Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008912.1 Hibiscus syriacus cultivar Beakdansim tig00112215_pilon, whole genome shotgun sequence
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: 3753803
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 18
Found at i:1083576 original size:32 final size:32
Alignment explanation
Indices: 1083480--1083576 Score: 104
Period size: 32 Copynumber: 3.0 Consensus size: 32
1083470 ATTTTGGATT
*
1083480 ATATGACACATGTCACATTATCACTTTGGGTG
1 ATATGACACATGTCACATCATCACTTTGGGTG
* * * * * *
1083512 ATGTGTCACCTCTCACATCGTCATTTTGGGTG
1 ATATGACACATGTCACATCATCACTTTGGGTG
* * *
1083544 ATATGACACATGACACATCATCGCTTTAGGTG
1 ATATGACACATGTCACATCATCACTTTGGGTG
1083576 A
1 A
1083577 CATGGCATGT
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (32 bp):
ATATGACACATGTCACATCATCACTTTGGGTG
Found at i:1084168 original size:16 final size:17
Alignment explanation
Indices: 1084147--1084184 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1084137 TGATGTTGTG
* *
1084147 AATAAAGCAACAA-AAA
1 AATAAAACAAAAATAAA
1084163 AATAAAACAAAAATAAA
1 AATAAAACAAAAATAAA
1084180 AATAA
1 AATAA
1084185 GAATGAAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.79, C:0.08, G:0.03, T:0.11
Consensus pattern (17 bp):
AATAAAACAAAAATAAA
Found at i:1086752 original size:7 final size:6
Alignment explanation
Indices: 1086721--1086761 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
1086711 TTAAAGTTTA
1086721 TAAATT TAGAA-T T-AATT TAAATT TAAATTT TAAATT TAAAT
1 TAAATT TA-AATT TAAATT TAAATT TAAA-TT TAAATT TAAAT
1086762 CGATCAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
4 2 0.06
5 2 0.06
6 19 0.61
7 8 0.26
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:1086754 original size:13 final size:13
Alignment explanation
Indices: 1086736--1086761 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1086726 TTAGAATTAA
1086736 TTTAAATTTAAAT
1 TTTAAATTTAAAT
1086749 TTTAAATTTAAAT
1 TTTAAATTTAAAT
1086762 CGATCAAATA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAAATTTAAAT
Found at i:1092935 original size:34 final size:33
Alignment explanation
Indices: 1092895--1092970 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 33
1092885 GTAGCATGTG
* * *
1092895 ACACATCATTACTTTAGGTGGCACATCACATGAC
1 ACACATCATTAATTTAGGTGACACAGCA-ATGAC
* *
1092929 ACACATCATTAATTTGGGTGACAGAGCAATGAC
1 ACACATCATTAATTTAGGTGACACAGCAATGAC
1092962 ACATCATCA
1 ACA-CATCA
1092971 ATTTAAAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
33 8 0.22
34 28 0.78
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.25
Consensus pattern (33 bp):
ACACATCATTAATTTAGGTGACACAGCAATGAC
Found at i:1093221 original size:32 final size:32
Alignment explanation
Indices: 1093133--1093223 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 32
1093123 AATACCATGT
* *
1093133 CATCAATTTGGGTGACATGAAACATGCCATGC
1 CATCAATTTGGGTGACATGACACATGCCACGC
* * * ** ** *
1093165 CATCACTTTCGGTGACGTCTCACATGTTACGT
1 CATCAATTTGGGTGACATGACACATGCCACGC
*
1093197 TATCAATTTGGGTGACATGACACATGC
1 CATCAATTTGGGTGACATGACACATGC
1093224 ACATGGGACG
Statistics
Matches: 42, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (32 bp):
CATCAATTTGGGTGACATGACACATGCCACGC
Found at i:1093336 original size:31 final size:32
Alignment explanation
Indices: 1093290--1093441 Score: 152
Period size: 32 Copynumber: 4.8 Consensus size: 32
1093280 TTTAAATGAC
*
1093290 ATGACACATAACACATCATCACTTTGA-TGAT
1 ATGACACATGACACATCATCACTTTGAGTGAT
* ** *
1093321 GTGGTACATGACACATCATCAC-TTGAGTGAC
1 ATGACACATGACACATCATCACTTTGAGTGAT
*
1093352 ATGACACGTGACATC-TCATCACTTTTG-GTGAT
1 ATGACACATGACA-CATCATCAC-TTTGAGTGAT
* *
1093384 ATGACACTTGACACATCATCACATTGAGTGAT
1 ATGACACATGACACATCATCACTTTGAGTGAT
* *
1093416 ATGGCACATGA-ATCATAATCACTTTG
1 ATGACACATGACA-CATCATCACTTTG
1093442 GTAACATGGC
Statistics
Matches: 98, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
30 4 0.04
31 42 0.43
32 49 0.50
33 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (32 bp):
ATGACACATGACACATCATCACTTTGAGTGAT
Found at i:1093340 original size:63 final size:63
Alignment explanation
Indices: 1093281--1093405 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 63
1093271 TGTCATCATT
* **
1093281 TTAAATGACATGACACATAACA-CATCATCAC-TTTGATGATGTGGTACATGACACATCATCAC
1 TTAAATGACATGACACATAACATC-TCATCACTTTTGATGATATGACACATGACACATCATCAC
* * * * * *
1093343 TTGAGTGACATGACACGTGACATCTCATCACTTTTGGTGATATGACACTTGACACATCATCAC
1 TTAAATGACATGACACATAACATCTCATCACTTTTGATGATATGACACATGACACATCATCAC
1093406 ATTGAGTGAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
62 25 0.48
63 27 0.52
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (63 bp):
TTAAATGACATGACACATAACATCTCATCACTTTTGATGATATGACACATGACACATCATCAC
Found at i:1093396 original size:32 final size:34
Alignment explanation
Indices: 1093273--1093440 Score: 135
Period size: 32 Copynumber: 5.3 Consensus size: 34
1093263 ACATGTCATG
* * * *
1093273 TCATCA-TTTTAAATGACATGACACATAACA-CA
1 TCATCACTTTTGAGTGATATGACACATGACATCA
* **
1093305 TCATCAC-TTTGA-TGATGTGGTACATGACA-CA
1 TCATCACTTTTGAGTGATATGACACATGACATCA
* *
1093336 TCATCAC--TTGAGTGACATGACACGTGACATC-
1 TCATCACTTTTGAGTGATATGACACATGACATCA
*
1093367 TCATCACTTTTG-GTGATATGACACTTGACA-CA
1 TCATCACTTTTGAGTGATATGACACATGACATCA
* *
1093399 TCATCAC-ATTGAGTGATATGGCACATGA-ATCA
1 TCATCACTTTTGAGTGATATGACACATGACATCA
*
1093431 TAATCACTTT
1 TCATCACTTT
1093441 GGTAACATGG
Statistics
Matches: 109, Mismatches: 18, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
30 4 0.04
31 45 0.41
32 56 0.51
33 4 0.04
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (34 bp):
TCATCACTTTTGAGTGATATGACACATGACATCA
Found at i:1093484 original size:24 final size:24
Alignment explanation
Indices: 1093452--1093497 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1093442 GTAACATGGC
*
1093452 ACATGTCATGTTATTACTTTAGTG
1 ACATGTCATGTCATTACTTTAGTG
1093476 ACATGTCATGTCATTACTTTAG
1 ACATGTCATGTCATTACTTTAG
1093498 GTGATATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (24 bp):
ACATGTCATGTCATTACTTTAGTG
Found at i:1095283 original size:2 final size:2
Alignment explanation
Indices: 1095276--1095321 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1095266 ATTTTAACCG
1095276 TA TA TA TA TA TA 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 TA TA TA TA TA TA
1095318 TA TA
1 TA TA
1095322 AACCTTTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1102578 original size:97 final size:97
Alignment explanation
Indices: 1102412--1102605 Score: 379
Period size: 97 Copynumber: 2.0 Consensus size: 97
1102402 ATCCAAAGAG
*
1102412 TCAGCAAATTTAACATTTTTTCTTAGACAAGAGAAATAAGTTTAACGTTCCTAGTAAAGTGAACC
1 TCAGCAAATTTAACATTTTTTCTTAGAAAAGAGAAATAAGTTTAACGTTCCTAGTAAAGTGAACC
1102477 AAACCATGGATTTGGGATTTGAGGTCATGGAA
66 AAACCATGGATTTGGGATTTGAGGTCATGGAA
1102509 TCAGCAAATTTAACATTTTTTCTTAGAAAAGAGAAATAAGTTTAACGTTCCTAGTAAAGTGAACC
1 TCAGCAAATTTAACATTTTTTCTTAGAAAAGAGAAATAAGTTTAACGTTCCTAGTAAAGTGAACC
1102574 AAACCATGGATTTGGGATTTGAGGTCATGGAA
66 AAACCATGGATTTGGGATTTGAGGTCATGGAA
1102606 AACGTTCCCC
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (97 bp):
TCAGCAAATTTAACATTTTTTCTTAGAAAAGAGAAATAAGTTTAACGTTCCTAGTAAAGTGAACC
AAACCATGGATTTGGGATTTGAGGTCATGGAA
Found at i:1116106 original size:17 final size:17
Alignment explanation
Indices: 1116086--1116128 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1116076 TTTTAATATT
1116086 TTAATAAAATTAAAATA
1 TTAATAAAATTAAAATA
*
1116103 TTAAAAAAATTAAAATA
1 TTAATAAAATTAAAATA
1116120 -T-ATAAAATT
1 TTAATAAAATT
1116129 TTGAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 7 0.29
16 1 0.04
17 16 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAATAAAATTAAAATA
Found at i:1116122 original size:19 final size:18
Alignment explanation
Indices: 1116080--1116126 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1116070 ATGAATTTTT
* *
1116080 AATATTTTAATAAAATTA
1 AATATATTAAAAAAATTA
1116098 AA-ATATTAAAAAAATTA
1 AATATATTAAAAAAATTA
1116115 AA-ATATATAAAA
1 AATATAT-TAAAA
1116127 TTTTGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATATATTAAAAAAATTA
Found at i:1116477 original size:9 final size:9
Alignment explanation
Indices: 1116459--1116487 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1116449 GTTCTATTTA
1116459 ATAT-ATAT
1 ATATAATAT
1116467 ATATAATAT
1 ATATAATAT
1116476 ATATAATAT
1 ATATAATAT
1116485 ATA
1 ATA
1116488 GTTTTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATATAATAT
Found at i:1116500 original size:38 final size:38
Alignment explanation
Indices: 1116466--1116869 Score: 286
Period size: 38 Copynumber: 10.9 Consensus size: 38
1116456 TTAATATATA
*
1116466 TATATAATATATATAATATATAGTTTTGAAAATATTTT
1 TATAAAATATATATAATATATAGTTTTGAAAATATTTT
* * *
1116504 TAAAAAATGTATATAATATATAGTTTTGAAAA-AGTTT
1 TATAAAATATATATAATATATAGTTTTGAAAATATTTT
* *
1116541 TATGAAAATATATATGATATATAG-TTTGAAAACATTTT
1 TAT-AAAATATATATAATATATAGTTTTGAAAATATTTT
* * *
1116579 TGA-AAAA-A-AGT-T-ATAAATAGTTTTAAAAACATTTT
1 T-ATAAAATATA-TATAATATATAGTTTTGAAAATATTTT
* * * * * *
1116614 T-GAAAATTTATAT-ATATATA--TAT--ATATATATA
1 TATAAAATATATATAATATATAGTTTTGAAAATATTTT
* *
1116646 TATATATATATATATATATATATAGTTTTGAAAACATTTT
1 TATA-AAATATATATA-ATATATAGTTTTGAAAATATTTT
**
1116686 TCGAAAATATATATAATATATAGTTTTGAAAATATTTT
1 TATAAAATATATATAATATATAGTTTTGAAAATATTTT
* * * * *
1116724 TAAAAAATATATATAAAATATGGTTTTAAAAACATTTT
1 TATAAAATATATATAATATATAGTTTTGAAAATATTTT
** * *
1116762 TGGAAAATATATATAATATATA-TTTTAGAAAACA-TGT
1 TATAAAATATATATAATATATAGTTTT-GAAAATATTTT
** * * * * *
1116799 TGGAAACTATATATAATATTTGGGTTTCGAAAATGTTTT
1 TATAAAATATATATAATATAT-AGTTTTGAAAATATTTT
* *
1116838 T-CAAAATATATATAATAT-CAGTTTT-AAAATAT
1 TATAAAATATATATAATATATAGTTTTGAAAATAT
1116870 ATTATAGTAT
Statistics
Matches: 291, Mismatches: 54, Indels: 45
0.75 0.14 0.12
Matches are distributed among these distances:
32 6 0.02
33 1 0.00
34 21 0.07
35 23 0.08
36 21 0.07
37 43 0.15
38 152 0.52
39 17 0.06
40 7 0.02
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.43
Consensus pattern (38 bp):
TATAAAATATATATAATATATAGTTTTGAAAATATTTT
Found at i:1116629 original size:2 final size:2
Alignment explanation
Indices: 1116622--1116669 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1116612 TTTGAAAATT
1116622 TA TA TA TA TA TA 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 TA TA TA TA TA TA
1116664 TA TA TA
1 TA TA TA
1116670 GTTTTGAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1116812 original size:182 final size:177
Alignment explanation
Indices: 1116459--1116817 Score: 447
Period size: 182 Copynumber: 2.0 Consensus size: 177
1116449 GTTCTATTTA
* *
1116459 ATATATATATATAATATATATAATATATAGTTTTGAAAATATTTTTAAAAAATGTATATAATATA
1 ATATATATATATAATATATATAATATATAGTTTTGAAAACATTTTTAAAAAATATATATAATATA
* * * *
1116524 TAGTTTTGAAAAAGTTTTATGAAAATATATATGATATATAGTTTGAAAACATTTTTGAAAAAAAG
66 TAGTTTTGAAAAAGTTTTATAAAAATATATATAAAATATAGTTTAAAAACATTTTTGAAAAAAAG
* *
1116589 TTATAAATAGTTTTAAAAACATTTTTGAAAATTTATATATATATATATAT
131 TTATAAATAATTTTAAAAACATTGTTGAAAA--TATATATATA-ATATAT
**
1116639 ATATATATATATATATATATATATATATATAGTTTTGAAAACATTTTTCGAAAATATATATAATA
1 ATATATATATATA-ATATATATA-ATATATAGTTTTGAAAACATTTTTAAAAAATATATATAATA
* * *
1116704 TATAGTTTTGAAAATATTTTTA-AAAAATATATATAAAATATGGTTTTAAAAACATTTTTGGAAA
64 TATAGTTTTGAAAA-AGTTTTATAAAAATATATATAAAATATAG-TTTAAAAACATTTTTGAAAA
* * *
1116768 ATA-TATATAATATATATTTTAGAAAACA-TGTTGGAAA-CTATATATAATAT
127 AAAGT-TATAA-ATA-ATTTTA-AAAACATTGTTGAAAATATATATATAATAT
1116818 TTGGGTTTCG
Statistics
Matches: 155, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
180 13 0.08
181 13 0.08
182 77 0.50
183 31 0.20
184 3 0.02
185 12 0.08
186 6 0.04
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.43
Consensus pattern (177 bp):
ATATATATATATAATATATATAATATATAGTTTTGAAAACATTTTTAAAAAATATATATAATATA
TAGTTTTGAAAAAGTTTTATAAAAATATATATAAAATATAGTTTAAAAACATTTTTGAAAAAAAG
TTATAAATAATTTTAAAAACATTGTTGAAAATATATATATAATATAT
Found at i:1116903 original size:16 final size:15
Alignment explanation
Indices: 1116882--1116923 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
1116872 TATAGTATAC
1116882 TTATTTTTTTATTCCT
1 TTATTTTTTTATT-CT
* *
1116898 TTATTTTTATATTTT
1 TTATTTTTTTATTCT
1116913 TTATTTTTTTA
1 TTATTTTTTTA
1116924 GGTCCAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (15 bp):
TTATTTTTTTATTCT
Found at i:1116922 original size:8 final size:8
Alignment explanation
Indices: 1116882--1116923 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
1116872 TATAGTATAC
1116882 TTATTTTT
1 TTATTTTT
**
1116890 TTATTCCT
1 TTATTTTT
1116898 TTATTTTT
1 TTATTTTT
*
1116906 ATA-TTTT
1 TTATTTTT
1116913 TTATTTTT
1 TTATTTTT
1116921 TTA
1 TTA
1116924 GGTCCAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (8 bp):
TTATTTTT
Found at i:1124474 original size:22 final size:22
Alignment explanation
Indices: 1124449--1124490 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1124439 CTTTAAATAA
*
1124449 GGTTTGAGAGCCAATTCAGACG
1 GGTTCGAGAGCCAATTCAGACG
1124471 GGTTCGAGAGCCAATTCAGA
1 GGTTCGAGAGCCAATTCAGA
1124491 ATGGGTTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (22 bp):
GGTTCGAGAGCCAATTCAGACG
Found at i:1125551 original size:38 final size:37
Alignment explanation
Indices: 1125501--1125700 Score: 219
Period size: 38 Copynumber: 5.3 Consensus size: 37
1125491 TATACATAAT
1125501 ATATATAATATATAGTTTTGAAAACATTTTTGAACAAA
1 ATATATAATATATAGTTTTGAAAACATTTTTGAA-AAA
*
1125539 ATATATAATATATAGTTTTAAAAACATTTTT-AAAAA
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAAA
*
1125575 ATATATATTATATATAGTTTTGAAAACATTTTTCGAAAAT
1 ATATATA--ATATATAGTTTTGAAAACATTTTT-GAAAAA
* **
1125615 ATATATAATATATA-TTTTAGAAAACA-TGTTGCAAACT
1 ATATATAATATATAGTTTT-GAAAACATTTTTG-AAAAA
* ** *
1125652 ATATATAATATTTAGGTTTTGAAAATGTTTTTCG-AAAT
1 ATATATAATATATA-GTTTTGAAAACATTTTT-GAAAAA
1125690 ATATATAATAT
1 ATATATAATAT
1125701 CAGTTTTAAA
Statistics
Matches: 142, Mismatches: 10, Indels: 20
0.83 0.06 0.12
Matches are distributed among these distances:
36 11 0.08
37 26 0.18
38 86 0.61
39 7 0.05
40 12 0.08
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (37 bp):
ATATATAATATATAGTTTTGAAAACATTTTTGAAAAA
Found at i:1125580 original size:76 final size:75
Alignment explanation
Indices: 1125498--1125711 Score: 274
Period size: 76 Copynumber: 2.9 Consensus size: 75
1125488 ATATATACAT
*
1125498 AATATATATAATATATAGTTTTGAAAACATTTTT-GAACAAAATATATAATATATAGTTTTAAAA
1 AATATATATAATATATAGTTTTGAAAACATTTTTCGAA-AATATATATAATATATAGTTTTAAAA
*
1125562 ACATTTTTAAAA
65 ACA-TGTTAAAA
*
1125574 AATATATATTATATATAGTTTTGAAAACATTTTTCGAAAATATATATAATATATA-TTTTAGAAA
1 AATATATATAATATATAGTTTTGAAAACATTTTTCGAAAATATATATAATATATAGTTTTA-AAA
**
1125638 ACATGTTGCAA
65 ACATGTTAAAA
* * ** *
1125649 ACTATATATAATATTTAGGTTTTGAAAATGTTTTTCG-AAATATATATAATAT-CAGTTTTAAAA
1 AATATATATAATATATA-GTTTTGAAAACATTTTTCGAAAATATATATAATATATAGTTTTAAAA
1125712 TATATTATAG
Statistics
Matches: 123, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
74 4 0.03
75 44 0.36
76 72 0.59
77 3 0.02
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (75 bp):
AATATATATAATATATAGTTTTGAAAACATTTTTCGAAAATATATATAATATATAGTTTTAAAAA
CATGTTAAAA
Found at i:1125757 original size:23 final size:24
Alignment explanation
Indices: 1125727--1125782 Score: 80
Period size: 22 Copynumber: 2.4 Consensus size: 24
1125717 TATAGTATAC
1125727 TTATTTTTTATTTTTTTAT-TCCT
1 TTATTTTTTATTTTTTTATGTCCT
**
1125750 TTA-TTTTTATTTTTTTATGTTTT
1 TTATTTTTTATTTTTTTATGTCCT
1125773 TTATTTTTTA
1 TTATTTTTTA
1125783 GGTCCAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 15 0.52
23 8 0.28
24 6 0.21
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (24 bp):
TTATTTTTTATTTTTTTATGTCCT
Found at i:1125772 original size:9 final size:8
Alignment explanation
Indices: 1125730--1125781 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 8
1125720 AGTATACTTA
1125730 TTTTTTAT
1 TTTTTTAT
1125738 TTTTTTAT
1 TTTTTTAT
**
1125746 TCCTTTA-
1 TTTTTTAT
1125753 -TTTTTAT
1 TTTTTTAT
1125760 TTTTTTAT
1 TTTTTTAT
1125768 GTTTTTTAT
1 -TTTTTTAT
1125777 TTTTT
1 TTTTT
1125782 AGGTCCAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
6 4 0.11
8 25 0.68
9 8 0.22
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.83
Consensus pattern (8 bp):
TTTTTTAT
Found at i:1137560 original size:31 final size:31
Alignment explanation
Indices: 1137525--1137587 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1137515 AAAAAATTAA
1137525 GAGTAAGATAGATTTTCTCTTGAATTAGATT
1 GAGTAAGATAGATTTTCTCTTGAATTAGATT
1137556 GAGTAAGATAGATTTTCTCTTGAATTAGATT
1 GAGTAAGATAGATTTTCTCTTGAATTAGATT
1137587 G
1 G
1137588 CTCGGGTAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (31 bp):
GAGTAAGATAGATTTTCTCTTGAATTAGATT
Found at i:1141409 original size:5 final size:5
Alignment explanation
Indices: 1141399--1141447 Score: 52
Period size: 5 Copynumber: 10.6 Consensus size: 5
1141389 TATAAAAAAG
* *
1141399 TTTTC TTTTC -TTTC ATTTC -TTT- TTTTC TTTTC TTTT- TTTTA TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
1141445 TTT
1 TTT
1141448 AAACAAAGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
4 14 0.36
5 25 0.64
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:1141419 original size:14 final size:13
Alignment explanation
Indices: 1141400--1141447 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
1141390 ATAAAAAAGT
1141400 TTTCTTTTCTTTCA
1 TTTCTTTT-TTTCA
*
1141414 TTTCTTTTTTTCT
1 TTTCTTTTTTTCA
*
1141427 TTTCTTTTTTTTA
1 TTTCTTTTTTTCA
1141440 TTTTCTTT
1 -TTTCTTT
1141448 AAACAAAGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 15 0.50
14 15 0.50
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTCTTTTTTTCA
Found at i:1141443 original size:22 final size:22
Alignment explanation
Indices: 1141399--1141443 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1141389 TATAAAAAAG
*
1141399 TTTTCTTTTCTTTCATTTCTTT
1 TTTTCTTTTCTTTCATTTATTT
**
1141421 TTTTCTTTTCTTTTTTTTATTT
1 TTTTCTTTTCTTTCATTTATTT
1141443 T
1 T
1141444 CTTTAAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTCTTTTCTTTCATTTATTT
Found at i:1147351 original size:5 final size:5
Alignment explanation
Indices: 1147341--1147372 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1147331 AGTCTTAGTT
1147341 TTATA TTATA TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TT
1147373 TTTCTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:1148720 original size:20 final size:22
Alignment explanation
Indices: 1148681--1148721 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1148671 ACACAAAAAA
1148681 GATGAATGCTTCAAATTAATGGT
1 GATGAATGCTTC-AATTAATGGT
1148704 GATGAATGC-TC-ATTAATG
1 GATGAATGCTTCAATTAATG
1148722 TGTTGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
22 2 0.11
23 9 0.50
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (22 bp):
GATGAATGCTTCAATTAATGGT
Found at i:1161498 original size:20 final size:20
Alignment explanation
Indices: 1161462--1161499 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1161452 GCTGGAAAAT
*
1161462 CGGTTTTACCAGTTTTGAAC
1 CGGTTTTACCAGGTTTGAAC
1161482 CGGTTTTGACC-GGTTTGA
1 CGGTTTT-ACCAGGTTTGA
1161500 CCAGTCTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (20 bp):
CGGTTTTACCAGGTTTGAAC
Found at i:1161538 original size:17 final size:17
Alignment explanation
Indices: 1161516--1161553 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1161506 TGAACCGGTC
1161516 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1161533 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1161550 GACC
1 GACC
1161554 GTTGACTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:1166272 original size:18 final size:18
Alignment explanation
Indices: 1166224--1166273 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1166214 TTTTATATTA
1166224 ATATATAATA-TATTTTG
1 ATATATAATATTATTTTG
1166241 ATATATAA-ATTTATATTT-
1 ATATATAATA-TTAT-TTTG
*
1166259 CTATATAATATTATT
1 ATATATAATATTATT
1166274 AAGAATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
16 1 0.04
17 9 0.32
18 14 0.50
19 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
ATATATAATATTATTTTG
Found at i:1166309 original size:18 final size:18
Alignment explanation
Indices: 1166286--1166320 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1166276 GAATAATATT
1166286 ATATATCTTATATATTAA
1 ATATATCTTATATATTAA
*
1166304 ATATATCTTATTTATTA
1 ATATATCTTATATATTA
1166321 TTTATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATATCTTATATATTAA
Found at i:1166331 original size:15 final size:14
Alignment explanation
Indices: 1166311--1166342 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
1166301 TAAATATATC
1166311 TTATTTATTATTTAT
1 TTATTTATTA-TTAT
1166326 TTATTTATTATTAT
1 TTATTTATTATTAT
1166340 TTA
1 TTA
1166343 AATTAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTTATTATTAT
Found at i:1166438 original size:37 final size:36
Alignment explanation
Indices: 1166362--1166445 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 36
1166352 ATACTGAAAG
** *
1166362 ATTTAAAGTATTATTTATAATTTATTATTATTTAATA
1 ATTTAAA-TATTATTTATAACATATTATAATTTAATA
*
1166399 ATTTAAATATTATTTATTACATATT-TAATTTAATTTA
1 ATTTAAATATTATTTATAACATATTATAATTTAA--TA
1166436 ATTTAAATAT
1 ATTTAAATAT
1166446 AATAATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 7 0.17
36 15 0.37
37 19 0.46
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (36 bp):
ATTTAAATATTATTTATAACATATTATAATTTAATA
Found at i:1169920 original size:38 final size:38
Alignment explanation
Indices: 1169847--1170025 Score: 162
Period size: 38 Copynumber: 4.9 Consensus size: 38
1169837 TAATATTCTA
* * * *
1169847 TTATTTAAGGATTTATATTCAATTTAAAT-TAGAATACG
1 TTATTTATGAATTTATATTCAATTAAAATAT-GAATATG
* *
1169885 TTATTTATGAATTTATATTCAATTGAAATATGAATATA
1 TTATTTATGAATTTATATTCAATTAAAATATGAATATG
* * **
1169923 TTATTTATAAATGTATATTTGATT--AA-AT--ATA--
1 TTATTTATGAATTTATATTCAATTAAAATATGAATATG
1169954 TTATTTATGAATTTATATTCAATTAAAATATGAATATG
1 TTATTTATGAATTTATATTCAATTAAAATATGAATATG
** *
1169992 TTA-TTACAAATTTATATTCGATTAAAATAT-AATA
1 TTATTTATGAATTTATATTCAATTAAAATATGAATA
1170026 ATGTAGTTTC
Statistics
Matches: 117, Mismatches: 16, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
31 20 0.17
33 5 0.04
34 2 0.02
35 2 0.02
36 9 0.08
37 24 0.21
38 54 0.46
39 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (38 bp):
TTATTTATGAATTTATATTCAATTAAAATATGAATATG
Found at i:1169958 original size:17 final size:15
Alignment explanation
Indices: 1169917--1169961 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
1169907 TTGAAATATG
1169917 AATATATTATTTATA
1 AATATATTATTTATA
*
1169932 AATGTA-TATTTGATTA
1 AATATATTATTT-A-TA
1169948 AATATATTATTTAT
1 AATATATTATTTAT
1169962 GAATTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 5 0.20
15 7 0.28
16 8 0.32
17 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (15 bp):
AATATATTATTTATA
Found at i:1169960 original size:69 final size:69
Alignment explanation
Indices: 1169885--1170022 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 69
1169875 TTAGAATACG
* * *
1169885 TTATTTATGAATTTATATTCAATTGAAATATGAATATATTATTTATAAATGTATATTTGATT-AA
1 TTATTTATGAATTTATATTCAATTAAAATATGAATATATTA-TTACAAATGTATATTCGATTAAA
1169949 ATATA
65 ATATA
* *
1169954 TTATTTATGAATTTATATTCAATTAAAATATGAATATGTTATTACAAATTTATATTCGATTAAAA
1 TTATTTATGAATTTATATTCAATTAAAATATGAATATATTATTACAAATGTATATTCGATTAAAA
1170019 TATA
66 TATA
1170023 ATAATGTAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 17 0.27
69 46 0.73
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (69 bp):
TTATTTATGAATTTATATTCAATTAAAATATGAATATATTATTACAAATGTATATTCGATTAAAA
TATA
Found at i:1169979 original size:31 final size:31
Alignment explanation
Indices: 1169917--1169984 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1169907 TTGAAATATG
**
1169917 AATATATTATTTATAAATGTATATTTGATTA
1 AATATATTATTTATAAATGTATATTCAATTA
* *
1169948 AATATATTATTTATGAATTTATATTCAATTA
1 AATATATTATTTATAAATGTATATTCAATTA
1169979 AA-ATAT
1 AATATAT
1169985 GAATATGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (31 bp):
AATATATTATTTATAAATGTATATTCAATTA
Found at i:1170686 original size:13 final size:13
Alignment explanation
Indices: 1170668--1170714 Score: 85
Period size: 13 Copynumber: 3.6 Consensus size: 13
1170658 AGTTTCGCTG
*
1170668 CTATCGGCGAAGA
1 CTATCGTCGAAGA
1170681 CTATCGTCGAAGA
1 CTATCGTCGAAGA
1170694 CTATCGTCGAAGA
1 CTATCGTCGAAGA
1170707 CTATCGTC
1 CTATCGTC
1170715 TTCTGGTGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (13 bp):
CTATCGTCGAAGA
Found at i:1177476 original size:17 final size:18
Alignment explanation
Indices: 1177454--1177487 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1177444 TTGAAAGGTC
*
1177454 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
1177471 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
1177488 ACAGAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:1183146 original size:15 final size:15
Alignment explanation
Indices: 1183128--1183158 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1183118 CCACGAGATT
1183128 GATGCTCCTCCTAAA
1 GATGCTCCTCCTAAA
1183143 GATGCTCCTCCTAAA
1 GATGCTCCTCCTAAA
1183158 G
1 G
1183159 TAAAAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (15 bp):
GATGCTCCTCCTAAA
Found at i:1186622 original size:21 final size:21
Alignment explanation
Indices: 1186598--1186646 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1186588 AATATGGAGA
1186598 ACTGATGCAGGGGGATCCGAG
1 ACTGATGCAGGGGGATCCGAG
1186619 ACTGATGCAGGGGGATCCGAG
1 ACTGATGCAGGGGGATCCGAG
*
1186640 ACAGATG
1 ACTGATG
1186647 ATGCTGAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.41, T:0.14
Consensus pattern (21 bp):
ACTGATGCAGGGGGATCCGAG
Found at i:1187049 original size:22 final size:21
Alignment explanation
Indices: 1186997--1187045 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1186987 AGCTCAGCAT
*
1186997 CATCTGTCTCGGATCCCCCTG
1 CATCAGTCTCGGATCCCCCTG
1187018 CATCAGTCTCGGATCCCCCTG
1 CATCAGTCTCGGATCCCCCTG
1187039 CATCAGT
1 CATCAGT
1187046 TCTCCATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.14, C:0.41, G:0.18, T:0.27
Consensus pattern (21 bp):
CATCAGTCTCGGATCCCCCTG
Found at i:1188529 original size:18 final size:18
Alignment explanation
Indices: 1188506--1188541 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1188496 CCTTAAATAC
1188506 ACATTCACAATAGTGTTT
1 ACATTCACAATAGTGTTT
*
1188524 ACATTCCCAATAGTGTTT
1 ACATTCACAATAGTGTTT
1188542 CCAATACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (18 bp):
ACATTCACAATAGTGTTT
Found at i:1192865 original size:25 final size:26
Alignment explanation
Indices: 1192837--1192887 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
1192827 AACATGCAAC
1192837 ATGAATTAATAACATGC-AATATTAT
1 ATGAATTAATAACATGCTAATATTAT
*
1192862 ATGAATTAATAACATGCTATTATTAT
1 ATGAATTAATAACATGCTAATATTAT
1192888 TTAATACACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (26 bp):
ATGAATTAATAACATGCTAATATTAT
Found at i:1193596 original size:43 final size:44
Alignment explanation
Indices: 1193548--1193659 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 44
1193538 ACTGAATTGA
* * *
1193548 CATTGATTCAACTCATTTTGTGAAGAAACAAG-AGAAAGATTT-T
1 CATTGATCCAACTCCTTTTGTGAAGAAACAAGTAAAAAG-TTTGT
* * *
1193591 CATTGATCCAACTCCTTCTGTGAAGGATCAAGTAAAAAGTTTGT
1 CATTGATCCAACTCCTTTTGTGAAGAAACAAGTAAAAAGTTTGT
* *
1193635 CACTGATCCAAATCCTTTTGTGAAG
1 CATTGATCCAACTCCTTTTGTGAAG
1193660 GATAGAATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
43 30 0.52
44 28 0.48
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (44 bp):
CATTGATCCAACTCCTTTTGTGAAGAAACAAGTAAAAAGTTTGT
Found at i:1193824 original size:43 final size:43
Alignment explanation
Indices: 1193769--1193928 Score: 133
Period size: 43 Copynumber: 3.7 Consensus size: 43
1193759 AAAAGGTTAC
*
1193769 GCTGATTCAACTCCTTCTGTGAAGAATCGAGCAGAATGAC-ATT
1 GCTGATCCAACTCCTTCTGTGAAGAATCGAGCAGAATGACTA-T
* * * * * * *
1193812 GTTGATCCAACTCCTTCTATAAAGAATCAAACAGGATGTCTAT
1 GCTGATCCAACTCCTTCTGTGAAGAATCGAGCAGAATGACTAT
* * * **
1193855 GCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAATAAGGTTAT
1 GCTGATCCAACTCCTTCTGTGA-AGAATCGAGCAGAAT--GACTAT
* * *
1193901 ACTAATTCAACTCCTTCTGTGAAGAATC
1 GCTGATCCAACTCCTTCTGTGAAGAATC
1193929 AAGAAAAAGA
Statistics
Matches: 89, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
43 50 0.56
44 12 0.13
45 6 0.07
46 21 0.24
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (43 bp):
GCTGATCCAACTCCTTCTGTGAAGAATCGAGCAGAATGACTAT
Found at i:1193841 original size:132 final size:131
Alignment explanation
Indices: 1193681--1193928 Score: 318
Period size: 132 Copynumber: 1.9 Consensus size: 131
1193671 ATGACAAATA
* * * * * *
1193681 TTGATCCAACTCCTTATGTGAAGGATCAAAACA-ATTGCCAACGTTGATCTACCTTCTTTTGTGA
1 TTGATCCAACTCCTTATATAAAGAATC-AAACAGA-TGCCAACGCTGATCTACCTCCTTCTGTGA
* *
1193745 TAGAATCAAACAAAAAAAGGTTACGCTGATTCAACTCCTTCTGTGAAGAATCGAGCAGAATGACA
64 TAGAATCAAACAAAAAAAGGTTACACTAATTCAACTCCTTCTGTGAAGAATCGAGCAGAATGACA
1193810 TTG
129 TTG
* * * *
1193813 TTGATCCAACTCCTTCTATAAAGAATCAAACAGGATGTCTATGCTGATCTACCTCCTTCTGTGAT
1 TTGATCCAACTCCTTATATAAAGAATCAAACA-GATGCCAACGCTGATCTACCTCCTTCTGTGAT
* * * *
1193878 AGAATCGAGCAAAATAAGGTTATACTAATTCAACTCCTTCTGTGAAGAATC
65 AGAATCAAACAAAAAAAGGTTACACTAATTCAACTCCTTCTGTGAAGAATC
1193929 AAGAAAAAGA
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
131 5 0.05
132 92 0.94
133 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (131 bp):
TTGATCCAACTCCTTATATAAAGAATCAAACAGATGCCAACGCTGATCTACCTCCTTCTGTGATA
GAATCAAACAAAAAAAGGTTACACTAATTCAACTCCTTCTGTGAAGAATCGAGCAGAATGACATT
G
Found at i:1194498 original size:19 final size:19
Alignment explanation
Indices: 1194476--1194532 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1194466 CTTTGGTTTT
1194476 TTCTTTTTTTTTTTCTTCC
1 TTCTTTTTTTTTTTCTTCC
* * **
1194495 TTCTTTCTTTTTCTCTTTT
1 TTCTTTTTTTTTTTCTTCC
*
1194514 TATCTTCTTTTTTTTCTTC
1 T-TCTTTTTTTTTTTCTTC
1194533 TTCATCGAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (19 bp):
TTCTTTTTTTTTTTCTTCC
Found at i:1195258 original size:13 final size:14
Alignment explanation
Indices: 1195215--1195258 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
1195205 TTTATTTTTA
*
1195215 TTTTCTTTTTTTCT
1 TTTTCTCTTTTTCT
*
1195229 CTTTCTCTTTTTCT
1 TTTTCTCTTTTTCT
1195243 TTTTC-CTTTTTCT
1 TTTTCTCTTTTTCT
1195256 TTT
1 TTT
1195259 GTTTTTCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTCTCTTTTTCT
Found at i:1195264 original size:19 final size:19
Alignment explanation
Indices: 1195220--1195266 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1195210 TTTTATTTTC
1195220 TTTTTTTCTCTTTCTCTTT
1 TTTTTTTCTCTTTCTCTTT
*
1195239 TTCTTTTTC-CTTTTTCTTT
1 TT-TTTTTCTCTTTCTCTTT
*
1195258 TGTTTTTCT
1 TTTTTTTCT
1195267 TCTTCAAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.25
19 12 0.50
20 6 0.25
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTTTCTCTTTCTCTTT
Found at i:1196424 original size:11 final size:11
Alignment explanation
Indices: 1196408--1196432 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1196398 GAATTTCCCC
1196408 ATCGAAAATAT
1 ATCGAAAATAT
1196419 ATCGAAAATAT
1 ATCGAAAATAT
1196430 ATC
1 ATC
1196433 CTACTACAAT
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:0.52, C:0.12, G:0.08, T:0.28
Consensus pattern (11 bp):
ATCGAAAATAT
Found at i:1216456 original size:32 final size:32
Alignment explanation
Indices: 1216417--1216480 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1216407 CGCATATAGT
*
1216417 TTTATTTCTTTTTGTTCTCTTTAAGCATTGAG
1 TTTATTTCTTTTCGTTCTCTTTAAGCATTGAG
1216449 TTTATTTCTTTTCGTTCTCTTTAAGCATTGAG
1 TTTATTTCTTTTCGTTCTCTTTAAGCATTGAG
1216481 GACAATGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.58
Consensus pattern (32 bp):
TTTATTTCTTTTCGTTCTCTTTAAGCATTGAG
Found at i:1220100 original size:25 final size:26
Alignment explanation
Indices: 1220072--1220123 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
1220062 TTAACATGCA
1220072 ACATGAATTAAAAACATG-TAATATT
1 ACATGAATTAAAAACATGCTAATATT
* *
1220097 ACATGAATTAATAACATGCTATTATT
1 ACATGAATTAAAAACATGCTAATATT
1220123 A
1 A
1220124 TTTAATACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.35
Consensus pattern (26 bp):
ACATGAATTAAAAACATGCTAATATT
Found at i:1223734 original size:23 final size:23
Alignment explanation
Indices: 1223699--1223747 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1223689 CTGTGGGTAT
*
1223699 GAACAAAATGAAAGAAAAGAAAA
1 GAACAAAAGGAAAGAAAAGAAAA
* * *
1223722 GAACAACAGGAAAGGAAAGGAAA
1 GAACAAAAGGAAAGAAAAGAAAA
1223745 GAA
1 GAA
1223748 AGGTGAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.67, C:0.06, G:0.24, T:0.02
Consensus pattern (23 bp):
GAACAAAAGGAAAGAAAAGAAAA
Found at i:1223865 original size:42 final size:41
Alignment explanation
Indices: 1223755--1223962 Score: 175
Period size: 42 Copynumber: 5.0 Consensus size: 41
1223745 GAAAGGTGAA
** ** * * *
1223755 TAAAGTAGAACAAAAGGAGGTATTGCACTTTCGATTCTCATC
1 TAAAGTAGAACGGAAGGAGGCGTCGCA-TTTTGATTCTCGTC
* * * * *
1223797 TAAAATAGAATGGAAGGAGG-GATCGCATTTTAAATTATTGTC
1 TAAAGTAGAACGGAAGGAGGCG-TCGCATTTT-GATTCTCGTC
1223839 TAAAGTAGAACGGAAGGAGGCGTCGCACTTTTGATTCTCGTC
1 TAAAGTAGAACGGAAGGAGGCGTCGCA-TTTTGATTCTCGTC
* * * *
1223881 TAAAGTAGAACGGAATGAGACATCGCACTTTCGATTCTCGTC
1 TAAAGTAGAACGGAAGGAGGCGTCGCA-TTTTGATTCTCGTC
* * * *
1223923 TAAAGTAGAACGGAATGAGACATCGCACTTTCGATTCTCG
1 TAAAGTAGAACGGAAGGAGGCGTCGCA-TTTTGATTCTCG
1223963 ATTACAAAAT
Statistics
Matches: 142, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
41 3 0.02
42 134 0.94
43 5 0.04
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (41 bp):
TAAAGTAGAACGGAAGGAGGCGTCGCATTTTGATTCTCGTC
Found at i:1223906 original size:84 final size:84
Alignment explanation
Indices: 1223755--1223962 Score: 245
Period size: 84 Copynumber: 2.5 Consensus size: 84
1223745 GAAAGGTGAA
** * * * * **
1223755 TAAAGTAGAACAAAAGGAGGTATTGCACTTTCGATTCTCATCTAAAATAGAATGGAAGGAGGGAT
1 TAAAGTAGAACGGAAGGAGGCATCGCACTTTCGATTCTCGTCTAAAATAGAACGGAAGGAGACAT
* *
1223820 CGCATTTTAAATTATTGTC
66 CGCACTTTAAATTATCGTC
* * * *
1223839 TAAAGTAGAACGGAAGGAGGCGTCGCACTTTTGATTCTCGTCTAAAGTAGAACGGAATGAGACAT
1 TAAAGTAGAACGGAAGGAGGCATCGCACTTTCGATTCTCGTCTAAAATAGAACGGAAGGAGACAT
** *
1223904 CGCACTTTCGATTCTCGTC
66 CGCACTTTAAATTATCGTC
* *
1223923 TAAAGTAGAACGGAATGAGACATCGCACTTTCGATTCTCG
1 TAAAGTAGAACGGAAGGAGGCATCGCACTTTCGATTCTCG
1223963 ATTACAAAAT
Statistics
Matches: 103, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
84 103 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (84 bp):
TAAAGTAGAACGGAAGGAGGCATCGCACTTTCGATTCTCGTCTAAAATAGAACGGAAGGAGACAT
CGCACTTTAAATTATCGTC
Found at i:1227244 original size:15 final size:16
Alignment explanation
Indices: 1227226--1227256 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1227216 TTTTTGTTAC
1227226 AATTTT-AAAAATTTA
1 AATTTTGAAAAATTTA
1227241 AATTTTGAAAAATTTA
1 AATTTTGAAAAATTTA
1227257 TACATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AATTTTGAAAAATTTA
Found at i:1228581 original size:3 final size:3
Alignment explanation
Indices: 1228573--1228663 Score: 182
Period size: 3 Copynumber: 30.3 Consensus size: 3
1228563 TGCATAAACT
1228573 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1228621 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1228664 CATCATGTCA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1228840 original size:17 final size:17
Alignment explanation
Indices: 1228818--1228870 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1228808 GCACTCGTTT
*
1228818 TGTTAATCATTATATTG
1 TGTTAATCATTATATTA
*
1228835 TGTTAATCATTTTATTA
1 TGTTAATCATTATATTA
* *
1228852 TGATAAACATTATTATTA
1 TGTTAATCATTA-TATTA
1228870 T
1 T
1228871 TATTCCTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 24 0.80
18 6 0.20
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.53
Consensus pattern (17 bp):
TGTTAATCATTATATTA
Found at i:1228972 original size:3 final size:3
Alignment explanation
Indices: 1228964--1228997 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1228954 TCTACAAAAA
1228964 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1228998 GTTGTTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1229002 original size:3 final size:3
Alignment explanation
Indices: 1228996--1229021 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1228986 ATTATTATTA
1228996 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
1229022 ATTTACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:1229776 original size:76 final size:75
Alignment explanation
Indices: 1229649--1229877 Score: 298
Period size: 76 Copynumber: 3.0 Consensus size: 75
1229639 GATTAAACTC
* * * * *
1229649 AAGTTTTAGGATAATATGTTAAACATTATATCTTTGTTTTAGATATTTTAGTTTAAATAGCTTTT
1 AAGTTTTAGGATATTATTTTTAA-ATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAG-TTTT
1229714 AGTATTTTAATT
64 AGTATTTTAATT
* *
1229726 AAGTTTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAAGAGGTTTTA
1 AAGTTTTAGGATATTATTTTTAAATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTA
1229791 GTATTTTAATT
65 GTATTTTAATT
* * * * *
1229802 AGGATTTAGGATATTA-TTTTAAATATTATTTTTGTTTTAGGTGTTTTAGTTTAAATAGTTTTAA
1 AAGTTTTAGGATATTATTTTTAAATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTT-A
*
1229866 GTGTTTTAATT
65 GTATTTTAATT
1229877 A
1 A
1229878 GTATTTAAGA
Statistics
Matches: 135, Mismatches: 15, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
74 5 0.04
75 48 0.36
76 62 0.46
77 20 0.15
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.55
Consensus pattern (75 bp):
AAGTTTTAGGATATTATTTTTAAATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAG
TATTTTAATT
Found at i:1229905 original size:21 final size:20
Alignment explanation
Indices: 1229851--1229894 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1229841 GGTGTTTTAG
*
1229851 TTTAAATAG-TTTTAAGTGT
1 TTTAATTAGTTTTTAAGTGT
*
1229870 TTTAATTAGTATTTAAGATGT
1 TTTAATTAGTTTTTAAG-TGT
1229891 TTTA
1 TTTA
1229895 GCTTGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (20 bp):
TTTAATTAGTTTTTAAGTGT
Found at i:1230610 original size:18 final size:19
Alignment explanation
Indices: 1230589--1230629 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1230579 TAGTTATTAT
* *
1230589 TTTATTATT-TCTCTTTTA
1 TTTATTATTATATATTTTA
1230607 TTTATTATTATATATTTTA
1 TTTATTATTATATATTTTA
1230626 TTTA
1 TTTA
1230630 ATTAAATCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTATTATTATATATTTTA
Found at i:1236278 original size:15 final size:15
Alignment explanation
Indices: 1236258--1236288 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1236248 TTTGAACAAT
*
1236258 ACAGTGTAGAAAAAA
1 ACAGTGCAGAAAAAA
1236273 ACAGTGCAGAAAAAA
1 ACAGTGCAGAAAAAA
1236288 A
1 A
1236289 TAGATTTGGT
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:0.61, C:0.10, G:0.19, T:0.10
Consensus pattern (15 bp):
ACAGTGCAGAAAAAA
Found at i:1238181 original size:76 final size:74
Alignment explanation
Indices: 1238054--1238282 Score: 316
Period size: 76 Copynumber: 3.0 Consensus size: 74
1238044 GATTAAACTC
*
1238054 AAGTTTTAGGATAATATTTTAAACATTATATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT
1 AAGTTTTAGGATATTATTTT-AA-ATT-TATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT
1238119 AGTATTTTAATT
63 AGTATTTTAATT
*
1238131 AAGTTTTAGAATATTATTTTTATAATTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
1 AAGTTTTAGGATATTA-TTTTA-AATTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
*
1238196 TTATTTTAATT
64 GTATTTTAATT
* * * *
1238207 AGGATTTAGGATATTATTTTAAATATTATTTTTGTTTTAGGTGTTTTAGTTTAAATA-GTTTTAA
1 AAGTTTTAGGATATTATTTTAAAT-TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-A
*
1238271 GTGTTTTAATT
64 GTATTTTAATT
1238282 A
1 A
1238283 GAATTTAAGA
Statistics
Matches: 138, Mismatches: 10, Indels: 10
0.87 0.06 0.06
Matches are distributed among these distances:
74 8 0.06
75 46 0.33
76 61 0.44
77 18 0.13
78 5 0.04
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (74 bp):
AAGTTTTAGGATATTATTTTAAATTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGT
ATTTTAATT
Found at i:1238209 original size:19 final size:19
Alignment explanation
Indices: 1238168--1238214 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1238158 TATCTTTGTT
*
1238168 TTAGGTATT-TTAGTTTAA
1 TTAGGTTTTATTAGTTTAA
* *
1238186 ATAGGTTTTATTATTTTAA
1 TTAGGTTTTATTAGTTTAA
*
1238205 TTAGGATTTA
1 TTAGGTTTTA
1238215 GGATATTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (19 bp):
TTAGGTTTTATTAGTTTAA
Found at i:1238278 original size:75 final size:75
Alignment explanation
Indices: 1238058--1238298 Score: 315
Period size: 75 Copynumber: 3.2 Consensus size: 75
1238048 AAACTCAAGT
* *
1238058 TTTAGGATAATATTTTAAACATTATATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTA
1 TTTAGGATATTATTTTAAATATTAT-T-TTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTA
* *
1238123 TTTTAATTAAGT
64 TTTTAATTAGGA
* * *
1238135 TTTAGAATATTATTTTTATAAT-TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTATTA
1 TTTAGGATATTA-TTTTA-AATATTATTTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTA
1238199 TTTTAATTAGGA
64 TTTTAATTAGGA
* *
1238211 TTTAGGATATTATTTTAAATATTATTTTTGTTTTAGGTGTTTTAGTTTAAATA-GTTTTAAGTGT
1 TTTAGGATATTATTTTAAATATTATTTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTAT
*
1238275 TTTAATTAGAA
65 TTTAATTAGGA
* *
1238286 TTTAAGATGTTAT
1 TTTAGGATATTAT
1238299 AGCTTGTTTT
Statistics
Matches: 145, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
74 8 0.06
75 59 0.41
76 57 0.39
77 10 0.07
78 9 0.06
79 2 0.01
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (75 bp):
TTTAGGATATTATTTTAAATATTATTTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAGGA
Found at i:1240506 original size:2 final size:2
Alignment explanation
Indices: 1240499--1240533 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1240489 TGTTTCCTTA
1240499 AT AT 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 A
1240534 CTTTCGAAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1246044 original size:34 final size:34
Alignment explanation
Indices: 1246001--1246068 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1245991 TTTCAAAAAA
1246001 TAAAATACAAACTTCATCATGACATCATAAACAT
1 TAAAATACAAACTTCATCATGACATCATAAACAT
1246035 TAAAATACAAACTTCATCATGACATCATAAACAT
1 TAAAATACAAACTTCATCATGACATCATAAACAT
1246069 CCAAAATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.50, C:0.21, G:0.03, T:0.26
Consensus pattern (34 bp):
TAAAATACAAACTTCATCATGACATCATAAACAT
Found at i:1246278 original size:36 final size:35
Alignment explanation
Indices: 1246235--1246338 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 35
1246225 AAAATTTATG
*
1246235 AAACAAATTTTGTCTCGCTTGAGTCAATTTTCTCTA
1 AAACAAATTTTGTCTCGCTTGAGACAATTTTCT-TA
*
1246271 AAACAAATTTTGTCTCGCTTGAGACAATTTATCTTG
1 AAACAAATTTTGTCTCGCTTGAGACAATTT-TCTTA
* *
1246307 AAACAAATTTCGTCTCGCTTGAGACATTTTTC
1 AAACAAATTTTGTCTCGCTTGAGACAATTTTC
1246339 CTTTGAGGTG
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 2 0.03
36 58 0.92
37 3 0.05
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.39
Consensus pattern (35 bp):
AAACAAATTTTGTCTCGCTTGAGACAATTTTCTTA
Found at i:1246297 original size:21 final size:21
Alignment explanation
Indices: 1246237--1246332 Score: 54
Period size: 21 Copynumber: 5.1 Consensus size: 21
1246227 AATTTATGAA
1246237 ACAAATTTTGTCTCGCTTGAG
1 ACAAATTTTGTCTCGCTTGAG
* * *
1246258 TC-AA-TTT-TCT--C-TAAA
1 ACAAATTTTGTCTCGCTTGAG
1246273 ACAAATTTTGTCTCGCTTGAG
1 ACAAATTTTGTCTCGCTTGAG
* *
1246294 AC-AA--TT-TAT--CTTGAA
1 ACAAATTTTGTCTCGCTTGAG
*
1246309 ACAAATTTCGTCTCGCTTGAG
1 ACAAATTTTGTCTCGCTTGAG
1246330 ACA
1 ACA
1246333 TTTTTCCTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 24
0.60 0.13 0.28
Matches are distributed among these distances:
15 10 0.19
16 5 0.10
17 5 0.10
18 9 0.17
19 5 0.10
20 5 0.10
21 13 0.25
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (21 bp):
ACAAATTTTGTCTCGCTTGAG
Found at i:1246603 original size:67 final size:66
Alignment explanation
Indices: 1246496--1246642 Score: 199
Period size: 67 Copynumber: 2.2 Consensus size: 66
1246486 TTTAAGATTG
* *
1246496 TTTCTCTTGAAACACAAATCTTGGAGTCTATTTCCCTTGAAACAAGTTGTT-TCTCTCTTGAGAC
1 TTTCTCTTGAAACACAAATCTTGGAGTCTATTTCCCTTGAAACAAATT-TTGTATCTCTTGAGAC
1246560 AA
65 AA
* * *
1246562 TTTCTCTTGAAACATAACATCTTTGAG-CATGTTTCCCTTGAAACAAATTTTGTATCTCTTGAGA
1 TTTCTCTTGAAACACAA-ATCTTGGAGTC-TATTTCCCTTGAAACAAATTTTGTATCTCTTGAGA
*
1246626 TAA
64 CAA
1246629 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
1246643 AATCCCTAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
66 19 0.26
67 53 0.74
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (66 bp):
TTTCTCTTGAAACACAAATCTTGGAGTCTATTTCCCTTGAAACAAATTTTGTATCTCTTGAGACA
A
Found at i:1246964 original size:135 final size:133
Alignment explanation
Indices: 1246643--1247003 Score: 431
Period size: 131 Copynumber: 2.7 Consensus size: 133
1246633 TCTTGAAACA
* ** * * * *
1246643 AATCCCTAAAGATGGCCAGCCATCCTCATTGCGTAGGAACCATGTCATCCACCAAACATACCTCC
1 AATCCCTAAAGATGGCTAGCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCATAACTCC
* * * * ** * *
1246708 TCATCGCGTAGGAGCCGTGTCACCCTTAGATAACCAACCGTCCTTATCATGTAGGAACTGTGTTA
66 TCATCACGTAAGAGTCGTGTCACCCTTAGATAACCAACCGTCCTCATCACATAAGAACCGTGTTA
1246773 T-C
131 TAC
* *
1246775 -ATCCCTAAAGATGGTCTA-TCATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCATAACTC
1 AATCCCTAAAGATGG-CTAGCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCATAACTC
* * * * *
1246838 TTCATCACGTAAGAGTCATGTCACCCCTAGATAACCAACTGTCCTCATCGCATAAGAACCGTGTT
65 CTCATCACGTAAGAGTCGTGTCACCCTTAGATAACCAACCGTCCTCATCACATAAGAACCGTGTT
1246903 ATCAC
130 AT-AC
* * * * *
1246908 AATTCCCTAAATATGGCTAGCCGTCCTCACCACGTAGAAACCGTGTCATCCACCGACCATATCTC
1 AA-TCCCTAAAGATGGCTAGCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCATAACTC
1246973 CTCATCACGTAAGAGTCGTGTCACCCTTAGA
65 CTCATCACGTAAGAGTCGTGTCACCCTTAGA
1247004 CGACCAGAAC
Statistics
Matches: 191, Mismatches: 32, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
131 105 0.55
132 2 0.01
133 1 0.01
134 4 0.02
135 79 0.41
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (133 bp):
AATCCCTAAAGATGGCTAGCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCATAACTCC
TCATCACGTAAGAGTCGTGTCACCCTTAGATAACCAACCGTCCTCATCACATAAGAACCGTGTTA
TAC
Found at i:1248766 original size:2 final size:2
Alignment explanation
Indices: 1248759--1248804 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
1248749 ATATTATGGC
*
1248759 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1248799 AT AT AT
1 AT AT AT
1248805 TATTATTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1248805 original size:14 final size:15
Alignment explanation
Indices: 1248764--1248814 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 15
1248754 ATGGCATATA
*
1248764 TATATATATATATATA
1 TATATATATAT-TATT
1248780 TATATATATATTATT
1 TATATATATATTATT
1248795 TAATATATATTATTATT
1 T-ATATATA-TATTATT
1248812 TAT
1 TAT
1248815 GATAAATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 4 0.12
16 20 0.62
17 8 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATATATATTATT
Found at i:1251156 original size:32 final size:32
Alignment explanation
Indices: 1251115--1251196 Score: 119
Period size: 32 Copynumber: 2.6 Consensus size: 32
1251105 AACCGAATGG
* **
1251115 AGTACCTTGGGGCCTTAGTTCCCATCGAAGGA
1 AGTACCTTGGGGCCTAAGGGCCCATCGAAGGA
* *
1251147 AGTACCTTGGGGCCTAAGGGCCTATCGAAGGG
1 AGTACCTTGGGGCCTAAGGGCCCATCGAAGGA
1251179 AGTACCTTGGGGCCTAAG
1 AGTACCTTGGGGCCTAAG
1251197 AGTCTATCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.22, C:0.23, G:0.33, T:0.22
Consensus pattern (32 bp):
AGTACCTTGGGGCCTAAGGGCCCATCGAAGGA
Found at i:1251204 original size:32 final size:31
Alignment explanation
Indices: 1251108--1251210 Score: 116
Period size: 32 Copynumber: 3.2 Consensus size: 31
1251098 AGGAGCCAAC
* * * *
1251108 CGAATGGAGTACCTTGGGGCCTTAGTTCCCAT
1 CGAAGGGAGTACCTTGGGGCCTAAGGT-CTAT
* *
1251140 CGAAGGAAGTACCTTGGGGCCTAAGGGCCTAT
1 CGAAGGGAGTACCTTGGGGCCTAA-GGTCTAT
1251172 CGAAGGGAGTACCTTGGGGCCTAAGAGTCTAT
1 CGAAGGGAGTACCTTGGGGCCTAAG-GTCTAT
*
1251204 CTAAGGG
1 CGAAGGG
1251211 TCACCATAGG
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
31 1 0.02
32 58 0.97
33 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (31 bp):
CGAAGGGAGTACCTTGGGGCCTAAGGTCTAT
Found at i:1257939 original size:22 final size:22
Alignment explanation
Indices: 1257891--1257945 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1257881 ATTTGATTTT
* * *
1257891 TTGGTTAAAATCAAAGTCAATA
1 TTGGTCAAAGTCAAAGCCAATA
* *
1257913 CTGGTCAAAGTCAAAGCCAGTA
1 TTGGTCAAAGTCAAAGCCAATA
1257935 TTGGTCAAAGT
1 TTGGTCAAAGT
1257946 TAACAGTCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (22 bp):
TTGGTCAAAGTCAAAGCCAATA
Found at i:1257978 original size:18 final size:19
Alignment explanation
Indices: 1257930--1257978 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1257920 AAGTCAAAGC
1257930 CAGTATTGGTCAAAGTTAA
1 CAGTATTGGTCAAAGTTAA
*
1257949 CAGTCA-T-ATCAAAGTTAA
1 CAGT-ATTGGTCAAAGTTAA
1257967 CAGT-TTGGTCAA
1 CAGTATTGGTCAA
1257979 GGCCAACAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
17 1 0.04
18 18 0.72
19 5 0.20
20 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (19 bp):
CAGTATTGGTCAAAGTTAA
Found at i:1260241 original size:227 final size:223
Alignment explanation
Indices: 1259798--1260290 Score: 676
Period size: 232 Copynumber: 2.2 Consensus size: 223
1259788 ATATTTTCGG
*
1259798 GTCGGGTTGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGT
1 GTCGGGTTGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTAATATTCGGGT
* * *
1259863 TGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATATTT
66 CGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATATATTT
* * *
1259928 ATGAATAATTATAATAATACCCCTCTATATATATATATATATTTTTCAATTAAGTCATCATTTTT
131 AGGAATAATTACAATAATACCCCTC-ATATATATATATATATTTTCCAATTAAGTCATCATTTTT
1259993 ATTGAATAAAAATAATTTTTTTATTA-TT
195 ATTGAATAAAAATAATTTTTTTATTATTT
*
1260021 -TCGGGTTGGGTGAAACTTTATTTTGGTCGGGTCGGGTCAGTTTTTTTTAAGTGTAATATTCGGG
1 GTCGGGTTGGGTGAAACTTTATTTTGGTCGGGTCGGGTC-GGTTTTTTTAAGTGTAATATTCGGG
* * *
1260085 TCGGGTTCGAGTTTAGGGTGAAAAATACCCTACCCGACTTGACCCATAAAATATATAATTTTACT
65 TCGAGTTCGAGTTTAGGGTGAAAAATACCCGA-CC--C--GA---A-AAAATATATAATTTTACC
*
1260150 TTATATATTTAGGAATAATTACAATAATACCCCTC-TCTATATAT-T-T-TTTTCCAATTAAGTC
121 TTATATATTTAGGAATAATTACAATAATACCCCTCATATATATATATATATTTTCCAATTAAGTC
*
1260211 A-CTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTT
186 ATC-ATTTTTATTGAATAAAAATAATTTTTTTATTA-TTT
*
1260250 GGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTC
1 --GTCGGGTTGGGTGAAACTTTATTTTGGTCGGGTCGGGTC
1260291 TCGGATGGAG
Statistics
Matches: 240, Mismatches: 14, Indels: 23
0.87 0.05 0.08
Matches are distributed among these distances:
222 38 0.16
223 51 0.21
224 2 0.01
226 2 0.01
227 46 0.19
228 3 0.01
229 3 0.01
230 8 0.03
231 1 0.00
232 86 0.36
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.42
Consensus pattern (223 bp):
GTCGGGTTGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTAATATTCGGGT
CGAGTTCGAGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATATATTT
AGGAATAATTACAATAATACCCCTCATATATATATATATATTTTCCAATTAAGTCATCATTTTTA
TTGAATAAAAATAATTTTTTTATTATTT
Found at i:1266560 original size:855 final size:854
Alignment explanation
Indices: 1264867--1266580 Score: 2905
Period size: 855 Copynumber: 2.0 Consensus size: 854
1264857 AATTGGGCGA
*
1264867 ATGGTGAATGGGTATGGAATATTGAATTGAGGCGTGACTTGTTTGAGTTGGAAAAGGTTACTTGG
1 ATGGTGAATGGGTATGGAATATTGAATTGAGGCGTGACTTGTTTGAGTGGGAAAAGGTTACTTGG
*
1264932 AATAATTTTTACCAAGTTCTGAAAAGAGGTGTTAGTTCAAATCCAAGTGTTGATAGATTGAAATG
66 AACAATTTTTACCAAGTTCTGAAAAGAGGTGTTAGTTCAAATCCAAGTGTTGATAGATTGAAATG
* * *
1264997 GATAGGTTCTTCTAATAGTATATATAATCCTAAAAATTTTTGCATTAAGTTGGCAACGGTAGGTA
131 GATAGGTTCTTCCAATAGCATATATAATCCTAAAAATTTCTGCATTAAGTTGGCAACGGTAGGTA
* *
1265062 AGATTGAAGACCCAATTTGGAAAAGGTTTGGAATAAGTTTTTCCCTCCTAAAGTGGCTACTTTTG
196 AGATTGAAGACCCAATTTGGAAAAGGTTTGGAATAAATTTGTCCCTCCTAAAGTGGCTACTTTTG
* * * *
1265127 TCTGGAAAGCTGTATATCAAAGGTTGCCGATTGCGACAGAATTGGTTAGGAGGGGCATCAATTGC
261 TCTGGAAAACTGTATATCAAAGGCTGCCGATTGCGACAGAATTAGTTAAGAGGGGCATCAATTGC
1265192 AATTTTCAACTATTGTGCTTGTTTTACAAAAGTCATATGGAAGATGTCAATCATGTGCTATGCCA
326 AATTTTCAACTATTGTGCTTGTTTTACAAAAGTCATATGGAAGATGTCAATCATGTGCTATGCC-
1265257 TTGTAATTTCTTTTGGCAAGTGTGGCAACGGTGGTGTTCTTTATGGAAAGCCTGGTTTATTTTTC
390 ---T-ATTTCTTTTGGCAAGTGTGGCAACGGTGGTGTTCTTTATGGAAAGCCTGGTTTATTTTTC
*
1265322 CAAGAATGTCAAAGATTTATTAGCGATATGGTGCTCTCAGAAAATTAGAAGAAAAACAAGGAACC
451 CAAGAATGTCAAAGATTTATTAGCGATATGGCGCTCTCAGAAAATTAGAAGAAAAACAAGGAACC
1265387 TTTGGCAGCTTGAGTTTTTCGGTTTAATTTGACAGATCTGGTTGTGCAGAAACAAGTCAACGTTC
516 TTTGGCAGCTTGAGTTTTTCGGTTTAATTTGACAGATCTGGTTGTGCAGAAACAAGTCAACGTTC
* *
1265452 AATGAGTGTCTTACAATGTGGATCAGATAGTTAACAGCATTTTACTGCAGATAGGGGTGTGGGCT
581 AATGAGTGTCTTACAATGTGGATCAGATAGTTAACAGCATTTTACTGCAGATAAGGGTGTGAGCT
*
1265517 AATGTATTATGACCATCGCTAGTTCCACATGTTCAAGAATTCGTTCGAAGCCCGGAATCTATCAT
646 AATGTATTATGACCATCGCTAGTTCCACATGTTCAAGAATTCGTTCAAAGCCCGGAATCTATCAT
1265582 TCTTATTGATCATTGGTAAGTGTTTTGGTTTTTATGTTATCCAGTATATTTTATCATTGATTTTC
711 TCTTATTGATCATTGGTAAGTGTTTTGGTTTTTATGTTATCCAGTATATTTTATCATTGATTTTC
* * *
1265647 ACAGGTTTCATTCGGATCAAGAGCTGTGGTTATAGTGCTGCTCTAGTTTATGCTGGGCTGCACAT
776 ACAGGTTTAATTCCGATCAAGAGCTGTGGTTATAGTGATGCTCTAGTTTATGCTGGGCTGCACAT
1265712 ATATTTATTTGTTT
841 ATATTTATTTGTTT
* *
1265726 ATGGTGAATGGGTATGGAATATTGAATTGAGGCGTGGCTTGTTTGGGTGGGAAAAGGTTACTTGG
1 ATGGTGAATGGGTATGGAATATTGAATTGAGGCGTGACTTGTTTGAGTGGGAAAAGGTTACTTGG
* *
1265791 AACAA-TTTTAGCAAGTTCTGAAAAGAGGTGTTAGTTCAAATCCAAGTGTTGATAGATTGAAGTG
66 AACAATTTTTACCAAGTTCTGAAAAGAGGTGTTAGTTCAAATCCAAGTGTTGATAGATTGAAATG
* *
1265855 GATAGGTTCTTCCAATGGCATATATAATCCTAAAAATTTCTGCATTAAGTTGGCAATGGTAGGTA
131 GATAGGTTCTTCCAATAGCATATATAATCCTAAAAATTTCTGCATTAAGTTGGCAACGGTAGGTA
* **
1265920 AGATTGAAGACCCAATTTGGAAAAAGGTTTGGAATAAATTTGTCCCTCCTAAAGTGGTTGTTTTT
196 AGATTGAAGACCCAATTTGG-AAAAGGTTTGGAATAAATTTGTCCCTCCTAAAGTGGCTACTTTT
*
1265985 GTCTGGAAAACTGTATATCAAAGGCTGCCGATTGCGACGGAATTAGTTAAGAGGGGCATCAATTG
260 GTCTGGAAAACTGTATATCAAAGGCTGCCGATTGCGACAGAATTAGTTAAGAGGGGCATCAATTG
1266050 CAATTTTCAACTATTGTGCTTGTTTTGA-AAAAGTCATCA-GGAAGATGTCAATCATGTGCTATG
325 CAATTTTCAACTATTGTGCTTGTTTT-ACAAAAGTCAT-ATGGAAGATGTCAATCATGTGCTATG
*
1266113 CC-ATTTCTTTTGGCAAGTGTGGCAACGGTGGTGTTCTTTATGGAAAGTCTGGTTTATTTTTCCC
388 CCTATTTCTTTTGGCAAGTGTGGCAACGGTGGTGTTCTTTATGGAAAGCCTGGTTTATTTTT-CC
1266177 AAGAATGTCAAAGATTTATTAGCGATATGGCGCTCTCAGAAAATTAGAAGAAAAACAAGGAACCT
452 AAGAATGTCAAAGATTTATTAGCGATATGGCGCTCTCAGAAAATTAGAAGAAAAACAAGGAACCT
* * * * *
1266242 TTGGCAGCTTGAGTTTTTCGGTTTGATTTGGCTGATCTGGTTGTGCAGAAACAAGTCAAGGTTTA
517 TTGGCAGCTTGAGTTTTTCGGTTTAATTTGACAGATCTGGTTGTGCAGAAACAAGTCAACGTTCA
* * * *
1266307 GTGATGTGTCTTACAATGTGGATCAGATATTTAACAGCGTTTTACTGCAGATAAGGTTGTGAGCT
582 ATGA-GTGTCTTACAATGTGGATCAGATAGTTAACAGCATTTTACTGCAGATAAGGGTGTGAGCT
* * *
1266372 AATGTATTATGGCCATCGCTAGTTCCACATGTTCAAGACTTCGTTCAAAGCTCGGAATCTATCAT
646 AATGTATTATGACCATCGCTAGTTCCACATGTTCAAGAATTCGTTCAAAGCCCGGAATCTATCAT
*
1266437 TCTTATTGATCATTGGTAAGTGTTTTGGTTTTTATGTTATCCAGTATCTTTTATCATTGATTTTC
711 TCTTATTGATCATTGGTAAGTGTTTTGGTTTTTATGTTATCCAGTATATTTTATCATTGATTTTC
* * *
1266502 ACAGGTTTAATTCCGATCAAGAGCTGTGGTTGTAGTGATGTTCTAGTTTCTGCTGGGCTGCACAT
776 ACAGGTTTAATTCCGATCAAGAGCTGTGGTTATAGTGATGCTCTAGTTTATGCTGGGCTGCACAT
1266567 ATATTTATTTGTTT
841 ATATTTATTTGTTT
1266581 TACACTTTAG
Statistics
Matches: 805, Mismatches: 45, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
853 58 0.07
854 129 0.16
855 253 0.31
858 137 0.17
859 226 0.28
860 2 0.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (854 bp):
ATGGTGAATGGGTATGGAATATTGAATTGAGGCGTGACTTGTTTGAGTGGGAAAAGGTTACTTGG
AACAATTTTTACCAAGTTCTGAAAAGAGGTGTTAGTTCAAATCCAAGTGTTGATAGATTGAAATG
GATAGGTTCTTCCAATAGCATATATAATCCTAAAAATTTCTGCATTAAGTTGGCAACGGTAGGTA
AGATTGAAGACCCAATTTGGAAAAGGTTTGGAATAAATTTGTCCCTCCTAAAGTGGCTACTTTTG
TCTGGAAAACTGTATATCAAAGGCTGCCGATTGCGACAGAATTAGTTAAGAGGGGCATCAATTGC
AATTTTCAACTATTGTGCTTGTTTTACAAAAGTCATATGGAAGATGTCAATCATGTGCTATGCCT
ATTTCTTTTGGCAAGTGTGGCAACGGTGGTGTTCTTTATGGAAAGCCTGGTTTATTTTTCCAAGA
ATGTCAAAGATTTATTAGCGATATGGCGCTCTCAGAAAATTAGAAGAAAAACAAGGAACCTTTGG
CAGCTTGAGTTTTTCGGTTTAATTTGACAGATCTGGTTGTGCAGAAACAAGTCAACGTTCAATGA
GTGTCTTACAATGTGGATCAGATAGTTAACAGCATTTTACTGCAGATAAGGGTGTGAGCTAATGT
ATTATGACCATCGCTAGTTCCACATGTTCAAGAATTCGTTCAAAGCCCGGAATCTATCATTCTTA
TTGATCATTGGTAAGTGTTTTGGTTTTTATGTTATCCAGTATATTTTATCATTGATTTTCACAGG
TTTAATTCCGATCAAGAGCTGTGGTTATAGTGATGCTCTAGTTTATGCTGGGCTGCACATATATT
TATTTGTTT
Found at i:1267705 original size:35 final size:35
Alignment explanation
Indices: 1267659--1267816 Score: 162
Period size: 35 Copynumber: 4.6 Consensus size: 35
1267649 AATTTATAAT
** *
1267659 AACTCAAAAGATGTGTATACATTGCATTACGTAAC
1 AACTCAAAAGATACGTATAAATTGCATTACGTAAC
***
1267694 AACTCAAAAGATACGTATAAATTGCATTAAACAAC
1 AACTCAAAAGATACGTATAAATTGCATTACGTAAC
* * * ***
1267729 AACCCAAAATATACGTATATATTGTGGTACGTAAC
1 AACTCAAAAGATACGTATAAATTGCATTACGTAAC
*
1267764 AACTCAAAA-ATACATATAAATTGCATTA---AAC
1 AACTCAAAAGATACGTATAAATTGCATTACGTAAC
*
1267795 AACTCAAAAAATACGTATAAAT
1 AACTCAAAAGATACGTATAAAT
1267817 ACTGAATAAC
Statistics
Matches: 100, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
31 12 0.12
32 11 0.11
34 14 0.14
35 63 0.63
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.26
Consensus pattern (35 bp):
AACTCAAAAGATACGTATAAATTGCATTACGTAAC
Found at i:1267828 original size:32 final size:30
Alignment explanation
Indices: 1267760--1267830 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 30
1267750 TTGTGGTACG
*
1267760 TAACAACTCAAAAATACATATAAATTGCAT
1 TAACAACTCAAAAATACATATAAATTGCAA
*
1267790 TAAACAACTCAAAAAATACGTATAAATACTG-AA
1 T-AACAACTC-AAAAATACATATAAAT--TGCAA
1267823 TAACAACT
1 TAACAACT
1267831 TAGAAGACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 1 0.03
31 8 0.23
32 22 0.63
33 2 0.06
34 2 0.06
ACGTcount: A:0.55, C:0.17, G:0.04, T:0.24
Consensus pattern (30 bp):
TAACAACTCAAAAATACATATAAATTGCAA
Found at i:1283966 original size:47 final size:48
Alignment explanation
Indices: 1283912--1284004 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 48
1283902 AATTTGAAAA
* * *
1283912 TTAGTTTAGATTAGTATAAACTCTATCTTAAGTTTAAA-TAAGAGTGG
1 TTAGTTTAGAGTAGAATAAACTCTATCCTAAGTTTAAATTAAGAGTGG
*
1283959 TTAGTTTAGAGTAGAATAAGCTCTATCCTAAGTTTAAATTAAGAGT
1 TTAGTTTAGAGTAGAATAAACTCTATCCTAAGTTTAAATTAAGAGT
1284005 TGTTTAACCG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.83
48 7 0.17
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.39
Consensus pattern (48 bp):
TTAGTTTAGAGTAGAATAAACTCTATCCTAAGTTTAAATTAAGAGTGG
Found at i:1288378 original size:18 final size:19
Alignment explanation
Indices: 1288355--1288397 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1288345 CAGTAATCCT
*
1288355 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGATAATCTTAC
1288373 ATTCCCACTGATAATCTTAC
1 ATT-CCACTGATAATCTTAC
1288393 ATTCC
1 ATTCC
1288398 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:1291251 original size:21 final size:21
Alignment explanation
Indices: 1291218--1291257 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1291208 TCTACTTTAC
** *
1291218 AGCCATTGTCATTTGACCAGT
1 AGCCATTCACATTTAACCAGT
1291239 AGCCATTCACATTTAACCA
1 AGCCATTCACATTTAACCA
1291258 TCCAGCAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (21 bp):
AGCCATTCACATTTAACCAGT
Found at i:1302861 original size:33 final size:33
Alignment explanation
Indices: 1302815--1302889 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
1302805 TTACAACTCT
*
1302815 CTAGTTTTCCACGGGCTAAACTAGAACCAATCC
1 CTAGTTTTTCACGGGCTAAACTAGAACCAATCC
1302848 CTAGTTTTTCACGGGCTAAACTAGAACCAATCC
1 CTAGTTTTTCACGGGCTAAACTAGAACCAATCC
*
1302881 CTAGCTTTT
1 CTAGTTTTT
1302890 AACAGGCTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (33 bp):
CTAGTTTTTCACGGGCTAAACTAGAACCAATCC
Found at i:1302910 original size:33 final size:33
Alignment explanation
Indices: 1302828--1302897 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
1302818 GTTTTCCACG
* * *
1302828 GGCTAAACTAGAACCAATCCCTAGTTTTTCACG
1 GGCTAAACTAGAACCAATCCCTAGCTTTTAACA
1302861 GGCTAAACTAGAACCAATCCCTAGCTTTTAACA
1 GGCTAAACTAGAACCAATCCCTAGCTTTTAACA
1302894 GGCT
1 GGCT
1302898 TAGCTATAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (33 bp):
GGCTAAACTAGAACCAATCCCTAGCTTTTAACA
Found at i:1306370 original size:33 final size:33
Alignment explanation
Indices: 1306310--1306375 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1306300 CCTTTACAAC
* * *
1306310 TCCCTAGTTTTTTACGGGCTAAACTAGAACCAA
1 TCCCTAGATTTTAACAGGCTAAACTAGAACCAA
* *
1306343 TCCCTAGATTTTAACAGGCTCAGCTAGAACCAA
1 TCCCTAGATTTTAACAGGCTAAACTAGAACCAA
1306376 AACCCCTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (33 bp):
TCCCTAGATTTTAACAGGCTAAACTAGAACCAA
Found at i:1312390 original size:2 final size:2
Alignment explanation
Indices: 1312385--1312421 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1312375 AGTTCAATCG
1312385 AT AT AT 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
1312422 CATACATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1313072 original size:30 final size:30
Alignment explanation
Indices: 1313031--1313098 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
1313021 ATATAATAAG
* **
1313031 CAGAGATCATATAAAAAATATACAGTAAAT
1 CAGATATCATATAAAAAATATACAAAAAAT
*
1313061 CAGATATCATATAAAAAATATTCAAAAAAT
1 CAGATATCATATAAAAAATATACAAAAAAT
1313091 CAGATATC
1 CAGATATC
1313099 GCGTCATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.25
Consensus pattern (30 bp):
CAGATATCATATAAAAAATATACAAAAAAT
Found at i:1315163 original size:10 final size:11
Alignment explanation
Indices: 1315138--1315170 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1315128 GTGCTAATTT
1315138 TTTAATGATAA
1 TTTAATGATAA
*
1315149 TTTAAT-ATTA
1 TTTAATGATAA
1315159 TTTAATGATAA
1 TTTAATGATAA
1315170 T
1 T
1315171 ATTTTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (11 bp):
TTTAATGATAA
Found at i:1315172 original size:16 final size:15
Alignment explanation
Indices: 1315146--1315191 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1315136 TTTTTAATGA
*
1315146 TAATTTAATATTATT
1 TAATATAATATTATT
*
1315161 TAATGATAATATTTTT
1 TAAT-ATAATATTATT
*
1315177 TAATATATTATTATT
1 TAATATAATATTATT
1315192 AATTTGTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TAATATAATATTATT
Found at i:1318815 original size:15 final size:15
Alignment explanation
Indices: 1318795--1318879 Score: 71
Period size: 15 Copynumber: 5.4 Consensus size: 15
1318785 ATGTTACAGA
1318795 TACCCGGTAATCGGG
1 TACCCGGTAATCGGG
* **
1318810 TACCCGAATTTTACGGG
1 TACCCG-GTAAT-CGGG
1318827 TACCCGGTAATCGGG
1 TACCCGGTAATCGGG
* **
1318842 TACTCGGATTTTGCGGG
1 TACCCGG-TAAT-CGGG
*
1318859 TATCCGGTAATCGGG
1 TACCCGGTAATCGGG
1318874 TACCCG
1 TACCCG
1318880 ATACTCGGTT
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
15 25 0.48
16 8 0.15
17 19 0.37
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.26
Consensus pattern (15 bp):
TACCCGGTAATCGGG
Found at i:1318831 original size:32 final size:32
Alignment explanation
Indices: 1318795--1318880 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
1318785 ATGTTACAGA
1318795 TACCCGGTAATCGGGTACCCGAATTTTACGGG
1 TACCCGGTAATCGGGTACCCGAATTTTACGGG
* * *
1318827 TACCCGGTAATCGGGTACTCGGATTTTGCGGG
1 TACCCGGTAATCGGGTACCCGAATTTTACGGG
*
1318859 TATCCGGTAATCGGGTACCCGA
1 TACCCGGTAATCGGGTACCCGA
1318881 TACTCGGTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (32 bp):
TACCCGGTAATCGGGTACCCGAATTTTACGGG
Found at i:1319484 original size:37 final size:37
Alignment explanation
Indices: 1319438--1319546 Score: 164
Period size: 37 Copynumber: 2.9 Consensus size: 37
1319428 AACATAACTT
1319438 TAGAATTTTACTATGATTCAAACTCCTAAAAATAGAA
1 TAGAATTTTACTATGATTCAAACTCCTAAAAATAGAA
* **
1319475 TAGAGTTTTACTAAAATTCAAACTCCTAAAAATAGAA
1 TAGAATTTTACTATGATTCAAACTCCTAAAAATAGAA
* * *
1319512 TATAATTCTACTATGATTTAAACTCCTAAAAATAG
1 TAGAATTTTACTATGATTCAAACTCCTAAAAATAG
1319547 GATCCACAAG
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (37 bp):
TAGAATTTTACTATGATTCAAACTCCTAAAAATAGAA
Found at i:1320051 original size:12 final size:13
Alignment explanation
Indices: 1319990--1320052 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 13
1319980 ATTTCAACAG
1319990 TATATTTATTATTA
1 TATATTT-TTATTA
*
1320004 TATATATTTAATTA
1 TATAT-TTTTATTA
1320018 TATATTTTTATTA
1 TATATTTTTATTA
1320031 TCTATTATTTTTATTA
1 --TA-TATTTTTATTA
1320047 T-TATTT
1 TATATTT
1320053 ATTCTTTTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
12 5 0.12
13 7 0.16
14 16 0.37
15 4 0.09
16 11 0.26
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TATATTTTTATTA
Found at i:1320054 original size:16 final size:16
Alignment explanation
Indices: 1319994--1320055 Score: 76
Period size: 16 Copynumber: 4.0 Consensus size: 16
1319984 CAACAGTATA
*
1319994 TTTATTATTATATATA
1 TTTATTATTATATATT
1320010 TTTA--ATTATATATT
1 TTTATTATTATATATT
1320024 TTTATTATCTAT-TATT
1 TTTATTAT-TATATATT
*
1320040 TTTATTATTATTTATT
1 TTTATTATTATATATT
1320056 CTTTTGTCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 13 0.32
15 3 0.07
16 22 0.54
17 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTATATATT
Found at i:1320107 original size:19 final size:18
Alignment explanation
Indices: 1320083--1320144 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 18
1320073 TATATATATA
1320083 TATATATATTTATCACTAT
1 TATATAT-TTTATCACTAT
1320102 TATATATTTTAT-A-TAT
1 TATATATTTTATCACTAT
1320118 TACTATATTTTATCACTAT
1 TA-TATATTTTATCACTAT
1320137 GTATATAT
1 -TATATAT
1320145 ACTTTTGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.13
17 11 0.28
18 6 0.15
19 15 0.38
20 2 0.05
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (18 bp):
TATATATTTTATCACTAT
Found at i:1320125 original size:36 final size:36
Alignment explanation
Indices: 1320075--1320144 Score: 108
Period size: 36 Copynumber: 1.9 Consensus size: 36
1320065 TTTTAATCTA
1320075 TATATATATATATATATTTATCACTAT-TATATATTT
1 TATATATATATATAT-TTTATCACTATGTATATATTT
1320111 TATATAT-TACTATATTTTATCACTATGTATATAT
1 TATATATATA-TATATTTTATCACTATGTATATAT
1320145 ACTTTTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 13 0.41
36 19 0.59
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.54
Consensus pattern (36 bp):
TATATATATATATATTTTATCACTATGTATATATTT
Found at i:1320145 original size:38 final size:37
Alignment explanation
Indices: 1320075--1320161 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 37
1320065 TTTTAATCTA
1320075 TATATATATATATATATTTATCACTATTATATA-TTT
1 TATATATATATATATATTTATCACTATTATATACTTT
1320111 TATATAT-TACTATAT-TTTATCACTATGTATATATACTTT
1 TATATATATA-TATATATTTATCACTA--T-TATATACTTT
*
1320150 TGATATTTATAT
1 T-ATATATATAT
1320162 TACTATATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
35 12 0.28
36 12 0.28
37 1 0.02
38 6 0.14
39 4 0.09
40 6 0.14
41 2 0.05
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (37 bp):
TATATATATATATATATTTATCACTATTATATACTTT
Found at i:1320259 original size:16 final size:16
Alignment explanation
Indices: 1320225--1320283 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
1320215 TTCTCTTTTT
1320225 TTTTC-TTTTCTACTTTA
1 TTTTCATTTT-TA-TTTA
1320242 TTTTCATTTTTATTTA
1 TTTTCATTTTTATTTA
* *
1320258 TTTT-ATATTTTCTTGA
1 TTTTCAT-TTTTATTTA
*
1320274 TGTTCATTTT
1 TTTTCATTTT
1320284 ATTACTTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
15 2 0.06
16 21 0.58
17 9 0.25
18 4 0.11
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTCATTTTTATTTA
Found at i:1324698 original size:32 final size:32
Alignment explanation
Indices: 1324624--1324713 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 32
1324614 CATCTTTGAA
* *
1324624 GATTCAACATCAGATGTTGGGGCACTTTTTTGT
1 GATTCAACATCAAATATTGGGGCA-TTTTTTGT
*
1324657 GATTTAACATCAAATATTGGGGCATTTTTTGAT
1 GATTCAACATCAAATATTGGGGCATTTTTTG-T
*
1324690 -ATTCAACATCGAATATTGGGGCAT
1 GATTCAACATCAAATATTGGGGCAT
1324714 CTTTGGGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
32 29 0.57
33 22 0.43
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (32 bp):
GATTCAACATCAAATATTGGGGCATTTTTTGT
Found at i:1324726 original size:32 final size:32
Alignment explanation
Indices: 1324611--1324732 Score: 90
Period size: 32 Copynumber: 3.8 Consensus size: 32
1324601 GGAACAATGA
* *
1324611 GGGCATCTTT-GAAGATTCAACATCAGATGTTG
1 GGGCATCTTTGGGAGATTCAACATCA-ATATTG
** * *
1324643 GGGCA-CTTTTTTGTGATTTAACATCAAATATTG
1 GGGCATC-TTTGGGAGATTCAACATC-AATATTG
** *
1324676 GGGCAT-TTTTTGATATTCAACATCGAATATTG
1 GGGCATCTTTGGGAGATTCAACATC-AATATTG
*
1324708 GGGCATCTTTGGGA-ATTCAATATCA
1 GGGCATCTTTGGGAGATTCAACATCA
1324733 TGATGTGAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
31 2 0.03
32 45 0.62
33 25 0.34
34 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (32 bp):
GGGCATCTTTGGGAGATTCAACATCAATATTG
Found at i:1326010 original size:36 final size:36
Alignment explanation
Indices: 1325899--1326020 Score: 122
Period size: 36 Copynumber: 3.4 Consensus size: 36
1325889 GTGCTCACCA
* *
1325899 TTGTCTCTCTTGAGACAGGTTCCCTT-GAAACAAATT
1 TTGTCTCTCTTGAGACA-GTTTCTTTAGAAACAAATT
** * **
1325935 TCATCTCCCTTGAGACAGTTTCTTTTAG-AACTATGTT
1 TTGTCTCTCTTGAGACAGTTTC-TTTAGAAAC-AAATT
*
1325972 TTGTCTCTCTTGAGATAGTTTCTTTAGAAACAAATT
1 TTGTCTCTCTTGAGACAGTTTCTTTAGAAACAAATT
*
1326008 TTGTCCCTCTTGA
1 TTGTCTCTCTTGA
1326021 AACATAAAAA
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
35 4 0.06
36 39 0.57
37 25 0.37
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCTTTAGAAACAAATT
Found at i:1326066 original size:30 final size:29
Alignment explanation
Indices: 1326027--1326084 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1326017 TTGAAACATA
*
1326027 AAAAAAAACTCTCGAAATTATTTCTCTTGG
1 AAAAAAAACT-TCGAAAATATTTCTCTTGG
* * *
1326057 AAAAGAAACTTTGAAAATGTTTCTCTTG
1 AAAAAAAACTTCGAAAATATTTCTCTTG
1326085 AAACACAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (29 bp):
AAAAAAAACTTCGAAAATATTTCTCTTGG
Found at i:1326294 original size:83 final size:83
Alignment explanation
Indices: 1326089--1326344 Score: 259
Period size: 83 Copynumber: 3.1 Consensus size: 83
1326079 CTCTTGAAAC
* * *
1326089 ACAAAG-CCTTCGAGTTTGATTACACTCAACTTC-GAGGGGACATCATTTGCAGCATAACTCAAG
1 ACAAAGACCTTCGAGTTAGATTACACTCAAC-TCAGA-GGCAAATCATTTGCAGCATAACTCAAG
*
1326152 GCTAGAAGGGTTATCTATCA
64 GCAAGAAGGGTTATCTATCA
* * * * *
1326172 ACAAAGACCTTCGAGTTAGACTACGCTCAGCTCTA-AGGCATATCATTTGTAGCATAACTCAAGG
1 ACAAAGACCTTCGAGTTAGATTACACTCAACTC-AGAGGCAAATCATTTGCAGCATAACTCAAGG
*
1326236 CAAGAAGGGTTATC-AGTTA
65 CAAGAAGGGTTATCTA-TCA
* * * * * *
1326255 TCAAATACCTTCGAGTTCGATTACATTCAACTCAGAGGCAAATCAAATTTGCAACATAGCTCAAG
1 ACAAAGACCTTCGAGTTAGATTACACTCAACTCAGAGGCAAATC--ATTTGCAGCATAACTCAAG
* **
1326320 GCAAGAAGGGCTATCTGCCA
64 GCAAGAAGGGTTATCTATCA
1326340 ACAAA
1 ACAAA
1326345 ATTGTCGAGT
Statistics
Matches: 140, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
82 2 0.01
83 82 0.59
84 21 0.15
85 35 0.25
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (83 bp):
ACAAAGACCTTCGAGTTAGATTACACTCAACTCAGAGGCAAATCATTTGCAGCATAACTCAAGGC
AAGAAGGGTTATCTATCA
Found at i:1326877 original size:37 final size:37
Alignment explanation
Indices: 1326831--1326942 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 37
1326821 AACATAACGT
*
1326831 TAGAATTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
*
1326868 TAGAGTTTTACTAGGATTCAAATTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* * *
1326905 TAGAGGTCTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1326942 T
1 T
1326943 CCACAAGCGT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:1327418 original size:14 final size:14
Alignment explanation
Indices: 1327391--1327432 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1327381 ATTCCAACAG
1327391 TATATTTATTATTATA
1 TATATTTA--ATTATA
1327407 TATATTTAATTATA
1 TATATTTAATTATA
*
1327421 TAT-TTTTATTAT
1 TATATTTAATTAT
1327433 CTATTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 8 0.32
14 9 0.36
16 8 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATATTTAATTATA
Found at i:1327506 original size:2 final size:2
Alignment explanation
Indices: 1327499--1327554 Score: 64
Period size: 2 Copynumber: 28.5 Consensus size: 2
1327489 TCTATCTATC
1327499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TCA CTA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A -TA TA TA
*
1327541 TA TA T- TT TA TA TA T
1 TA TA TA TA TA TA TA T
1327555 TACTATATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
1 3 0.06
2 42 0.88
3 2 0.04
4 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1327593 original size:38 final size:35
Alignment explanation
Indices: 1327498--1327581 Score: 107
Period size: 35 Copynumber: 2.3 Consensus size: 35
1327488 ATCTATCTAT
*
1327498 CTATATATATATATATATATATATA-TATATATTATCA
1 CTAT-TATATAT-TTTATATAT-TACTATATATTATCA
*
1327535 CTATTATATATTTTATATATTACTATATTTTATCA
1 CTATTATATATTTTATATATTACTATATATTATCA
1327570 CTATGTATATAT
1 CTAT-TATATAT
1327582 ACTTTTGATA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
34 2 0.05
35 23 0.53
36 14 0.33
37 4 0.09
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (35 bp):
CTATTATATATTTTATATATTACTATATATTATCA
Found at i:1327695 original size:16 final size:16
Alignment explanation
Indices: 1327660--1327719 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
1327650 TTTTCTTTTT
*
1327660 TTTTCCTTTTCTACTTTA
1 TTTTCATTTT-TA-TTTA
1327678 TTTTCATTTTTATTTA
1 TTTTCATTTTTATTTA
* *
1327694 TTTT-ATATTTTCTTGA
1 TTTTCAT-TTTTATTTA
*
1327710 TGTTCATTTT
1 TTTTCATTTT
1327720 ATTACTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 2 0.06
16 21 0.58
17 4 0.11
18 9 0.25
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTCATTTTTATTTA
Found at i:1332380 original size:19 final size:18
Alignment explanation
Indices: 1332337--1332380 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
1332327 ATATTTATTT
1332337 TATTAATATTAAAAATCA
1 TATTAATATTAAAAATCA
1332355 TACTTAATATTTCAAAAATCA
1 TA-TTAATA-TT-AAAAATCA
1332376 T-TTAA
1 TATTAA
1332381 ACACTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.09
19 10 0.43
20 2 0.09
21 9 0.39
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (18 bp):
TATTAATATTAAAAATCA
Found at i:1342294 original size:26 final size:27
Alignment explanation
Indices: 1342258--1342319 Score: 117
Period size: 26 Copynumber: 2.3 Consensus size: 27
1342248 TGTACATTAG
1342258 ATTCTAAACTTGTTGGACAAAA-AAAA
1 ATTCTAAACTTGTTGGACAAAATAAAA
1342284 ATTCTAAACTTGTTGGACAAAATAAAA
1 ATTCTAAACTTGTTGGACAAAATAAAA
1342311 ATTCTAAAC
1 ATTCTAAAC
1342320 ATATGTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 22 0.63
27 13 0.37
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (27 bp):
ATTCTAAACTTGTTGGACAAAATAAAA
Found at i:1347908 original size:59 final size:60
Alignment explanation
Indices: 1347794--1347908 Score: 137
Period size: 59 Copynumber: 1.9 Consensus size: 60
1347784 GTATAAATTG
* * * * *
1347794 TAATAGTCAGTAGACTCAACAAAATAATATCATATAGTCGAGGGATCACTTTGTAACTTT
1 TAATAGTCAGTAGACTCAACAAAATAACACCATATAATCGAGGGACCAATTTGTAACTTT
*
1347854 TAATAGTCAG-AGACTCAAC-AAATCAACACCCTATAATCGA-GGACCAATTATGTAA
1 TAATAGTCAGTAGACTCAACAAAAT-AACACCATATAATCGAGGGACCAATT-TGTAA
1347909 TTTATCCTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
58 11 0.23
59 26 0.55
60 10 0.21
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (60 bp):
TAATAGTCAGTAGACTCAACAAAATAACACCATATAATCGAGGGACCAATTTGTAACTTT
Done.