Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 217 of 240
Found at i:65455357 original size:23 final size:23
Alignment explanation
Indices: 65455345--65455389 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
65455335 TTAAATTTAT
65455345 TATTAAGATAAATATTATTTAAA
1 TATTAAGATAAATATTATTTAAA
*
65455368 TATTAAGATAAGTATTATTTAA
1 TATTAAGATAAATATTATTTAA
65455390 CTTTATTAAT
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:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (23 bp):
TATTAAGATAAATATTATTTAAA
Found at i:65455401 original size:29 final size:27
Alignment explanation
Indices: 65455333--65455402 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 27
65455323 TAAACGCTAA
65455333 ATTTAAATTTATTATTAAGATAAATATT
1 ATTT-AATTTATTATTAAGATAAATATT
*
65455361 ATTTAA---A-TATTAAGATAAGTATT
1 ATTTAATTTATTATTAAGATAAATATT
65455384 ATTTAACTTTATTAATTAA
1 ATTTAA-TTTATT-ATTAA
65455403 ATATGACTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
23 21 0.60
24 1 0.03
27 3 0.09
28 5 0.14
29 5 0.14
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (27 bp):
ATTTAATTTATTATTAAGATAAATATT
Found at i:65458438 original size:13 final size:13
Alignment explanation
Indices: 65458420--65458444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65458410 TTGCTCATCT
65458420 TTTATTTACTTTC
1 TTTATTTACTTTC
65458433 TTTATTTACTTT
1 TTTATTTACTTT
65458445 TTTCCGGAAC
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:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTACTTTC
Found at i:65480533 original size:17 final size:15
Alignment explanation
Indices: 65480495--65480534 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
65480485 TAATATTTAG
65480495 GTGTTAAAAAAATAA
1 GTGTTAAAAAAATAA
*
65480510 GTATTAAAAAGAATTAA
1 GTGTTAAAAA-AA-TAA
65480527 GTGTTAAA
1 GTGTTAAA
65480535 TTTAAGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 9 0.43
16 2 0.10
17 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (15 bp):
GTGTTAAAAAAATAA
Found at i:65486707 original size:19 final size:18
Alignment explanation
Indices: 65486672--65486707 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
65486662 GAAGCAAGCA
*
65486672 ATGATTGAAGAAATCAGG
1 ATGATTGAAAAAATCAGG
65486690 ATGATTGAAAAGAATCAG
1 ATGATTGAAAA-AATCAG
65486708 ACCTGGAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (18 bp):
ATGATTGAAAAAATCAGG
Found at i:65490655 original size:18 final size:18
Alignment explanation
Indices: 65490626--65490720 Score: 136
Period size: 18 Copynumber: 5.3 Consensus size: 18
65490616 TACGACCGTT
*
65490626 TACAGTACTATTCACGTA
1 TACAGCACTATTCACGTA
*
65490644 TACGGCACTATTCACGTA
1 TACAGCACTATTCACGTA
*
65490662 TACAGTACTATTCACGTA
1 TACAGCACTATTCACGTA
65490680 TACAGCACTATTCACGTA
1 TACAGCACTATTCACGTA
* * *
65490698 TACGGTACTGTTCACGTA
1 TACAGCACTATTCACGTA
65490716 TACAG
1 TACAG
65490721 TAGTTGGGAT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (18 bp):
TACAGCACTATTCACGTA
Found at i:65490673 original size:36 final size:36
Alignment explanation
Indices: 65490626--65490720 Score: 163
Period size: 36 Copynumber: 2.6 Consensus size: 36
65490616 TACGACCGTT
*
65490626 TACAGTACTATTCACGTATACGGCACTATTCACGTA
1 TACAGTACTATTCACGTATACAGCACTATTCACGTA
65490662 TACAGTACTATTCACGTATACAGCACTATTCACGTA
1 TACAGTACTATTCACGTATACAGCACTATTCACGTA
* *
65490698 TACGGTACTGTTCACGTATACAG
1 TACAGTACTATTCACGTATACAG
65490721 TAGTTGGGAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (36 bp):
TACAGTACTATTCACGTATACAGCACTATTCACGTA
Found at i:65500047 original size:24 final size:23
Alignment explanation
Indices: 65499997--65500049 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
65499987 TTAATTTTTT
*
65499997 TATATTTTTTAATTAATTAAATAA
1 TATATTTTTTAATT-ATCAAATAA
65500021 TATATTTTTATAATT-TCAAATATA
1 TATATTTTT-TAATTATCAAATA-A
65500045 TATAT
1 TATAT
65500050 GTGCTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 6 0.23
24 15 0.58
25 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TATATTTTTTAATTATCAAATAA
Found at i:65511500 original size:953 final size:958
Alignment explanation
Indices: 65509636--65511942 Score: 3761
Period size: 953 Copynumber: 2.4 Consensus size: 958
65509626 TGTTGTTCAG
* *
65509636 CTTGTATGCATACTACAACAATTGTGCATGTTGCAGCAACATAT-TTTCTGTTTTAGTTGCAATT
1 CTTGTATGCATGCTACAACAATTGTGCATGTTGCAGCAACATATGTTT-TGTTTTAGTTGCAATG
* *
65509700 TAATTTGGTTTGGTTGAAAATGAACTTAGTTGTTGATGTTTTGATGGGTTTAGGTGATGATTGAG
65 TAATTTAGTTTGGTTGAAAATGAACTTAGTTGTTGATGTTTTGATGGGTTTAGGTGATGATTGAA
* * * *
65509765 CTGATAAGTCAGCTTATTCATGTGTACAAGCAATGTTTTACTATTCCCAATGCTGATTAGTGGGA
130 CTGATAAGTCAGCTTATTCTTGTGTACAAGCAATGTTTTAATAGTCCTAATGCTGATTAGTGGGA
* * *
65509830 TTACTTAAATATTTGGTGATGTATTTTGATTATAAATGTATTGTTTTCATACTGAATGAGAAAGC
195 TTAGTTGAATATTTGGTGATGTATTTTGATTATAAATGTATTGTTTTCATATTGAATGAGAAAGC
*
65509895 ATATCAGTTGTGTAAAGTAGATTGCTTCCTTAATGCACGTTTGTGAGCAAGTAAATTATGTCAAG
260 ATATCAGTTGTGTAAAGTAGATTGCTTCCTTAATGCACATTTGTGAGCAAGTAAATTATGTCAAG
65509960 CTTCTTGCTCCTTTGTTCTCTGTCTTGTTCTCTTCTTTTGCTGTTGTCAAAACCCAACAAATTGT
325 CTTCTTGCTCCTTTGTTCTCTGTCTTGTTCTCTTCTTTTGCTGTTGTCAAAACCCAACAAATTGT
*
65510025 ATCATAAGCCCAAGTCTTTAAAGGTTTGTTTTTTGCTTATGTTGCTTGTTAAGAAAGACAAGAAG
390 ATCATAAGCCCAAGTC-------------TTTTTGCTTATGTTGCTTGTTAAGAAAGACAAAAAG
* *
65510090 CTGTTAAAGCTTGTCATCTTTAAGGGTTGTTTGTAAAAGATAGAGCAATAACTCACCCTTGTGAG
442 CTGTTAAAGCTTGTCATCTTTAAGGGTTGTTTGTAAAAGATAGAGCAACAACTCACCCATGTGAG
*
65510155 ACTCCTAAACAAGCTTGGGATAAGCTGAAGGAGGAGTTGATGGGGTATGTGCATGAAGACACTCC
507 ACTCCTAAACAAGCTTGAGATAAGCTGAAGGAGGAGTTGATGGGGTATGTGCATGAAGACACTCC
* *
65510220 ACAGTAGGAGGGAGTATGTGCAAGAAGAAACAGGACTATAATGAACAAAGAAACAAGGTAAGATA
572 ACAGCAGGAGGGAGTATGTGCAAGAAGAAACAGGACTATAATGAACAAAGAAACAAGGCAAGATA
*
65510285 TGTTTGAAGGCAAGTTGCCAACCAAGGCTGTGAAGAAGGAGAAGACTCCATTTGATGAACAACTC
637 TGTTTGAAGGCAAGTTGCCAACCAAGGCTATGAAGAAGGAGAAGACTCCATTTGATGAACAACTC
* * * *
65510350 TTTGGCACAAAAGAATGAGATAATCAAGTGTGTAAGTCATATTTTGTTTAGAATGAAGATAAGGT
702 TTTGGCACAAAAGAATGAGATAATCAAGTATGTAAGTCATATTTGGTTGAGAATGAAGACAAGGT
*
65510415 TGAAAATGAATTGCTTGAGTAGAGTCAGCTTGAAATAAAGCATCTAAGGACTGCCAAGCTAAAAA
767 TGAAAATGAATTGCTTGAGCAGAGTCAGCTTGAAATAAAGCATCTAAGGACTGCCAAGCTAAAAA
* *
65510480 AAACTTGATGAATGATTGGTATTTTCAACATGGAGGCCAAGAAGGAGTGTTGAAAATGGCCAACC
832 AAACTTGATGAATGATTGGTATTTTCAACATGGAGGCCAAGAAGGACTGTTGAAAATGACCAACC
* **
65510545 ATGCTGCTATTATGTTTTGTTAAAGTGCATGTTGTTATGATGATTTTGCTGAGTGCATACAA
897 ATGCTACTATTATGTTTTGTTAAAGTGCATACTGTTATGATGATTTTGCTGAGTGCATACAA
* *
65510607 CTTGTATGCATGCTACAACAATTGTGCATGTTGCAACAACATATGTTTTGTTTTAGTTGTAATGT
1 CTTGTATGCATGCTACAACAATTGTGCATGTTGCAGCAACATATGTTTTGTTTTAGTTGCAATGT
65510672 AATTTAGTTTGGTTGAAAATGAACTTAGTTGTTGATGTTTTGATGGGTTTAGGTGATGATTGAAC
66 AATTTAGTTTGGTTGAAAATGAACTTAGTTGTTGATGTTTTGATGGGTTTAGGTGATGATTGAAC
* *
65510737 TGACAAGTCAGCTTATTCTTGTGTACAAGCAATGTTTTAATAGTCCTAATGCTGACTAGTGGGAT
131 TGATAAGTCAGCTTATTCTTGTGTACAAGCAATGTTTTAATAGTCCTAATGCTGATTAGTGGGAT
* *
65510802 TAGTTGAATATTTGGTGATGTATTTTGATTATAAATGTGTTATTTTCATATTGAATGAGAAAGCA
196 TAGTTGAATATTTGGTGATGTATTTTGATTATAAATGTATTGTTTTCATATTGAATGAGAAAGCA
* * * * *
65510867 TATCAGTTGTGTAAAGCAGATTACTTCATTGATAG-ACATTTGTGAGCAAGTACATTATGTCAAG
261 TATCAGTTGTGTAAAGTAGATTGCTTCCTTAAT-GCACATTTGTGAGCAAGTAAATTATGTCAAG
*
65510931 CTTCTTGCTCCTTTGTTCTCTGTCTTGTTCTATTCTTTTGCTGTTGTCAAAACCCAACAAATTGT
325 CTTCTTGCTCCTTTGTTCTCTGTCTTGTTCTCTTCTTTTGCTGTTGTCAAAACCCAACAAATTGT
*
65510996 ATCATGAGCCCAAGTC-TTTT-C-T-T-TTGCTTGTTAAGAAAGACAAAAAGCTGTTAAAGCTTG
390 ATCATAAGCCCAAGTCTTTTTGCTTATGTTGCTTGTTAAGAAAGACAAAAAGCTGTTAAAGCTTG
* *
65511056 TCATCTTTGAGGGTTGTTTGTAAAAGATAGAGCAACAGCTCACCCATGTGAGACTCCTAAACAAG
455 TCATCTTTAAGGGTTGTTTGTAAAAGATAGAGCAACAACTCACCCATGTGAGACTCCTAAACAAG
* *
65511121 CTTGAGATAAGCTGAAGGAGGAGTTGATGGGGTATGTGCATGAAGACACTCCATAGCGGGAGGGA
520 CTTGAGATAAGCTGAAGGAGGAGTTGATGGGGTATGTGCATGAAGACACTCCACAGCAGGAGGGA
* * * *
65511186 GTATGTGCAAGAAGAAACATGACTGTAATGAACAAGGAAACAAGGCAAGATGTGTTTGAAGGCAA
585 GTATGTGCAAGAAGAAACAGGACTATAATGAACAAAGAAACAAGGCAAGATATGTTTGAAGGCAA
* * *
65511251 GTTGCCAACCAAGGCTATGAA-AGAGGAGAAGACTCTATTTGATGAACAACTTTTTGGCATAAAA
650 GTTGCCAACCAAGGCTATGAAGA-AGGAGAAGACTCCATTTGATGAACAACTCTTTGGCACAAAA
* *
65511315 GAATGGGATAATCAAGTATGTAATTCATATTTGGTTGAGAATGAAGACAAGGTTGAAAATGAATT
714 GAATGAGATAATCAAGTATGTAAGTCATATTTGGTTGAGAATGAAGACAAGGTTGAAAATGAATT
65511380 GCTTGAGCAGAGTCAGCTTGAAATAAAGCATCTAAGGACTGCCAAGCTAAAAAAAACTTGATGAA
779 GCTTGAGCAGAGTCAGCTTGAAATAAAGCATCTAAGGACTGCCAAGCTAAAAAAAACTTGATGAA
* * *
65511445 TGATTGGTATTTTCAACATGGAGGCCAAGGAGGACTGTTGAAAATGACCAACCATGTTACTGTTA
844 TGATTGGTATTTTCAACATGGAGGCCAAGAAGGACTGTTGAAAATGACCAACCATGCTACTATTA
* * *
65511510 TGTTTTGTTAAAGTGCATACTGTTATGATGATTTTGTTGAGTGCATATAG
909 TGTTTTGTTAAAGTGCATACTGTTATGATGATTTTGCTGAGTGCATACAA
* * *
65511560 CTTGTATGCATGCTACAAAAATTGTGCATGTTGCAGCAACATATGTTCTCTTTTAGTTGCAATGT
1 CTTGTATGCATGCTACAACAATTGTGCATGTTGCAGCAACATATGTTTTGTTTTAGTTGCAATGT
*
65511625 AATTTAGTTTGGTTGAAAATGAACTTAGTTGTTGATGTTTTGATGGGTTTAAGTGATGATTGAAC
66 AATTTAGTTTGGTTGAAAATGAACTTAGTTGTTGATGTTTTGATGGGTTTAGGTGATGATTGAAC
*
65511690 TGATAAGTCAGCTTATTCTTGTGTACAAGCAATATTTTAATAGT-CTCAATGCTGATTAGTGGGA
131 TGATAAGTCAGCTTATTCTTGTGTACAAGCAATGTTTTAATAGTCCT-AATGCTGATTAGTGGGA
*
65511754 TTAGTTGAATATTTGGTGATGTAGTTTGATTATAAATGTATTGTTTTCATATTGAATGAGAAAGC
195 TTAGTTGAATATTTGGTGATGTATTTTGATTATAAATGTATTGTTTTCATATTGAATGAGAAAGC
*
65511819 ATATCAGTTGTGTAAAGTAGATTGCTTCCTTAATGCATATTTGTGAGCAAGTAAATTATGTCAAG
260 ATATCAGTTGTGTAAAGTAGATTGCTTCCTTAATGCACATTTGTGAGCAAGTAAATTATGTCAAG
*
65511884 CTTCTTGCT-CTTTGTTCTCTGTCTTGTTCTCTTCTTTTGTTGTTGTCAAAACCCCAACA
325 CTTCTTGCTCCTTTGTTCTCTGTCTTGTTCTCTTCTTTTGCTGTTGTCAAAA-CCCAACA
65511943 TGTATCCAAG
Statistics
Matches: 1249, Mismatches: 81, Indels: 30
0.92 0.06 0.02
Matches are distributed among these distances:
952 44 0.04
953 820 0.66
954 1 0.00
955 1 0.00
956 1 0.00
957 4 0.00
971 374 0.30
972 4 0.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (958 bp):
CTTGTATGCATGCTACAACAATTGTGCATGTTGCAGCAACATATGTTTTGTTTTAGTTGCAATGT
AATTTAGTTTGGTTGAAAATGAACTTAGTTGTTGATGTTTTGATGGGTTTAGGTGATGATTGAAC
TGATAAGTCAGCTTATTCTTGTGTACAAGCAATGTTTTAATAGTCCTAATGCTGATTAGTGGGAT
TAGTTGAATATTTGGTGATGTATTTTGATTATAAATGTATTGTTTTCATATTGAATGAGAAAGCA
TATCAGTTGTGTAAAGTAGATTGCTTCCTTAATGCACATTTGTGAGCAAGTAAATTATGTCAAGC
TTCTTGCTCCTTTGTTCTCTGTCTTGTTCTCTTCTTTTGCTGTTGTCAAAACCCAACAAATTGTA
TCATAAGCCCAAGTCTTTTTGCTTATGTTGCTTGTTAAGAAAGACAAAAAGCTGTTAAAGCTTGT
CATCTTTAAGGGTTGTTTGTAAAAGATAGAGCAACAACTCACCCATGTGAGACTCCTAAACAAGC
TTGAGATAAGCTGAAGGAGGAGTTGATGGGGTATGTGCATGAAGACACTCCACAGCAGGAGGGAG
TATGTGCAAGAAGAAACAGGACTATAATGAACAAAGAAACAAGGCAAGATATGTTTGAAGGCAAG
TTGCCAACCAAGGCTATGAAGAAGGAGAAGACTCCATTTGATGAACAACTCTTTGGCACAAAAGA
ATGAGATAATCAAGTATGTAAGTCATATTTGGTTGAGAATGAAGACAAGGTTGAAAATGAATTGC
TTGAGCAGAGTCAGCTTGAAATAAAGCATCTAAGGACTGCCAAGCTAAAAAAAACTTGATGAATG
ATTGGTATTTTCAACATGGAGGCCAAGAAGGACTGTTGAAAATGACCAACCATGCTACTATTATG
TTTTGTTAAAGTGCATACTGTTATGATGATTTTGCTGAGTGCATACAA
Found at i:65517221 original size:56 final size:56
Alignment explanation
Indices: 65517142--65517300 Score: 291
Period size: 56 Copynumber: 2.8 Consensus size: 56
65517132 CTTTGAGAAT
* *
65517142 TCATGGGTTAGTAATGGTTGATGCAGCAAACTCTTTTCATAAATTAATAAGAATTC
1 TCATGGGTTAGTAATGGTTGATGCAACAAACTCTTTTCATAAATTAATAAAAATTC
65517198 TCATGGGTTAGTAATGGTTGATGCAACAAACTCTTTTCATAAATTAATAAAAATTC
1 TCATGGGTTAGTAATGGTTGATGCAACAAACTCTTTTCATAAATTAATAAAAATTC
*
65517254 TCATGGGTTAGTAATGGTTGATGCAACCAACTCTTTTCATAAATTAA
1 TCATGGGTTAGTAATGGTTGATGCAACAAACTCTTTTCATAAATTAA
65517301 AGATTGAATT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 100 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (56 bp):
TCATGGGTTAGTAATGGTTGATGCAACAAACTCTTTTCATAAATTAATAAAAATTC
Found at i:65519635 original size:20 final size:21
Alignment explanation
Indices: 65519585--65519642 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
65519575 AAAAGAGAAA
65519585 GAAAAACTTGGGATTTTATAGG
1 GAAAAACTTGGG-TTTTATAGG
**
65519607 GAATTACTTGGGTTTTATA-G
1 GAAAAACTTGGGTTTTATAGG
*
65519627 GAAAAACTTGAGTTTT
1 GAAAAACTTGGGTTTT
65519643 TACAAGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 14 0.45
21 7 0.23
22 10 0.32
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (21 bp):
GAAAAACTTGGGTTTTATAGG
Found at i:65533892 original size:22 final size:22
Alignment explanation
Indices: 65533864--65533908 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
65533854 TACAGAAAGC
65533864 TTATAGAGATATACACAAGGAA
1 TTATAGAGATATACACAAGGAA
**
65533886 TTATAGAGATATACTGAAGGAA
1 TTATAGAGATATACACAAGGAA
65533908 T
1 T
65533909 GAAATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (22 bp):
TTATAGAGATATACACAAGGAA
Found at i:65534235 original size:10 final size:11
Alignment explanation
Indices: 65534208--65534233 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
65534198 TTTAAAAATA
65534208 AAAAATATTTT
1 AAAAATATTTT
65534219 AAAAATATTTT
1 AAAAATATTTT
65534230 AAAA
1 AAAA
65534234 TAAAATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:65537551 original size:20 final size:20
Alignment explanation
Indices: 65537528--65537570 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
65537518 TTAAAAAACA
* **
65537528 TATAATTATTCATTTAATAT
1 TATAACTATTCAAATAATAT
65537548 TATAACTATTCAAATAATAT
1 TATAACTATTCAAATAATAT
65537568 TAT
1 TAT
65537571 TTGAACAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
TATAACTATTCAAATAATAT
Found at i:65543182 original size:20 final size:21
Alignment explanation
Indices: 65543157--65543199 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
65543147 TTAGATTGGC
* *
65543157 TTGATTTTTTTTTAA-TAATA
1 TTGATTTTGTTATAAGTAATA
65543177 TTGATTTTGTTATAAGTAATA
1 TTGATTTTGTTATAAGTAATA
65543198 TT
1 TT
65543200 TTATTATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.60
Consensus pattern (21 bp):
TTGATTTTGTTATAAGTAATA
Found at i:65544912 original size:26 final size:27
Alignment explanation
Indices: 65544862--65544936 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
65544852 TTTTGTGTAG
65544862 ATTAAGATAATTAGGAGTTTAAATTAA
1 ATTAAGATAATTAGGAGTTTAAATTAA
* * *
65544889 ATTAGGATAATTA-GAGTTTTAATTTAG
1 ATTAAGATAATTAGGAG-TTTAAATTAA
* *
65544916 A-TGAGATAATTAGGAATTTAA
1 ATTAAGATAATTAGGAGTTTAA
65544937 GTTTTGCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 17 0.43
27 23 0.57
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (27 bp):
ATTAAGATAATTAGGAGTTTAAATTAA
Found at i:65547455 original size:11 final size:11
Alignment explanation
Indices: 65547439--65547469 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
65547429 TAGAATATAC
65547439 CCCATACCTTG
1 CCCATACCTTG
*
65547450 CCCATACCTTT
1 CCCATACCTTG
65547461 CCCATACCT
1 CCCATACCT
65547470 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:65548041 original size:18 final size:18
Alignment explanation
Indices: 65548014--65548106 Score: 159
Period size: 18 Copynumber: 5.2 Consensus size: 18
65548004 TACGACCGTT
65548014 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
65548032 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
65548050 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
65548068 TACGGAACTATTCACGTA
1 TACGGTACTATTCACGTA
*
65548086 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
65548104 TAC
1 TAC
65548107 AGTAGTTGGG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:65552170 original size:11 final size:11
Alignment explanation
Indices: 65552154--65552184 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
65552144 TAGAATATAC
65552154 CCCATACCTTG
1 CCCATACCTTG
*
65552165 CCCATACCTTT
1 CCCATACCTTG
65552176 CCCATACCT
1 CCCATACCT
65552185 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:65557018 original size:17 final size:16
Alignment explanation
Indices: 65556985--65557015 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65556975 TTATTTTAAC
65556985 AATAAATTTTAAAAAT
1 AATAAATTTTAAAAAT
*
65557001 AATAATTTTTAAAAA
1 AATAAATTTTAAAAA
65557016 ATATTATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAAATTTTAAAAAT
Found at i:65557090 original size:25 final size:27
Alignment explanation
Indices: 65557038--65557090 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
65557028 TATTATTGAA
* *
65557038 AAATATTTATATTAATATTTTACGAAT
1 AAATATATATATTAATATTTTACAAAT
*
65557065 AAATATAT-TATTAA-ATTTTATAAAT
1 AAATATATATATTAATATTTTACAAAT
65557090 A
1 A
65557091 TTATAGTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 10 0.43
26 6 0.26
27 7 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
AAATATATATATTAATATTTTACAAAT
Found at i:65559347 original size:21 final size:23
Alignment explanation
Indices: 65559323--65559369 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
65559313 TTACACGGCC
*
65559323 GTGTGGCTGAGGGACAC-G-CAT
1 GTGTGACTGAGGGACACAGCCAT
*
65559344 GTGTGACTGAGGTACACAGCCAT
1 GTGTGACTGAGGGACACAGCCAT
65559367 GTG
1 GTG
65559370 AGTAAGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 1 0.05
23 6 0.27
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (23 bp):
GTGTGACTGAGGGACACAGCCAT
Found at i:65559370 original size:21 final size:20
Alignment explanation
Indices: 65559269--65559370 Score: 55
Period size: 21 Copynumber: 4.8 Consensus size: 20
65559259 CGTGTGACAA
*
65559269 AGGTACACAGCCATGTGACTA
1 AGGTACAC-GCCATGTGACTG
* **
65559290 AGAG-ATACGCCCATACGACTG
1 AG-GTACACG-CCATGTGACTG
* * *
65559311 AGTTACACGGCCGTGTGGCTG
1 AGGTACAC-GCCATGTGACTG
*
65559332 AGGGACACG-CATGTGTGACTG
1 AGGTACACGCCA--TGTGACTG
65559353 AGGTACACAGCCATGTGA
1 AGGTACAC-GCCATGTGA
65559371 GTAAGTATTG
Statistics
Matches: 58, Mismatches: 15, Indels: 16
0.65 0.17 0.18
Matches are distributed among these distances:
19 1 0.02
20 2 0.03
21 50 0.86
22 3 0.05
23 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.30, T:0.19
Consensus pattern (20 bp):
AGGTACACGCCATGTGACTG
Found at i:65559648 original size:30 final size:30
Alignment explanation
Indices: 65559573--65559722 Score: 129
Period size: 30 Copynumber: 5.0 Consensus size: 30
65559563 AGTTTTTAAG
* * * * *
65559573 GCGGCACACGACCATGTGGATCGCTCATGC
1 GCGGCACACGCCCGTGTGGACCGCCCGTGC
* * * *
65559603 GAGACACATGGCCGTGTGGACCGCCCGTGC
1 GCGGCACACGCCCGTGTGGACCGCCCGTGC
* *
65559633 GCGGCACACGCCCGTGTGGACTGCCCTTGC
1 GCGGCACACGCCCGTGTGGACCGCCCGTGC
* * *
65559663 GTGGAACATGCCCGTGTGGACCGCCCGTGC
1 GCGGCACACGCCCGTGTGGACCGCCCGTGC
* * * * *
65559693 ACGGCACACACCCGTATGGACAGTCCGTGC
1 GCGGCACACGCCCGTGTGGACCGCCCGTGC
65559723 CCGGAACGCT
Statistics
Matches: 93, Mismatches: 27, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
30 93 1.00
ACGTcount: A:0.17, C:0.35, G:0.33, T:0.15
Consensus pattern (30 bp):
GCGGCACACGCCCGTGTGGACCGCCCGTGC
Found at i:65559651 original size:60 final size:60
Alignment explanation
Indices: 65559573--65559713 Score: 169
Period size: 60 Copynumber: 2.4 Consensus size: 60
65559563 AGTTTTTAAG
* * * *
65559573 GCGGCACACGACCATGTGGA-TCGCTCATGCG-AGACACATGGCCGTGTGGACCGCCCGTGC
1 GCGGCACACGCCCGTGTGGACT-GCCCATGCGTAGA-ACATGCCCGTGTGGACCGCCCGTGC
* *
65559633 GCGGCACACGCCCGTGTGGACTGCCCTTGCGTGGAACATGCCCGTGTGGACCGCCCGTGC
1 GCGGCACACGCCCGTGTGGACTGCCCATGCGTAGAACATGCCCGTGTGGACCGCCCGTGC
* * *
65559693 ACGGCACACACCCGTATGGAC
1 GCGGCACACGCCCGTGTGGAC
65559714 AGTCCGTGCC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
60 67 0.96
61 3 0.04
ACGTcount: A:0.17, C:0.35, G:0.33, T:0.15
Consensus pattern (60 bp):
GCGGCACACGCCCGTGTGGACTGCCCATGCGTAGAACATGCCCGTGTGGACCGCCCGTGC
Found at i:65559729 original size:60 final size:60
Alignment explanation
Indices: 65559608--65559729 Score: 163
Period size: 60 Copynumber: 2.0 Consensus size: 60
65559598 CATGCGAGAC
* * * * * * **
65559608 ACATGGCCGTGTGGACCGCCCGTGCGCGGCACACGCCCGTGTGGACTGCCCTTGCGTGGA
1 ACATGCCCGTGTGGACCGCCCGTGCACGGCACACACCCGTATGGACAGCCCGTGCCCGGA
*
65559668 ACATGCCCGTGTGGACCGCCCGTGCACGGCACACACCCGTATGGACAGTCCGTGCCCGGA
1 ACATGCCCGTGTGGACCGCCCGTGCACGGCACACACCCGTATGGACAGCCCGTGCCCGGA
65559728 AC
1 AC
65559730 GCTCCCAAGT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.16, C:0.37, G:0.33, T:0.15
Consensus pattern (60 bp):
ACATGCCCGTGTGGACCGCCCGTGCACGGCACACACCCGTATGGACAGCCCGTGCCCGGA
Found at i:65565337 original size:21 final size:21
Alignment explanation
Indices: 65565304--65565351 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
65565294 TTGATTTTTT
* * * *
65565304 TTCGAATCGAGTCGAGTGAAA
1 TTCGAGTCAAGTCAAGTCAAA
65565325 TTCGAGTCAAGTCAAGTCAAA
1 TTCGAGTCAAGTCAAGTCAAA
65565346 TT-GAGT
1 TTCGAGT
65565352 GAAATTGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (21 bp):
TTCGAGTCAAGTCAAGTCAAA
Found at i:65565579 original size:10 final size:10
Alignment explanation
Indices: 65565564--65565599 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
65565554 AAATTTGAAC
65565564 TTTTTATATT
1 TTTTTATATT
* *
65565574 TTTTTAGAAT
1 TTTTTATATT
65565584 TTTTTATATT
1 TTTTTATATT
65565594 TTTTTA
1 TTTTTA
65565600 AATATAAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (10 bp):
TTTTTATATT
Found at i:65565626 original size:19 final size:19
Alignment explanation
Indices: 65565609--65565656 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
65565599 AAATATAAAC
65565609 TTTTGAAATTTTTATAAATA
1 TTTTG-AATTTTTATAAATA
*
65565629 TTTTGAA-TTTTAAAAATTA
1 TTTTGAATTTTTATAAA-TA
65565648 TTTTGAATT
1 TTTTGAATT
65565657 ATTTTATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 8 0.32
19 11 0.44
20 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTTGAATTTTTATAAATA
Found at i:65570814 original size:21 final size:22
Alignment explanation
Indices: 65570760--65570817 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 22
65570750 GGGGTTCATG
65570760 TATATAAATATTTTTTTTAATT
1 TATATAAATATTTTTTTTAATT
65570782 TA-ATACACATAAATATTTTTTTAATT
1 TATATA-A-AT--AT-TTTTTTTAATT
65570808 TATATAAATA
1 TATATAAATA
65570818 AAAAGTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
21 3 0.10
22 3 0.10
23 3 0.10
25 4 0.13
26 14 0.47
27 3 0.10
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (22 bp):
TATATAAATATTTTTTTTAATT
Found at i:65571557 original size:63 final size:62
Alignment explanation
Indices: 65571438--65571557 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 62
65571428 GGACAAAAAA
* * * **
65571438 ATCAAATATAAATTTAAAAAAAAACTCAGATACCAAAATGAATATTGAAGCCAAACTTATGT
1 ATCAAATATAAATTTAAAAAAAAACTCAAACACCAAAATGAACATTGAAGAAAAACTTATGT
*
65571500 ATCAAAT-TAAAATTTAAAAAAAAAACTCAAACACCAAACTGAACATTGCAA-AAAAACT
1 ATCAAATAT-AAATTT-AAAAAAAAACTCAAACACCAAAATGAACATTG-AAGAAAAACT
65571558 AGTACCTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
61 1 0.02
62 13 0.27
63 33 0.67
64 2 0.04
ACGTcount: A:0.57, C:0.15, G:0.06, T:0.23
Consensus pattern (62 bp):
ATCAAATATAAATTTAAAAAAAAACTCAAACACCAAAATGAACATTGAAGAAAAACTTATGT
Found at i:65572107 original size:21 final size:22
Alignment explanation
Indices: 65572065--65572109 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
65572055 GAGAGAAAGG
*
65572065 AAAGGAAAGGAAAATGGAGAGA
1 AAAGGAAAGGAAAAGGGAGAGA
* *
65572087 AAAGGAAGGGAAAGGGGGAGAGA
1 AAAGGAAAGGAAA-AGGGAGAGA
65572110 TTTTCCACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.02
Consensus pattern (22 bp):
AAAGGAAAGGAAAAGGGAGAGA
Found at i:65573439 original size:28 final size:25
Alignment explanation
Indices: 65573390--65573454 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 25
65573380 GATTTTTAAA
65573390 AAAAAATTATATAATTTTTTTG-TAC
1 AAAAAATTATATAATTTTTTTGCT-C
*
65573415 AAAATATTATATAAATTTTATTTTGCTC
1 AAAAAATTATAT-AA-TTT-TTTTGCTC
65573443 AAAAAATTATAT
1 AAAAAATTATAT
65573455 TGTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 11 0.32
26 2 0.06
27 3 0.09
28 17 0.50
29 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (25 bp):
AAAAAATTATATAATTTTTTTGCTC
Found at i:65574747 original size:11 final size:11
Alignment explanation
Indices: 65574733--65574758 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
65574723 TATTTTTTTA
65574733 TTTTAAAATAT
1 TTTTAAAATAT
65574744 TTTTAAAATAT
1 TTTTAAAATAT
65574755 TTTT
1 TTTT
65574759 TTATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:65574778 original size:20 final size:19
Alignment explanation
Indices: 65574741--65574780 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
65574731 TATTTTAAAA
*
65574741 TATTTTTAAAATATTTTTT
1 TATTTTTAAAATAATTTTT
*
65574760 TATTTTTAAAATAAATTTT
1 TATTTTTAAAATAATTTTT
65574779 TA
1 TA
65574781 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTTAAAATAATTTTT
Found at i:65574787 original size:20 final size:19
Alignment explanation
Indices: 65574745--65574787 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
65574735 TTAAAATATT
** *
65574745 TTTAAAATATTTTTTTATT
1 TTTAAAATAAATTTTTATG
65574764 TTTAAAATAAATTTTTAGTG
1 TTTAAAATAAATTTTTA-TG
65574784 TTTA
1 TTTA
65574788 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTAAAATAAATTTTTATG
Found at i:65575527 original size:17 final size:17
Alignment explanation
Indices: 65575507--65575539 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
65575497 ATTCTTTGAA
65575507 TTTTTTA-AATTTTAAT
1 TTTTTTATAATTTTAAT
65575523 TTTTTTATAATTTTAAT
1 TTTTTTATAATTTTAAT
65575540 AATTTAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTTATAATTTTAAT
Found at i:65575850 original size:16 final size:14
Alignment explanation
Indices: 65575806--65575853 Score: 57
Period size: 11 Copynumber: 3.5 Consensus size: 14
65575796 AATTGAATTT
65575806 ATTGATAAAATTAA
1 ATTGATAAAATTAA
65575820 A-T--TAAAATTAA
1 ATTGATAAAATTAA
65575831 ATTGATAAAATCTAA
1 ATTGATAAAAT-TAA
65575846 CATTGATA
1 -ATTGATA
65575854 TCACGTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 10 0.34
12 1 0.03
13 1 0.03
14 7 0.24
15 3 0.10
16 7 0.24
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.35
Consensus pattern (14 bp):
ATTGATAAAATTAA
Found at i:65579728 original size:47 final size:47
Alignment explanation
Indices: 65579662--65579755 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 47
65579652 GCCTTTATTT
*
65579662 TTTCAATTCCCATCAAAAC-TATCTCCTATTTCAATTCCGACTTCTA
1 TTTCAATTCCCACCAAAACTTATCTCCTATTTCAATTCCGACTTCTA
*
65579708 TTTCAAATTCCCACCAAAACTTATCTCCTATTTCAATTTCGACTTCTA
1 TTTC-AATTCCCACCAAAACTTATCTCCTATTTCAATTCCGACTTCTA
65579756 AATTTGCTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 4 0.09
47 14 0.32
48 26 0.59
ACGTcount: A:0.29, C:0.30, G:0.02, T:0.39
Consensus pattern (47 bp):
TTTCAATTCCCACCAAAACTTATCTCCTATTTCAATTCCGACTTCTA
Found at i:65586343 original size:24 final size:26
Alignment explanation
Indices: 65586308--65586363 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
65586298 TGGTGCTTCT
65586308 CGTTA-AGTGCTCTTCG-GAGCTACC
1 CGTTATAGTGCTCTTCGTGAGCTACC
* *
65586332 CGTTATAG-GCTCTTTGTGAGCTTCC
1 CGTTATAGTGCTCTTCGTGAGCTACC
*
65586357 CATTATA
1 CGTTATA
65586364 TTACTCGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (26 bp):
CGTTATAGTGCTCTTCGTGAGCTACC
Found at i:65600971 original size:45 final size:45
Alignment explanation
Indices: 65600922--65601037 Score: 187
Period size: 45 Copynumber: 2.6 Consensus size: 45
65600912 TCGGCCATGG
* * * *
65600922 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
65600967 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
65601012 TGCTTCCTTAAATTCTTCCATGAATT
1 TGCTTCCTTAAATTCTTCCATGAATT
65601038 CAAGGCACAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (45 bp):
TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
Found at i:65606482 original size:15 final size:15
Alignment explanation
Indices: 65606464--65606501 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
65606454 TTAATTTCGA
65606464 TTTTTTTTGAAACTC
1 TTTTTTTTGAAACTC
65606479 TTTTTTTTGAAACTC
1 TTTTTTTTGAAACTC
65606494 TTTTTTTT
1 TTTTTTTT
65606502 TCAATACCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.68
Consensus pattern (15 bp):
TTTTTTTTGAAACTC
Found at i:65607292 original size:45 final size:45
Alignment explanation
Indices: 65607237--65607352 Score: 223
Period size: 45 Copynumber: 2.6 Consensus size: 45
65607227 TTGGCCATGG
65607237 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
65607282 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
65607327 TGCTTCCTTAAATTCTTCCATGAATT
1 TGCTTCCTTAAATTCTTCCATGAATT
65607353 CAAGGCACAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (45 bp):
TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
Found at i:65615166 original size:9 final size:9
Alignment explanation
Indices: 65615142--65615178 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
65615132 TTGAGTTTCA
*
65615142 AATTCGAAT
1 AATTCAAAT
*
65615151 AACTCAAAT
1 AATTCAAAT
65615160 AATTCAAAT
1 AATTCAAAT
65615169 AATTCAAAT
1 AATTCAAAT
65615178 A
1 A
65615179 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.30
Consensus pattern (9 bp):
AATTCAAAT
Found at i:65615426 original size:30 final size:31
Alignment explanation
Indices: 65615392--65615451 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
65615382 AAACCTTTTA
*
65615392 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
65615422 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
65615452 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:65615721 original size:9 final size:9
Alignment explanation
Indices: 65615707--65615735 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
65615697 AATTTCACAT
65615707 TTTATATTA
1 TTTATATTA
65615716 TTTATATTA
1 TTTATATTA
65615725 TTTATATTA
1 TTTATATTA
65615734 TT
1 TT
65615736 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:65616966 original size:23 final size:23
Alignment explanation
Indices: 65616939--65616984 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
65616929 AGGATTATGA
*
65616939 GATACCTGTGGATAGATTAATTC
1 GATACCTGCGGATAGATTAATTC
65616962 GATACCTGCGGATAGATTAATTC
1 GATACCTGCGGATAGATTAATTC
65616985 AATTATGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (23 bp):
GATACCTGCGGATAGATTAATTC
Found at i:65619847 original size:22 final size:24
Alignment explanation
Indices: 65619803--65619848 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
65619793 GCAACTTATC
*
65619803 TCAAACAGTATCATAGATAACATA
1 TCAAACAGTATCAGAGATAACATA
65619827 TCAAACAGT-TCAGA-ATAACATA
1 TCAAACAGTATCAGAGATAACATA
65619849 GAGAATTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 4 0.19
24 9 0.43
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (24 bp):
TCAAACAGTATCAGAGATAACATA
Found at i:65624057 original size:16 final size:19
Alignment explanation
Indices: 65624036--65624072 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
65624026 TTGTTTTAAG
65624036 AACAAGA-AG-AAAAA-AA
1 AACAAGACAGTAAAAAGAA
65624052 AACAAGACAGTAAAAAGAA
1 AACAAGACAGTAAAAAGAA
65624071 AA
1 AA
65624073 ACGGAACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 5 0.28
19 4 0.22
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.03
Consensus pattern (19 bp):
AACAAGACAGTAAAAAGAA
Found at i:65625050 original size:45 final size:45
Alignment explanation
Indices: 65625004--65625492 Score: 355
Period size: 45 Copynumber: 11.0 Consensus size: 45
65624994 TATAACTTCA
**
65625004 ATCTACTTCGCCACTAGTATGGGAAGACAAGATCTGCTTTCTTCA
1 ATCTACTTCGCCACTAGTATGGGAAGACAAGATCTGCTTTCTTTG
* * * * * * *
65625049 ATCTACTCCACCACCAGTATGGGGAGGCAATATCTG-TTGTATTTG
1 ATCTACTTCGCCACTAGTATGGGAAGACAAGATCTGCTT-TCTTTG
* * *** * * *
65625094 ATCTACTTC-ACGCT-GATACATGAAGACAAGATTTGTTTTCTTCG
1 ATCTACTTCGCCACTAG-TATGGGAAGACAAGATCTGCTTTCTTTG
* * * * *
65625138 ATCTGCTTCGCCACCAATATGGGAAGACAAGATCTGGTATCTTTG
1 ATCTACTTCGCCACTAGTATGGGAAGACAAGATCTGCTTTCTTTG
* * *
65625183 ATCTACTTCACGCCAGTA-CAT--GAAGACAAGATCTGCTTTCTTCG
1 ATCTACTT--CGCCACTAGTATGGGAAGACAAGATCTGCTTTCTTTG
* * * * *
65625227 ATCTGCTTCGCCGCCAGTATGGGAAGGCAAGATCTGCTATCTTTG
1 ATCTACTTCGCCACTAGTATGGGAAGACAAGATCTGCTTTCTTTG
* * *
65625272 ATCTACTTCACGCCAGTA-CAT--GAAGACAAGATCTGTTTTCTTTG
1 ATCTACTT--CGCCACTAGTATGGGAAGACAAGATCTGCTTTCTTTG
* * * *
65625316 ATCTACTTCGCCACCAGTATGGGAAGACAAAATCTTCTATCTTTG
1 ATCTACTTCGCCACTAGTATGGGAAGACAAGATCTGCTTTCTTTG
* *
65625361 ATCTACTTCACGCCAGTA-CAT--GAAGACAAGATCTG-TTT-TTTCG
1 ATCTACTT--CGCCACTAGTATGGGAAGACAAGATCTGCTTTCTTT-G
* * *
65625404 ATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTG
1 ATCTACTTCGCCACTAGTATGGGAAGACAAGATCTGCTTTCTTTG
* *
65625449 ATCTACTTTACGCCAGTA-CAT--GAAGACAAGATCTGCTTTTCTTT
1 ATCTAC-TT-CGCCACTAGTATGGGAAGACAAGATCTGC-TTTCTTT
65625493 TCAGCCTGCT
Statistics
Matches: 339, Mismatches: 79, Indels: 52
0.72 0.17 0.11
Matches are distributed among these distances:
41 6 0.02
42 16 0.05
43 16 0.05
44 123 0.36
45 142 0.42
46 13 0.04
47 23 0.07
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (45 bp):
ATCTACTTCGCCACTAGTATGGGAAGACAAGATCTGCTTTCTTTG
Found at i:65625122 original size:89 final size:89
Alignment explanation
Indices: 65625026--65625487 Score: 676
Period size: 89 Copynumber: 5.2 Consensus size: 89
65625016 ACTAGTATGG
* * * * * * * * *
65625026 GAAGACAAGATCTGCTTTCTTCAATCTACTCCACCACCAGTATGGGGAGGCAATATCTGTTGTAT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCT
*
65625091 TTGATCTACTTCACG-CTGATACAT
66 TTGATCTACTTCACGCCAG-TACAT
* * * *
65625115 GAAGACAAGATTTGTTTTCTTCGATCTGCTTCGCCACCAATATGGGAAGACAAGATCTGGTATCT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCT
65625180 TTGATCTACTTCACGCCAGTACAT
66 TTGATCTACTTCACGCCAGTACAT
* * * *
65625204 GAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCGCCAGTATGGGAAGGCAAGATCTGCTATCT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCT
65625269 TTGATCTACTTCACGCCAGTACAT
66 TTGATCTACTTCACGCCAGTACAT
* * * **
65625293 GAAGACAAGATCTGTTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAAATCTTCTATCT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCT
65625358 TTGATCTACTTCACGCCAGTACAT
66 TTGATCTACTTCACGCCAGTACAT
*
65625382 GAAGACAAGATCTG-TTTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCT
*
65625446 TTGATCTACTTTACGCCAGTACAT
66 TTGATCTACTTCACGCCAGTACAT
65625470 GAAGACAAGATCTGCTTT
1 GAAGACAAGATCTGCTTT
65625488 TCTTTTCAGC
Statistics
Matches: 338, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
88 82 0.24
89 254 0.75
90 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (89 bp):
GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCT
TTGATCTACTTCACGCCAGTACAT
Found at i:65625215 original size:44 final size:44
Alignment explanation
Indices: 65625090--65625485 Score: 375
Period size: 44 Copynumber: 8.9 Consensus size: 44
65625080 ATCTGTTGTA
* * * *
65625090 TTTGATCTACTTCACG-CTGATACATGAAGACAAGATTTGTTTTC
1 TTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTATC
* * * * * *** *
65625134 TTCGATCTGCTTCGCCACCAATATGGGAAGACAAGATCTGGTATC
1 TTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTATC
*
65625179 TTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTC
1 TTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTATC
* * * *** *
65625223 TTCGATCTGCTTCGCCGCCAGTATGGGAAGGCAAGATCTGCTATC
1 TTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTATC
* *
65625268 TTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTC
1 TTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTATC
* * *** * *
65625312 TTTGATCTACTTCGCCACCAGTATGGGAAGACAAAATCTTCTATC
1 TTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTATC
*
65625357 TTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG-T-TT
1 TTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTATC
* * *** *
65625399 TTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATC
1 TTT-GATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTATC
*
65625445 TTTGATCTACTTTACGCCAGTACATGAAGACAAGATCTGCT
1 TTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT
65625486 TTTCTTTTCA
Statistics
Matches: 275, Mismatches: 69, Indels: 16
0.76 0.19 0.04
Matches are distributed among these distances:
42 4 0.01
43 11 0.04
44 144 0.52
45 111 0.40
46 5 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
TTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTATC
Found at i:65626799 original size:48 final size:47
Alignment explanation
Indices: 65626755--65626848 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
65626745 GTTTTCACTT
* * *
65626755 TAGCCTCTCTTTTTTTTACCTCAAGGCTCCCTTTGTAGGGTTTCACCC
1 TAGCCTCTCTTTTTTTTA-CTCAAAGCGCCCTTTGTAGGCTTTCACCC
* *
65626803 TAGTCTCTTTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACC
1 TAGCCTCTCTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACC
65626849 TTGGTCCCAC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 25 0.61
48 16 0.39
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.44
Consensus pattern (47 bp):
TAGCCTCTCTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCC
Found at i:65626864 original size:48 final size:48
Alignment explanation
Indices: 65626763--65626865 Score: 118
Period size: 47 Copynumber: 2.1 Consensus size: 48
65626753 TTTAGCCTCT
* * * * *
65626763 CTTTTTTTTACCTCAAGGCTCCCTTTGTAGGGTTTCACCCTAGTCTCT
1 CTTTTTTTTACCTCAAAGCGCCCTTTGTAGGCTTTCACCCTAGTCCCC
* * *
65626811 TTTTTTTTTA-CTCAAAGCGCCCTTTGTAGGCTTTCACCTTGGTCCCAC
1 CTTTTTTTTACCTCAAAGCGCCCTTTGTAGGCTTTCACCCTAGTCCC-C
65626859 CTTTTTT
1 CTTTTTT
65626866 AAGCAGAGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
47 30 0.67
48 15 0.33
ACGTcount: A:0.13, C:0.28, G:0.14, T:0.46
Consensus pattern (48 bp):
CTTTTTTTTACCTCAAAGCGCCCTTTGTAGGCTTTCACCCTAGTCCCC
Found at i:65632321 original size:16 final size:19
Alignment explanation
Indices: 65632300--65632336 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
65632290 TTGTTTTAAG
65632300 AACAAGA-AG-AAAAA-AA
1 AACAAGACAGTAAAAAGAA
65632316 AACAAGACAGTAAAAAGAA
1 AACAAGACAGTAAAAAGAA
65632335 AA
1 AA
65632337 ACGGAACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 5 0.28
19 4 0.22
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.03
Consensus pattern (19 bp):
AACAAGACAGTAAAAAGAA
Found at i:65633139 original size:26 final size:26
Alignment explanation
Indices: 65633108--65633189 Score: 164
Period size: 26 Copynumber: 3.2 Consensus size: 26
65633098 TAAACATTTT
65633108 AACTCTCATTCTTTCAATTTTGGTCA
1 AACTCTCATTCTTTCAATTTTGGTCA
65633134 AACTCTCATTCTTTCAATTTTGGTCA
1 AACTCTCATTCTTTCAATTTTGGTCA
65633160 AACTCTCATTCTTTCAATTTTGGTCA
1 AACTCTCATTCTTTCAATTTTGGTCA
65633186 AACT
1 AACT
65633190 GATAATTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.24, C:0.23, G:0.07, T:0.45
Consensus pattern (26 bp):
AACTCTCATTCTTTCAATTTTGGTCA
Found at i:65639159 original size:30 final size:30
Alignment explanation
Indices: 65639125--65639182 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
65639115 GTAATTTTTT
65639125 CGTAAATATAATAATCTTATTTCAAATTCA
1 CGTAAATATAATAATCTTATTTCAAATTCA
65639155 CGTAAATATAATAATCTTATTTCAAATT
1 CGTAAATATAATAATCTTATTTCAAATT
65639183 AGTTAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.41
Consensus pattern (30 bp):
CGTAAATATAATAATCTTATTTCAAATTCA
Found at i:65640792 original size:30 final size:30
Alignment explanation
Indices: 65640747--65640804 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
65640737 AAATTGATAG
* * *
65640747 AATATAGATTATTAGTTACTGAATTCGTAT
1 AATACAGATGATTAGTTACCGAATTCGTAT
*
65640777 AATACAGATGATTAGTTACCGAGTTCGT
1 AATACAGATGATTAGTTACCGAATTCGT
65640805 TTCAATGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (30 bp):
AATACAGATGATTAGTTACCGAATTCGTAT
Found at i:65650590 original size:20 final size:20
Alignment explanation
Indices: 65650567--65650620 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
65650557 AAGCCATTTT
65650567 AAAATTTAAAAATTATTAAA-
1 AAAATTTAAAAATTA-TAAAC
*
65650587 AAAATCATAAAAATTATAAAC
1 AAAAT-TTAAAAATTATAAAC
*
65650608 AAAATTTATAAAT
1 AAAATTTAAAAAT
65650621 AAAAGGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATTTAAAAATTATAAAC
Found at i:65650599 original size:21 final size:21
Alignment explanation
Indices: 65650573--65650612 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
65650563 TTTTAAAATT
65650573 TAAAAATTATTAAA-AAAATCA
1 TAAAAATTA-TAAACAAAATCA
65650594 TAAAAATTATAAACAAAAT
1 TAAAAATTATAAACAAAAT
65650613 TTATAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAATTATAAACAAAATCA
Found at i:65650809 original size:20 final size:20
Alignment explanation
Indices: 65650766--65650809 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
65650756 AATAAAAAAT
**
65650766 ATAAATTTATAATTTTTCTT
1 ATAAATTTATAATTTTTCAA
65650786 ATAAATTTATAATTATTT-AA
1 ATAAATTTATAATT-TTTCAA
65650806 ATAA
1 ATAA
65650810 TTTTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAAATTTATAATTTTTCAA
Found at i:65651406 original size:11 final size:12
Alignment explanation
Indices: 65651343--65651407 Score: 68
Period size: 11 Copynumber: 5.8 Consensus size: 12
65651333 AACTAATCCT
65651343 CTCTCAAATTTC
1 CTCTCAAATTTC
65651355 CTCTC-AATTTC
1 CTCTCAAATTTC
*
65651366 CTCTC-AATTTG
1 CTCTCAAATTTC
*
65651377 CTTTCAAA-TTC
1 CTCTCAAATTTC
65651388 CT-TCCAAATTT-
1 CTCT-CAAATTTC
65651399 CTCTCAAAT
1 CTCTCAAAT
65651408 CCATATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
10 1 0.02
11 35 0.76
12 10 0.22
ACGTcount: A:0.25, C:0.31, G:0.02, T:0.43
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:65652613 original size:7 final size:7
Alignment explanation
Indices: 65652601--65652626 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
65652591 TAGTCAATTG
65652601 GTATTTA
1 GTATTTA
65652608 GTATTTA
1 GTATTTA
65652615 GTATTTA
1 GTATTTA
65652622 GTATT
1 GTATT
65652627 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:65654105 original size:125 final size:125
Alignment explanation
Indices: 65653879--65654253 Score: 606
Period size: 125 Copynumber: 3.0 Consensus size: 125
65653869 TCCAAACATG
* * * *
65653879 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGCTTTCACAAATTCTTCTCAAATAGCATACTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTATCAAACAGCATTCTGC
* * * *
65653944 TAGAAGCAATTTTATACTATTTGCTCAGAAATGTCAACTCAAAATTATTTCTTCTAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
*
65654004 CTACTGTAGCAAAAGCGCGTCCATGAGGGCGCGATTTCACAAATTCTTATCAAACAGCATTCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTATCAAACAGCATTCTGC
* *
65654069 TAGAAACGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAAGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
* * * *
65654129 CTACTGTAGCAAAAGCGCGTCCACGGGGGCGCGATTTCATAAATTATTATCAAACAACATTCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTATCAAACAGCATTCTGC
*
65654194 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
65654254 TTAAAACCCT
Statistics
Matches: 231, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 231 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTATCAAACAGCATTCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
Found at i:65656244 original size:42 final size:42
Alignment explanation
Indices: 65656187--65656450 Score: 366
Period size: 42 Copynumber: 6.2 Consensus size: 42
65656177 CTAACTTTTT
* * * * *
65656187 GCGGCGCTTACAGAAAAAAGCGCCGCTAAAGGTCATGTTTTTTG
1 GCGGCGCTT--AGAAAAAAACGCCACTAAAGATCATGTTCTTTA
65656231 GCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
* *
65656273 GCGGCGCTTAGAAAAAAACGCCGCTAAATATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
* * *
65656315 GCGGCGCTTGTGCAAAAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTT-AGAAAAAAACGCCACTAAAGATCATGTTCTTTA
*
65656358 GCGGCGCTAAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
* * * *
65656400 GCGGCGGTAAGAAAAAAACGCCACCAAAGATCGTGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
65656442 GCGGCGCTT
1 GCGGCGCTT
65656451 TATCTACAAA
Statistics
Matches: 200, Mismatches: 19, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
42 153 0.76
43 38 0.19
44 9 0.05
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (42 bp):
GCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
Found at i:65656351 original size:127 final size:128
Alignment explanation
Indices: 65656200--65656450 Score: 405
Period size: 127 Copynumber: 2.0 Consensus size: 128
65656190 GCGCTTACAG
* * * *
65656200 AAAAAAGCGCCGCTAAAGGTCATGTTTTTTGGCGGCGCTTAGAAAAAAACGCCACTAAAGATCAT
1 AAAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCCACTAAAGATCAT
* * * *
65656265 GTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAATATCATGTTCTTTAGCGGCGCTTGTGC
66 GTTCTTTAGCGGCGCTAAGAAAAAAACGCCACCAAAGATCATGTTCTTTAGCGGCGCTTGTGC
65656328 AAAAAA-CGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCCACTAAAGATCAT
1 AAAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCCACTAAAGATCAT
* *
65656392 GTTCTTTAGCGGCGGTAAGAAAAAAACGCCACCAAAGATCGTGTTCTTTAGCGGCGCTT
66 GTTCTTTAGCGGCGCTAAGAAAAAAACGCCACCAAAGATCATGTTCTTTAGCGGCGCTT
65656451 TATCTACAAA
Statistics
Matches: 113, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
127 107 0.95
128 6 0.05
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (128 bp):
AAAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCCACTAAAGATCAT
GTTCTTTAGCGGCGCTAAGAAAAAAACGCCACCAAAGATCATGTTCTTTAGCGGCGCTTGTGC
Found at i:65656353 original size:85 final size:84
Alignment explanation
Indices: 65656187--65656494 Score: 377
Period size: 85 Copynumber: 3.6 Consensus size: 84
65656177 CTAACTTTTT
* * * *
65656187 GCGGCGCTTACAGAAAAAAGCGCCGCTAAAGGTCATGTTTTTTGGCGGCGCTTAGAAAAAAACGC
1 GCGGCGCTT--AGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGC
65656252 CACTAAAGATCATGTTCTTTA
64 CACTAAAGATCATGTTCTTTA
* * *
65656273 GCGGCGCTTAGAAAAAAACGCCGCTAAATATCATGTTCTTTAGCGGCGCTTGTGCAAAAAACGCC
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-AGAAAAAAACGCC
*
65656338 GCTAAAGATCATGTTCTTTA
65 ACTAAAGATCATGTTCTTTA
* * * *
65656358 GCGGCGCTAAGAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGGTAAGAAAAAAACGCCA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCA
* *
65656423 CCAAAGATCGTGTTCTTTA
66 CTAAAGATCATGTTCTTTA
*** * *
65656442 GCGGCGCTTTATCTACAAACGCCGCTAAA-AGT-AGTGTGCTTTAGCGGCGCTTA
1 GCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
65656495 TTTCAGAAAT
Statistics
Matches: 191, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
84 74 0.39
85 108 0.57
86 9 0.05
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (84 bp):
GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCA
CTAAAGATCATGTTCTTTA
Found at i:65656462 original size:127 final size:127
Alignment explanation
Indices: 65656200--65656492 Score: 403
Period size: 127 Copynumber: 2.3 Consensus size: 127
65656190 GCGCTTACAG
* * * *
65656200 AAAAAAGCGCCGCTAAAGGTCATGTTTTTTGGCGGCGCTTAGAAAAAAACGCCACTAAAGATCAT
1 AAAAAA-CGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCCACTAAAGATCAT
* * * *
65656265 GTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAATATCATGTTCTTTAGCGGCGCTTGTGC
65 GTTCTTTAGCGGCGCTAAGAAAAAAACGCCACCAAAGATCATGTTCTTTAGCGGCGCTTGTGC
65656328 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCCACTAAAGATCATG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCCACTAAAGATCATG
* * *
65656393 TTCTTTAGCGGCGGTAAGAAAAAAACGCCACCAAAGATCGTGTTCTTTAGCGGCGCTT-TATC
66 TTCTTTAGCGGCGCTAAGAAAAAAACGCCACCAAAGATCATGTTCTTTAGCGGCGCTTGT-GC
* * *
65656455 TACAAACGCCGCTAAA-AGT-AGTGTGCTTTAGCGGCGCT
1 AAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCT
65656493 TATTTCAGAA
Statistics
Matches: 148, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
126 3 0.02
127 139 0.94
128 6 0.04
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (127 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCCACTAAAGATCATG
TTCTTTAGCGGCGCTAAGAAAAAAACGCCACCAAAGATCATGTTCTTTAGCGGCGCTTGTGC
Found at i:65656946 original size:12 final size:12
Alignment explanation
Indices: 65656929--65656956 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
65656919 TTTTGAACCT
65656929 CTGCTTCTCTCG
1 CTGCTTCTCTCG
65656941 CTGCTTCTCTCG
1 CTGCTTCTCTCG
65656953 CTGC
1 CTGC
65656957 GGCATCTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.43, G:0.18, T:0.39
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:65656965 original size:21 final size:21
Alignment explanation
Indices: 65656941--65656998 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
65656931 GCTTCTCTCG
65656941 CTGCTTCTCTCGCTGC-GGCAT
1 CTGCTTCTCTCGCTGCAGGC-T
* * *
65656962 CTGCTTCTCTTGTTGCAGTCT
1 CTGCTTCTCTCGCTGCAGGCT
*
65656983 CTGCTTCCCTCGCTGC
1 CTGCTTCTCTCGCTGC
65656999 TGCCTTTGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.03, C:0.38, G:0.21, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGGCT
Found at i:65662532 original size:9 final size:9
Alignment explanation
Indices: 65662518--65662672 Score: 110
Period size: 9 Copynumber: 17.8 Consensus size: 9
65662508 TTTTTATGTA
65662518 TTATGTAAG
1 TTATGTAAG
*
65662527 TTATGTAAC
1 TTATGTAAG
*
65662536 TTACGTAAG
1 TTATGTAAG
** *
65662545 TTA-CCAAA
1 TTATGTAAG
*
65662553 TTAATGTATG
1 TT-ATGTAAG
65662563 TTATGTAAG
1 TTATGTAAG
65662572 -T-TGTAAG
1 TTATGTAAG
*
65662579 TTAT-TATG
1 TTATGTAAG
65662587 TATTATGTAAG
1 --TTATGTAAG
65662598 TTATGT-A-
1 TTATGTAAG
*
65662605 TTATGTAGG
1 TTATGTAAG
65662614 TTATGTAAG
1 TTATGTAAG
*
65662623 TTGTGTAAG
1 TTATGTAAG
* *
65662632 ATATTTAAG
1 TTATGTAAG
65662641 TTATGTAAG
1 TTATGTAAG
* *
65662650 TTTTG-CAG
1 TTATGTAAG
65662658 -TATGTAAG
1 TTATGTAAG
65662666 TTATGTA
1 TTATGTA
65662673 TGCTATGTAT
Statistics
Matches: 110, Mismatches: 25, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
7 15 0.14
8 14 0.13
9 71 0.65
10 7 0.06
11 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:65662532 original size:16 final size:16
Alignment explanation
Indices: 65662511--65662739 Score: 102
Period size: 16 Copynumber: 14.1 Consensus size: 16
65662501 TGATATATTT
65662511 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
*
65662527 TTATGTAACTTACGTAAG
1 TTATGT-A-TTATGTAAG
*** *
65662545 TTACCAAATTAATGTATG
1 TTA-TGTATT-ATGTAAG
*
65662563 TTATGTAAGT-TGTAAG
1 TTATGT-ATTATGTAAG
65662579 TTATTATGTATTATGTAAG
1 ---TTATGTATTATGTAAG
*
65662598 TTATGTATTATGTAGG
1 TTATGTATTATGTAAG
*
65662614 TTATGTAAGTTGTGTAAG
1 TTATGT-A-TTATGTAAG
* *
65662632 ATATTTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
* * *
65662650 TTTTGCAGTATGTAAG
1 TTATGTATTATGTAAG
65662666 TTATGTATGCTATGT-A-
1 TTATGTAT--TATGTAAG
* *
65662682 TAATGTA--A-GT-TG
1 TTATGTATTATGTAAG
*
65662694 TTATGTATAATGTAAG
1 TTATGTATTATGTAAG
65662710 TTA---A-TATGTAAG
1 TTATGTATTATGTAAG
*
65662722 TAATGTATTATGTAAG
1 TTATGTATTATGTAAG
65662738 TT
1 TT
65662740 TATATAAAAA
Statistics
Matches: 158, Mismatches: 33, Indels: 44
0.67 0.14 0.19
Matches are distributed among these distances:
11 2 0.01
12 16 0.10
13 1 0.01
14 1 0.01
15 3 0.02
16 64 0.41
17 6 0.04
18 53 0.34
19 12 0.08
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:65662587 original size:19 final size:19
Alignment explanation
Indices: 65662563--65662601 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
65662553 TTAATGTATG
65662563 TTATGTAAGT-TGTAAGTTA
1 TTATGT-AGTATGTAAGTTA
*
65662582 TTATGTATTATGTAAGTTA
1 TTATGTAGTATGTAAGTTA
65662601 T
1 T
65662602 GTATTATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (19 bp):
TTATGTAGTATGTAAGTTA
Found at i:65662623 original size:25 final size:24
Alignment explanation
Indices: 65662583--65662688 Score: 79
Period size: 25 Copynumber: 4.2 Consensus size: 24
65662573 TGTAAGTTAT
65662583 TATGTA-TTATGTAAGTTATGTAT
1 TATGTAGTTATGTAAGTTATGTAT
* *
65662606 TATGTAGGTTATGTAAGTTGTGTAAGA
1 TATGTA-GTTATGTAAGTTATGT-A-T
* * * *
65662633 TATTTAAGTTATGTAAGTTTTGCAG
1 TATGT-AGTTATGTAAGTTATGTAT
* *
65662658 TATGTAAGTTATGTATGCTATGTAT
1 TATGT-AGTTATGTAAGTTATGTAT
*
65662683 AATGTA
1 TATGTA
65662689 AGTTGTTATG
Statistics
Matches: 65, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
23 6 0.09
24 1 0.02
25 37 0.57
26 2 0.03
27 18 0.28
28 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.46
Consensus pattern (24 bp):
TATGTAGTTATGTAAGTTATGTAT
Found at i:65662649 original size:27 final size:25
Alignment explanation
Indices: 65662556--65662672 Score: 94
Period size: 25 Copynumber: 4.6 Consensus size: 25
65662546 TACCAAATTA
*
65662556 ATGTATGTTATGTAAGTTGT-AAGTT
1 ATGTAAGTTATGTAAGTTGTGAAG-T
* * * *
65662581 AT-TATGTATTATGTAAGTTATGTATT
1 ATGTAAG--TTATGTAAGTTGTGAAGT
*
65662607 ATGTAGGTTATGTAAGTTGTGTAAGAT
1 ATGTAAGTTATGTAAGTTGTG-AAG-T
* * *
65662634 ATTTAAGTTATGTAAGTTTTGCAGT
1 ATGTAAGTTATGTAAGTTGTGAAGT
65662659 ATGTAAGTTATGTA
1 ATGTAAGTTATGTA
65662673 TGCTATGTAT
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
24 4 0.05
25 29 0.39
26 18 0.24
27 23 0.31
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.47
Consensus pattern (25 bp):
ATGTAAGTTATGTAAGTTGTGAAGT
Found at i:65662717 original size:19 final size:19
Alignment explanation
Indices: 65662676--65662719 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
65662666 TTATGTATGC
**
65662676 TATGTATAATGTAAGTTGT
1 TATGTATAATGTAAGTTAA
65662695 TATGTATAATGTAAGTTAA
1 TATGTATAATGTAAGTTAA
65662714 TATGTA
1 TATGTA
65662720 AGTAATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (19 bp):
TATGTATAATGTAAGTTAA
Found at i:65662810 original size:13 final size:13
Alignment explanation
Indices: 65662792--65662837 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
65662782 ATATAAGTTT
65662792 ATGTAAGTTATGA
1 ATGTAAGTTATGA
65662805 ATGTAAG-T-T--
1 ATGTAAGTTATGA
65662814 ATGTAAGTTATGA
1 ATGTAAGTTATGA
65662827 ATGTAAGTTAT
1 ATGTAAGTTAT
65662838 TTAAATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 7 0.24
10 1 0.03
11 2 0.07
12 1 0.03
13 18 0.62
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
ATGTAAGTTATGA
Found at i:65662815 original size:22 final size:22
Alignment explanation
Indices: 65662785--65662846 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
65662775 AGGTAACATA
65662785 TAAGTTTATGTAAGTTATGAATG
1 TAAG-TTATGTAAGTTATGAATG
65662808 TAAGTTATGTAAGTTATGAATG
1 TAAGTTATGTAAGTTATGAATG
* *
65662830 TAAGTTATTTAAATTAT
1 TAAGTTATGTAAGTTAT
65662847 TTAAGTTGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 33 0.89
23 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (22 bp):
TAAGTTATGTAAGTTATGAATG
Found at i:65664376 original size:19 final size:19
Alignment explanation
Indices: 65664352--65664393 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
65664342 AAATTGAATT
65664352 TTCTGTTTTCATTTGCATC
1 TTCTGTTTTCATTTGCATC
65664371 TTCTGTTTTCATTTGCATC
1 TTCTGTTTTCATTTGCATC
65664390 TTCT
1 TTCT
65664394 AATTTCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.10, C:0.21, G:0.10, T:0.60
Consensus pattern (19 bp):
TTCTGTTTTCATTTGCATC
Found at i:65664399 original size:19 final size:19
Alignment explanation
Indices: 65664358--65664399 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
65664348 AATTTTCTGT
**
65664358 TTTCATTTGCATCTTCTGT
1 TTTCATTTGCATCTTCTAA
65664377 TTTCATTTGCATCTTCTAA
1 TTTCATTTGCATCTTCTAA
65664396 TTTC
1 TTTC
65664400 TAATTTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (19 bp):
TTTCATTTGCATCTTCTAA
Found at i:65666236 original size:7 final size:7
Alignment explanation
Indices: 65666224--65666347 Score: 65
Period size: 7 Copynumber: 17.0 Consensus size: 7
65666214 CTTAATTGAC
65666224 ACCCTAA
1 ACCCTAA
65666231 ACCCTAA
1 ACCCTAA
65666238 ATCCCT-A
1 A-CCCTAA
65666245 ACCCTTAA
1 ACCC-TAA
*
65666253 CCCCTAA
1 ACCCTAA
*
65666260 ATCTCCTAG
1 A-C-CCTAA
*
65666269 CCCCTAA
1 ACCCTAA
*
65666276 ATTCCTAA
1 A-CCCTAA
*
65666284 CCCCT-A
1 ACCCTAA
65666290 ACTCCTAA
1 AC-CCTAA
*
65666298 CCCCTAA
1 ACCCTAA
65666305 ATCCCTAA
1 A-CCCTAA
*
65666313 CCCCTAA
1 ACCCTAA
*
65666320 CCCCTAA
1 ACCCTAA
*
65666327 ACCTTATA
1 ACCCTA-A
*
65666335 TCCC-AA
1 ACCCTAA
65666341 ACCCTAA
1 ACCCTAA
65666348 TAATCATATA
Statistics
Matches: 88, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
6 9 0.10
7 49 0.56
8 26 0.30
9 4 0.05
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.22
Consensus pattern (7 bp):
ACCCTAA
Found at i:65666249 original size:14 final size:15
Alignment explanation
Indices: 65666225--65666319 Score: 99
Period size: 15 Copynumber: 6.4 Consensus size: 15
65666215 TTAATTGACA
*
65666225 CCCTAAA-CCCTAAAT
1 CCCTAAATCCCT-AAC
65666240 CCCT-AA-CCCTTAAC
1 CCCTAAATCCC-TAAC
*
65666254 CCCTAAATCTCCTAGC
1 CCCTAAATC-CCTAAC
*
65666270 CCCTAAATTCCTAAC
1 CCCTAAATCCCTAAC
*
65666285 CCCTAACT-CCTAAC
1 CCCTAAATCCCTAAC
65666299 CCCTAAATCCCTAAC
1 CCCTAAATCCCTAAC
65666314 CCCTAA
1 CCCTAA
65666320 CCCCTAAACC
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
14 24 0.35
15 31 0.45
16 12 0.17
17 2 0.03
ACGTcount: A:0.32, C:0.45, G:0.01, T:0.22
Consensus pattern (15 bp):
CCCTAAATCCCTAAC
Found at i:65666260 original size:22 final size:21
Alignment explanation
Indices: 65666224--65666327 Score: 102
Period size: 22 Copynumber: 4.7 Consensus size: 21
65666214 CTTAATTGAC
*
65666224 ACCCTAAACCCTAAATCCCTA
1 ACCCTAACCCCTAAATCCCTA
65666245 ACCCTTAACCCCTAAATCTCCTA
1 ACCC-TAACCCCTAAATC-CCTA
* ** *
65666268 GCCCCTAAATTCCT-AACCCCTA
1 -ACCCT-AACCCCTAAATCCCTA
65666290 ACTCCTAACCCCTAAATCCCTA
1 AC-CCTAACCCCTAAATCCCTA
65666312 ACCCCTAACCCCTAAA
1 A-CCCTAACCCCTAAA
65666328 CCTTATATCC
Statistics
Matches: 67, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
21 10 0.15
22 40 0.60
23 9 0.13
24 8 0.12
ACGTcount: A:0.33, C:0.45, G:0.01, T:0.21
Consensus pattern (21 bp):
ACCCTAACCCCTAAATCCCTA
Found at i:65666301 original size:29 final size:29
Alignment explanation
Indices: 65666250--65666344 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
65666240 CCCTAACCCT
* *
65666250 TAACCCCTAAATCTCCTAGCCCCTAAATTCC
1 TAACCCCT-AA-CTCCTAACCCCTAAATCCC
65666281 TAACCCCTAACTCCTAACCCCTAAATCCC
1 TAACCCCTAACTCCTAACCCCTAAATCCC
* * * *
65666310 TAACCCCTAACCCCTAAACCTTATATCCC
1 TAACCCCTAACTCCTAACCCCTAAATCCC
*
65666339 AAACCC
1 TAACCC
65666345 TAATAATCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 47 0.82
30 2 0.04
31 8 0.14
ACGTcount: A:0.32, C:0.45, G:0.01, T:0.22
Consensus pattern (29 bp):
TAACCCCTAACTCCTAACCCCTAAATCCC
Found at i:65666343 original size:22 final size:22
Alignment explanation
Indices: 65666224--65666344 Score: 86
Period size: 22 Copynumber: 5.5 Consensus size: 22
65666214 CTTAATTGAC
*
65666224 ACCCTAAA-CCCTAAATCCCTA
1 ACCCCAAACCCCTAAATCCCTA
**
65666245 ACCCTTAACCCCTAAATCTCCTA
1 ACCCCAAACCCCTAAATC-CCTA
* ** *
65666268 GCCCCTAAATTCCT-AACCCCTA
1 ACCCC-AAACCCCTAAATCCCTA
* *
65666290 ACTCCTAACCCCTAAATCCCTA
1 ACCCCAAACCCCTAAATCCCTA
* *
65666312 ACCCCTAACCCCTAAA-CCTTA
1 ACCCCAAACCCCTAAATCCCTA
*
65666333 TATCCCAAACCC
1 -ACCCCAAACCC
65666345 TAATAATCAT
Statistics
Matches: 78, Mismatches: 17, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
21 16 0.21
22 47 0.60
23 10 0.13
24 5 0.06
ACGTcount: A:0.32, C:0.45, G:0.01, T:0.21
Consensus pattern (22 bp):
ACCCCAAACCCCTAAATCCCTA
Found at i:65677697 original size:13 final size:13
Alignment explanation
Indices: 65677665--65677689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65677655 ATAAAATATT
65677665 TTTATAATTTGTG
1 TTTATAATTTGTG
65677678 TTTATAATTTGT
1 TTTATAATTTGT
65677690 TTATATAAAA
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:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
TTTATAATTTGTG
Found at i:65685527 original size:29 final size:30
Alignment explanation
Indices: 65685492--65685549 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
65685482 TAATTTAATT
65685492 TGTAATTATATACATA-AACTTTGATTTTG
1 TGTAATTATATACATATAACTTTGATTTTG
* * *
65685521 TGTAATTTTATATATATAATTTTGATTTT
1 TGTAATTATATACATATAACTTTGATTTT
65685550 ATCTAATTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (30 bp):
TGTAATTATATACATATAACTTTGATTTTG
Found at i:65685557 original size:30 final size:31
Alignment explanation
Indices: 65685497--65685557 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
65685487 TAATTTGTAA
* *
65685497 TTATATACATAAACTTTGATTTTGTGTAATT
1 TTATATACATAAACTTTGATTTTATCTAATT
* *
65685528 TTATATATAT-AATTTTGATTTTATCTAATT
1 TTATATACATAAACTTTGATTTTATCTAATT
65685558 CTTGTAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.56
Consensus pattern (31 bp):
TTATATACATAAACTTTGATTTTATCTAATT
Found at i:65686908 original size:3 final size:3
Alignment explanation
Indices: 65686900--65686929 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
65686890 TTATAGTTTA
65686900 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
65686930 GAATTACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:65688312 original size:20 final size:20
Alignment explanation
Indices: 65688261--65688320 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
65688251 ATGGTCTTAT
65688261 AAATTTTGATA-TCAATTAA
1 AAATTTTGATATTCAATTAA
* * ** *
65688280 AAATATTGTTATTGTATTAG
1 AAATTTTGATATTCAATTAA
65688300 AAATTTTGATATT--ATTAA
1 AAATTTTGATATTCAATTAA
65688318 AAA
1 AAA
65688321 AATATTGATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
18 7 0.22
19 9 0.28
20 16 0.50
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (20 bp):
AAATTTTGATATTCAATTAA
Found at i:65688341 original size:40 final size:39
Alignment explanation
Indices: 65688261--65688343 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 39
65688251 ATGGTCTTAT
* * *
65688261 AAATTTTGATATCAATTAAAAATATTGTTATTGTATTAG
1 AAATTTTGATATCAATTAAAAATATTGATATTGCAGTAG
* *
65688300 AAATTTTGATAT-TATTAAAAAAATATTGATATTGCGGTAG
1 AAATTTTGATATCAATT--AAAAATATTGATATTGCAGTAG
65688340 AAAT
1 AAAT
65688344 ATTGGTACTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 3 0.08
39 12 0.32
40 22 0.59
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.42
Consensus pattern (39 bp):
AAATTTTGATATCAATTAAAAATATTGATATTGCAGTAG
Found at i:65690346 original size:16 final size:16
Alignment explanation
Indices: 65690308--65690344 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
65690298 TATTTTTATG
*
65690308 AATTTTAAAAATAATT
1 AATTTTAAAAATAAGT
65690324 AATTTTAAAAA-AAGT
1 AATTTTAAAAATAAGT
65690339 AATTTT
1 AATTTT
65690345 TATAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AATTTTAAAAATAAGT
Found at i:65690378 original size:18 final size:20
Alignment explanation
Indices: 65690341--65690379 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
65690331 AAAAAAGTAA
*
65690341 TTTTTATAATTTATTTAAAT
1 TTTTTATAATTTATTAAAAT
65690361 TTTTTA-AATTT-TTAAAAT
1 TTTTTATAATTTATTAAAAT
65690379 T
1 T
65690380 AATTAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 5 0.28
20 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTATAATTTATTAAAAT
Found at i:65691095 original size:28 final size:28
Alignment explanation
Indices: 65691018--65691096 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 28
65691008 TATGTTAAGA
*
65691018 ATATTTTAATTATGATTCAA-AAATTTT
1 ATATTTTAATTATGATTCAATAAATTAT
* *
65691045 ATATTATAATATTTGAGTT-AATAAGATTAT
1 ATATTTTAAT-TATGA-TTCAATAA-ATTAT
65691075 ATATTTTAATTAT-ATTCAATAA
1 ATATTTTAATTATGATTCAATAA
65691097 TTCATACAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 11 0.26
28 12 0.29
29 6 0.14
30 13 0.31
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (28 bp):
ATATTTTAATTATGATTCAATAAATTAT
Found at i:65708048 original size:20 final size:20
Alignment explanation
Indices: 65707997--65708056 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
65707987 ATGGTCTTAT
65707997 AAATTTTGATA-TCAATTAA
1 AAATTTTGATATTCAATTAA
* * ** *
65708016 AAATATTGTTATTGTATTAG
1 AAATTTTGATATTCAATTAA
65708036 AAATTTTGATATT--ATTAA
1 AAATTTTGATATTCAATTAA
65708054 AAA
1 AAA
65708057 AATATTGATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
18 7 0.22
19 9 0.28
20 16 0.50
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (20 bp):
AAATTTTGATATTCAATTAA
Found at i:65708077 original size:40 final size:39
Alignment explanation
Indices: 65707997--65708079 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 39
65707987 ATGGTCTTAT
* * *
65707997 AAATTTTGATATCAATTAAAAATATTGTTATTGTATTAG
1 AAATTTTGATATCAATTAAAAATATTGATATTGCAGTAG
* *
65708036 AAATTTTGATAT-TATTAAAAAAATATTGATATTGCGGTAG
1 AAATTTTGATATCAATT--AAAAATATTGATATTGCAGTAG
65708076 AAAT
1 AAAT
65708080 ATTGGTACTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
38 3 0.08
39 12 0.32
40 22 0.59
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.42
Consensus pattern (39 bp):
AAATTTTGATATCAATTAAAAATATTGATATTGCAGTAG
Found at i:65710082 original size:16 final size:16
Alignment explanation
Indices: 65710044--65710080 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
65710034 TATTTTTATG
*
65710044 AATTTTAAAAATAATT
1 AATTTTAAAAATAAGT
65710060 AATTTTAAAAA-AAGT
1 AATTTTAAAAATAAGT
65710075 AATTTT
1 AATTTT
65710081 TATAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AATTTTAAAAATAAGT
Found at i:65710114 original size:18 final size:20
Alignment explanation
Indices: 65710077--65710115 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
65710067 AAAAAAGTAA
*
65710077 TTTTTATAATTTATTTAAAT
1 TTTTTATAATTTATTAAAAT
65710097 TTTTTA-AATTT-TTAAAAT
1 TTTTTATAATTTATTAAAAT
65710115 T
1 T
65710116 AATTAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 5 0.28
20 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTATAATTTATTAAAAT
Found at i:65710831 original size:28 final size:28
Alignment explanation
Indices: 65710754--65710832 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 28
65710744 TATGTTAAGA
*
65710754 ATATTTTAATTATGATTCAA-AAATTTT
1 ATATTTTAATTATGATTCAATAAATTAT
* *
65710781 ATATTATAATATTTGAGTT-AATAAGATTAT
1 ATATTTTAAT-TATGA-TTCAATAA-ATTAT
65710811 ATATTTTAATTAT-ATTCAATAA
1 ATATTTTAATTATGATTCAATAA
65710833 TTCATACAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 11 0.26
28 12 0.29
29 6 0.14
30 13 0.31
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (28 bp):
ATATTTTAATTATGATTCAATAAATTAT
Found at i:65730679 original size:20 final size:20
Alignment explanation
Indices: 65730656--65730709 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
65730646 AAGCCATTTT
65730656 AAAATTTAAAAATTATTAAA-
1 AAAATTTAAAAATTA-TAAAC
*
65730676 AAAATCATAAAAATTATAAAC
1 AAAAT-TTAAAAATTATAAAC
*
65730697 AAAATTTATAAAT
1 AAAATTTAAAAAT
65730710 AAAAGGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATTTAAAAATTATAAAC
Found at i:65730688 original size:21 final size:21
Alignment explanation
Indices: 65730662--65730701 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
65730652 TTTTAAAATT
65730662 TAAAAATTATTAAA-AAAATCA
1 TAAAAATTA-TAAACAAAATCA
65730683 TAAAAATTATAAACAAAAT
1 TAAAAATTATAAACAAAAT
65730702 TTATAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAATTATAAACAAAATCA
Found at i:65730895 original size:20 final size:20
Alignment explanation
Indices: 65730852--65730895 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
65730842 AATAAAAAAT
**
65730852 ATAAATTTATAATTTTTCTT
1 ATAAATTTATAATTTTTCAA
65730872 ATAAATTTATAATTATTT-AA
1 ATAAATTTATAATT-TTTCAA
65730892 ATAA
1 ATAA
65730896 TTTTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAAATTTATAATTTTTCAA
Found at i:65731490 original size:11 final size:12
Alignment explanation
Indices: 65731427--65731491 Score: 68
Period size: 11 Copynumber: 5.8 Consensus size: 12
65731417 AACTAATCCT
65731427 CTCTCAAATTTC
1 CTCTCAAATTTC
65731439 CTCTC-AATTTC
1 CTCTCAAATTTC
*
65731450 CTCTC-AATTTG
1 CTCTCAAATTTC
*
65731461 CTTTCAAA-TTC
1 CTCTCAAATTTC
65731472 CT-TCCAAATTT-
1 CTCT-CAAATTTC
65731483 CTCTCAAAT
1 CTCTCAAAT
65731492 CCATATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
10 1 0.02
11 35 0.76
12 10 0.22
ACGTcount: A:0.25, C:0.31, G:0.02, T:0.43
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:65732696 original size:7 final size:7
Alignment explanation
Indices: 65732684--65732709 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
65732674 TAGTCAATTG
65732684 GTATTTA
1 GTATTTA
65732691 GTATTTA
1 GTATTTA
65732698 GTATTTA
1 GTATTTA
65732705 GTATT
1 GTATT
65732710 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:65734188 original size:125 final size:125
Alignment explanation
Indices: 65733962--65734336 Score: 579
Period size: 125 Copynumber: 3.0 Consensus size: 125
65733952 TCCAAACATG
* * * *
65733962 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGCTTTCACAAATTCTTCTGAAATAGCATACTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTATCAAATAGCATTCTGC
* * * *
65734027 TAGAAGCAATTTTATACTATTTGCTCAGAAATGTCAACTCAAAATTATTTCTTCTAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
* *
65734087 CTACTGTAGCAAAAGCGCGTCCATGAGGGCGCGATTTCACAAATTCTTATCAAACAGCATTCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTATCAAATAGCATTCTGC
* *
65734152 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTTGAAATTATTTCTTCCAAGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
* * * *
65734212 CTACTGTAGCAAAAGCGCGTCCACGGGGGCGTGATTTCACAAATTATTATCAAATAACATTCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTATCAAATAGCATTCTGC
* * *
65734277 TAGAAGAGATTTTATACTATTTGATCAAAAACGTCAACTCGAAATTATTTCTTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
65734337 TTAAAACCTT
Statistics
Matches: 227, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
125 227 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTATCAAATAGCATTCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
Found at i:65736372 original size:42 final size:42
Alignment explanation
Indices: 65736271--65736619 Score: 402
Period size: 42 Copynumber: 8.2 Consensus size: 42
65736261 CTAACTTTTT
* * * *
65736271 GCGGCGCTTATAGAAAAAAGCACCGCTAAAGGTCATGTT-TGTTG
1 GCGGCGC-T-TAGAAAAAAACGCCGCTAAAGATCATGTTCT-TTA
*
65736315 GCGGCGCTTAG-AAAAAACGCCACTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
*
65736356 GCGGCGCTTAGAAAAAAACGCCGCTAAATATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
* *
65736398 GCGGCGCTTGTGCAAAAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTT-AGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
*
65736441 GCGGCG-TTAAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
1 GCGGCGCTT-AGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
* * * * *
65736483 GCGGCGGTAAGAAAAAAACGCCACCAAAGATCGTGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
* *
65736525 GCGGCGCTTGGGAAAAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
*** * *
65736567 GCGGCGCTTTATCTACAAACGCCGCTAAA-AGT-AGTGTGCTTTA
1 GCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTA
65736610 GCGGCGCTTA
1 GCGGCGCTTA
65736620 TTTCAGAAAC
Statistics
Matches: 268, Mismatches: 30, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
41 34 0.13
42 157 0.59
43 70 0.26
44 7 0.03
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (42 bp):
GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
Found at i:65736427 original size:85 final size:84
Alignment explanation
Indices: 65736271--65736619 Score: 411
Period size: 85 Copynumber: 4.1 Consensus size: 84
65736261 CTAACTTTTT
* * * *
65736271 GCGGCGCTTATAGAAAAAAGCACCGCTAAAGGTCATGTT-TGTTGGCGGCGCTTAG-AAAAAACG
1 GCGGCGC-T-TAGAAAAAAACGCCGCTAAAGATCATGTTCT-TTAGCGGCGCTTAGCAAAAAACG
65736334 CCACTAAAGATCATGTTCTTTA
63 CCACTAAAGATCATGTTCTTTA
* *
65736356 GCGGCGCTTAGAAAAAAACGCCGCTAAATATCATGTTCTTTAGCGGCGCTTGTGCAAAAAACGCC
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-AGCAAAAAACGCC
*
65736421 GCTAAAGATCATGTTCTTTA
65 ACTAAAGATCATGTTCTTTA
* * * *
65736441 GCGGCG-TTAAGAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGGTAAGAAAAAAACGCC
1 GCGGCGCTT-AGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGCAAAAAACGCC
* *
65736505 ACCAAAGATCGTGTTCTTTA
65 ACTAAAGATCATGTTCTTTA
* * * * *
65736525 GCGGCGCTTGGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTATCTACAAACGCC
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTAGCAAAAAACGCC
* *
65736590 GCTAAA-AGT-AGTGTGCTTTA
65 ACTAAAGA-TCA-TGTTCTTTA
65736610 GCGGCGCTTA
1 GCGGCGCTTA
65736620 TTTCAGAAAC
Statistics
Matches: 226, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
83 36 0.16
84 76 0.34
85 114 0.50
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (84 bp):
GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGCAAAAAACGCCA
CTAAAGATCATGTTCTTTA
Found at i:65736472 original size:127 final size:125
Alignment explanation
Indices: 65736271--65736575 Score: 443
Period size: 127 Copynumber: 2.4 Consensus size: 125
65736261 CTAACTTTTT
* * * *
65736271 GCGGCGCTTATAGAAAAAAGCACCGCTAAAGGTCATGTT-TGTTGGCGGCGCTTAGAAAAAACGC
1 GCGGCGCTTGT-GAAAAAA-CGCCGCTAAAGATCATGTTCT-TTAGCGGCGCTTAGAAAAAACGC
* * * *
65736335 CACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAATATCATGTTCTTTA
63 CACTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCCACCAAAGATCATGTTCTTTA
65736398 GCGGCGCTTGTGCAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-TTAAGAAAAAAACGC
1 GCGGCGCTTGTG-AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-AG-AAAAAACGC
* *
65736462 CACTAAAGATCATGTTCTTTAGCGGCGGTAAGAAAAAAACGCCACCAAAGATCGTGTTCTTTA
63 CACTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCCACCAAAGATCATGTTCTTTA
*
65736525 GCGGCGCTTGGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
1 GCGGCGCTTGTGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
65736576 TATCTACAAA
Statistics
Matches: 162, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
125 2 0.01
126 64 0.40
127 96 0.59
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (125 bp):
GCGGCGCTTGTGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAACGCCAC
TAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAAAACGCCACCAAAGATCATGTTCTTTA
Found at i:65737070 original size:12 final size:12
Alignment explanation
Indices: 65737053--65737079 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
65737043 TTTTGAACCT
65737053 CTGCTTCTCTCG
1 CTGCTTCTCTCG
65737065 CTGCTTCTCTCG
1 CTGCTTCTCTCG
65737077 CTG
1 CTG
65737080 TGGCATCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.19, T:0.41
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:65738766 original size:22 final size:22
Alignment explanation
Indices: 65738736--65738788 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
65738726 AACTCATTAC
*
65738736 AACAACATTGTCAAAGAACTCT
1 AACAGCATTGTCAAAGAACTCT
65738758 AACAGCATTGTCAAAGAACTCT
1 AACAGCATTGTCAAAGAACTCT
65738780 AACAGCATT
1 AACAGCATT
65738789 TTATCTGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (22 bp):
AACAGCATTGTCAAAGAACTCT
Found at i:65739571 original size:9 final size:9
Alignment explanation
Indices: 65739557--65739711 Score: 92
Period size: 9 Copynumber: 17.8 Consensus size: 9
65739547 TTTTTATGTA
65739557 TTATGTAAG
1 TTATGTAAG
*
65739566 TTATGTAAC
1 TTATGTAAG
*
65739575 TTACGTAAG
1 TTATGTAAG
** *
65739584 TTA-CCAAA
1 TTATGTAAG
*
65739592 TTAATGTATG
1 TT-ATGTAAG
*
65739602 CTATGTAAG
1 TTATGTAAG
65739611 -T-TGTAAG
1 TTATGTAAG
*
65739618 TTAT-TATG
1 TTATGTAAG
65739626 TATTATGTAAG
1 --TTATGTAAG
65739637 TTATGT-A-
1 TTATGTAAG
*
65739644 TTATGTAGG
1 TTATGTAAG
65739653 TTATGTAAG
1 TTATGTAAG
*
65739662 TTGTGTAAG
1 TTATGTAAG
* *
65739671 ATATTTAAG
1 TTATGTAAG
65739680 TTATGTAAG
1 TTATGTAAG
* *
65739689 TTTTG-CAG
1 TTATGTAAG
*
65739697 -TAAGTAAG
1 TTATGTAAG
65739705 TTATGTA
1 TTATGTA
65739712 TGCTATGTAT
Statistics
Matches: 107, Mismatches: 28, Indels: 22
0.68 0.18 0.14
Matches are distributed among these distances:
7 14 0.13
8 14 0.13
9 70 0.65
10 6 0.06
11 3 0.03
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:65739571 original size:16 final size:16
Alignment explanation
Indices: 65739550--65739797 Score: 86
Period size: 16 Copynumber: 15.1 Consensus size: 16
65739540 TGATATATTT
65739550 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
*
65739566 TTATGTAACTTACGTAAG
1 TTATGT-A-TTATGTAAG
*** *
65739584 TTACCAAATTAATGTATG
1 TTA-TGTATT-ATGTAAG
* *
65739602 CTATGTAAGT-TGTAAG
1 TTATGT-ATTATGTAAG
65739618 TTATTATGTATTATGTAAG
1 -T--TATGTATTATGTAAG
*
65739637 TTATGTATTATGTAGG
1 TTATGTATTATGTAAG
*
65739653 TTATGTAAGTTGTGTAAG
1 TTATGT-A-TTATGTAAG
* *
65739671 ATATTTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
* * * *
65739689 TTTTGCAGTAAGTAAG
1 TTATGTATTATGTAAG
65739705 TTATGTATGCTATGT-A-
1 TTATGTAT--TATGTAAG
* *
65739721 TAATGTA--A-GT-TG
1 TTATGTATTATGTAAG
*
65739733 TTATGTATAATGTAAGTTG
1 TTATGTATTATGTAA---G
*
65739752 TTATGTATAATGTAAG
1 TTATGTATTATGTAAG
65739768 TTA---A-TATGTAAG
1 TTATGTATTATGTAAG
*
65739780 TAATGTATTATGTAAG
1 TTATGTATTATGTAAG
65739796 TT
1 TT
65739798 TATATAAAAA
Statistics
Matches: 170, Mismatches: 37, Indels: 50
0.66 0.14 0.19
Matches are distributed among these distances:
11 2 0.01
12 16 0.09
13 1 0.01
14 1 0.01
15 3 0.02
16 62 0.36
17 6 0.04
18 52 0.31
19 27 0.16
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.45
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:65739627 original size:19 final size:19
Alignment explanation
Indices: 65739603--65739777 Score: 52
Period size: 19 Copynumber: 9.3 Consensus size: 19
65739593 TAATGTATGC
65739603 TATGTAAGT-TGTAAGTTAT
1 TATGT-AGTATGTAAGTTAT
*
65739622 TATGTATTATGTAAG---T
1 TATGTAGTATGTAAGTTAT
* *
65739638 TATGTATTATGTAGGTTAT
1 TATGTAGTATGTAAGTTAT
* * *
65739657 GTAAGT--TGTGTAAGATAT
1 -TATGTAGTATGTAAGTTAT
*
65739675 T-T-AAGTTATGTAAG-T-T
1 TATGTAG-TATGTAAGTTAT
* *
65739691 T-TGCAGTAAGTAAGTTAT
1 TATGTAGTATGTAAGTTAT
*
65739709 GTATGCTATGTATAATGTAAGTTGT
1 -TATG-TA-G--T-ATGTAAGTTAT
*
65739734 TATGTA-TAATGTAAGTTGT
1 TATGTAGT-ATGTAAGTTAT
*
65739753 TATGTA-TAATGTAAGTTAA
1 TATGTAGT-ATGTAAGTTAT
65739772 TATGTA
1 TATGTA
65739778 AGTAATGTAT
Statistics
Matches: 122, Mismatches: 16, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
16 25 0.20
17 5 0.04
18 19 0.16
19 49 0.40
20 6 0.05
21 1 0.01
22 1 0.01
23 2 0.02
24 5 0.04
25 9 0.07
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.46
Consensus pattern (19 bp):
TATGTAGTATGTAAGTTAT
Found at i:65739662 original size:25 final size:24
Alignment explanation
Indices: 65739622--65739727 Score: 70
Period size: 25 Copynumber: 4.2 Consensus size: 24
65739612 TGTAAGTTAT
65739622 TATGTA-TTATGTAAGTTATGTAT
1 TATGTAGTTATGTAAGTTATGTAT
* *
65739645 TATGTAGGTTATGTAAGTTGTGTAAGA
1 TATGTA-GTTATGTAAGTTATGT-A-T
* * * *
65739672 TATTTAAGTTATGTAAGTTTTGCAG
1 TATGT-AGTTATGTAAGTTATGTAT
* * *
65739697 TAAGTAAGTTATGTATGCTATGTAT
1 TATGT-AGTTATGTAAGTTATGTAT
*
65739722 AATGTA
1 TATGTA
65739728 AGTTGTTATG
Statistics
Matches: 63, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
23 6 0.10
24 1 0.02
25 35 0.56
26 2 0.03
27 18 0.29
28 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (24 bp):
TATGTAGTTATGTAAGTTATGTAT
Found at i:65739868 original size:13 final size:13
Alignment explanation
Indices: 65739850--65739895 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
65739840 ATATAAGTTT
65739850 ATGTAAGTTATGA
1 ATGTAAGTTATGA
65739863 ATGTAAG-T-T--
1 ATGTAAGTTATGA
65739872 ATGTAAGTTATGA
1 ATGTAAGTTATGA
65739885 ATGTAAGTTAT
1 ATGTAAGTTAT
65739896 TTAAATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 7 0.24
10 1 0.03
11 2 0.07
12 1 0.03
13 18 0.62
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
ATGTAAGTTATGA
Found at i:65739873 original size:22 final size:22
Alignment explanation
Indices: 65739843--65739904 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
65739833 AGGTAACATA
65739843 TAAGTTTATGTAAGTTATGAATG
1 TAAG-TTATGTAAGTTATGAATG
65739866 TAAGTTATGTAAGTTATGAATG
1 TAAGTTATGTAAGTTATGAATG
* *
65739888 TAAGTTATTTAAATTAT
1 TAAGTTATGTAAGTTAT
65739905 TTAAGTTGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 33 0.89
23 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (22 bp):
TAAGTTATGTAAGTTATGAATG
Found at i:65741057 original size:16 final size:16
Alignment explanation
Indices: 65741031--65741068 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
65741021 TTGAACTTAT
*
65741031 ATAAC-TGTTCCGAAA
1 ATAACATGTTCCCAAA
65741046 ATAACATGTTCCCAAA
1 ATAACATGTTCCCAAA
65741062 ATAACAT
1 ATAACAT
65741069 TTGTCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (16 bp):
ATAACATGTTCCCAAA
Found at i:65741404 original size:19 final size:19
Alignment explanation
Indices: 65741380--65741421 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
65741370 AAATTGAATT
65741380 TTCTGTTTTCATTTGCATC
1 TTCTGTTTTCATTTGCATC
65741399 TTCTGTTTTCATTTGCATC
1 TTCTGTTTTCATTTGCATC
65741418 TTCT
1 TTCT
65741422 AATTTCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.10, C:0.21, G:0.10, T:0.60
Consensus pattern (19 bp):
TTCTGTTTTCATTTGCATC
Found at i:65741427 original size:19 final size:19
Alignment explanation
Indices: 65741386--65741427 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
65741376 AATTTTCTGT
**
65741386 TTTCATTTGCATCTTCTGT
1 TTTCATTTGCATCTTCTAA
65741405 TTTCATTTGCATCTTCTAA
1 TTTCATTTGCATCTTCTAA
65741424 TTTC
1 TTTC
65741428 TAATTTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (19 bp):
TTTCATTTGCATCTTCTAA
Found at i:65743263 original size:7 final size:7
Alignment explanation
Indices: 65743251--65743374 Score: 65
Period size: 7 Copynumber: 17.0 Consensus size: 7
65743241 CTTAATTGAC
65743251 ACCCTAA
1 ACCCTAA
65743258 ACCCTAA
1 ACCCTAA
65743265 ATCCCT-A
1 A-CCCTAA
65743272 ACCCTTAA
1 ACCC-TAA
*
65743280 CCCCTAA
1 ACCCTAA
*
65743287 ATCTCCTAG
1 A-C-CCTAA
*
65743296 CCCCTAA
1 ACCCTAA
*
65743303 ATTCCTAA
1 A-CCCTAA
*
65743311 CCCCT-A
1 ACCCTAA
65743317 ACTCCTAA
1 AC-CCTAA
*
65743325 CCCCTAA
1 ACCCTAA
65743332 ATCCCTAA
1 A-CCCTAA
*
65743340 CCCCTAA
1 ACCCTAA
*
65743347 CCCCTAA
1 ACCCTAA
*
65743354 ACCTTATA
1 ACCCTA-A
*
65743362 TCCC-AA
1 ACCCTAA
65743368 ACCCTAA
1 ACCCTAA
65743375 TAATCATATA
Statistics
Matches: 88, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
6 9 0.10
7 49 0.56
8 26 0.30
9 4 0.05
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.22
Consensus pattern (7 bp):
ACCCTAA
Done.