Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 6 of 145
Found at i:2055504 original size:22 final size:22
Alignment explanation
Indices: 2055479--2055528 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
2055469 TTGATTTCAC
* *
2055479 ATTATTTTGCTACCATTTTGTT
1 ATTATTTTACTACCATTTTATT
* *
2055501 ATTATATTACTACTATTTTATT
1 ATTATTTTACTACCATTTTATT
*
2055523 GTTATT
1 ATTATT
2055529 GTTTGGATAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.60
Consensus pattern (22 bp):
ATTATTTTACTACCATTTTATT
Found at i:2057181 original size:27 final size:26
Alignment explanation
Indices: 2057131--2057191 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
2057121 ACCAAAAATT
*
2057131 TATTTTAAAAATAAAAAACAAAAAAG
1 TATTTTAAAAATAAAAAACAAAAAAA
*
2057157 TATTTTAAAATTAAAAAA-ATTAAAAAA
1 TATTTTAAAAATAAAAAACA--AAAAAA
2057184 TATATTTA
1 TAT-TTTA
2057192 TTTATTCGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 1 0.03
26 17 0.57
27 8 0.27
28 4 0.13
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (26 bp):
TATTTTAAAAATAAAAAACAAAAAAA
Found at i:2057461 original size:23 final size:25
Alignment explanation
Indices: 2057425--2057480 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
2057415 TTAATATTTA
*
2057425 TAATTTTTTTATT-AATTTGGTT-T
1 TAATTTTTTAATTAAATTTGGTTAT
* *
2057448 TCATTTTTTAATTAAATTTTGTTAT
1 TAATTTTTTAATTAAATTTGGTTAT
2057473 TAATTTTT
1 TAATTTTT
2057481 CAAAAGAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 11 0.41
24 8 0.30
25 8 0.30
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (25 bp):
TAATTTTTTAATTAAATTTGGTTAT
Found at i:2057480 original size:13 final size:12
Alignment explanation
Indices: 2057421--2057480 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
2057411 GTCTTTAATA
2057421 TTTA-TAATTTT
1 TTTATTAATTTT
*
2057432 TTTATTAATTTG
1 TTTATTAATTTT
* *
2057444 GTT-TTCATTTT
1 TTTATTAATTTT
*
2057455 TTAATTAAATTTT
1 TTTATT-AATTTT
*
2057468 GTTATTAATTTT
1 TTTATTAATTTT
2057480 T
1 T
2057481 CAAAAGAGTA
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
11 11 0.31
12 16 0.44
13 9 0.25
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (12 bp):
TTTATTAATTTT
Found at i:2060159 original size:12 final size:13
Alignment explanation
Indices: 2060130--2060167 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
2060120 TAAAAAACAT
*
2060130 TAATTTGTTTATA
1 TAATTTTTTTATA
2060143 TAATTTTTTTA-A
1 TAATTTTTTTATA
*
2060155 TAATTTTATTATA
1 TAATTTTTTTATA
2060168 CATTTTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (13 bp):
TAATTTTTTTATA
Found at i:2062912 original size:20 final size:19
Alignment explanation
Indices: 2062887--2062934 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
2062877 TCAAAACACG
*
2062887 TTTATAATAATATAACTAAT
1 TTTATAATAAAATAA-TAAT
2062907 TTTATATATAAAATAATAAT
1 TTTATA-ATAAAATAATAAT
*
2062927 TTAATAAT
1 TTTATAAT
2062935 TTTTGAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 15 0.60
21 8 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTATAATAAAATAATAAT
Found at i:2064386 original size:6 final size:6
Alignment explanation
Indices: 2064375--2064401 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2064365 CAAAGCTAAA
2064375 CCATCT CCATCT CCATCT CCATCT CCA
1 CCATCT CCATCT CCATCT CCATCT CCA
2064402 ACCGCTACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.52, G:0.00, T:0.30
Consensus pattern (6 bp):
CCATCT
Found at i:2070439 original size:23 final size:22
Alignment explanation
Indices: 2070407--2070468 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
2070397 GCCCGGCCCG
*
2070407 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
2070431 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
2070453 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
2070469 TTGTTATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 15 0.42
24 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:2070481 original size:16 final size:16
Alignment explanation
Indices: 2070442--2070482 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
2070432 TTTTATTAAA
*
2070442 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
2070458 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
2070474 ATTAAAATT
1 ATTAAAATT
2070483 GTATCAGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:2070604 original size:34 final size:37
Alignment explanation
Indices: 2070565--2070650 Score: 115
Period size: 40 Copynumber: 2.3 Consensus size: 37
2070555 TTGTTAATTG
2070565 TATTAATTGTTACTAA-A-ATT-ATCAAATTATTAAT
1 TATTAATTGTTACTAACATATTAATCAAATTATTAAT
*
2070599 TATTAATTGTTACTAACATTTTGTTAATCAAATTATTAAT
1 TATTAATTGTTACTAACA---TATTAATCAAATTATTAAT
2070639 TATTAATTGTTA
1 TATTAATTGTTA
2070651 ATTGTATTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
34 16 0.36
35 1 0.02
39 2 0.04
40 26 0.58
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.50
Consensus pattern (37 bp):
TATTAATTGTTACTAACATATTAATCAAATTATTAAT
Found at i:2076595 original size:31 final size:31
Alignment explanation
Indices: 2076555--2076615 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2076545 TTGGACAAAA
*
2076555 AAGCTAAGTTCAAGTA-ATAATTTGAATCAAG
1 AAGCCAAGTTCAAGTACATAATTTG-ATCAAG
* *
2076586 AAGCCAAGTTCAGGTACTTAATTTGATCAA
1 AAGCCAAGTTCAAGTACATAATTTGATCAA
2076616 AATAAACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (31 bp):
AAGCCAAGTTCAAGTACATAATTTGATCAAG
Found at i:2086242 original size:18 final size:18
Alignment explanation
Indices: 2086219--2086254 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2086209 CAATTAAACC
2086219 ATTTGATTGATATATTTA
1 ATTTGATTGATATATTTA
* *
2086237 ATTTGATTTATTTATTTA
1 ATTTGATTGATATATTTA
2086255 TAAATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
ATTTGATTGATATATTTA
Found at i:2086317 original size:20 final size:20
Alignment explanation
Indices: 2086294--2086332 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2086284 CAATTTAAAA
2086294 TATAAAAAATTATTAATATG
1 TATAAAAAATTATTAATATG
* **
2086314 TATATAATTTTATTAATAT
1 TATAAAAAATTATTAATAT
2086333 ATGTAAAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAAATTATTAATATG
Found at i:2086389 original size:30 final size:33
Alignment explanation
Indices: 2086354--2086429 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
2086344 ACTTTTCCGA
*
2086354 AAAATATTTTCAGGA-ACT-A-CCAAACAACAG
1 AAAATATTTTCAGCAGACTCATCCAAACAACAG
* *
2086384 AAAATATTTTACA-CAGATTCATCCAAACACCAG
1 AAAATATTTT-CAGCAGACTCATCCAAACAACAG
2086417 AAAATATTTTCAG
1 AAAATATTTTCAG
2086430 TAAATCATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 11 0.29
31 4 0.11
32 3 0.08
33 20 0.53
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (33 bp):
AAAATATTTTCAGCAGACTCATCCAAACAACAG
Found at i:2086454 original size:20 final size:20
Alignment explanation
Indices: 2086429--2086467 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2086419 AATATTTTCA
2086429 GTAAATCATTTTCCAGAAAT
1 GTAAATCATTTTCCAGAAAT
*
2086449 GTAAATCATTTTCCGGAAA
1 GTAAATCATTTTCCAGAAA
2086468 ATATTTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
GTAAATCATTTTCCAGAAAT
Found at i:2097596 original size:4 final size:4
Alignment explanation
Indices: 2097589--2097614 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2097579 TTACAGTTGG
2097589 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
2097615 TTATTATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:2102185 original size:22 final size:22
Alignment explanation
Indices: 2102153--2102196 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2102143 TATATAAAAA
2102153 GAGCTTAAATACAAATGAGTTT
1 GAGCTTAAATACAAATGAGTTT
* *
2102175 GAGCTTGAATACTAATGAGTTT
1 GAGCTTAAATACAAATGAGTTT
2102197 AATTGAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (22 bp):
GAGCTTAAATACAAATGAGTTT
Found at i:2114393 original size:2 final size:2
Alignment explanation
Indices: 2114345--2114374 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2114335 AGCAATAATG
2114345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2114375 AAGGTATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2114616 original size:236 final size:235
Alignment explanation
Indices: 2114331--2114801 Score: 917
Period size: 236 Copynumber: 2.0 Consensus size: 235
2114321 TTAAGTATAT
2114331 ACATAGCAATAATGTATATATATATATATATATATATATATATAAAGGTATTCAAGCATATATGA
1 ACATAGCAATAATGTATATATATATATATATATATATATATATAAAGGTATTCAAGCATATATGA
2114396 AAACTATCCTGTGCACAGAACTTCATAGTGTGAAAAATGGCAGGCTTAATTGATCAGCGAAATGT
66 AAACTATCCTGTGCACAGAACTTCATAGTGTGAAAAATGGCAGGCTTAATTGATCAGCGAAATGT
2114461 AACTATCAAATATGTGTCTATTTTTTAATATGCTTTGTTTCGGTGAAAAGATATTTGTGGTATAA
131 AACTATCAAATATGTGTCTATTTTTTAATATGCTTTGTTTCGGTGAAAAGATATTTGTGGTATAA
2114526 TAACAAGTTTAGCTCTTGATGTTTATATATTTTAGGTAAA
196 TAACAAGTTTAGCTCTTGATGTTTATATATTTTAGGTAAA
2114566 ACATAGCAAT-ATGTATATATATATATATATATATATATATATATAAAGGTATTCAAGCATATAT
1 ACATAGCAATAATG--TATATATATATATATATATATATATATATAAAGGTATTCAAGCATATAT
2114630 GAAAACTATCCTGTGCACAGAACTTCATAGTGTGAAAAATGGCAGGCTTAATTGATCAGCGAAAT
64 GAAAACTATCCTGTGCACAGAACTTCATAGTGTGAAAAATGGCAGGCTTAATTGATCAGCGAAAT
2114695 GTAACTATCAAATATGTGTCTATTTTTTAATATGCTTTGTTTCGGTGAAAAGATATTTGTGGTAT
129 GTAACTATCAAATATGTGTCTATTTTTTAATATGCTTTGTTTCGGTGAAAAGATATTTGTGGTAT
2114760 AATAACAAGTTTAGCTCTTGATGTTTATATATTTTAGGTAAA
194 AATAACAAGTTTAGCTCTTGATGTTTATATATTTTAGGTAAA
2114802 TGATGACAAA
Statistics
Matches: 234, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
234 3 0.01
235 10 0.04
236 221 0.94
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (235 bp):
ACATAGCAATAATGTATATATATATATATATATATATATATATAAAGGTATTCAAGCATATATGA
AAACTATCCTGTGCACAGAACTTCATAGTGTGAAAAATGGCAGGCTTAATTGATCAGCGAAATGT
AACTATCAAATATGTGTCTATTTTTTAATATGCTTTGTTTCGGTGAAAAGATATTTGTGGTATAA
TAACAAGTTTAGCTCTTGATGTTTATATATTTTAGGTAAA
Found at i:2114629 original size:2 final size:2
Alignment explanation
Indices: 2114574--2114610 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2114564 AAACATAGCA
*
2114574 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2114611 AAGGTATTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2119232 original size:30 final size:29
Alignment explanation
Indices: 2119175--2119256 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 29
2119165 AAATTGTGGA
* *
2119175 TTTAATTTTTATACTTTT-AATTGATCAAT
1 TTTAATCTTTATATTTTTGAA-TGATCAAT
2119204 TTTAATCTTTATATTTTTTGAATGATCAAT
1 TTTAATCTTTATA-TTTTTGAATGATCAAT
*
2119234 TTTAGTCTTTATACTTTTTGAAT
1 TTTAATCTTTATA-TTTTTGAAT
2119257 TATGAAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
29 12 0.26
30 33 0.70
31 2 0.04
ACGTcount: A:0.28, C:0.07, G:0.06, T:0.59
Consensus pattern (29 bp):
TTTAATCTTTATATTTTTGAATGATCAAT
Found at i:2126277 original size:20 final size:20
Alignment explanation
Indices: 2126254--2126292 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2126244 CATTAAATAA
2126254 ATTATTAAAAATTTAAAAAT
1 ATTATTAAAAATTTAAAAAT
*
2126274 ATTATTACAAATTTAAAAA
1 ATTATTAAAAATTTAAAAA
2126293 AATAGTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTATTAAAAATTTAAAAAT
Found at i:2126319 original size:21 final size:20
Alignment explanation
Indices: 2126295--2126352 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
2126285 TTTAAAAAAA
2126295 TAGTTCGATCAATTCAACTAT
1 TAGTTCGATCAATTCAACT-T
* * *
2126316 TAGTTCAATCGATTTTAACTT
1 TAGTTCGATC-AATTCAACTT
2126337 TA-TTCGTATCAATTCA
1 TAGTTCG-ATCAATTCA
2126353 CAAATCAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 7 0.24
21 15 0.52
22 7 0.24
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (20 bp):
TAGTTCGATCAATTCAACTT
Found at i:2126884 original size:82 final size:83
Alignment explanation
Indices: 2126774--2126950 Score: 331
Period size: 82 Copynumber: 2.2 Consensus size: 83
2126764 AAAATATATA
*
2126774 AAAAAATACA-AATAAATAAATTTAATTAATTGTAAACCCAAAAAGAATAAATTTATAATATAAT
1 AAAAAATAAACAATAAATAAATTTAATTAATTGTAAACCCAAAAAGAATAAATTTATAATATAAT
2126838 TTATCTATTTCTATTTAT
66 TTATCTATTTCTATTTAT
2126856 AAAAAATAAACAATAAATAAA-TTAATTAATTGTAAACCCAAAAAGAATAAATTTATAATATAAT
1 AAAAAATAAACAATAAATAAATTTAATTAATTGTAAACCCAAAAAGAATAAATTTATAATATAAT
2126920 TTATCTATTTCTATTTAT
66 TTATCTATTTCTATTTAT
2126938 AAAAAATAAACAA
1 AAAAAATAAACAA
2126951 AAAAGTTATT
Statistics
Matches: 93, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
82 83 0.89
83 10 0.11
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.35
Consensus pattern (83 bp):
AAAAAATAAACAATAAATAAATTTAATTAATTGTAAACCCAAAAAGAATAAATTTATAATATAAT
TTATCTATTTCTATTTAT
Found at i:2138240 original size:14 final size:14
Alignment explanation
Indices: 2138215--2138251 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2138205 TTCTCATTTT
2138215 TCATTTTCTTTCTC
1 TCATTTTCTTTCTC
* *
2138229 TCGTTTTTTTTCTC
1 TCATTTTCTTTCTC
2138243 TCATTTTCT
1 TCATTTTCT
2138252 CCTATTACCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.05, C:0.24, G:0.03, T:0.68
Consensus pattern (14 bp):
TCATTTTCTTTCTC
Found at i:2138570 original size:21 final size:24
Alignment explanation
Indices: 2138520--2138575 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 24
2138510 GGATAATTAA
2138520 CTTAATTAA-TTTAAACTAATCATG
1 CTTAATTAACTTTAAACTAA-CATG
2138544 CTTTAATTAACTTTAAACT-A-AT-
1 C-TTAATTAACTTTAAACTAACATG
2138566 CTTAATTAAC
1 CTTAATTAAC
2138576 ATAAGTAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 9 0.30
22 1 0.03
23 2 0.07
24 1 0.03
25 9 0.30
26 8 0.27
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
CTTAATTAACTTTAAACTAACATG
Found at i:2138574 original size:25 final size:25
Alignment explanation
Indices: 2138515--2138574 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
2138505 ATTAGGGATA
2138515 ATTAACTTAATTAATTTAAACTAATC
1 ATTAA-TTAATTAATTTAAACTAATC
***
2138541 ATGCTTTAATTAACTTTAAACTAATC
1 ATTAATTAATTAA-TTTAAACTAATC
2138567 -TTAATTAA
1 ATTAATTAA
2138575 CATAAGTAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTAATTAATTAATTTAAACTAATC
Found at i:2140492 original size:41 final size:42
Alignment explanation
Indices: 2140352--2140502 Score: 151
Period size: 42 Copynumber: 3.6 Consensus size: 42
2140342 AAGGCTTAAT
* * *
2140352 AGAACCTCATGAGAGCTAAACAGAAACCCATAAGGGTTGAAC
1 AGAAGCTCATGAGAGCTGAACAGAAACCCATAAGGGTTAAAC
* * * * *
2140394 GGAAGCTCGTAAAAGCTGAACGGAAACCCATAAGGGTTAAAC
1 AGAAGCTCATGAGAGCTGAACAGAAACCCATAAGGGTTAAAC
* * * * *
2140436 AGAAGCACATTAGAGCTGAAC-GAAACTCATATGAGTTAAAC
1 AGAAGCTCATGAGAGCTGAACAGAAACCCATAAGGGTTAAAC
* * *
2140477 AGAAGCTCGTGAGAGCTAAATAGAAA
1 AGAAGCTCATGAGAGCTGAACAGAAA
2140503 GAAACACAAA
Statistics
Matches: 87, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
41 33 0.38
42 54 0.62
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (42 bp):
AGAAGCTCATGAGAGCTGAACAGAAACCCATAAGGGTTAAAC
Found at i:2150948 original size:2 final size:2
Alignment explanation
Indices: 2150943--2150967 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2150933 GAAGCATCTA
2150943 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2150968 GTTAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2151574 original size:31 final size:31
Alignment explanation
Indices: 2151536--2151604 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
2151526 ATACCGATTA
*
2151536 TTGAATAGTCTAGTGACTTAAATAAAAACTT
1 TTGAATAGTCTAGTGACTTAAACAAAAACTT
* *
2151567 TTGAATAGTTTAGTGACTTAAACAAAATCTT
1 TTGAATAGTCTAGTGACTTAAACAAAAACTT
*
2151598 TCGAATA
1 TTGAATA
2151605 ATTCAGTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (31 bp):
TTGAATAGTCTAGTGACTTAAACAAAAACTT
Found at i:2151613 original size:31 final size:31
Alignment explanation
Indices: 2151547--2151613 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
2151537 TGAATAGTCT
* * * *
2151547 AGTGACTTAAATAAAAACTTTTGAATAGTTT
1 AGTGACTTAAACAAAAACTTTCGAATAATTC
*
2151578 AGTGACTTAAACAAAATCTTTCGAATAATTC
1 AGTGACTTAAACAAAAACTTTCGAATAATTC
2151609 AGTGA
1 AGTGA
2151614 TCATTCTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (31 bp):
AGTGACTTAAACAAAAACTTTCGAATAATTC
Found at i:2152911 original size:17 final size:18
Alignment explanation
Indices: 2152880--2152913 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2152870 GTCTCACATC
*
2152880 ATTTTCATATCAAGATAG
1 ATTTTCATATAAAGATAG
2152898 ATTTT-ATATAAAGATA
1 ATTTTCATATAAAGATA
2152914 TTTACATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (18 bp):
ATTTTCATATAAAGATAG
Found at i:2153589 original size:22 final size:21
Alignment explanation
Indices: 2153563--2153619 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
2153553 GCTATGCGAG
2153563 TAAAAATGAAAATAATATATT-T
1 TAAAAA-GAAAATAATA-ATTAT
*
2153585 T-AAAAGAAACTAATAATTAT
1 TAAAAAGAAAATAATAATTAT
2153605 TAATAAAGAAAATAA
1 TAA-AAAGAAAATAA
2153620 AAAATACATG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 3 0.10
20 11 0.37
21 5 0.17
22 11 0.37
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAAAAGAAAATAATAATTAT
Found at i:2153700 original size:34 final size:31
Alignment explanation
Indices: 2153637--2153714 Score: 106
Period size: 34 Copynumber: 2.5 Consensus size: 31
2153627 ATGAATGGTT
*
2153637 ATTGATAAAAG-A-TTTTTTTTTGACGATTA
1 ATTGATAAAAGAATTTTTTTTTTGACAATTA
2153666 ATTGATAAAAGAATTTTTTTTTTGAACCAAATTA
1 ATTGATAAAAGAATTTTTTTTTTG-A-C-AATTA
2153700 ATTGATAAAAGAATT
1 ATTGATAAAAGAATT
2153715 GTATGAGAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 11 0.26
30 1 0.02
31 10 0.23
32 1 0.02
33 1 0.02
34 19 0.44
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.44
Consensus pattern (31 bp):
ATTGATAAAAGAATTTTTTTTTTGACAATTA
Found at i:2164075 original size:5 final size:5
Alignment explanation
Indices: 2164065--2164092 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2164055 TATTTAAAAA
2164065 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
2164093 TAAGGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:2164831 original size:30 final size:29
Alignment explanation
Indices: 2164778--2164834 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
2164768 ATGTTAAAAA
*
2164778 TAATTTTTAGTTATTTTTATATTTTTTGG
1 TAATTTTTAATTATTTTTATATTTTTTGG
* *
2164807 TAATTTTATAATTGTTTTTCTATTTTTT
1 TAATTTT-TAATTATTTTTATATTTTTT
2164835 AAATAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.70
Consensus pattern (29 bp):
TAATTTTTAATTATTTTTATATTTTTTGG
Found at i:2165626 original size:27 final size:27
Alignment explanation
Indices: 2165588--2165642 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2165578 AGGATGGAGT
2165588 TATTTTTGGTAAAAGTATCATAAAGGC
1 TATTTTTGGTAAAAGTATCATAAAGGC
2165615 TATTTTTGGTAAAAGTATCATAAAGGC
1 TATTTTTGGTAAAAGTATCATAAAGGC
2165642 T
1 T
2165643 CTTATATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.38
Consensus pattern (27 bp):
TATTTTTGGTAAAAGTATCATAAAGGC
Found at i:2167420 original size:30 final size:29
Alignment explanation
Indices: 2167354--2167425 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 29
2167344 GTACTCTCTA
2167354 TATATTT-AGAATTTAATCCTCAATTTTT
1 TATATTTAAGAATTTAATCCTCAATTTTT
* * *
2167382 TATTTTTAAGAATTTAGTCTCTCTATTTTT
1 TATATTTAAGAATTTAATC-CTCAATTTTT
*
2167412 TGA-ATTTAAAAATT
1 T-ATATTTAAGAATT
2167426 CGGGTCTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 6 0.17
29 10 0.28
30 19 0.53
31 1 0.03
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (29 bp):
TATATTTAAGAATTTAATCCTCAATTTTT
Found at i:2172778 original size:16 final size:16
Alignment explanation
Indices: 2172759--2172800 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2172749 TCTCATGTTA
*
2172759 TTTTTT-ATTCATAAT
1 TTTTTTAATTAATAAT
2172774 TTTTTTAATTAATAAT
1 TTTTTTAATTAATAAT
**
2172790 TACTTTAATTA
1 TTTTTTAATTA
2172801 TATTCATACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTTAATTAATAAT
Found at i:2180606 original size:184 final size:184
Alignment explanation
Indices: 2180192--2180712 Score: 714
Period size: 184 Copynumber: 2.8 Consensus size: 184
2180182 AGACAAGACC
* * *
2180192 TGATTGTACATAAAAAATATACATTAGATACCATACGACAATCGAACCGGAACTAGAGACATAAC
1 TGATTGCACATGAAAAATATACATTAGATACCATACGACAATCGAACCGGAACTAGAGCCATAAC
* *
2180257 GACCATAAACACAAATTATATGCACTTTTGTATCCCAAAACAAACCAGCAGATACCGCATTAAGT
66 GACCATAAACACAATTTATATGCACTTTTGTATCCCACAACAAACCAGCAGATACCG-ATTAAGT
2180322 GCATCATCACTAAGATATTTAGGAAATATTCAACAGAACCGGAATCTAAGGTTCT
130 GCATCATCACTAAGATATTTAGGAAATATTCAACAGAACCGGAATCTAAGGTTCT
* *
2180377 TGATTGCACATGAAAAATATACATTAGATACCATATGACAATCGAACCGGAACTCGAGCCATAAC
1 TGATTGCACATGAAAAATATACATTAGATACCATACGACAATCGAACCGGAACTAGAGCCATAAC
* * *
2180442 GACCATAAACACAATTTATATGCACTTTTGTATCCCACAACGATCCAGCAGATACTG-TGTAAGT
66 GACCATAAACACAATTTATATGCACTTTTGTATCCCACAACAAACCAGCAGATACCGAT-TAAGT
* * *
2180506 GCAT-AGTCACTAAGA-ACTTTAGGAAATATTTAA-AGGAACTGGCATCTAAGGTTCT
130 GCATCA-TCACTAAGATA-TTTAGGAAATATTCAACA-GAACCGGAATCTAAGGTTCT
*
2180561 TGATTGCACATGAAAAATATACATTAGATACCATAGGGA-AATCGAACCGGAACTAGAGCCATAA
1 TGATTGCACATGAAAAATATACATTAGATACCATA-CGACAATCGAACCGGAACTAGAGCCATAA
* * * * * * *
2180625 CAACCATTAGCACAATTTATATGCAATTTTGTATCCCACAATAAACCAGCAAATACC-ACATAAG
65 CGACCATAAACACAATTTATATGCACTTTTGTATCCCACAACAAACCAGCAGATACCGA-TTAAG
* *
2180689 TGCAT-AGTCATTAACATATTTAGG
129 TGCATCA-TCACTAAGATATTTAGG
2180713 CCACTTATAC
Statistics
Matches: 301, Mismatches: 27, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
183 4 0.01
184 182 0.60
185 115 0.38
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (184 bp):
TGATTGCACATGAAAAATATACATTAGATACCATACGACAATCGAACCGGAACTAGAGCCATAAC
GACCATAAACACAATTTATATGCACTTTTGTATCCCACAACAAACCAGCAGATACCGATTAAGTG
CATCATCACTAAGATATTTAGGAAATATTCAACAGAACCGGAATCTAAGGTTCT
Found at i:2184091 original size:13 final size:13
Alignment explanation
Indices: 2184073--2184097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2184063 ATTTTTAATA
2184073 TTATTTTGTGTGT
1 TTATTTTGTGTGT
2184086 TTATTTTGTGTG
1 TTATTTTGTGTG
2184098 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:2185702 original size:41 final size:40
Alignment explanation
Indices: 2185672--2185817 Score: 120
Period size: 41 Copynumber: 3.6 Consensus size: 40
2185662 GGTTATGTAC
*
2185672 CTAGCAGGCTTAATGCTGGTGAAGTAATTCAGACTTTACG
1 CTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTACG
* *
2185712 TCTAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTATATG
1 -CTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTTTACG
* * * *
2185753 TCTAGCAGGC-TAAGTGCCGGTGTACTGAA-TCAGGCTTTAAG
1 -CTAGCAGGCTTAA-TGCCGGTGAAGT-AATTCAGACTTTACG
* *
2185794 CCTAGCAGGCTAAATGCCAGTGAA
1 -CTAGCAGGCTTAATGCCGGTGAA
2185818 TCTGTTTAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
39 2 0.02
40 5 0.06
41 75 0.85
42 3 0.03
43 2 0.02
44 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTACG
Found at i:2186118 original size:2 final size:2
Alignment explanation
Indices: 2186111--2186162 Score: 50
Period size: 2 Copynumber: 25.0 Consensus size: 2
2186101 TGCATTTGAG
* * * *
2186111 AT AT AT AT AT AT AT AT AT AT AC AT GT ACT CAT TT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT
2186155 AT AT AT AT
1 AT AT AT AT
2186163 TCGAATGTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
2 37 0.93
3 2 0.05
4 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2192901 original size:10 final size:9
Alignment explanation
Indices: 2192848--2192913 Score: 51
Period size: 10 Copynumber: 6.7 Consensus size: 9
2192838 AGGTTACAAA
*
2192848 AAAAAATTC
1 AAAAAATTT
2192857 AAAATAATTTT
1 AAAA-AA-TTT
*
2192868 AAAATATTT
1 AAAAAATTT
2192877 ATAAAAATTT
1 A-AAAAATTT
*
2192887 TAAAAATTCT
1 AAAAAATT-T
2192897 AAAAAATATAT
1 AAAAAAT-T-T
2192908 AAAAAA
1 AAAAAA
2192914 AGTTAAGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
9 15 0.33
10 17 0.37
11 14 0.30
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAAATTT
Found at i:2192912 original size:20 final size:19
Alignment explanation
Indices: 2192849--2192903 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
2192839 GGTTACAAAA
2192849 AAAAATTC-AAAATAATTTT
1 AAAAATTCTAAAA-AATTTT
2192868 AAAATATT-TATAAAAATTTT
1 AAAA-ATTCTA-AAAAATTTT
2192888 AAAAATTCTAAAAAAT
1 AAAAATTCTAAAAAAT
2192904 ATATAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 13 0.41
20 16 0.50
21 3 0.09
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATTCTAAAAAATTTT
Found at i:2195496 original size:2 final size:2
Alignment explanation
Indices: 2195489--2195523 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2195479 CTGTGTTTCT
2195489 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
2195524 TCAAATAGAT
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:2199872 original size:38 final size:38
Alignment explanation
Indices: 2199817--2199896 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
2199807 TCTAATGATG
*
2199817 ATTA-GTGTTCACCTTCTATACTATGTCGTGGATTCGA
1 ATTATGTGTTCACCTTCTAGACTATGTCGTGGATTCGA
* *
2199854 GTTATGTGTTCACCTTCTAGACTATGTTGTGGATTCGA
1 ATTATGTGTTCACCTTCTAGACTATGTCGTGGATTCGA
2199892 ATTAT
1 ATTAT
2199897 AGTACCAGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 3 0.08
38 35 0.92
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.42
Consensus pattern (38 bp):
ATTATGTGTTCACCTTCTAGACTATGTCGTGGATTCGA
Found at i:2208992 original size:17 final size:16
Alignment explanation
Indices: 2208970--2209008 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
2208960 AATGCAGGTG
2208970 AAAAATAAATTTATATA
1 AAAAATAAATTTATA-A
*
2208987 AAAAATATATTTATAA
1 AAAAATAAATTTATAA
2209003 AAAAAT
1 AAAAAT
2209009 TGGTATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATAAATTTATAA
Found at i:2211240 original size:14 final size:15
Alignment explanation
Indices: 2211217--2211259 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
2211207 ATTTTAGAAG
*
2211217 TTTTTATATATTCTA
1 TTTTTATATATTATA
2211232 TTTTT-TATATTATA
1 TTTTTATATATTATA
2211246 TTTTATGATATATT
1 TTTT-T-ATATATT
2211260 TCAATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.50
15 6 0.25
17 6 0.25
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTTATATATTATA
Found at i:2217212 original size:3 final size:3
Alignment explanation
Indices: 2217204--2217243 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
2217194 TGGTGTTTTA
*
2217204 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT TGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
2217244 TAGTAGCCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
GGT
Found at i:2220691 original size:7 final size:7
Alignment explanation
Indices: 2220679--2220703 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2220669 ATATATTTTT
2220679 TTTATAA
1 TTTATAA
2220686 TTTATAA
1 TTTATAA
2220693 TTTATAA
1 TTTATAA
2220700 TTTA
1 TTTA
2220704 ACAAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTATAA
Found at i:2228873 original size:22 final size:23
Alignment explanation
Indices: 2228820--2228875 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
2228810 GCCGTTTTTA
* * *
2228820 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
2228843 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
2228865 ATTAAAATTAA
1 ATTAAAATTAA
2228876 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:2228888 original size:16 final size:16
Alignment explanation
Indices: 2228851--2228890 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
2228841 TTAATAAAAT
* *
2228851 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
2228867 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
2228883 TAAAATTA
1 TAAAATTA
2228891 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:2228960 original size:66 final size:58
Alignment explanation
Indices: 2228893--2229011 Score: 186
Period size: 58 Copynumber: 2.1 Consensus size: 58
2228883 TAAAATTATC
* *
2228893 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAA-AAAATCTAACATTTGATTAGTA
* *
2228951 AATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAAAAAATCTAACATTTGATTAGTA
2229009 AAA
1 AAA
2229012 CAAACTTGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 29 0.53
59 26 0.47
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (58 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAAAAAATCTAACATTTGATTAGTA
Found at i:2229107 original size:24 final size:24
Alignment explanation
Indices: 2229077--2229122 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
2229067 AAATAAATTT
2229077 AAAATAAAAAACTAT-TATATTTTA
1 AAAATAAAAAA-TATATATATTTTA
2229101 AAAATAAAAAATATATATATTT
1 AAAATAAAAAATATATATATTT
2229123 AATATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAAAATATATATATTTTA
Found at i:2229123 original size:23 final size:23
Alignment explanation
Indices: 2229073--2229124 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
2229063 AAGTAAATAA
2229073 ATTT-AAAATAAAAAACTATTAT
1 ATTTAAAAATAAAAAACTATTAT
2229095 ATTTTAAAAATAAAAAA-TATATAT
1 A-TTTAAAAATAAAAAACTAT-TAT
2229119 ATTTAA
1 ATTTAA
2229125 TATTTTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 1 0.04
23 11 0.41
24 15 0.56
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTTAAAAATAAAAAACTATTAT
Found at i:2235614 original size:15 final size:17
Alignment explanation
Indices: 2235578--2235614 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
2235568 CTTTTTAAAT
2235578 TTAATTTTATATAAAAA
1 TTAATTTTATATAAAAA
*
2235595 ATAATTTTA-A-AAAAA
1 TTAATTTTATATAAAAA
2235610 TTAAT
1 TTAAT
2235615 ACAGATAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.50
16 1 0.06
17 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTTTATATAAAAA
Found at i:2248454 original size:30 final size:31
Alignment explanation
Indices: 2248420--2248483 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
2248410 CCTTTGGGGC
*
2248420 AATATAATTGAAAAAT-ACGTAATTAATTTG
1 AATATAATTAAAAAATGACGTAATTAATTTG
2248450 AATATAATTAAAAAATGACGTAATTAATTTG
1 AATATAATTAAAAAATGACGTAATTAATTTG
2248481 AAT
1 AAT
2248484 TTAGTAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (31 bp):
AATATAATTAAAAAATGACGTAATTAATTTG
Found at i:2248492 original size:30 final size:30
Alignment explanation
Indices: 2248420--2248492 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
2248410 CCTTTGGGGC
* *
2248420 AATATAATTGAAAAATACGTAATTAATTTG
1 AATATAAGTAAAAAATACGTAATTAATTTG
*
2248450 AATATAATTAAAAAATGACGTAATTAATTTG
1 AATATAAGTAAAAAAT-ACGTAATTAATTTG
*
2248481 AAT-TTAGTAAAA
1 AATATAAGTAAAA
2248493 TAATTTTAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 22 0.56
31 17 0.44
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.36
Consensus pattern (30 bp):
AATATAAGTAAAAAATACGTAATTAATTTG
Found at i:2262506 original size:15 final size:14
Alignment explanation
Indices: 2262486--2262515 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2262476 CCGTTCTCTT
2262486 TCCTTCTCCTTTCTC
1 TCCTTCTCC-TTCTC
2262501 TCCTTCTCCTTCTC
1 TCCTTCTCCTTCTC
2262515 T
1 T
2262516 TTCCGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (14 bp):
TCCTTCTCCTTCTC
Found at i:2266288 original size:1 final size:1
Alignment explanation
Indices: 2266282--2266368 Score: 174
Period size: 1 Copynumber: 87.0 Consensus size: 1
2266272 CTGATAAGAC
2266282 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2266347 AAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAA
2266369 CAGTGACAAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 86 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2270658 original size:127 final size:127
Alignment explanation
Indices: 2270432--2270686 Score: 474
Period size: 127 Copynumber: 2.0 Consensus size: 127
2270422 TGATCAGCAT
*
2270432 AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACATGGCATA
1 AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACAAGGCATA
*
2270497 ACCTCGTTATATTTCTGTTTAGCATACTATTTTATATCCTAGGAATGAGGACTTACTGTATC
66 ACCTCGTTATATTTCTGTTTAGCATACTATTTTATATCCCAGGAATGAGGACTTACTGTATC
2270559 AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACAAGGCATA
1 AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACAAGGCATA
* *
2270624 ACCTTGTTATATTTCTGTTTAGCATACTATTTTATATCCCAGGGATGAGGACTTACTGTATC
66 ACCTCGTTATATTTCTGTTTAGCATACTATTTTATATCCCAGGAATGAGGACTTACTGTATC
2270686 A
1 A
2270687 GCAGAAGAAG
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 124 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (127 bp):
AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACAAGGCATA
ACCTCGTTATATTTCTGTTTAGCATACTATTTTATATCCCAGGAATGAGGACTTACTGTATC
Found at i:2277205 original size:78 final size:78
Alignment explanation
Indices: 2277076--2277232 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
2277066 GGGTTGTTAA
2277076 GTTTTTATTCTTTTTAAAGTTTGGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
1 GTTTTTATTCTTTTTAAAGTTTGGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
2277141 ATCAATATCTATC
66 ATCAATATCTATC
2277154 GTTTTTATTCTTTTTAAAGTTTGGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
1 GTTTTTATTCTTTTTAAAGTTTGGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
2277219 ATCAATATCTATC
66 ATCAATATCTATC
2277232 G
1 G
2277233 ATGAGTAAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.41
Consensus pattern (78 bp):
GTTTTTATTCTTTTTAAAGTTTGGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
ATCAATATCTATC
Found at i:2277826 original size:13 final size:12
Alignment explanation
Indices: 2277800--2277833 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
2277790 TGTTTTTAAG
*
2277800 TTTTTTATTTTA
1 TTTTTAATTTTA
2277812 TTTTTAATTTATA
1 TTTTTAATTT-TA
2277825 TTTTTAATT
1 TTTTTAATT
2277834 AATAACTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTAATTTTA
Found at i:2288050 original size:139 final size:139
Alignment explanation
Indices: 2287791--2288064 Score: 392
Period size: 139 Copynumber: 2.0 Consensus size: 139
2287781 GTCCTATAAA
* * * *
2287791 GGAAATGGCTCCTATGACTAAGAAGGGAAAGAAAGCTAAATCTGTGAAGAAGGCTCGGAAAGTGA
1 GGAAATGCCTCCTATGACTAAGAAGGGAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGTGA
* * * * *
2287856 TAAAGAGTATGTATCCTCTAGTCAAACGCACAAAGAAATTGAAATCTACTTCCTCTTAGCAGAGT
66 AAAAGAATATGTATCCTCTAGTCAAACGAACAAAGAAATTGAAATCCACTCCCTCTTAGCAGAGT
2287921 CTGCTCAAG
131 CTGCTCAAG
*
2287930 GGAAATGCCTCCTATGTA-TAAGATGGTG-AAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGT
1 GGAAATGCCTCCTATG-ACTAAGAAGG-GAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGT
* *
2287993 GAAAAAGAATGTGTATCCTCTAGTCAAACGAACGAAGAAATTGAAATCCA-TGCCCTCTTAGCAG
64 GAAAAAGAATATGTATCCTCTAGTCAAACGAACAAAGAAATTGAAATCCACT-CCCTCTTAGCAG
2288057 AGTCTGCT
128 AGTCTGCT
2288065 TTGTGAGTTT
Statistics
Matches: 120, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
138 1 0.01
139 117 0.98
140 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (139 bp):
GGAAATGCCTCCTATGACTAAGAAGGGAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGTGA
AAAAGAATATGTATCCTCTAGTCAAACGAACAAAGAAATTGAAATCCACTCCCTCTTAGCAGAGT
CTGCTCAAG
Found at i:2300723 original size:30 final size:29
Alignment explanation
Indices: 2300689--2300747 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2300679 TTATGGGATC
*
2300689 TGGATCAAATTAGTCCTTTTTATAATTAAA
1 TGGATCAAATTAGT-CTTTATATAATTAAA
* * *
2300719 TGGATGAATTTAGTCTTTATATTATTAAA
1 TGGATCAAATTAGTCTTTATATAATTAAA
2300748 AAGGATGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.46
Consensus pattern (29 bp):
TGGATCAAATTAGTCTTTATATAATTAAA
Found at i:2300754 original size:30 final size:30
Alignment explanation
Indices: 2300698--2300756 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2300688 CTGGATCAAA
* *
2300698 TTAGTCCTTTTTATAATTAAATGGATGAAT
1 TTAGTCCTTTATATAATTAAAAGGATGAAT
*
2300728 TTAGT-CTTTATATTATTAAAAAGGATGAA
1 TTAGTCCTTTATATAATT-AAAAGGATGAA
2300757 ATAAGTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (30 bp):
TTAGTCCTTTATATAATTAAAAGGATGAAT
Found at i:2301800 original size:30 final size:30
Alignment explanation
Indices: 2301756--2301816 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 30
2301746 TAGACCTGAA
*
2301756 TTTTGAAATCTAAAAAGTA-AAGAGACTAAAT
1 TTTTGAAATAT-AAAAGTATAAGAG-CTAAAT
*
2301787 TTTTGAAA-ATAAAAGTATATGAGCTAAAT
1 TTTTGAAATATAAAAGTATAAGAGCTAAAT
2301816 T
1 T
2301817 CTAAAGTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 14 0.52
30 5 0.19
31 8 0.30
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (30 bp):
TTTTGAAATATAAAAGTATAAGAGCTAAAT
Found at i:2304545 original size:21 final size:21
Alignment explanation
Indices: 2304516--2304557 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2304506 TTCAAGTTTT
2304516 TGTTCTTGAGGTCTAGAGACA
1 TGTTCTTGAGGTCTAGAGACA
* * *
2304537 TGTTTTTGATGTCTCGAGACA
1 TGTTCTTGAGGTCTAGAGACA
2304558 CATGTCCGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.38
Consensus pattern (21 bp):
TGTTCTTGAGGTCTAGAGACA
Found at i:2310457 original size:126 final size:127
Alignment explanation
Indices: 2310281--2310534 Score: 501
Period size: 126 Copynumber: 2.0 Consensus size: 127
2310271 ATCATGCTTC
2310281 TTGTTGATTTAACTTTGTAAATTCCGTGAACAAGTCTAAACCTTTTCTGCTGATTTCAATGACAT
1 TTGTTGATTTAACTTTGTAAATTCCGTGAACAAGTCTAAACCTTTTCTGCTGATTTCAATGACAT
2310346 AGCTGCAGCTGTAATTCACTGCTGATTCTTGTGATCCAGGCATGCATGCTCTGTTAGCGGCT
66 AGCTGCAGCTGTAATTCACTGCTGATTCTTGTGATCCAGGCATGCATGCTCTGTTAGCGGCT
2310408 TTGTTGATTT-ACTTTGTAAATTCCGTGAACAAGTCTAAACCTTTTCTGCTGATTTCAATGACAT
1 TTGTTGATTTAACTTTGTAAATTCCGTGAACAAGTCTAAACCTTTTCTGCTGATTTCAATGACAT
2310472 AGCTGCAGCTGTAATTCACTGCTGATTCTTGTGATCCAGGCATGCATGCTCTGTTAGCGGCT
66 AGCTGCAGCTGTAATTCACTGCTGATTCTTGTGATCCAGGCATGCATGCTCTGTTAGCGGCT
2310534 T
1 T
2310535 GACTTGCAGT
Statistics
Matches: 127, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
126 117 0.92
127 10 0.08
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (127 bp):
TTGTTGATTTAACTTTGTAAATTCCGTGAACAAGTCTAAACCTTTTCTGCTGATTTCAATGACAT
AGCTGCAGCTGTAATTCACTGCTGATTCTTGTGATCCAGGCATGCATGCTCTGTTAGCGGCT
Found at i:2317664 original size:25 final size:25
Alignment explanation
Indices: 2317630--2317679 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2317620 CCTTACTGTT
* *
2317630 TTTTTTTTTTTTTTCCTTTTTTTCA
1 TTTTTTTTTTTTTTCCATTTGTTCA
2317655 TTTTTTTTTTTTTTCCATTTGTTCA
1 TTTTTTTTTTTTTTCCATTTGTTCA
2317680 GGTTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.06, C:0.12, G:0.02, T:0.80
Consensus pattern (25 bp):
TTTTTTTTTTTTTTCCATTTGTTCA
Found at i:2317996 original size:112 final size:113
Alignment explanation
Indices: 2317798--2318021 Score: 344
Period size: 112 Copynumber: 2.0 Consensus size: 113
2317788 TATTCTGTTA
* * * *
2317798 AATTAGGGTTACATGTGACTCTGGATTTGGGGGATTTTTTTTAATTTCTGCTGGGTTTAAGGTTT
1 AATTAGGGTTACAGGTGACTCTCGATTTGGGGAATTTTTTTTAATTTCTGCTAGGTTTAAGGTTT
2317863 CTAAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
66 CTAAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
* * * *
2317911 AATTAGGGTTACAGGTGACTGTCGATTT-GGGAATTTTTTTTACTTTCTGTTAGGTTTAGGGTTT
1 AATTAGGGTTACAGGTGACTCTCGATTTGGGGAATTTTTTTTAATTTCTGCTAGGTTTAAGGTTT
*
2317975 CTAAG-CTTCTTTGTTTTCAATTCCAGTGGTATAATATTTCTAGGGTT
66 CTAAGTC-TCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTT
2318022 TTAGAGCTGT
Statistics
Matches: 101, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
111 1 0.01
112 75 0.74
113 25 0.25
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.46
Consensus pattern (113 bp):
AATTAGGGTTACAGGTGACTCTCGATTTGGGGAATTTTTTTTAATTTCTGCTAGGTTTAAGGTTT
CTAAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
Found at i:2323048 original size:161 final size:159
Alignment explanation
Indices: 2322813--2323411 Score: 620
Period size: 160 Copynumber: 3.7 Consensus size: 159
2322803 TGTTCTTTGG
* * * ** * *
2322813 CTTGCTGCTCTAGTGATCCTCATATAATATTTTATGTTAGCCAT-GATTGTAAATCATAATTCTT
1 CTTGCTGGTCTAGTGAACCTCATATAATTTTTTATCATAGCC-TGGATTGTTAATCAT-ACTCTT
* * * * * *
2322877 CATCAAAGTATACCCAGTGAAGCTTCTTCTTTATCGTCTCCTTTCAAAGCTTTTTTTTATTGCTT
64 CATCAAAGTATACCTATTGAAGCTTTTTCTTTATTGTCTCCTTTCAAAGCTTTTCTTTATTGCCT
* *
2322942 TAGAATTTTTATGTT-TGTCATGTTATTTATGA
129 TAGAATTTATATGTTCTATCAT-TT-TTTATGA
*
2322974 CTTTCTGGTCTAGTGAACCTCATATAATTTTTTATCATAGCCTGGATTGTTAATCATACTCCTTC
1 CTTGCTGGTCTAGTGAACCTCATATAATTTTTTATCATAGCCTGGATTGTTAATCATACT-CTTC
* * * * *
2323039 ATTAAAGTATACTTTTTGAAGCTTTTTCTTTATTGCCTCCGTTT-GAAGCTTTTCTTTATTGCCT
65 ATCAAAGTATACCTATTGAAGCTTTTTCTTTATTGTCTCC-TTTCAAAGCTTTTCTTTATTGCCT
2323103 TAGAATTTATATGTTCTATCATTTTGTT-TGA
129 TAGAATTTATATGTTCTATCATTTT-TTATGA
* * * * * *
2323134 CTTGCTGATCTAGTGTACCTCAGATAATTTTTTATCATAGCCAGGATTTTTAGTCATACTCTGTC
1 CTTGCTGGTCTAGTGAACCTCATATAATTTTTTATCATAGCCTGGATTGTTAATCATACTCT-TC
* * * *
2323199 ATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCCTTTCGAAGCGTTTCTTTATTGCCTT
65 ATCAAAGTATACCTATTGAAGCTTTTTCTTTATTGTCTCCTTTCAAAGCTTTTCTTTATTGCCTT
*
2323264 AGAATTTATATTTTCTATCATATTGTTTATGA
130 AGAATTTATATGTTCTATCAT-TT-TTTATGA
* * * * *
2323296 CTTGCTTGTCTAGCGAACCACATATATATATTTATCTTAATTCTTAG-CTGGGATTGTTGATCAT
1 CTTGCTGGTCTAGTGAACCTC--ATATA-ATTT-T-TT-A-TCATAGCCT-GGATTGTTAATCAT
* * *
2323360 A--CTTCATCAAAGTATGCCTAATGGAGC-TTTTCTTTATTGTCTCCTTTCAAAG
58 ACTCTTCATCAAAGTATACCTATTGAAGCTTTTTCTTTATTGTCTCCTTTCAAAG
2323412 TTAACTATAG
Statistics
Matches: 370, Mismatches: 50, Indels: 32
0.82 0.11 0.07
Matches are distributed among these distances:
159 5 0.01
160 139 0.38
161 123 0.33
162 28 0.08
164 4 0.01
165 27 0.07
166 21 0.06
167 4 0.01
168 2 0.01
169 17 0.05
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (159 bp):
CTTGCTGGTCTAGTGAACCTCATATAATTTTTTATCATAGCCTGGATTGTTAATCATACTCTTCA
TCAAAGTATACCTATTGAAGCTTTTTCTTTATTGTCTCCTTTCAAAGCTTTTCTTTATTGCCTTA
GAATTTATATGTTCTATCATTTTTTATGA
Found at i:2327070 original size:6 final size:6
Alignment explanation
Indices: 2327052--2327091 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
2327042 GCCCCACACC
*
2327052 CCCCAT CCTCAT CCCCAT CCCCAT CCCCAT CCCCAT CCCC
1 CCCCAT CCCCAT CCCCAT CCCCAT CCCCAT CCCCAT CCCC
2327092 CATTCTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.15, C:0.68, G:0.00, T:0.17
Consensus pattern (6 bp):
CCCCAT
Found at i:2333045 original size:20 final size:20
Alignment explanation
Indices: 2333020--2333064 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2333010 TAATTTTGAA
2333020 AATTTTT-TATAATTTTTTG
1 AATTTTTATATAATTTTTTG
** *
2333039 AATTTTTATATGTTTTTTTT
1 AATTTTTATATAATTTTTTG
2333059 AATTTT
1 AATTTT
2333065 AAGAGCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (20 bp):
AATTTTTATATAATTTTTTG
Found at i:2333412 original size:23 final size:23
Alignment explanation
Indices: 2333382--2333427 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2333372 CTGTAGAATG
2333382 ACCAAAATGCAAT-TCGAAGTATA
1 ACCAAAATGCAATCT-GAAGTATA
2333405 ACCAAAATGCAATCTGAAGTATA
1 ACCAAAATGCAATCTGAAGTATA
2333428 GTTTAGGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (23 bp):
ACCAAAATGCAATCTGAAGTATA
Found at i:2345910 original size:18 final size:18
Alignment explanation
Indices: 2345873--2345922 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
2345863 GAGGTAACTA
* * *
2345873 ATGATCCTCATCACCGTC
1 ATGATCATCATCATCATC
2345891 ATGATCATCATCATCATC
1 ATGATCATCATCATCATC
**
2345909 ATTTTCATCATCAT
1 ATGATCATCATCAT
2345923 AGTCAAGCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.36
Consensus pattern (18 bp):
ATGATCATCATCATCATC
Found at i:2354846 original size:8 final size:7
Alignment explanation
Indices: 2354816--2354842 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2354806 CAATCAACGC
2354816 AAAAAAG
1 AAAAAAG
2354823 AAAAAAG
1 AAAAAAG
2354830 AAAAAAG
1 AAAAAAG
2354837 AAAAAA
1 AAAAAA
2354843 AGAATTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:2364958 original size:22 final size:24
Alignment explanation
Indices: 2364923--2364971 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2364913 ATGATGAAAT
2364923 AAATAATAATATAT-TAGATTTAA
1 AAATAATAATATATATAGATTTAA
2364946 AAATAA-AATATATAATAGATTTAA
1 AAATAATAATATAT-ATAGATTTAA
2364970 AA
1 AA
2364972 CATCAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 7 0.29
23 6 0.25
24 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAATAATATATATAGATTTAA
Found at i:2371755 original size:41 final size:41
Alignment explanation
Indices: 2371693--2371808 Score: 160
Period size: 41 Copynumber: 2.8 Consensus size: 41
2371683 TTTTGTAAGT
*
2371693 TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAAATATA
* * *
2371734 TCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAAATATA
* ** *
2371775 TCGGGCTTGGTGCCTAGCAGGCTTTATGCCGGTG
1 TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTG
2371809 TTATATACAA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAAATATA
Found at i:2376933 original size:18 final size:17
Alignment explanation
Indices: 2376879--2376946 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 17
2376869 GTATTTAATT
*
2376879 AATTTTTAAAAATTTAA
1 AATTTTTAAAAAATTAA
**
2376896 AATTTCAAAAAATTATTAA
1 AATTTTTAAAAA--ATTAA
2376915 AACTTTTTAAAAAATTAA
1 AA-TTTTTAAAAAATTAA
2376933 AATTATTTAAAAAA
1 AATT-TTTAAAAAA
2376947 AATATATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
17 12 0.29
18 16 0.38
19 6 0.14
20 8 0.19
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTTTTAAAAAATTAA
Found at i:2389969 original size:44 final size:44
Alignment explanation
Indices: 2389906--2390024 Score: 175
Period size: 44 Copynumber: 2.7 Consensus size: 44
2389896 AAACTCATTG
* * *
2389906 TTATCTGATCAGTGACAAGTGATGAGTGATTGTTTTAGTTACAC
1 TTATCTGATCAGTGACAAGTGATGAGTGATAGCTTTAGCTACAC
*
2389950 TTATCTGATCAGTGACAAGTGATGAGTGGTAGCTTTAGCTACAC
1 TTATCTGATCAGTGACAAGTGATGAGTGATAGCTTTAGCTACAC
* **
2389994 TTATCTGATCAGGGACAAGTGACAAGTGATA
1 TTATCTGATCAGTGACAAGTGATGAGTGATA
2390025 AATGTGACCC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (44 bp):
TTATCTGATCAGTGACAAGTGATGAGTGATAGCTTTAGCTACAC
Found at i:2392903 original size:11 final size:11
Alignment explanation
Indices: 2392887--2392911 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2392877 TCTATCTTGG
2392887 TACCTCTATGT
1 TACCTCTATGT
2392898 TACCTCTATGT
1 TACCTCTATGT
2392909 TAC
1 TAC
2392912 GTTCACCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.28, G:0.08, T:0.44
Consensus pattern (11 bp):
TACCTCTATGT
Found at i:2399695 original size:20 final size:21
Alignment explanation
Indices: 2399672--2399714 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2399662 TCAATTCGAT
2399672 TTAAAAAAAT-AAATTTTAAA
1 TTAAAAAAATCAAATTTTAAA
** *
2399692 TTAACTAAATCGAATTTTAAA
1 TTAAAAAAATCAAATTTTAAA
2399713 TT
1 TT
2399715 TATTTGATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAAAAAAATCAAATTTTAAA
Found at i:2401878 original size:21 final size:21
Alignment explanation
Indices: 2401852--2401895 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2401842 GAAATTTTGA
2401852 ATCGATTTAATATATTAT-TAT
1 ATCGATTTAA-ATATTATATAT
2401873 ATCGATTTAAATATTATATAT
1 ATCGATTTAAATATTATATAT
2401894 AT
1 AT
2401896 TAATATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
ATCGATTTAAATATTATATAT
Found at i:2403102 original size:24 final size:22
Alignment explanation
Indices: 2403075--2403122 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2403065 AATATATTAT
*
2403075 TTTTTAATTTAATATTTGTATATA
1 TTTTTAA-TTAAAATTT-TATATA
*
2403099 TTTTTTATTAAAATTTTATATA
1 TTTTTAATTAAAATTTTATATA
2403121 TT
1 TT
2403123 GTCATCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTTAATTAAAATTTTATATA
Found at i:2408937 original size:29 final size:28
Alignment explanation
Indices: 2408898--2409022 Score: 99
Period size: 29 Copynumber: 4.2 Consensus size: 28
2408888 GGTTGCTCAC
* *
2408898 ATAATGGCCAAACATTTCAAAATGGTCAT
1 ATAA-GGCCAAACATTTCAAAATGATCAA
*
2408927 ATAAGGCCCAAACATTTACAAAAGTGCTCAA
1 ATAAGG-CCAAACATTT-CAAAA-TGATCAA
* * *
2408958 ATGAAGGCCAAACCTTTCTAAATGATCAG
1 AT-AAGGCCAAACATTTCAAAATGATCAA
* *
2408987 ATAAAAGCCAAACCTTTTCAAAATG-TACAA
1 AT-AAGGCCAAA-CATTTCAAAATGAT-CAA
2409017 ATAAGG
1 ATAAGG
2409023 GTTAAACCTT
Statistics
Matches: 78, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.03
29 33 0.42
30 23 0.29
31 16 0.21
32 4 0.05
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (28 bp):
ATAAGGCCAAACATTTCAAAATGATCAA
Found at i:2418783 original size:30 final size:28
Alignment explanation
Indices: 2418716--2418785 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
2418706 TCCTCATAAA
*
2418716 TTGAAAATTTAGTCTCTATACTTTTATT
1 TTGAAAATTTAATCTCTATACTTTTATT
* *
2418744 TCT-AGAAATTTAATCTCTTTATTTTTTATAT
1 T-TGA-AAATTTAATCTCTATA-CTTTTAT-T
2418775 TTGAAAATTTA
1 TTGAAAATTTA
2418786 TGTCTAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
28 2 0.06
29 15 0.44
30 14 0.41
31 3 0.09
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (28 bp):
TTGAAAATTTAATCTCTATACTTTTATT
Found at i:2421862 original size:20 final size:19
Alignment explanation
Indices: 2421837--2421889 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
2421827 TTCATTATAT
2421837 ATTTTTAGAATTTTTATGAA
1 ATTTTTAGAATTTTTATG-A
* *
2421857 ATTTTTATAATTTGTTTTGA
1 ATTTTTAGAATTT-TTATGA
2421877 A-TTTT-GAATTTTT
1 ATTTTTAGAATTTTT
2421890 GTAATTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 2 0.07
18 5 0.17
19 4 0.14
20 14 0.48
21 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (19 bp):
ATTTTTAGAATTTTTATGA
Found at i:2427437 original size:2 final size:2
Alignment explanation
Indices: 2427430--2427463 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
2427420 TTTGATCAAG
2427430 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
2427464 GCCAATAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2430560 original size:91 final size:93
Alignment explanation
Indices: 2430433--2430617 Score: 356
Period size: 91 Copynumber: 2.0 Consensus size: 93
2430423 GACTGAGATA
2430433 AGTGGAACTTAACAAGCAAATGCCTCTAAAATAATAACAAAATTAAAGAGTTATATGATATCCAA
1 AGTGGAACTTAACAAGCAAATGCCTCTAAAATAATAACAAAATTAAAGAGTTATATGATATCCAA
2430498 ATAATAACAACAAAATAGTAGTAATTAG
66 ATAATAACAACAAAATAGTAGTAATTAG
2430526 AGTGGAACTT-A-AAGCAAATGCCTCTAAAATAATAACAAAATTAAAGAGTTATATGATATCCAA
1 AGTGGAACTTAACAAGCAAATGCCTCTAAAATAATAACAAAATTAAAGAGTTATATGATATCCAA
2430589 ATAATAACAACAAAATAGTAGTAATTAG
66 ATAATAACAACAAAATAGTAGTAATTAG
2430617 A
1 A
2430618 CCTGATCATG
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
91 81 0.88
92 1 0.01
93 10 0.11
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.25
Consensus pattern (93 bp):
AGTGGAACTTAACAAGCAAATGCCTCTAAAATAATAACAAAATTAAAGAGTTATATGATATCCAA
ATAATAACAACAAAATAGTAGTAATTAG
Found at i:2446067 original size:20 final size:20
Alignment explanation
Indices: 2446042--2446082 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2446032 ATTTTAATAA
2446042 ATGAAA-ATTAATATAAAAAT
1 ATGAAATATTAA-ATAAAAAT
*
2446062 ATGAAATATTAAATTAAAAT
1 ATGAAATATTAAATAAAAAT
2446082 A
1 A
2446083 ATATAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
ATGAAATATTAAATAAAAAT
Found at i:2449209 original size:2 final size:2
Alignment explanation
Indices: 2449202--2449226 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2449192 CAATCAATCA
2449202 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2449227 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2449231 original size:2 final size:2
Alignment explanation
Indices: 2449226--2449254 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2449216 ATATATATAT
2449226 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2449255 TAGGATGGTT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2449303 original size:2 final size:2
Alignment explanation
Indices: 2449298--2449328 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2449288 ATATATATAT
2449298 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2449329 CTGCAGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2453588 original size:4 final size:4
Alignment explanation
Indices: 2453579--2453603 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2453569 TTATTAGGAA
2453579 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
2453604 TACACTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:2453645 original size:18 final size:18
Alignment explanation
Indices: 2453622--2453657 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2453612 AAGTCACTGG
2453622 CAATTATAACCATCCATC
1 CAATTATAACCATCCATC
2453640 CAATTATAACCATCCATC
1 CAATTATAACCATCCATC
2453658 AAGACAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (18 bp):
CAATTATAACCATCCATC
Found at i:2459934 original size:26 final size:26
Alignment explanation
Indices: 2459905--2459970 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
2459895 TATGTAAATA
*
2459905 TAATAAATATAATTATTGATTATATT
1 TAATAAATATAATTATTAATTATATT
* * *
2459931 TAATAACT-TAATTTAGTAATTATGTT
1 TAATAAATATAA-TTATTAATTATATT
2459957 T-AT-AATATAATTAT
1 TAATAAATATAATTAT
2459971 AAAAAATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
24 5 0.16
25 8 0.25
26 19 0.59
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (26 bp):
TAATAAATATAATTATTAATTATATT
Found at i:2462138 original size:23 final size:23
Alignment explanation
Indices: 2462111--2462155 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2462101 CTCGTTACAC
2462111 GGCTCTTCCTGAGCTTCCCGATA
1 GGCTCTTCCTGAGCTTCCCGATA
*
2462134 GGCTCTTCGTGAGCTTCCCGAT
1 GGCTCTTCCTGAGCTTCCCGAT
2462156 CAAATGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.33, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCTCTTCCTGAGCTTCCCGATA
Found at i:2465081 original size:15 final size:15
Alignment explanation
Indices: 2465061--2465092 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2465051 TATATATGAA
2465061 TCTTCATGTAAGAGT
1 TCTTCATGTAAGAGT
2465076 TCTTCATGTAAGAGT
1 TCTTCATGTAAGAGT
2465091 TC
1 TC
2465093 GCCGAAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (15 bp):
TCTTCATGTAAGAGT
Found at i:2467364 original size:14 final size:14
Alignment explanation
Indices: 2467345--2467371 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2467335 TGAAATGAAA
2467345 TCGAGTTAAATTAT
1 TCGAGTTAAATTAT
2467359 TCGAGTTAAATTA
1 TCGAGTTAAATTA
2467372 AAATTTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (14 bp):
TCGAGTTAAATTAT
Found at i:2474986 original size:24 final size:24
Alignment explanation
Indices: 2474933--2474994 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
2474923 CACAGCTCGA
* *
2474933 ATGAGCATCCCGTTATTATCTCTC
1 ATGAGCATCCCGTTATTAGCCCTC
*
2474957 ATGAGCATCCTGTTATTAGCCCTC
1 ATGAGCATCCCGTTATTAGCCCTC
*
2474981 -TCGAGCTTCCCGTT
1 AT-GAGCATCCCGTT
2474995 GTGTGGTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 1 0.03
24 31 0.97
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (24 bp):
ATGAGCATCCCGTTATTAGCCCTC
Found at i:2476491 original size:41 final size:41
Alignment explanation
Indices: 2476444--2476561 Score: 114
Period size: 41 Copynumber: 2.9 Consensus size: 41
2476434 TGGCGCTAAC
* * *
2476444 AGAAAAACGTCGCAATAGGTAAAGCAGTAGCAGG-GTTTATG
1 AGAAAAACGCCGCAAAAAGTAAAGCAGTAGC-GGCGTTTATG
* *
2476485 AGAAAAACGCCTCAAAAAGTCAAGCAGTAGCGGCGTTTATG
1 AGAAAAACGCCGCAAAAAGTAAAGCAGTAGCGGCGTTTATG
* ** * * *
2476526 AAAAAAATACCGCAAAAGGT-AAGCAATAGTGGCGTT
1 AGAAAAACGCCGCAAAAAGTAAAGCAGTAGCGGCGTT
2476562 CAAAAACGTC
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
40 16 0.25
41 48 0.75
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (41 bp):
AGAAAAACGCCGCAAAAAGTAAAGCAGTAGCGGCGTTTATG
Found at i:2477035 original size:33 final size:33
Alignment explanation
Indices: 2476998--2477066 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
2476988 TATCATGCAT
2476998 CATCCTGTTTTGTTTATATTTGCATATAATCAA
1 CATCCTGTTTTGTTTATATTTGCATATAATCAA
2477031 CATCCTGTTTTGTTTATATTTGCATATAATCAA
1 CATCCTGTTTTGTTTATATTTGCATATAATCAA
2477064 CAT
1 CAT
2477067 TCTTTCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.48
Consensus pattern (33 bp):
CATCCTGTTTTGTTTATATTTGCATATAATCAA
Found at i:2478221 original size:92 final size:92
Alignment explanation
Indices: 2478064--2478254 Score: 301
Period size: 92 Copynumber: 2.1 Consensus size: 92
2478054 TTTGAACCTG
* * * * *
2478064 TTGAATCGGTAGAGGTACCAATCTAGAGAGAGGCATCAAACTTATTAACTTGCAAATTGGTACGA
1 TTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTCATTAACTTGCAAACTGGTACGA
*
2478129 GCTGGTAGAACTAGACTAAAAAACCGA
66 GCTGGTAGAACTAAACTAAAAAACCGA
* *
2478156 TTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTCATTGACTTGCAAGCTGGTACGA
1 TTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTCATTAACTTGCAAACTGGTACGA
*
2478221 GCTGGTAGAACTAAACTAAAAAATCGA
66 GCTGGTAGAACTAAACTAAAAAACCGA
2478248 TTGAACC
1 TTGAACC
2478255 CAAATTTTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (92 bp):
TTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTCATTAACTTGCAAACTGGTACGA
GCTGGTAGAACTAAACTAAAAAACCGA
Found at i:2484635 original size:85 final size:85
Alignment explanation
Indices: 2484492--2484659 Score: 300
Period size: 85 Copynumber: 2.0 Consensus size: 85
2484482 GTCACTTCAC
* *
2484492 TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCTTTGGGCCTTCTTTAGACATGTTGC
1 TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCCTTGGGCCTTCTTTAGACATGCTGC
2484557 AGCTTGAACAATGATAGACT
66 AGCTTGAACAATGATAGACT
* *
2484577 TTAATCGCTAAAACCTAGTACTTCTGTTTATGTCTGATCCCTTGGGCCTTCTTTAGACATGCTGC
1 TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCCTTGGGCCTTCTTTAGACATGCTGC
2484642 AGCTTGAACAATGATAGA
66 AGCTTGAACAATGATAGA
2484660 ATTGGGCTAT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (85 bp):
TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCCTTGGGCCTTCTTTAGACATGCTGC
AGCTTGAACAATGATAGACT
Found at i:2491008 original size:17 final size:17
Alignment explanation
Indices: 2490986--2491049 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
2490976 AATCTTAGAG
2490986 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
2491003 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
*
2491022 TTTTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
2491039 TTTTAATTGTA
1 TTCTAATTGTA
2491050 GCCTTTGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 1 0.03
17 22 0.58
18 4 0.11
19 10 0.26
20 1 0.03
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:2491029 original size:36 final size:36
Alignment explanation
Indices: 2490978--2491048 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
2490968 GATTATGTAA
2490978 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
* *
2491014 TCTTAGAGTTTTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGT
2491049 AGCCTTTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:2491317 original size:48 final size:48
Alignment explanation
Indices: 2491242--2491336 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
2491232 TGAAGGAATT
2491242 CTGTTGAATCATTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
1 CTGTTGAATCATTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
*
2491290 CTGTTGAATCATTTATCATTGCGAGTTAGGCTGACTTAGGCGTTTTT
1 CTGTTGAATCATTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTT
2491337 AAGCAAAGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (48 bp):
CTGTTGAATCATTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
Found at i:2491903 original size:21 final size:21
Alignment explanation
Indices: 2491877--2491929 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2491867 AACAGTGGCA
* *
2491877 GTGAGATTAGTTATTGTAACG
1 GTGAGATTAGATACTGTAACG
* *
2491898 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAACG
2491919 GTGAGATTAGA
1 GTGAGATTAGA
2491930 AACAATGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.06, G:0.34, T:0.32
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAACG
Found at i:2496295 original size:31 final size:30
Alignment explanation
Indices: 2496230--2496344 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
2496220 NNNNNNNNNN
2496230 TTTTTTTATTTTTAAAATACACTACATATA
1 TTTTTTTATTTTTAAAATACACTACATATA
*
2496260 TTTTTTTATTTTTGAAATACACTACATATA
1 TTTTTTTATTTTTAAAATACACTACATATA
2496290 TTTTTTTATTTTTAAAATACACTACATATA
1 TTTTTTTATTTTTAAAATACACTACATATA
*
2496320 TTTTTTTTATTTTTAAAATAAACTA
1 -TTTTTTTATTTTTAAAATACACTA
2496345 ATACAGTGCA
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
30 58 0.72
31 23 0.28
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.55
Consensus pattern (30 bp):
TTTTTTTATTTTTAAAATACACTACATATA
Found at i:2498869 original size:22 final size:21
Alignment explanation
Indices: 2498844--2498909 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
2498834 CCAAGAACAA
2498844 AGCAAAAAAGAGGGGAGAAACC
1 AGCAAAAAAGA-GGGAGAAACC
* * *
2498866 AGCAAAAACGAAGGACAAACC
1 AGCAAAAAAGAGGGAGAAACC
*
2498887 AGCAAGAACA-AGGGAGAAACC
1 AGCAA-AAAAGAGGGAGAAACC
2498908 AG
1 AG
2498910 TATGGGTATA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 24 0.67
22 12 0.33
ACGTcount: A:0.55, C:0.18, G:0.27, T:0.00
Consensus pattern (21 bp):
AGCAAAAAAGAGGGAGAAACC
Found at i:2499432 original size:24 final size:24
Alignment explanation
Indices: 2499379--2499434 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
2499369 ATGTATATGC
* *
2499379 AATTTAATATTTTTTATTCTTTAT
1 AATTTAATATTATTTATTATTTAT
*
2499403 ATTTTAATATTATTTATTA-TTAT
1 AATTTAATATTATTTATTATTTAT
2499426 AAATTTAAT
1 -AATTTAAT
2499435 TTTTATGTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
AATTTAATATTATTTATTATTTAT
Found at i:2499902 original size:22 final size:21
Alignment explanation
Indices: 2499858--2499902 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
2499848 CATGTAATTC
*
2499858 ATAAAAAATTAAAATAAATAA
1 ATAAAAAATTAAAATAAACAA
* *
2499879 ATAAAAATTTAAAAATCAACAA
1 ATAAAAAATT-AAAATAAACAA
2499901 AT
1 AT
2499903 TCCAAAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (21 bp):
ATAAAAAATTAAAATAAACAA
Found at i:2505106 original size:38 final size:37
Alignment explanation
Indices: 2505055--2505130 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 37
2505045 GTGGCTCATG
*
2505055 AAACGAGGTTGAAGTCCTCTCCCACACCCCCCCCCCCC
1 AAACGAGGTTGAAGTCCCCTCCC-CACCCCCCCCCCCC
*
2505093 AAACGAGGTTGAAGTCCCCTCCCCCCCCCCCCCCCCC
1 AAACGAGGTTGAAGTCCCCTCCCCACCCCCCCCCCCC
2505130 A
1 A
2505131 GATTGCTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 14 0.39
38 22 0.61
ACGTcount: A:0.20, C:0.55, G:0.13, T:0.12
Consensus pattern (37 bp):
AAACGAGGTTGAAGTCCCCTCCCCACCCCCCCCCCCC
Found at i:2506736 original size:83 final size:83
Alignment explanation
Indices: 2506605--2506790 Score: 259
Period size: 83 Copynumber: 2.2 Consensus size: 83
2506595 CTATATGCAT
* * * *
2506605 AGTACAAG-ACTAGTAATTTAGTTTAATCAAATGGATTTAAGCATTACTATTTTGGGTTAGGACT
1 AGTACAAGAACTA-AAATTGAGTTTAATCAAACGGATTTAAGCACTACTATTTTGGGTTAGGACT
* *
2506669 AAAATTTCAAATTTTGAAA
65 AAAATTTAAAAATTTGAAA
* *
2506688 AGTAGAGGAACTAAAATTGAGTTTAATCAAACGGATTTAA-CTACTACTATTTTGGGTTAGGACT
1 AGTACAAGAACTAAAATTGAGTTTAATCAAACGGATTTAAGC-ACTACTATTTTGGGTTAGGACT
2506752 AAAATTTAAAAATTTGAAA
65 AAAATTTAAAAATTTGAAA
*
2506771 AGTACAATAACTAAAATTGA
1 AGTACAAGAACTAAAATTGA
2506791 CTATTTCGAA
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
82 1 0.01
83 85 0.94
84 4 0.04
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.34
Consensus pattern (83 bp):
AGTACAAGAACTAAAATTGAGTTTAATCAAACGGATTTAAGCACTACTATTTTGGGTTAGGACTA
AAATTTAAAAATTTGAAA
Found at i:2519911 original size:24 final size:25
Alignment explanation
Indices: 2519882--2519931 Score: 79
Period size: 22 Copynumber: 2.1 Consensus size: 25
2519872 TTCTTATGAA
2519882 TATTTTTTTA--TTTTGAAT-TTTT
1 TATTTTTTTATTTTTTGAATATTTT
2519904 TATTTTTTTATTTTTTGAATATTTT
1 TATTTTTTTATTTTTTGAATATTTT
2519929 TAT
1 TAT
2519932 AATTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 10 0.40
24 8 0.32
25 7 0.28
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (25 bp):
TATTTTTTTATTTTTTGAATATTTT
Found at i:2519926 original size:19 final size:20
Alignment explanation
Indices: 2519903--2519950 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2519893 TTTGAATTTT
* *
2519903 TTATTTTTTTATTTTTTGAA
1 TTATTTTTTTAATTTTTAAA
*
2519923 -TATTTTTATAATTTTTAAA
1 TTATTTTTTTAATTTTTAAA
2519942 TTATTTTTT
1 TTATTTTTT
2519951 GGCGTGGCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TTATTTTTTTAATTTTTAAA
Found at i:2521715 original size:28 final size:28
Alignment explanation
Indices: 2521679--2521748 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
2521669 AAATAAAAAA
*
2521679 TTACCAAAATGT-TATACATTTTTTTTAT
1 TTACCAAAATATATATA-ATTTTTTTTAT
2521707 TTACCAAAATATATATAATTTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTTAT
2521735 TTACCAAAATATAT
1 TTACCAAAATATAT
2521749 CAAAAAAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 36 0.90
29 4 0.10
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (28 bp):
TTACCAAAATATATATAATTTTTTTTAT
Found at i:2521827 original size:27 final size:27
Alignment explanation
Indices: 2521786--2521864 Score: 117
Period size: 27 Copynumber: 2.9 Consensus size: 27
2521776 TTCCCTGGGT
2521786 CAAGGGAACAC-TGTTGGCGGCACCAAA
1 CAAGGGAAC-CTTGTTGGCGGCACCAAA
2521813 CAAGGGAACCTTGTTGGCGGCACCAAA
1 CAAGGGAACCTTGTTGGCGGCACCAAA
*
2521840 CAA-GGATTCCTTGTTGGCGGCACCA
1 CAAGGGA-ACCTTGTTGGCGGCACCA
2521865 CCTTAAATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
26 4 0.08
27 45 0.92
ACGTcount: A:0.28, C:0.27, G:0.29, T:0.16
Consensus pattern (27 bp):
CAAGGGAACCTTGTTGGCGGCACCAAA
Done.