 CCAATATCGTTGGCCGTGAATCAACATATTGGCA
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCA
1349486 TCTTTATCAC
Statistics
Matches: 241, Mismatches: 26, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
43 38 0.16
45 1 0.00
49 159 0.66
50 3 0.01
52 40 0.17
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (49 bp):
CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
Found at i:1349599 original size:115 final size:116
Alignment explanation
Indices: 1349382--1349600 Score: 296
Period size: 115 Copynumber: 1.9 Consensus size: 116
1349372 ACTCAGCACA
* * * *
1349382 TTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCAT
* * *
1349447 TAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTT
66 TAAGCCCAATATAGCTGGCCGTGAATCAACACATTGGCATCTTTATCACTT
* * * *
1349498 TTGGCACC-TCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCAT
* * * *
1349562 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
66 TAAGCCCAATATAGCTGGCCGTGAATCAACACATTGGCA
1349601 CCTCATCTTT
Statistics
Matches: 88, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
115 80 0.91
116 8 0.09
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (116 bp):
TTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCAT
TAAGCCCAATATAGCTGGCCGTGAATCAACACATTGGCATCTTTATCACTT
Found at i:1349632 original size:48 final size:48
Alignment explanation
Indices: 1349498--1349740 Score: 343
Period size: 48 Copynumber: 5.1 Consensus size: 48
1349488 TTTATCACTT
*
1349498 TTGGCACCTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACA
1 TTGGCACCTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
* *
1349546 TTGGCACCTTCACCATTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
1 TTGGCACC-TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
1349595 TTGGCACCTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
1 TTGGCACCTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
* * *
1349643 TT-G-A---CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAA
1 TTGGCACCTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
*
1349686 TTGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACA
1 TTGGCACC---T-CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
1349738 TTG
1 TTG
1349741 ACATCTTTTT
Statistics
Matches: 173, Mismatches: 12, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
43 38 0.22
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 48 0.28
49 45 0.26
52 38 0.22
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (48 bp):
TTGGCACCTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
Found at i:1349668 original size:43 final size:43
Alignment explanation
Indices: 1349556--1349748 Score: 197
Period size: 43 Copynumber: 4.2 Consensus size: 43
1349546 TTGGCACCTT
*
1349556 CACCATTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
1 CACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-A
*
1349601 CCTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGA
1 ---CACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGA
* *
1349647 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGGCA
1 CACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-A
* *
1349692 CCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGA
1 -------CACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGA
*
1349742 CATCTTT
1 CACCTTT
1349749 TTTCATCATC
Statistics
Matches: 127, Mismatches: 9, Indels: 23
0.80 0.06 0.14
Matches are distributed among these distances:
43 45 0.35
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 39 0.31
50 1 0.01
51 1 0.01
52 37 0.29
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (43 bp):
CACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGA
Found at i:1349728 original size:52 final size:52
Alignment explanation
Indices: 1349650--1349788 Score: 161
Period size: 52 Copynumber: 2.6 Consensus size: 52
1349640 ACATTGACAC
*
1349650 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGACACCTTTTCCAT
* * * *
1349702 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCTTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGACA-C-CTTTTC--CAT
* * * *
1349758 CTTTAAGCCCAATATCGTTGGCCATGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
1349789 ACATATTGGC
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
52 38 0.53
53 1 0.01
54 5 0.07
56 28 0.39
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGACACCTTTTCCAT
Found at i:1349740 original size:95 final size:91
Alignment explanation
Indices: 1349556--1349748 Score: 305
Period size: 95 Copynumber: 2.1 Consensus size: 91
1349546 TTGGCACCTT
* * *
1349556 CACCATTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGGCACCTCATCTTTAAGTCCAATG
1349621 TAGCTGGCCTTGAATCAGCACATTGA
66 TAGCTGGCCTTGAATCAGCACATTGA
*
1349647 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGGCACCTTTTCCATCTTTAAGTTC
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGGCACC---T-CATCTTTAAGTCC
1349712 AATGTAGCTGGCCTTGAATCAGCACATTGA
62 AATGTAGCTGGCCTTGAATCAGCACATTGA
*
1349742 CATCTTT
1 CACCTTT
1349749 TTTCATCATC
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
91 44 0.47
94 1 0.01
95 48 0.52
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (91 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGGCACCTCATCTTTAAGTCCAATG
TAGCTGGCCTTGAATCAGCACATTGA
Found at i:1349786 original size:56 final size:54
Alignment explanation
Indices: 1349650--1349804 Score: 179
Period size: 56 Copynumber: 2.9 Consensus size: 54
1349640 ACATTGACAC
*
1349650 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGGCA-C-CTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGGCATCTTTTTTCCAT
* * * *
1349702 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCTTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGGCATCTTTTTTC--CAT
* * * * * *
1349758 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGGCATCTTT
1349805 ATCACTTTTC
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
52 38 0.45
53 1 0.01
54 5 0.06
56 41 0.48
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (54 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAAATTGGCATCTTTTTTCCAT
Found at i:1350696 original size:13 final size:13
Alignment explanation
Indices: 1350678--1350702 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1350668 CATAAAATGT
1350678 TGTATCGATACAA
1 TGTATCGATACAA
1350691 TGTATCGATACA
1 TGTATCGATACA
1350703 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1350700 original size:33 final size:33
Alignment explanation
Indices: 1350658--1350727 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1350648 TTCAACGATT
1350658 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1350691 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1350724 TGTA
1 TGTA
1350728 AGCTACTGCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1350786 original size:13 final size:13
Alignment explanation
Indices: 1350768--1350792 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1350758 ATTACTCACA
1350768 TGTATCGATACAT
1 TGTATCGATACAT
1350781 TGTATCGATACA
1 TGTATCGATACA
1350793 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1350857 original size:52 final size:52
Alignment explanation
Indices: 1350801--1350921 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1350791 CACTGATCTT
*
1350801 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1350853 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1350905 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1350922 TAACTTTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1356230 original size:17 final size:17
Alignment explanation
Indices: 1356204--1356236 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1356194 AGGGTTCAAT
1356204 AAGAAAATGATGGAAAG
1 AAGAAAATGATGGAAAG
*
1356221 AAGAAGATGATGGAAA
1 AAGAAAATGATGGAAA
1356237 AAATTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.30, T:0.12
Consensus pattern (17 bp):
AAGAAAATGATGGAAAG
Found at i:1357987 original size:57 final size:57
Alignment explanation
Indices: 1357813--1358248 Score: 405
Period size: 57 Copynumber: 7.7 Consensus size: 57
1357803 ACTCTTAAAT
* * * * * *
1357813 CTTTGGCAATAGCAAGATAAAAATTTTGGACCTTAGCAAATGTTCAAGCTCTCAAG-
1 CTTTAGCAATGGCAAGATAATAATTTTGGACCTTAGCAAATGATCGAGTTCTCAAGC
* * * * * *
1357869 CTTTTGACAGTGGCAAGATAATAATTTTGG-CTTTAGCAAATGGTCGAATTTTCAAGC
1 CTTTAG-CAATGGCAAGATAATAATTTTGGACCTTAGCAAATGATCGAGTTCTCAAGC
* * * * ** *
1357926 CTTTAGTAGTGGTAAGATAATAATTTTAGACCTTAGCAAACAATCAAGTTCTCAAGC
1 CTTTAGCAATGGCAAGATAATAATTTTGGACCTTAGCAAATGATCGAGTTCTCAAGC
* * * * * * * * *
1357983 CTTTAGTAATGGCAAGAAAATAATTGTAGACTTTAGCGAATGATTGAGCTCTCAAGT
1 CTTTAGCAATGGCAAGATAATAATTTTGGACCTTAGCAAATGATCGAGTTCTCAAGC
* * * * *
1358040 CTTTGGCAATGGCAAGATGACAA-TTTGGACCTTAGCAAATGGTTGAGTT-TCAAGC
1 CTTTAGCAATGGCAAGATAATAATTTTGGACCTTAGCAAATGATCGAGTTCTCAAGC
* * * * * * *
1358095 CTTTGGTAGTGGCCAGATAATAATTTTGGATCTTATCAAATGATCGAGTTTTCAAGC
1 CTTTAGCAATGGCAAGATAATAATTTTGGACCTTAGCAAATGATCGAGTTCTCAAGC
* *
1358152 CTTTGAG-AATGGCAAGATAATATTTTTGGACCTTAGCAAATGATTGAGTTCTCAAGC
1 CTTT-AGCAATGGCAAGATAATAATTTTGGACCTTAGCAAATGATCGAGTTCTCAAGC
* * * *
1358209 TTTTAGCAATGGCAAGATAACAATTTTGAACTTTAGCAAA
1 CTTTAGCAATGGCAAGATAATAATTTTGGACCTTAGCAAA
1358249 AGGTCAAGGA
Statistics
Matches: 306, Mismatches: 67, Indels: 13
0.79 0.17 0.03
Matches are distributed among these distances:
55 23 0.08
56 89 0.29
57 193 0.63
58 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (57 bp):
CTTTAGCAATGGCAAGATAATAATTTTGGACCTTAGCAAATGATCGAGTTCTCAAGC
Found at i:1358152 original size:169 final size:171
Alignment explanation
Indices: 1357824--1358253 Score: 505
Period size: 169 Copynumber: 2.5 Consensus size: 171
1357814 TTTGGCAATA
* * * * *
1357824 GCAAGATAAA-AATTTTGGACCTTAGCAAATG-TTCAAGCTCTCAAGCTTTTGACAGTGGCAAGA
1 GCAAGA-AAATAATTGTAGACCTTAGCAAATGATT-GAGCTCTCAAGCTTTTGGCAATGGCAAGA
* * *
1357887 TAATAATTTTGG-CTTTAGCAAATGGTCGAATTTTCAAGCCTTTAGTAGTGGTAAGATAATAATT
64 TAACAATTTTGGACTTTAGCAAATGGTCGAAGTTTCAAGCCTTTAGTAGTGGCAAGATAATAATT
1357951 TTAGACCTTAGCAAACAATCAAGTTCTCAAGCCTTT-AGTAATG
129 TTAGACCTTAGCAAACAATCAAGTTCTCAAGCCTTTGAG-AATG
* *
1357994 GCAAGAAAATAATTGTAGACTTTAGCGAATGATTGAGCTCTCAAG-TCTTTGGCAATGGCAAGAT
1 GCAAGAAAATAATTGTAGACCTTAGCAAATGATTGAGCTCTCAAGCT-TTTGGCAATGGCAAGAT
* * * * *
1358058 GACAA-TTTGGACCTTAGCAAATGGTTG-AGTTTCAAGCCTTTGGTAGTGGCCAGATAATAATTT
65 AACAATTTTGGACTTTAGCAAATGGTCGAAGTTTCAAGCCTTTAGTAGTGGCAAGATAATAATTT
* * * ** * *
1358121 TGGATCTTATCAAATGATCGAGTTTTCAAGCCTTTGAGAATG
130 TAGACCTTAGCAAACAATCAAGTTCTCAAGCCTTTGAGAATG
* * * * * *
1358163 GCAAGATAATATTTTTGGACCTTAGCAAATGATTGAGTTCTCAAGCTTTTAGCAATGGCAAGATA
1 GCAAGAAAATAATTGTAGACCTTAGCAAATGATTGAGCTCTCAAGCTTTTGGCAATGGCAAGATA
* *
1358228 ACAATTTTGAACTTTAGCAAAAGGTC
66 ACAATTTTGGACTTTAGCAAATGGTC
1358254 AAGGAATAAT
Statistics
Matches: 218, Mismatches: 35, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
169 131 0.60
170 85 0.39
171 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (171 bp):
GCAAGAAAATAATTGTAGACCTTAGCAAATGATTGAGCTCTCAAGCTTTTGGCAATGGCAAGATA
ACAATTTTGGACTTTAGCAAATGGTCGAAGTTTCAAGCCTTTAGTAGTGGCAAGATAATAATTTT
AGACCTTAGCAAACAATCAAGTTCTCAAGCCTTTGAGAATG
Found at i:1358245 original size:226 final size:227
Alignment explanation
Indices: 1357812--1358233 Score: 564
Period size: 226 Copynumber: 1.9 Consensus size: 227
1357802 AACTCTTAAA
*
1357812 TCTTTGGCAATAGCAAGATAAAAATTTTGGACCTTAGCAAATGTTCAAGCTCTCAAGCTTTTGAC
1 TCTTTGGCAATAGCAAGATAAAAATTTTGGACCTTAGCAAATGTTCAAGCTCTCAAGCCTTTGAC
* * * *
1357877 AGTGGCAAGATAATAATTTTGGCTTTAGCAAATGGTCGAATTTTCAAGCCTTTAGTAGTGGTAAG
66 AGTGGCAAGATAATAATTTTGGATTTAGCAAATGATCGAATTTTCAAGCCTTTAGTAATGGCAAG
* *
1357942 ATAATAATTTTAGACCTTAGCAAACAATCAAGTTCTCAAGCCTTTAGTAATGGCAAGAAAATAAT
131 ATAATAATTTTAGACCTTAGCAAACAATCAAGTTCTCAAGCCTTTAGCAATGGCAAGAAAACAAT
1358007 TGTAGACTTTAGCGAATGATTGAGCTCTCAAG
196 TGTAGACTTTAGCGAATGATTGAGCTCTCAAG
* * * * * *
1358039 TCTTTGGCAATGGCAAGATGACAA-TTTGGACCTTAGCAAATGGTT-GAG-TTTCAAGCCTTTGG
1 TCTTTGGCAATAGCAAGATAAAAATTTTGGACCTTAGCAAAT-GTTCAAGCTCTCAAGCCTTTGA
* * * *
1358101 TAGTGGCCAGATAATAATTTTGGATCTTATCAAATGATCGAGTTTTCAAGCCTTTGAG-AATGGC
65 CAGTGGCAAGATAATAATTTTGGAT-TTAGCAAATGATCGAATTTTCAAGCCTTT-AGTAATGGC
* * ** ** * *
1358165 AAGATAATATTTTTGGACCTTAGCAAATGATTGAGTTCTCAAGCTTTTAGCAATGGCAAGATAAC
128 AAGATAATAATTTTAGACCTTAGCAAACAATCAAGTTCTCAAGCCTTTAGCAATGGCAAGAAAAC
1358230 AATT
193 AATT
1358234 TTGAACTTTA
Statistics
Matches: 167, Mismatches: 25, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
225 33 0.20
226 108 0.65
227 26 0.16
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (227 bp):
TCTTTGGCAATAGCAAGATAAAAATTTTGGACCTTAGCAAATGTTCAAGCTCTCAAGCCTTTGAC
AGTGGCAAGATAATAATTTTGGATTTAGCAAATGATCGAATTTTCAAGCCTTTAGTAATGGCAAG
ATAATAATTTTAGACCTTAGCAAACAATCAAGTTCTCAAGCCTTTAGCAATGGCAAGAAAACAAT
TGTAGACTTTAGCGAATGATTGAGCTCTCAAG
Found at i:1362925 original size:11 final size:10
Alignment explanation
Indices: 1362901--1362975 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 10
1362891 AGGCCACATA
*
1362901 TTTTTTTTAC
1 TTTTTTTTAT
*
1362911 TTTTTATTAT
1 TTTTTTTTAT
*
1362921 TTTTTTGTAT
1 TTTTTTTTAT
*
1362931 TTTTTTGTCTCT
1 TTTTTT-T-TAT
1362943 TTTTTTTATAT
1 TTTTTTT-TAT
1362954 TTTATTATATTAT
1 TTT-TT-T-TTAT
*
1362967 TATTTTTTA
1 TTTTTTTTA
1362976 AAAAAACGTG
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
10 25 0.49
11 7 0.14
12 12 0.24
13 6 0.12
14 1 0.02
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.77
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:1368855 original size:21 final size:22
Alignment explanation
Indices: 1368829--1368873 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1368819 GATCTATTCA
*
1368829 TTTCTCCTTCTTCCTCC-TCCT
1 TTTCTCCTTCCTCCTCCTTCCT
*
1368850 TTTCTCCTTCCTCTTCCTTCCT
1 TTTCTCCTTCCTCCTCCTTCCT
1368872 TT
1 TT
1368874 CCCAAATTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTCTCCTTCCTCCTCCTTCCT
Found at i:1369126 original size:6 final size:6
Alignment explanation
Indices: 1369115--1369165 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
1369105 TATGCTATTC
* * *
1369115 CCATTG CCATTG CCATTG CCATTG CCATTG CTATTG CTATTG CTATTG
1 CCATTG CCATTG CCATTG CCATTG CCATTG CCATTG CCATTG CCATTG
1369163 CCA
1 CCA
1369166 GTAGATGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.37
Consensus pattern (6 bp):
CCATTG
Found at i:1377483 original size:52 final size:52
Alignment explanation
Indices: 1377427--1377547 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
1377417 GAAAATTTAT
*
1377427 CTGCATGTATCAATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCAATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1377479 CTGCATGTATCAATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCAATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1377531 CTGCATGTATCGATACA
1 CTGCATGTATCAATACA
1377548 AAGATCAATG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCAATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1377558 original size:52 final size:52
Alignment explanation
Indices: 1377427--1377567 Score: 196
Period size: 52 Copynumber: 2.7 Consensus size: 52
1377417 GAAAATTTAT
* *
1377427 CTGCATGTATCAATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCAATACA-TAAGATAATGTATCGATACATCTGGGCAAATTTGC
***
1377479 CTGCATGTATCAATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCAATACATAAGATAATGTATCGATACATCTGGGCAAATTTGC
*
1377531 CTGCATGTATCGATACA-AAGATCAATGTATCGATACA
1 CTGCATGTATCAATACATAAGAT-AATGTATCGATACA
1377568 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 4 0.05
52 77 0.95
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCAATACATAAGATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1377571 original size:13 final size:13
Alignment explanation
Indices: 1377553--1377580 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1377543 ATACAAAGAT
1377553 CAATGTATCGATA
1 CAATGTATCGATA
1377566 CAATGTATCGATA
1 CAATGTATCGATA
1377579 CA
1 CA
1377581 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1377647 original size:20 final size:20
Alignment explanation
Indices: 1377622--1377675 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1377612 TAGCTTAAAT
1377622 TGTATCGATACAAAAAACTA
1 TGTATCGATACAAAAAACTA
* ***
1377642 TGTATCGATACAACATTTTA
1 TGTATCGATACAAAAAACTA
1377662 TGTATCGATACAAA
1 TGTATCGATACAAA
1377676 TCGTTGAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (20 bp):
TGTATCGATACAAAAAACTA
Found at i:1378483 original size:82 final size:82
Alignment explanation
Indices: 1378341--1379399 Score: 1540
Period size: 82 Copynumber: 12.8 Consensus size: 82
1378331 AGTACTGTGA
* * * *
1378341 CCTTTTAAAGTCCACAACTCCGTGGTATCCTTTTAAAGTCCACAACTCCATGGTACCCTTTTAAA
1 CCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AA
*
1378406 GTCCACAACTCCATGGCA-C
63 GTCCACAACTCCGTGGCATC
* * *
1378425 CCTTTAAAATCCACAACTCCGTGGCACCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGT
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
1378490 CCACAACTCCGTGGCA-C
65 CCACAACTCCGTGGCATC
* * *
1378507 CCTTTTAAAGTCCATAACTTCATGGCACCCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTTAA
1 CCTTTT-AAGTCCACAACTCCGTGGCACCC-TTTTAAGTCCACAACTCCGTGGCACCC-TTTTAA
1378572 GTCCACAACTCCGTGGCA-C
63 GTCCACAACTCCGTGGCATC
* * *
1378591 CCTTTTAAGGTCCATAACTCCATGGCACCCTTTTAAGTCCATAACTCCGTGGCACCCTTTTAAGT
1 CCTTTTAA-GTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
*
1378656 CCACAACTACGT-GCA-C
65 CCACAACTCCGTGGCATC
*
1378672 CCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
**
1378737 CACAACTTGGTGGCATC
66 CACAACTCCGTGGCATC
*
1378754 CCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1378819 CACAACTCCGTGGCATC
66 CACAACTCCGTGGCATC
* * * *
1378836 CCTTTTAAGTTCACGACTCCGCGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAATC
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1378901 CACAACTCCGTGGCATC
66 CACAACTCCGTGGCATC
* *
1378918 CCTTTTAAGTCCGCAACTCCGTGGCACCCTTTTAAGTCCGCAACTCCGTGGCACCCTTTTAAGTC
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* *
1378983 CATAACTCTGTGGCATC
66 CACAACTCCGTGGCATC
* * * *
1379000 TCTTTTAAGTCCATAACTTTC-TGGCACCCTTTTAAAGTCCACAACTTCGTGGCACCCTTTTAAA
1 CCTTTTAAGTCCACAAC-TCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AA
*
1379064 GTCCACAACTTCGTGGCA-C
63 GTCCACAACTCCGTGGCATC
*
1379083 CCTTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
1 CC-TTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AA
1379148 GTCCACAACTCCGTGGCA-C
63 GTCCACAACTCCGTGGCATC
* *
1379167 CCTTTTAAGTCTACAAGTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
1379232 CACAACTTCGTGGCATC
66 CACAACTCCGTGGCATC
1379249 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
1379314 CATAACTCCGTGGCATC
66 CACAACTCCGTGGCATC
* * * * *
1379331 TCTTTTAAAGTCCATAACTCTGTGGCACCCTTTTAAGTTCACAACTTCGTGGCACCCTTTTTAAG
1 CCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCC-TTTTAAG
1379396 TCCA
64 TCCA
1379400 TAAGATGGTG
Statistics
Matches: 897, Mismatches: 64, Indels: 28
0.91 0.06 0.03
Matches are distributed among these distances:
80 62 0.07
81 34 0.04
82 439 0.49
83 175 0.20
84 183 0.20
85 4 0.00
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (82 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
CACAACTCCGTGGCATC
Found at i:1379412 original size:28 final size:27
Alignment explanation
Indices: 1378341--1379399 Score: 1528
Period size: 27 Copynumber: 38.5 Consensus size: 27
1378331 AGTACTGTGA
* *
1378341 CCTTTTAAAGTCCACAACTCCGTGGTAT
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* *
1378369 CCTTTTAAAGTCCACAACTCCATGGTAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
*
1378397 CCTTTTAAAGTCCACAACTCCATGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* *
1378425 CCTTTAAAATCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1378452 CTTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1378479 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* * *
1378507 CCTTTTAAAGTCCATAACTTCATGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
1378535 CCTTTTTAAGTCCACAACTCCGTGGCAC
1 CC-TTTTAAGTCCACAACTCCGTGGCAC
1378563 CCTTTTTAAGTCCACAACTCCGTGGCAC
1 CC-TTTTAAGTCCACAACTCCGTGGCAC
* *
1378591 CCTTTTAAGGTCCATAACTCCATGGCAC
1 CCTTTTAA-GTCCACAACTCCGTGGCAC
*
1378619 CCTTTTAAGTCCATAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1378646 CCTTTTAAGTCCACAACTACGT-GCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1378672 CCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1378699 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
**
1378726 CCTTTTAAGTCCACAACTTGGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
*
1378754 CCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1378781 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1378808 CCTTTTAAGTCCACAACTCCGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
* * *
1378836 CCTTTTAAGTTCACGACTCCGCGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1378863 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1378890 CCTTTTAAATCCACAACTCCGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
*
1378918 CCTTTTAAGTCCGCAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1378945 CCTTTTAAGTCCGCAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* *
1378972 CCTTTTAAGTCCATAACTCTGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
* * *
1379000 TCTTTTAAGTCCATAACTTTC-TGGCAC
1 CCTTTTAAGTCCACAAC-TCCGTGGCAC
*
1379027 CCTTTTAAAGTCCACAACTTCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
*
1379055 CCTTTTAAAGTCCACAACTTCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
*
1379083 CCTTTTTAAGTCCACAACTTCGTGGCAC
1 CC-TTTTAAGTCCACAACTCCGTGGCAC
1379111 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
1379139 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* *
1379167 CCTTTTAAGTCTACAAGTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1379194 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1379221 CCTTTTAAGTCCACAACTTCGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
1379249 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1379276 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
1379303 CCTTTTAAGTCCATAACTCCGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
* * *
1379331 TCTTTTAAAGTCCATAACTCTGTGGCAC
1 CCTTTT-AAGTCCACAACTCCGTGGCAC
* *
1379359 CCTTTTAAGTTCACAACTTCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
1379386 CCTTTTTAAGTCCA
1 CC-TTTTAAGTCCA
1379400 TAAGATGGTG
Statistics
Matches: 952, Mismatches: 62, Indels: 34
0.91 0.06 0.03
Matches are distributed among these distances:
26 24 0.03
27 454 0.48
28 446 0.47
29 28 0.03
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:1379520 original size:28 final size:28
Alignment explanation
Indices: 1379422--1379691 Score: 234
Period size: 28 Copynumber: 9.4 Consensus size: 28
1379412 ATTCCCTTCT
*
1379422 AAAGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTTAGTGGCA-TCTTTTC
*
1379451 AAAGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTTAGTGGCA-TCTTTTC
* *
1379480 AAAGCCCATAAGTTAATGGCATCTTTTC
1 AAAGCCCACAAGTTAGTGGCATCTTTTC
* *
1379508 AAAGCCTACAAGTCAGTGGCATCTTTTC
1 AAAGCCCACAAGTTAGTGGCATCTTTTC
* *
1379536 AAAGTCCACACAAGTTGGTGGCATCCTTTC
1 AAAG-CC-CACAAGTTAGTGGCATCTTTTC
* * *
1379566 AAAACCCACAAGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTTAGTGGCATCTTTTC
* * * * * *
1379594 ATAGCCCACAAGTCAATGACACCATTTC
1 AAAGCCCACAAGTTAGTGGCATCTTTTC
* * * * *
1379622 AAAACCCACAAGTCAGTGACACCATTTC
1 AAAGCCCACAAGTTAGTGGCATCTTTTC
** * *
1379650 AAAGCCTGCACAAGTCGGTGGCAACCCATTTC
1 AAAGCC--CACAAGTTAGTGGC-A-TCTTTTC
1379682 AAAGCCCACA
1 AAAGCCCACA
1379692 CAAGTCGGTA
Statistics
Matches: 209, Mismatches: 26, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
28 106 0.51
29 52 0.25
30 37 0.18
31 1 0.00
32 13 0.06
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (28 bp):
AAAGCCCACAAGTTAGTGGCATCTTTTC
Found at i:1379662 original size:86 final size:84
Alignment explanation
Indices: 1379407--1379852 Score: 309
Period size: 86 Copynumber: 4.9 Consensus size: 84
1379397 CCATAAGATG
* * *
1379407 GTGGCATTCCCTTCTAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTTAGTGGCA
1 GTGGCA-TCCTTTC-AAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAACCCACAAGTTAGTGGCA
* *
1379472 CCCTTTTCAAAGCCCATAAGTTA
63 CCC-TTTCAAAGCCCACAAGTCA
* * * * * * *
1379495 ATGGCATCTTTTCAAAGCCTACAAGTCAGTGGCATCTTTTCAAAGTCCACACAAGTTGGTGGCAT
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAA-ACC-CACAAGTTAGTGGCAC
*
1379560 CCTTTCAAAACCCACAAGTCA
64 CCTTTCAAAGCCCACAAGTCA
* * * * * * *
1379581 GTGGCATCCTTTCATAGCCCACAAGTCAATGACACCATTTCAAAACCCACAAGTCAGTGACACCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAACCCACAAGTTAGTGGCACCC
*
1379646 TTTCAAAGCCTGCACAAGTCG
66 TTTCAAAGCC--CACAAGTCA
* * * * *
1379667 GTGGCAACCCATTTCAAAGCCCACACAAGTCGGTAGCAACCCCTTTTCAAAGCCTACACAAG-TC
1 GTGGC-ATCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A--CCTTTTCAAAACC--CACAAGTTA
* *
1379731 GATGGCAACCTATTTCAAAGCCCACACAAGTCG
57 G-TGGC-ACC-CTTTCAAAG-CC-CACAAGTCA
* * **
1379764 GTGGCAATCCATTTCAAAGCCCACACAAGTCGGTGGCAATCCTTTTCAAAGCCCACACAAGTCGG
1 GTGGC-ATCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A-CCTTTTCAAA-ACC-CACAAGTTAG
1379829 TGGCAACCCTTTTCAAAGCCCACA
58 TGGC-ACCC-TTTCAAAGCCCACA
1379853 CAAGTTGATG
Statistics
Matches: 291, Mismatches: 47, Indels: 34
0.78 0.13 0.09
Matches are distributed among these distances:
84 22 0.08
85 11 0.04
86 86 0.30
87 24 0.08
88 12 0.04
89 2 0.01
90 10 0.03
91 1 0.00
93 11 0.04
94 5 0.02
95 11 0.04
96 36 0.12
97 58 0.20
98 2 0.01
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (84 bp):
GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAACCCACAAGTTAGTGGCACCC
TTTCAAAGCCCACAAGTCA
Found at i:1379682 original size:32 final size:32
Alignment explanation
Indices: 1379532--1379942 Score: 359
Period size: 32 Copynumber: 13.2 Consensus size: 32
1379522 AGTGGCATCT
* * *
1379532 TTTCAAAGTCCACACAAGTTGGTGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
1379562 TTTCAAA-ACC-CACAAGTCAGTGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* ** *
1379590 TTTCATAG-CC-CACAAGTCAATGAC-A-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
1379618 TTTCAAA-ACC-CACAAGTCAGTGAC-A-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
**
1379646 TTTCAAAGCCTGCACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1379678 TTTCAAAGCCCACACAAGTCGGTAGCAACCCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAA-CCCA
* * *
1379711 TTTCAAAGCCTACACAAGTCGATGGCAACCTA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1379743 TTTCAAAGCCCACACAAGTCGGTGGCAATCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1379775 TTTCAAAGCCCACACAAGTCGGTGGCAATCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1379807 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
1379839 TTTCAAAGCCCACACAAGTTGATGGGAACCTC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACC-CA
* ** *
1379871 TTTCAAAAGTCCACAC-TTTCGGTGGCAACCCTT
1 TTTC-AAAGCCCACACAAGTCGGTGGCAACCC-A
* * * *
1379904 TTTAAAAGCCCACGCAAGTCAGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1379936 TTTCAAA
1 TTTCAAA
1379943 TCACCATTTT
Statistics
Matches: 325, Mismatches: 43, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
27 2 0.01
28 69 0.21
29 3 0.01
30 19 0.06
31 2 0.01
32 176 0.54
33 54 0.17
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:1379759 original size:97 final size:97
Alignment explanation
Indices: 1379646--1379942 Score: 379
Period size: 97 Copynumber: 3.1 Consensus size: 97
1379636 AGTGACACCA
** *
1379646 TTTCAAAGCCTGCACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTAGCAACCCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCCT
*
1379711 TTTCAAAGCCTACACAAGTCGATGGCAA-CCT
66 TTTCAAAGCCCACACAAGTCGATGGCAACCCT
* *
1379742 ATTTCAAAGCCCACACAAGTCGGTGGCAATCCATTTCAAAGCCCACACAAGTCGGTGGCAA-TCC
1 -TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCC
*
1379806 TTTTCAAAGCCCACACAAGTCGGTGGCAACCCT
65 TTTTCAAAGCCCACACAAGTCGATGGCAACCCT
* * * * **
1379839 TTTCAAAGCCCACACAAGTTGATGGGAACCTC-TTTCAAAAGTCCACAC-TTTCGGTGGCAACCC
1 TTTCAAAGCCCACACAAGTCGGTGGCAACC-CATTTC-AAAGCCCACACAAGTCGGTGGCAACCC
* * *
1379902 TTTTTAAAAGCCCACGCAAGTC-AGTGGCAACCCT
64 CTTTTCAAAGCCCACACAAGTCGA-TGGCAACCCT
1379936 TTTCAAA
1 TTTCAAA
1379943 TCACCATTTT
Statistics
Matches: 176, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
96 69 0.39
97 107 0.61
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.22
Consensus pattern (97 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCCT
TTTCAAAGCCCACACAAGTCGATGGCAACCCT
Found at i:1379811 original size:64 final size:63
Alignment explanation
Indices: 1379428--1379942 Score: 392
Period size: 64 Copynumber: 8.4 Consensus size: 63
1379418 TTCTAAAGCC
** * **
1379428 CACAAGTTAGTGGCACCCTTTTCAAAG-CC-CACAAGTTAGTGGC-ACCCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* *** * * * * *
1379486 CATAAGTTAATGGC-ATCTTTTCAAAG-CC-TACAAGTCAGTGGC-A-TCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* * * * * *
1379544 CACAAGTTGGTGGCATCC-TTTCAAA-ACC-CACAAGTCAGTGGC-ATCC-TTTCATAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
** * * * * * * **
1379600 CACAAGTCAATGAC-ACCATTTCAAA-ACC-CACAAGTCAGTGAC-A-CCATTTCAAAGCCTG
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* * *
1379658 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTAGCAACCCCTTTTCAAAGCCTA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCACACAAGTCGGTGGCAA-CCCTTTTCAAAGCCCA
* * *
1379723 CACAAGTCGATGGCAACCTATTTCAAAGCCCACACAAGTCGGTGGCAATCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCT-TTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1379787 CACAAGTCGGTGGCAATCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* * * * ** *
1379851 CACAAGTTGATGGGAACCTCTTTCAAAAGTCCACAC-TTTCGGTGGCAACCCTTTTTAAAAGCCC
1 CACAAGTCGGTGGCAACCT-TTTC-AAAGCCCACACAAGTCGGTGGCAACCC-TTTTCAAAGCCC
1379915 A
63 A
* *
1379916 CGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAA-CCTTTTCAAA
1379943 TCACCATTTT
Statistics
Matches: 382, Mismatches: 53, Indels: 38
0.81 0.11 0.08
Matches are distributed among these distances:
55 4 0.01
56 51 0.13
57 30 0.08
58 64 0.17
59 3 0.01
60 10 0.03
61 2 0.01
62 11 0.03
63 4 0.01
64 105 0.27
65 95 0.25
66 3 0.01
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (63 bp):
CACAAGTCGGTGGCAACCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
Found at i:1381200 original size:17 final size:15
Alignment explanation
Indices: 1381180--1381228 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
1381170 TTAGATAAGA
1381180 AAGAAAGAAAGAAGATG
1 AAGAAAGAAAGAA-A-G
1381197 AAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAG
1381211 AA-AAAGAAA-AAA-
1 AAGAAAGAAAGAAAG
1381223 AAGAAA
1 AAGAAA
1381229 AAATATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.07
13 6 0.20
14 9 0.30
15 1 0.03
16 9 0.30
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:1381227 original size:15 final size:17
Alignment explanation
Indices: 1381180--1381230 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 17
1381170 TTAGATAAGA
1381180 AAGAAAGAAAGAAGATGAAG
1 AAGAAAGAAAGAA-A--AAG
1381200 AAGAAAGAAAGAAAAAG
1 AAGAAAGAAAGAAAAAG
1381217 AA-AAA-AAAGAAAAA
1 AAGAAAGAAAGAAAAA
1381231 ATATGAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.29
16 3 0.10
17 5 0.16
19 1 0.03
20 13 0.42
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (17 bp):
AAGAAAGAAAGAAAAAG
Found at i:1387651 original size:23 final size:23
Alignment explanation
Indices: 1387625--1387668 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1387615 GAAAAATGCA
1387625 TATTATCATAAGAAAAAAATATG
1 TATTATCATAAGAAAAAAATATG
*
1387648 TATTATCATAAGGAAAAAATA
1 TATTATCATAAGAAAAAAATA
1387669 AAATTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (23 bp):
TATTATCATAAGAAAAAAATATG
Found at i:1389350 original size:55 final size:56
Alignment explanation
Indices: 1389291--1389397 Score: 137
Period size: 55 Copynumber: 1.9 Consensus size: 56
1389281 GGAGTAGCTA
* * * *
1389291 GTAAGTTTAGCTCCAGTTGAAA-TTGACACCTA-ATATAATAGCCTAAGAGTAATTG
1 GTAAGTTTAGCTCCAGTTAAAATTTG-CACCTAGATAAAAAAACCTAAGAGTAATTG
* *
1389346 GTAAGTTTATCTCTAGTTAAAATTTGCACCTAGATAAAAAAACCTAAGAGTA
1 GTAAGTTTAGCTCCAGTTAAAATTTGCACCTAGATAAAAAAACCTAAGAGTA
1389398 GCAAATAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
55 25 0.57
56 19 0.43
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (56 bp):
GTAAGTTTAGCTCCAGTTAAAATTTGCACCTAGATAAAAAAACCTAAGAGTAATTG
Found at i:1389480 original size:111 final size:112
Alignment explanation
Indices: 1389350--1389561 Score: 252
Period size: 111 Copynumber: 1.9 Consensus size: 112
1389340 TAATTGGTAA
* * * *
1389350 GTTTATCTCTAGTTAAAATT-TGCACCTAGATAAAAAAACCT-AAGAGTAGCAAATAAGTTTT-G
1 GTTTAGCTCAAGTTAAAATTGT-CACCTAAAT-AAAAAACCTCAAAAGTAGCAAAT-AGTTTTAG
* * *
1389412 CCCTAGTTGAAATT-GCATCTAAATAAGAGAGCCCAAGAACAACTTGTAG
63 CCCAAGTTGAAATTGGCACCTAAATAAGAAAGCCCAAGAACAACTTGTAG
* * * * *
1389461 GTTTAGCTCAAGTTGAAATTGTCACCTAAATGAGAAAGCTCAAAAGTAGCAAATAGTTTTAGCTC
1 GTTTAGCTCAAGTTAAAATTGTCACCTAAATAAAAAACCTCAAAAGTAGCAAATAGTTTTAGCCC
*
1389526 AAGTTGAAATTGGCACCTAGATAAGAAAGCCCAAGA
66 AAGTTGAAATTGGCACCTAAATAAGAAAGCCCAAGA
1389562 GTAACTAATA
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
110 12 0.14
111 50 0.60
112 22 0.26
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (112 bp):
GTTTAGCTCAAGTTAAAATTGTCACCTAAATAAAAAACCTCAAAAGTAGCAAATAGTTTTAGCCC
AAGTTGAAATTGGCACCTAAATAAGAAAGCCCAAGAACAACTTGTAG
Found at i:1389820 original size:111 final size:112
Alignment explanation
Indices: 1389653--1389934 Score: 281
Period size: 111 Copynumber: 2.5 Consensus size: 112
1389643 AAAATTGGCC
* * * *
1389653 CCCATATGAGAAAACCC-AAAAGTAGCTAGTATGTTTAGC-TCTAGTTGAAATTGGCACCATAAG
1 CCCAAATGA-AAAACCCTAAGAGTAGCTGGTAGGTTTAGCTTC-AGTTGAAATTGGCACCAT-AG
* * *
1389716 -GAGAAAGCCAAAGAGTAGCTAGTAAGTTTAGATC-AAGTTGAAA-TATGCA
63 TGAAAAAGCCAAAGAGTAGCTACTAAGTTTAGATCTAA-TTGAAATTA-ACA
** * *
1389765 -CCAGTTGAAAAACCCTAAGAGTAGCTGGTAGGTTTAACTTCAGTTAAAATTGGCACC-TAGTTG
1 CCCAAATGAAAAACCCTAAGAGTAGCTGGTAGGTTTAGCTTCAGTTGAAATTGGCACCATAG-TG
* * * *
1389828 AAAAAGTCTAAGAGTAGCTACTAGGTTTAGCTCTAATTGAAATTAACA
65 AAAAAGCCAAAGAGTAGCTACTAAGTTTAGATCTAATTGAAATTAACA
* * * * *
1389876 CCCAAATGAAAAATCCTAAGAATAGTTGATAGGTTTAGCTTTAGTTGAAATTGGCACCA
1 CCCAAATGAAAAACCCTAAGAGTAGCTGGTAGGTTTAGCTTCAGTTGAAATTGGCACCA
1389935 AAATGATTAA
Statistics
Matches: 139, Mismatches: 23, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
109 2 0.01
110 8 0.06
111 75 0.54
112 54 0.39
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (112 bp):
CCCAAATGAAAAACCCTAAGAGTAGCTGGTAGGTTTAGCTTCAGTTGAAATTGGCACCATAGTGA
AAAAGCCAAAGAGTAGCTACTAAGTTTAGATCTAATTGAAATTAACA
Found at i:1389871 original size:56 final size:56
Alignment explanation
Indices: 1389273--1389933 Score: 307
Period size: 56 Copynumber: 11.9 Consensus size: 56
1389263 CCTAAATAAG
** * * * *
1389273 AAAGCCTTGGAGTAGCTAGTAAGTTTAGCTCCAGTTGAAATTGACACCTA-AT-ATA
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGA-A
* ** * * * * * * *
1389328 ATAGCCTAAGAGTAATTGGTAAGTTTATCTCTAGTTAAAATTTGCACCTAGATAAA
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGAA
* * * * * * * **
1389384 AAAACCTAAGAGTAGCAAATAAGTTTTGCCCTAGTTGAAATT-GCATCTAAAT-AA
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGAA
* * ** * * * * ** *
1389438 GAGAGCCCAAGAACAACTTGTAGGTTTAGCTCAAGTTGAAATTGTCACCTAAATGAG
1 -AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGAA
* * * * * *
1389495 AAAG-CTCAAAAGTAGCAAATAGTTTTAGCTCAAGTTGAAATTGGCACCTAGAT-AA
1 AAAGCCT-AAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGAA
* * * * * * **
1389550 GAAAGCCCAAGAGTAACTAATATGTTTCA-CCCTAATTGAAATTGGCATCC-AAATGAA
1 -AAAGCCTAAGAGTAGCTAGTAGGTTT-AGCTCTAGTTGAAATTGGCA-CCTAGTTGAA
* * ** * * * *
1389607 AGAA-CCTAAAATTATTTAGTAAGTTTCA-C-CTGAGTTAAAATTGGCCCCCA-TATGAGA
1 A-AAGCCTAAGAGTAGCTAGTAGGTTT-AGCTCT-AGTTGAAATTGGCACCTAGT-TGA-A
* * * *
1389664 AAA-CCCAAAAGTAGCTAGTATGTTTAGCTCTAGTTGAAATTGGCACCATAAG--GAG
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACC-T-AGTTGAA
* * * *
1389719 AAAGCCAAAGAGTAGCTAGTAAGTTTAGATCAAGTTGAAATAT-GCACC-AGTTGAA
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAAT-TGGCACCTAGTTGAA
* * * *
1389774 AAACCCTAAGAGTAGCTGGTAGGTTTAACT-TCAGTTAAAATTGGCACCTAGTTGAA
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCT-AGTTGAAATTGGCACCTAGTTGAA
* * * ** * **
1389830 AAAGTCTAAGAGTAGCTACTAGGTTTAGCTCTAATTGAAATTAACACCCAAATGAA
1 AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGAA
* * * *
1389886 AAATCCTAAGAATAG-TTGATAGGTTTAGCTTTAGTTGAAATTGGCACC
1 AAAGCCTAAGAGTAGCTAG-TAGGTTTAGCTCTAGTTGAAATTGGCACC
1389934 AAAATGATTA
Statistics
Matches: 458, Mismatches: 118, Indels: 59
0.72 0.19 0.09
Matches are distributed among these distances:
53 2 0.00
54 3 0.01
55 126 0.28
56 310 0.68
57 16 0.03
58 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (56 bp):
AAAGCCTAAGAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCTAGTTGAA
Found at i:1392289 original size:76 final size:75
Alignment explanation
Indices: 1392152--1392330 Score: 180
Period size: 76 Copynumber: 2.3 Consensus size: 75
1392142 ATCGAGTCTA
* * * * * * *
1392152 AGGTCATGAAAGAATTTTCATTTAGATATATGTCCGTTAAGGTCATTTAAGTAATATTACATCAA
1 AGGTCATGTAA-AACTTTCATGTCGATACATGTCCGTTAAGGTCATTTAAGCAATAGTACATCAA
1392217 AAACAAG-TCT
65 AAACAAGCTCT
* * * * *
1392227 ACGGTCATGTGAAAACTTTCTTGTCGATACATGTCTGTTAAGGTCATTTAGGCAATGGTACATTA
1 A-GGTCATGT-AAAACTTTCATGTCGATACATGTCCGTTAAGGTCATTTAAGCAATAGTACATCA
*
1392292 AAACCAAGCTTCT
64 AAAACAAGC-TCT
**
1392305 AGGTTTTGTAAAACTTTCATGTCGAT
1 AGGTCATGTAAAACTTTCATGTCGAT
1392331 GGATGTCTTT
Statistics
Matches: 84, Mismatches: 16, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
75 1 0.01
76 71 0.85
77 8 0.10
78 4 0.05
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (75 bp):
AGGTCATGTAAAACTTTCATGTCGATACATGTCCGTTAAGGTCATTTAAGCAATAGTACATCAAA
AACAAGCTCT
Found at i:1393783 original size:13 final size:13
Alignment explanation
Indices: 1393765--1393789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1393755 CATAAAATGT
1393765 TGTATCGATACAA
1 TGTATCGATACAA
1393778 TGTATCGATACA
1 TGTATCGATACA
1393790 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.