Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007776.1 Hibiscus syriacus cultivar Beakdansim tig00110057_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: 2207776
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1152407 original size:18 final size:19
Alignment explanation
Indices: 1152384--1152421 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
1152374 CCGAACCTGA
1152384 AAAAAAAAAAGAAG-ACAG
1 AAAAAAAAAAGAAGAACAG
1152402 AAAAAAAAAAGAAGAACAG
1 AAAAAAAAAAGAAGAACAG
1152421 A
1 A
1152422 GAGACAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAAGAACAG
Found at i:1155516 original size:65 final size:65
Alignment explanation
Indices: 1155226--1155488 Score: 391
Period size: 65 Copynumber: 4.0 Consensus size: 65
1155216 GCTGCACCGA
* * * *
1155226 TACAGATCACTCATATGACTCATGTACTTTTGTGGTGCATGAGGTGGAGTGATAATTGAGTATTG
1 TACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
*
1155291 TACAAATCACTCATATAACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
1 TACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
* * * *
1155356 TACAAATTACTTATATGACTCAAGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATTG
1 TACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
* * ** * *
1155421 TACAGATCACTCATATGACTTAAATACCTTTGTGGTTCATGAGGTGAAGTGATAATTGAATACTG
1 TACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
1155486 TAC
1 TAC
1155489 TTCTCACTCA
Statistics
Matches: 180, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 180 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34
Consensus pattern (65 bp):
TACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
Found at i:1155536 original size:130 final size:130
Alignment explanation
Indices: 1155226--1155537 Score: 349
Period size: 130 Copynumber: 2.4 Consensus size: 130
1155216 GCTGCACCGA
* * * * * * * *
1155226 TACAGATCACTCATATGACTCATGTACTTTTGTGGTGCATGAGGTGGAGTGATAATTGAGTATTG
1 TACAAATCACTCAGATGACTCAAGTACCTTTGTGGTGCATAAGATAGAGTGATAATTGAATATTG
** *
1155291 TACAAATCACTCATATAACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
66 TACAAATCACTCATATAACTCAAATACCTTTGTGGTGCATGAGGTGAAGTGATAATTGAATACTG
* * * * * *
1155356 TACAAATTACTTATATGACTCAAGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATTG
1 TACAAATCACTCAGATGACTCAAGTACCTTTGTGGTGCATAAGATAGAGTGATAATTGAATATTG
* * * *
1155421 TACAGATCACTCATATGACTTAAATACCTTTGTGGTTCATGAGGTGAAGTGATAATTGAATACTG
66 TACAAATCACTCATATAACTCAAATACCTTTGTGGTGCATGAGGTGAAGTGATAATTGAATACTG
*** ***
1155486 TACTTCTCACTCACGA-GACTTGTGTACCTTTAG-GGTGCATAAGATAGAGTGA
1 TACAAATCACTCA-GATGACTCAAGTACCTTT-GTGGTGCATAAGATAGAGTGA
1155538 CTATATGATA
Statistics
Matches: 155, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
130 153 0.99
131 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (130 bp):
TACAAATCACTCAGATGACTCAAGTACCTTTGTGGTGCATAAGATAGAGTGATAATTGAATATTG
TACAAATCACTCATATAACTCAAATACCTTTGTGGTGCATGAGGTGAAGTGATAATTGAATACTG
Found at i:1156994 original size:25 final size:25
Alignment explanation
Indices: 1156966--1157018 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1156956 ACTAGGCAGA
1156966 AATAT-TAGAACAAGGCTTTGAAAAG
1 AATATATA-AACAAGGCTTTGAAAAG
* *
1156991 AATATATATATAAGGCTTTGAAAAG
1 AATATATAAACAAGGCTTTGAAAAG
1157016 AAT
1 AAT
1157019 GTGTGTGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (25 bp):
AATATATAAACAAGGCTTTGAAAAG
Found at i:1162812 original size:36 final size:36
Alignment explanation
Indices: 1162779--1162846 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
1162769 TACAAATTGT
*
1162779 AAAATATTTATAT-ATTTTTTTAAAAAATTAAATTC
1 AAAATATTTATATAATATTTTTAAAAAATTAAATTC
* *
1162814 ATAATATTTATATAATATTTTTACAAAATTAAA
1 AAAATATTTATATAATATTTTTAAAAAATTAAA
1162847 AATATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 12 0.41
36 17 0.59
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (36 bp):
AAAATATTTATATAATATTTTTAAAAAATTAAATTC
Found at i:1163661 original size:96 final size:97
Alignment explanation
Indices: 1163510--1163705 Score: 312
Period size: 97 Copynumber: 2.0 Consensus size: 97
1163500 TAAAATCAGA
*
1163510 ATTTAATATTTTTTTAAATTAATATTAGAAAGAATTTTTTAAATAAAGAGGTGATA-TTTTTTAG
1 ATTTAATATTTTTTTAAATTAATATTAGAAAGAATATTTTAAATAAAGAGGTGATATTTTTTTAG
1163574 CTTTACATTCTT-TTTCATTAGAATT-TAATATTT
66 CTTTACATTCTTATTT-ATT-GAATTATAAT-TTT
1163607 ATTTAATA-TTTTTTAACATTAATATTAGAAA-AATATTTTAAATAAAGAGGTGATATTTTTTTA
1 ATTTAATATTTTTTTAA-ATTAATATTAGAAAGAATATTTTAAATAAAGAGGTGATATTTTTTTA
1163670 GCTTTACATTCTTATTTATTGAATTATAATTTT
65 GCTTTACATTCTTATTTATTGAATTATAATTTT
1163703 ATT
1 ATT
1163706 AAAAATGAAT
Statistics
Matches: 94, Mismatches: 1, Indels: 9
0.90 0.01 0.09
Matches are distributed among these distances:
96 42 0.45
97 49 0.52
98 3 0.03
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (97 bp):
ATTTAATATTTTTTTAAATTAATATTAGAAAGAATATTTTAAATAAAGAGGTGATATTTTTTTAG
CTTTACATTCTTATTTATTGAATTATAATTTT
Found at i:1163721 original size:96 final size:97
Alignment explanation
Indices: 1163527--1163723 Score: 276
Period size: 96 Copynumber: 2.0 Consensus size: 97
1163517 ATTTTTTTAA
*
1163527 ATTAATATTAGAAAGAATTTTTTAAATAAAGAGGTGATATTTTTTAGCTTTACATTCTTTTTCAT
1 ATTAATATTAGAAAGAATATTTTAAATAAAGAGGTGATATTTTTTAGCTTTACATTCTTTTTCAT
* * *** *
1163592 TAGAATTTAATATTTATTTAATATTTTTTAAC
66 TAGAATTTAATATTTATTAAAAATGAATAAAC
1163624 ATTAATATTAGAAA-AATATTTTAAATAAAGAGGTGATATTTTTTTAGCTTTACATTCTTATTT-
1 ATTAATATTAGAAAGAATATTTTAAATAAAGAGGTGATA-TTTTTTAGCTTTACATTCTT-TTTC
1163687 ATT-GAATTATAAT-TTTATTAAAAATGAATAAAC
64 ATTAGAATT-TAATATTTATTAAAAATGAATAAAC
1163720 ATTA
1 ATTA
1163724 TTAATTGTTG
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
96 46 0.51
97 41 0.46
98 3 0.03
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.48
Consensus pattern (97 bp):
ATTAATATTAGAAAGAATATTTTAAATAAAGAGGTGATATTTTTTAGCTTTACATTCTTTTTCAT
TAGAATTTAATATTTATTAAAAATGAATAAAC
Found at i:1163738 original size:30 final size:28
Alignment explanation
Indices: 1163692--1163747 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
1163682 TATTTATTGA
1163692 ATTATAATTTTATTAAAAATGAATAAAC
1 ATTATAATTTTATTAAAAATGAATAAAC
* *
1163720 ATTATTAATTGTTGTTAAAAATTAATAA
1 ATTA-TAATT-TTATTAAAAATGAATAA
1163748 TTAATGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 5 0.21
30 15 0.62
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (28 bp):
ATTATAATTTTATTAAAAATGAATAAAC
Found at i:1165364 original size:16 final size:18
Alignment explanation
Indices: 1165343--1165382 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1165333 ATGAAATTTA
1165343 TAAAATTATA-AA-AATT
1 TAAAATTATACAAGAATT
*
1165359 TAAAA-TATACAAGGATT
1 TAAAATTATACAAGAATT
1165376 TAAAATT
1 TAAAATT
1165383 TATAGAGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 8 0.40
18 1 0.05
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (18 bp):
TAAAATTATACAAGAATT
Found at i:1169216 original size:31 final size:31
Alignment explanation
Indices: 1169181--1169248 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
1169171 AAATGAAAGG
* *
1169181 AATAAA-AATAAAGATAAAATAGAATAA-GATA
1 AATAAAGAAAAAAGAT-AAATAAAATAAGGA-A
1169212 AATAAAGAAAAAAGATAAATAAAATAAGGAA
1 AATAAAGAAAAAAGATAAATAAAATAAGGAA
1169243 AATAAA
1 AATAAA
1169249 TAGATCAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 23 0.70
32 10 0.30
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (31 bp):
AATAAAGAAAAAAGATAAATAAAATAAGGAA
Found at i:1169228 original size:17 final size:17
Alignment explanation
Indices: 1169181--1169234 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
1169171 AAATGAAAGG
*
1169181 AATAAA-AATAAAGATA
1 AATAAAGAAAAAAGATA
* *
1169197 AA-ATAG-AATAAGATA
1 AATAAAGAAAAAAGATA
1169212 AATAAAGAAAAAAGATA
1 AATAAAGAAAAAAGATA
1169229 AATAAA
1 AATAAA
1169235 ATAAGGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 11 0.37
16 5 0.17
17 14 0.47
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
AATAAAGAAAAAAGATA
Found at i:1169441 original size:3 final size:3
Alignment explanation
Indices: 1169412--1169515 Score: 92
Period size: 3 Copynumber: 34.3 Consensus size: 3
1169402 GTATCATATA
* * *
1169412 AAT AA- AAT AAGT AAAT AGT AA- AAT AAT AAT AAT ACAT GTAT GAAC
1 AAT AAT AAT AA-T -AAT AAT AAT AAT AAT AAT AAT A-AT -AAT -AAT
1169457 AAT AA- AAT -AT AAGT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1169500 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
1169516 TGAAGGAATA
Statistics
Matches: 85, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
2 10 0.12
3 62 0.73
4 11 0.13
5 2 0.02
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1169478 original size:43 final size:47
Alignment explanation
Indices: 1169361--1169493 Score: 130
Period size: 43 Copynumber: 2.8 Consensus size: 47
1169351 AAATAAAATA
* *
1169361 AAATAAAATATTAAGAAATAAAATATATACATATATATAATGTATCATAT
1 AAATAAAATAGTAAGTAATAAAATA-ATA-ATA-ATATAATGTATCATAT
* * * *
1169411 AAATAAAATAAGTAAATAGTAAAATAATAATAATA-CATGTATGA-A-
1 AAATAAAAT-AGTAAGTAATAAAATAATAATAATATAATGTATCATAT
*
1169456 CAATAAAATA-TAAGTAATAAAATAATAATAATAATAAT
1 AAATAAAATAGTAAGTAATAAAATAATAATAAT-ATAAT
1169494 AATAATAATA
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
43 20 0.29
44 2 0.03
45 10 0.14
46 1 0.01
47 7 0.10
48 3 0.04
49 3 0.04
50 12 0.17
51 12 0.17
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (47 bp):
AAATAAAATAGTAAGTAATAAAATAATAATAATATAATGTATCATAT
Found at i:1171337 original size:32 final size:32
Alignment explanation
Indices: 1171294--1171374 Score: 119
Period size: 32 Copynumber: 2.5 Consensus size: 32
1171284 GTTGGGTATC
*
1171294 CTTCGTCGTGAAGTTGAAACCGCAGGTGGCC-
1 CTTCGTTGTGAAGTTGAAACCGCAGGTGGCCT
* *
1171325 CATTCGTTGTGAAGTTGAAATCGCGGGTGGCCT
1 C-TTCGTTGTGAAGTTGAAACCGCAGGTGGCCT
1171358 CTTCGTTGTGAAGTTGA
1 CTTCGTTGTGAAGTTGA
1171375 GCCTGAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.02
32 43 0.96
33 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.30
Consensus pattern (32 bp):
CTTCGTTGTGAAGTTGAAACCGCAGGTGGCCT
Found at i:1172801 original size:21 final size:20
Alignment explanation
Indices: 1172760--1172804 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1172750 CCTAAACGTT
*
1172760 TTTTCTTTTTTTGATTGTTC
1 TTTTCTTTTTTTCATTGTTC
* *
1172780 TTTTCATTTTTTTCTTTTTTC
1 TTTTC-TTTTTTTCATTGTTC
1172801 TTTT
1 TTTT
1172805 TTTAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.80
Consensus pattern (20 bp):
TTTTCTTTTTTTCATTGTTC
Found at i:1180180 original size:20 final size:20
Alignment explanation
Indices: 1180143--1180181 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1180133 AGATTGAGTG
* * *
1180143 GATTTTGATGTTGTTTGCAT
1 GATTTTAATGATGATTGCAT
1180163 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
1180182 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAT
Found at i:1180367 original size:21 final size:21
Alignment explanation
Indices: 1180341--1180380 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1180331 CAGAACCCCA
*
1180341 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1180362 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1180381 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1180409 original size:20 final size:21
Alignment explanation
Indices: 1180363--1180423 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
1180353 TTCCCCTGTG
1180363 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
1180386 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1180406 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1180424 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1189453 original size:21 final size:20
Alignment explanation
Indices: 1189400--1189446 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1189390 AAAACATGGA
*
1189400 AAATATAAAA-ATAAACATG
1 AAATATAAAATGTAAACATG
1189419 AAATATAAAATGTAAAGCATG
1 AAATATAAAATGTAAA-CATG
*
1189440 CAATATA
1 AAATATA
1189447 TGATGTATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.42
20 4 0.17
21 10 0.42
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.23
Consensus pattern (20 bp):
AAATATAAAATGTAAACATG
Found at i:1192795 original size:31 final size:31
Alignment explanation
Indices: 1192760--1192827 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1192750 AAATAAAAGG
* * *
1192760 AATAAA-AATAAAGACAAAATAGAATAAGATA
1 AATAAAGAAAAAAGA-AAAATAAAATAAGAAA
*
1192791 AATAAAGAAAAAAGATAAATAAAATAAGAAA
1 AATAAAGAAAAAAGAAAAATAAAATAAGAAA
1192822 AATAAA
1 AATAAA
1192828 TCAATCAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 25 0.78
32 7 0.22
ACGTcount: A:0.75, C:0.01, G:0.09, T:0.15
Consensus pattern (31 bp):
AATAAAGAAAAAAGAAAAATAAAATAAGAAA
Found at i:1192814 original size:13 final size:14
Alignment explanation
Indices: 1192782--1192827 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
1192772 GACAAAATAG
*
1192782 AATAAGATAA-ATA
1 AATAAAATAAGATA
*
1192795 AAGAAAA-AAGATA
1 AATAAAATAAGATA
*
1192808 AATAAAATAAGAAA
1 AATAAAATAAGATA
1192822 AATAAA
1 AATAAA
1192828 TCAATCAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 2 0.07
13 14 0.52
14 11 0.41
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (14 bp):
AATAAAATAAGATA
Found at i:1192815 original size:22 final size:23
Alignment explanation
Indices: 1192764--1192855 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 23
1192754 AAAAGGAATA
1192764 AAAATAAAGACAAAATAGAATAAGAT
1 AAAATAAAGA-AAAATA-AATAA-AT
*
1192790 -AAATAAAGAAAAA-AGATAAAT
1 AAAATAAAGAAAAATAAATAAAT
*
1192811 AAAAT-AAGAAAAATAAATCAAT
1 AAAATAAAGAAAAATAAATAAAT
*
1192833 -CAATAAAG-AAAATAAAATAAAT
1 AAAATAAAGAAAAAT-AAATAAAT
1192855 A
1 A
1192856 TACCAAAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
21 18 0.32
22 24 0.43
23 1 0.02
24 4 0.07
25 9 0.16
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (23 bp):
AAAATAAAGAAAAATAAATAAAT
Found at i:1192827 original size:35 final size:37
Alignment explanation
Indices: 1192775--1192852 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 37
1192765 AAATAAAGAC
*
1192775 AAAAT-AGAATAAGATAAAT-AAAGAAAAAAGATAAAT
1 AAAATAAGAATAAGATAAATCAAACAAAAAAGA-AAAT
* *
1192811 AAAATAAGAA-AA-ATAAATCAATCAATAAAGAAAAT
1 AAAATAAGAATAAGATAAATCAAACAAAAAAGAAAAT
1192846 AAAATAA
1 AAAATAA
1192853 ATATACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 17 0.46
36 16 0.43
37 4 0.11
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.17
Consensus pattern (37 bp):
AAAATAAGAATAAGATAAATCAAACAAAAAAGAAAAT
Found at i:1192854 original size:9 final size:9
Alignment explanation
Indices: 1192775--1192855 Score: 55
Period size: 9 Copynumber: 9.1 Consensus size: 9
1192765 AAATAAAGAC
1192775 AAAATAGAAT
1 AAAATA-AAT
*
1192785 AAGATAAAT
1 AAAATAAAT
1192794 AAAGA-AAA-
1 AAA-ATAAAT
*
1192802 AAGATAAAT
1 AAAATAAAT
1192811 AAAATAAGA-
1 AAAATAA-AT
1192820 AAAATAAAT
1 AAAATAAAT
* *
1192829 -CAATCAAT
1 AAAATAAAT
1192837 AAAGA-AAAT
1 AAA-ATAAAT
1192846 AAAATAAAT
1 AAAATAAAT
1192855 A
1 A
1192856 TACCAAAATG
Statistics
Matches: 55, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
7 1 0.02
8 13 0.24
9 33 0.60
10 8 0.15
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (9 bp):
AAAATAAAT
Found at i:1192993 original size:50 final size:44
Alignment explanation
Indices: 1192935--1193067 Score: 121
Period size: 43 Copynumber: 2.9 Consensus size: 44
1192925 ACTTGTAAAC
1192935 TAAA-AAAATATTAAGAAATAAAATATATACATATATATAATGTAT-CATA
1 TAAATAAAATA-TAAGAAATAAAATA-ATA-ATA-ATAT-ATGTATGC--A
*
1192984 TAAATAAAATAAGTAA-ATAGTAAAATAATAATAATATATGTATGCA
1 TAAATAAAAT-A-TAAGA-AATAAAATAATAATAATATATGTATGCA
*
1193030 -CAATAAAATATAAGAAATAAAATAATAATAATAATATG
1 TAAATAAAATATAAGAAATAAAATAATAATAAT-ATATG
1193068 AAGGAATAAC
Statistics
Matches: 74, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
43 19 0.26
44 7 0.09
45 8 0.11
46 1 0.01
47 6 0.08
48 5 0.07
49 7 0.09
50 9 0.12
51 12 0.16
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (44 bp):
TAAATAAAATATAAGAAATAAAATAATAATAATATATGTATGCA
Found at i:1194881 original size:240 final size:240
Alignment explanation
Indices: 1194458--1194936 Score: 922
Period size: 240 Copynumber: 2.0 Consensus size: 240
1194448 GCTTATGATC
1194458 GAATTAATAGAATGTATACGTAATGAGGACTAATTATATAATTGTATTAATTTTTTAACAGCCAC
1 GAATTAATAGAATGTATACGTAATGAGGACTAATTATATAATTGTATTAATTTTTTAACAGCCAC
*
1194523 ATCAACTCTTTTATTAGATGTTAATGGCTAATGGCTTGATCGCAACACTTAAATAGTTAAGTGAT
66 ATCAACTCTTCTATTAGATGTTAATGGCTAATGGCTTGATCGCAACACTTAAATAGTTAAGTGAT
*
1194588 TTATTTGACAAAACTAAAATATCAATGGTCAAAATGAAAAAGGGACAATAGTTAAGTGGTCAAAG
131 TTATTTGACAAAACTAAAAGATCAATGGTCAAAATGAAAAAGGGACAATAGTTAAGTGGTCAAAG
1194653 ATAAAGTTTACCCATTTAAATAAGACTTTTAAATTAATTTTTTTT
196 ATAAAGTTTACCCATTTAAATAAGACTTTTAAATTAATTTTTTTT
1194698 GAATTAATAGAATGTATACGTAATGAGGACTAATTATATAATTGTATTAATTTTTTAACAGCCAC
1 GAATTAATAGAATGTATACGTAATGAGGACTAATTATATAATTGTATTAATTTTTTAACAGCCAC
*
1194763 ATCAACTCTTCTATTAGATGTTAATGGCTAATGGCTTGATTGCAACACTTAAATAGTTAAGTGAT
66 ATCAACTCTTCTATTAGATGTTAATGGCTAATGGCTTGATCGCAACACTTAAATAGTTAAGTGAT
*
1194828 TTATTTGACAAAACTAAAAGATCAATGGTCAAAATGAAAAAGGGACTATAGTTAAGTGGTCAAAG
131 TTATTTGACAAAACTAAAAGATCAATGGTCAAAATGAAAAAGGGACAATAGTTAAGTGGTCAAAG
1194893 ATAAAGTTTACCCATTTAAATAAGACTTTTAAATTAATTTTTTT
196 ATAAAGTTTACCCATTTAAATAAGACTTTTAAATTAATTTTTTT
1194937 GAAGGAAATA
Statistics
Matches: 235, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
240 235 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (240 bp):
GAATTAATAGAATGTATACGTAATGAGGACTAATTATATAATTGTATTAATTTTTTAACAGCCAC
ATCAACTCTTCTATTAGATGTTAATGGCTAATGGCTTGATCGCAACACTTAAATAGTTAAGTGAT
TTATTTGACAAAACTAAAAGATCAATGGTCAAAATGAAAAAGGGACAATAGTTAAGTGGTCAAAG
ATAAAGTTTACCCATTTAAATAAGACTTTTAAATTAATTTTTTTT
Found at i:1196082 original size:35 final size:35
Alignment explanation
Indices: 1196029--1196096 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
1196019 AATAAGATGG
* * *
1196029 AAAATATATAAAAATAAATAAATAAATAAATGAGC
1 AAAATATACAAAAATAAATAAACAAACAAATGAGC
1196064 AAAATA-ACAAAAAGTAAATAAACAAACAAATGA
1 AAAATATACAAAAA-TAAATAAACAAACAAATGA
1196097 AAAAAGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 6 0.21
35 23 0.79
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (35 bp):
AAAATATACAAAAATAAATAAACAAACAAATGAGC
Found at i:1196385 original size:3 final size:3
Alignment explanation
Indices: 1196377--1196402 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1196367 ATATATACAT
1196377 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1196403 GCATATAACA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1199811 original size:15 final size:16
Alignment explanation
Indices: 1199787--1199819 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1199777 TGAACCCACC
*
1199787 TTATT-TTTTTTTCTT
1 TTATTATTTTTCTCTT
1199802 TTATTATTTTTCTCTT
1 TTATTATTTTTCTCTT
1199818 TT
1 TT
1199820 TTCCCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (16 bp):
TTATTATTTTTCTCTT
Found at i:1206739 original size:21 final size:21
Alignment explanation
Indices: 1206713--1206757 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1206703 GACTAAGGAT
*
1206713 TCCTGGCTTTTCTTGATGGAC
1 TCCTGGCTTTTCTTGATGAAC
1206734 TCCTGGCTTTTCTTGATGAAC
1 TCCTGGCTTTTCTTGATGAAC
1206755 TCC
1 TCC
1206758 ATGGTACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.11, C:0.27, G:0.20, T:0.42
Consensus pattern (21 bp):
TCCTGGCTTTTCTTGATGAAC
Found at i:1210593 original size:3 final size:3
Alignment explanation
Indices: 1210585--1210672 Score: 155
Period size: 3 Copynumber: 30.3 Consensus size: 3
1210575 TATACATATC
1210585 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1210633 ATA ATA ATA AT- ATA ATA AT- ATA ATA AT- ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1210673 ATAGAAAGCG
Statistics
Matches: 82, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
2 6 0.07
3 76 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1218168 original size:99 final size:100
Alignment explanation
Indices: 1218037--1218237 Score: 289
Period size: 102 Copynumber: 2.0 Consensus size: 100
1218027 TAAGGCTTTT
* *
1218037 TAGGTTAAGGCCACTTTTCTTCCTTCTGTCCTTATAGAATC-CC-GTAGAGTAATTAAGGAGTGT
1 TAGGTTAAGGCCACTTTTCTTCCTTATGTCCTTATAGAATCTCCACTAGAGTAATTAAGGAGTGT
* * *
1218100 TGCTAGCATATTTCATATAAGAATCAATTCATTTG
66 TGCTAACATATGTCATATAAGAACCAATTCATTTG
* * *
1218135 TAGGTTAAAGGCTACTTTTCTTCCTTATGTCCTTTTAGAATCTCCATCTCGAGTAATTAAGGAGT
1 TAGGTT-AAGGCCACTTTTCTTCCTTATGTCCTTATAGAATCTCCA-CTAGAGTAATTAAGGAGT
*
1218200 GTTGGTAACATATGTCATATAAGAACCAATTCATTTG
64 GTTGCTAACATATGTCATATAAGAACCAATTCATTTG
1218237 T
1 T
1218238 TTTGTCCTGC
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
98 6 0.07
99 32 0.36
100 2 0.02
102 50 0.56
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (100 bp):
TAGGTTAAGGCCACTTTTCTTCCTTATGTCCTTATAGAATCTCCACTAGAGTAATTAAGGAGTGT
TGCTAACATATGTCATATAAGAACCAATTCATTTG
Found at i:1227213 original size:2 final size:2
Alignment explanation
Indices: 1227206--1227231 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1227196 TTGATAAGAA
1227206 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1227232 TTGTTTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1227817 original size:21 final size:21
Alignment explanation
Indices: 1227800--1227854 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
1227790 TAACCATTTC
*
1227800 AGATGGCATCGCAGCCATATA
1 AGATGGCACCGCAGCCATATA
1227821 AGATGGCACCGCAGCCATATA
1 AGATGGCACCGCAGCCATATA
1227842 AGATGGCACCGCA
1 AGATGGCACCGCA
1227855 TCTATTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.15
Consensus pattern (21 bp):
AGATGGCACCGCAGCCATATA
Found at i:1228210 original size:3 final size:3
Alignment explanation
Indices: 1228204--1228238 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1228194 TGACGACGAC
*
1228204 GAT GAT GAT GGT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1228239 GAGTGGAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.37, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:1230563 original size:19 final size:17
Alignment explanation
Indices: 1230541--1230585 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
1230531 TGAAACAAAT
1230541 ATAAAAAAAATGAAATTGA
1 ATAAAAAAAAT-AAA-TGA
1230560 ATAAAATAAAATAAATGA
1 ATAAAA-AAAATAAATGA
*
1230578 AGAAAAAA
1 ATAAAAAA
1230586 TATATATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.08
18 8 0.33
19 9 0.38
20 5 0.21
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (17 bp):
ATAAAAAAAATAAATGA
Found at i:1230705 original size:26 final size:26
Alignment explanation
Indices: 1230686--1230746 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
1230676 AAATAAATAG
1230686 TATAAATAAAATATAAAAATATAAAAA
1 TATAAA-AAAATATAAAAATATAAAAA
1230713 TATAAAAAAATATAAAAATATAAAAA
1 TATAAAAAAATATAAAAATATAAAAA
1230739 TATAAAAA
1 TATAAAAA
1230747 TGTATGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 28 0.82
27 6 0.18
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (26 bp):
TATAAAAAAATATAAAAATATAAAAA
Found at i:1230706 original size:8 final size:8
Alignment explanation
Indices: 1230693--1230747 Score: 92
Period size: 8 Copynumber: 6.6 Consensus size: 8
1230683 TAGTATAAAT
1230693 AAAATATA
1 AAAATATA
1230701 AAAATATA
1 AAAATATA
1230709 AAAATATAAA
1 AAAATAT--A
1230719 AAAATATA
1 AAAATATA
1230727 AAAATATA
1 AAAATATA
1230735 AAAATATA
1 AAAATATA
1230743 AAAAT
1 AAAAT
1230748 GTATGTATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
8 37 0.82
10 8 0.18
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATATA
Found at i:1230932 original size:17 final size:18
Alignment explanation
Indices: 1230910--1230943 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1230900 TATAGTAAAA
1230910 AAACATAG-TAAATAATT
1 AAACATAGATAAATAATT
1230927 AAACATAGATAAATAAT
1 AAACATAGATAAATAAT
1230944 AATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (18 bp):
AAACATAGATAAATAATT
Found at i:1231558 original size:37 final size:37
Alignment explanation
Indices: 1231465--1231566 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
1231455 ATGTTTGTGG
* * ** * * *
1231465 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
*
1231502 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
1231539 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
1231567 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
Found at i:1232503 original size:106 final size:106
Alignment explanation
Indices: 1232318--1232941 Score: 876
Period size: 106 Copynumber: 5.9 Consensus size: 106
1232308 AGCATTGTTC
* * * * *
1232318 CGAGTCCAATATCATCCG-TCGTGAAGTTAAAATTGGCT-CTAGAATCGGGAAATTGTTTGTTGA
1 CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCCGA-AATTGGGAAATTGTTTGTTGA
* * * * *
1232381 CGACCAGCCGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * *
1232424 CGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGACTCCGAAATTAGGAAATTATTTGTTGATA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
*
1232489 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
1232530 CGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
*
1232595 ACCAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * ** * * * * *
1232636 GGAGTCCAATACCCTTCATTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGATA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
*
1232701 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
1232742 -GAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGAC
1 CG-AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGAC
* *
1232806 AACCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCATTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
1232848 GGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1232913 ACCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAA
1232942 ATTGGCTCTG
Statistics
Matches: 466, Mismatches: 48, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
105 1 0.00
106 461 0.99
107 4 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:1232946 original size:63 final size:63
Alignment explanation
Indices: 1232868--1233004 Score: 247
Period size: 63 Copynumber: 2.2 Consensus size: 63
1232858 ATCTTTCGCT
*
1232868 GTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTC
1 GTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTAACAACCAGCGGTCCCTTCGTC
* *
1232931 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTAACAACCAGCGGTCCCTTCGTC
1 GTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTAACAACCAGCGGTCCCTTCGTC
1232994 GTGAAGTTGAA
1 GTGAAGTTGAA
1233005 CTTGCGTTGT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (63 bp):
GTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTAACAACCAGCGGTCCCTTCGTC
Found at i:1232980 original size:169 final size:169
Alignment explanation
Indices: 1232754--1233110 Score: 590
Period size: 169 Copynumber: 2.1 Consensus size: 169
1232744 AGTCCAATAT
*
1232754 CCTTCG-CTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAACCAGCGGTCC
1 CCTTCGTC-GTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTAACAACCAGCGGTCC
*
1232818 CTTCTTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTG
65 CTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTG
* *
1232883 GCTCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTC
130 GCTCCGAAATTGAGAAACTGTTTGTTGACAACCAGCGGTC
* * *
1232923 CCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTAACAACCAGCGGTCCC
1 CCTTCGTCGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTAACAACCAGCGGTCCC
* * *
1232988 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTTTGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGG
* *
1233053 CTCTGAAATTGAGAAGCTGTTTGTTGACAACCAGCGGTC
131 CTCCGAAATTGAGAAACTGTTTGTTGACAACCAGCGGTC
1233092 CCTTCGTCGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
1233111 CTTGCGTTGT
Statistics
Matches: 175, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
169 174 0.99
170 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (169 bp):
CCTTCGTCGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTAACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGG
CTCCGAAATTGAGAAACTGTTTGTTGACAACCAGCGGTC
Found at i:1232992 original size:275 final size:275
Alignment explanation
Indices: 1232647--1233216 Score: 906
Period size: 275 Copynumber: 2.1 Consensus size: 275
1232637 GAGTCCAATA
* * * * *
1232647 CCCTTCATTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGATAACCAGCGGTCC
1 CCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTAACAACCAGCGGTCC
1232712 CTTCGTCGTGAAGTTGAACTTGCATTGTCTGAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
66 CTTCGTCGTGAAGTTGAACTTGCATTGTCTGAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* * *
1232777 GCTCCGAAATTGGGAAATTATTTGTTGACAACCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCA
131 GCTCCGAAATTGAGAAACTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCA
* ** *
1232842 TTGTCTGGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTG
196 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTCACTCCGAAATTGGGAAATTGTTTA
*
1232907 TTGACAACCAGCGGT
261 TTGACAACCAGCGAT
*
1232922 CCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTAACAACCAGCGGTCC
1 CCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTAACAACCAGCGGTCC
* * * * *
1232987 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTTTGAAGTTGAAATTG
66 CTTCGTCGTGAAGTTGAACTTGCATTGTCTGAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* * * *
1233052 GCTCTGAAATTGAGAAGCTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
131 GCTCCGAAATTGAGAAACTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCA
* *
1233117 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTCACTCTGAAATTGGGAAGTTGTTTA
196 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTCACTCCGAAATTGGGAAATTGTTTA
1233182 TTGACAACCAGCGAT
261 TTGACAACCAGCGAT
*
1233197 CCCTTCGTCATGAAGTTGAA
1 CCCTTCGTCGTGAAGTTGAA
1233217 CTTGCGTTGT
Statistics
Matches: 269, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
275 269 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (275 bp):
CCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTAACAACCAGCGGTCC
CTTCGTCGTGAAGTTGAACTTGCATTGTCTGAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
GCTCCGAAATTGAGAAACTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCA
TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTCACTCCGAAATTGGGAAATTGTTTA
TTGACAACCAGCGAT
Found at i:1233044 original size:381 final size:373
Alignment explanation
Indices: 1232550--1233314 Score: 1224
Period size: 381 Copynumber: 2.0 Consensus size: 373
1232540 ATCCTTCACT
*
1232550 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCATTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTAACAACCAGCGGTCCATTCGTCGT
1232615 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATACCCTTCATTGTGAAGTTAAAATTGGCTCTGAAA
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATACCCTTCATTGTGAAGTTAAAATTGGCTCTGAAA
* *
1232680 TTGAGAAGTTGTTTGTTGATAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGAA
131 TTGAGAAGCTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGAA
** *
1232745 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAACC
196 GTCCAATATCCTTCGCTGTGAAGTTGAAATTCACTCCGAAATTGGGAAATTATTTATTGACAACC
* * * * *
1232810 AGCGGTCCCTTCTTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCTTTCGCTGTGAAGT
261 AGCGATCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCACTGTGAAGT
*
1232875 TGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTC
326 TGAAATTGGCT-C-----T--GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTC
*
1232931 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTAACAACCAGCGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTAACAACCAGCGGTCCATTCGTCGT
* * * * *
1232996 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTTTGAAGTTGAAATTGGCTCTGAAA
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATACCCTTCATTGTGAAGTTAAAATTGGCTCTGAAA
* *
1233061 TTGAGAAGCTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
131 TTGAGAAGCTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGAA
* * *
1233126 GTCCAATATCCTTCGCTGTGAAGTTGAAATTCACTCTGAAATTGGGAAGTTGTTTATTGACAACC
196 GTCCAATATCCTTCGCTGTGAAGTTGAAATTCACTCCGAAATTGGGAAATTATTTATTGACAACC
* *
1233191 AGCGATCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCACTGTGAAGT
261 AGCGATCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCACTGTGAAGT
*
1233256 TGAAATTGGCTCTGAAATTGTTTATTGACAACCAGTGGTCCCTTCGTC
326 TGAAATTGGCTCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTC
1233304 GTGAAGTTGAA
1 GTGAAGTTGAA
1233315 CTTGAGTTGT
Statistics
Matches: 358, Mismatches: 26, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
373 44 0.12
375 1 0.00
380 1 0.00
381 312 0.87
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (373 bp):
GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTAACAACCAGCGGTCCATTCGTCGT
GAAGTTGAACTTGCGTTGTCTGGAGTCCAATACCCTTCATTGTGAAGTTAAAATTGGCTCTGAAA
TTGAGAAGCTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGAA
GTCCAATATCCTTCGCTGTGAAGTTGAAATTCACTCCGAAATTGGGAAATTATTTATTGACAACC
AGCGATCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCACTGTGAAGT
TGAAATTGGCTCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTC
Found at i:1233110 original size:106 final size:106
Alignment explanation
Indices: 1232923--1233574 Score: 903
Period size: 106 Copynumber: 6.2 Consensus size: 106
1232913 ACCAGCGGTC
*
1232923 CCTTCG-TCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTAACAACCAGCGGTCC
1 CCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
1232987 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * *
1233029 CTTTCGTTTTGAAGTTGAAATTGGCTCTGAAATTGAGAAGCTGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
1233094 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
** * *
1233135 CCTTCGCTGTGAAGTTGAAATTCACTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGATCCC
1 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
* *
1233200 TTCGTCATGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
1233241 CCTTCACTGTGAAGTTGAAATTGGCTCTG--A-----AA-TTGTTTATTGACAACCAGTGGTCCC
1 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
*
1233298 TTCGTCGTGAAGTTGAACTTGAGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
1233339 CTTTC-ATCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
1 CCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
** *
1233403 CTTTTTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATAT
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* **
1233445 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAACCAGCCATCCC
1 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
* * *
1233510 TTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGACACAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT--C-CAATAT
* *
1233554 CCTCCG-TCGTGGAGTTGAAAT
1 CCTTCGCT-GTGAAGTTGAAAT
1233575 CGCGGATAGC
Statistics
Matches: 488, Mismatches: 43, Indels: 27
0.87 0.08 0.05
Matches are distributed among these distances:
97 1 0.00
98 86 0.18
99 2 0.00
100 1 0.00
104 1 0.00
105 2 0.00
106 368 0.75
107 2 0.00
108 2 0.00
109 23 0.05
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:1233392 original size:204 final size:204
Alignment explanation
Indices: 1232923--1233574 Score: 856
Period size: 204 Copynumber: 3.1 Consensus size: 204
1232913 ACCAGCGGTC
*
1232923 CCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTAACAACCAGCGGTCCC
1 CCTTC-TCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
* * *
1232988 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTTTGAAGTTGAAATTGG
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
* *
1233053 CTCTGAAATTGAGAAGCTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
130 CTC------TGA-AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGT
1233118 TGTCTGGAGTCCAATAT
188 TGTCTGGAGTCCAATAT
* ** * *
1233135 CCTTCGCTGTGAAGTTGAAATTCACTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGATCCC
1 CCTTCTC-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
* * *
1233200 TTCGTCATGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGG
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
* *
1233265 CTCTGAAA-TTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTGG
130 CTCTGAAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTGG
1233329 AGTCCAATAT
195 AGTCCAATAT
* *
1233339 CTTTCATCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
1 CCTTC-TCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCC
** *
1233404 TTTTTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
** * *
1233469 CTCTGAATTTGGGAAGTTGTTTGTTGACAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGT
130 CTCTG-A------AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGT
*
1233534 TGTCTCGAGTGACACAATAT
188 TGTCTGGAGT--C-CAATAT
* *
1233554 CCTCCGTCGTGGAGTTGAAAT
1 CCTTC-TCGTGAAGTTGAAAT
1233575 CGCGGATAGC
Statistics
Matches: 387, Mismatches: 40, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
204 182 0.47
205 4 0.01
206 3 0.01
211 3 0.01
212 171 0.44
214 1 0.00
215 23 0.06
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (204 bp):
CCTTCTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCT
TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC
TCTGAAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTGGA
GTCCAATAT
Found at i:1233421 original size:310 final size:310
Alignment explanation
Indices: 1232963--1233543 Score: 982
Period size: 310 Copynumber: 1.9 Consensus size: 310
1232953 AATTGGGAAG
* *
1232963 TTGTTTGTTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTGGAGTCCAATA
* **
1233028 TCTTTCGTTTTGAAGTTGAAATTGGCTCTGAAATTGAGAAGCTGTTTGTTGACAACCAGCGGTCC
66 TCTTTCATCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGCTGTTTGTTGACAACCAGCGGTCC
1233093 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTC
131 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTC
*
1233158 ACTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGATCCCTTCGTCATGAAGTTGAACTTGCG
196 ACTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCCATCCCTTCGTCATGAAGTTGAACTTGCG
*
1233223 TTGTCTTGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAA
261 TTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAA
* *
1233273 TTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTGGAGTCCAATA
1 TTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTGGAGTCCAATA
*
1233338 TCTTTCATCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
66 TCTTTCATCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGCTGTTTGTTGACAACCAGCGGTCC
** * *
1233403 CTTTTTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
131 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTC
* * * ** *
1233468 GCTCTGAATTTGGGAAGTTGTTTGTTGACAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTG
196 ACTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCCATCCCTTCGTCATGAAGTTGAACTTGCG
1233533 TTGTCTCGAGT
261 TTGTCTCGAGT
1233544 GACACAATAT
Statistics
Matches: 251, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
310 251 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (310 bp):
TTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTGGAGTCCAATA
TCTTTCATCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGCTGTTTGTTGACAACCAGCGGTCC
CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTC
ACTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCCATCCCTTCGTCATGAAGTTGAACTTGCG
TTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAA
Found at i:1234530 original size:22 final size:22
Alignment explanation
Indices: 1234505--1234559 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1234495 TTGTGTTTGG
1234505 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1234527 TCAAAGGTTTGTCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1234549 TCAAAGGTTTG
1 TCAAAGGTTTG
1234560 ATGGGGTAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1235157 original size:13 final size:13
Alignment explanation
Indices: 1235141--1235191 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
1235131 TTTTTGTCCC
*
1235141 TTTTTCTTTTTGA
1 TTTTTCTTTTTGT
* *
1235154 TTTTTGTTCTTTCT
1 TTTTTCTT-TTTGT
1235168 TTTTTC-TTTTGT
1 TTTTTCTTTTTGT
1235180 TTTCTTCTTTTT
1 TTT-TTCTTTTT
1235192 TGCTTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
12 7 0.23
13 11 0.37
14 12 0.40
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTTGT
Found at i:1235176 original size:11 final size:10
Alignment explanation
Indices: 1235154--1235201 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
1235144 TTCTTTTTGA
*
1235154 TTTTTGTTCT
1 TTTTTTTTCT
1235164 TTCTTTTTTCT
1 TT-TTTTTTCT
*
1235175 TTTGTTTTCT
1 TTTTTTTTCT
*
1235185 TCTTTTTTGCT
1 T-TTTTTTTCT
1235196 TTTTTT
1 TTTTTT
1235202 CCCTTTTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 15 0.47
11 17 0.53
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:1235184 original size:21 final size:20
Alignment explanation
Indices: 1235143--1235199 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1235133 TTTGTCCCTT
**
1235143 TTTCTTTTTGATTTTTGTTC
1 TTTCTTTTTTCTTTTTGTTC
*
1235163 TTTCTTTTTTC-TTTTGTTT
1 TTTCTTTTTTCTTTTTGTTC
1235182 TCTTCTTTTTTGCTTTTT
1 T-TTCTTTTTT-CTTTTT
1235200 TTCCCTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 8 0.26
20 18 0.58
21 1 0.03
22 4 0.13
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.79
Consensus pattern (20 bp):
TTTCTTTTTTCTTTTTGTTC
Found at i:1238622 original size:19 final size:19
Alignment explanation
Indices: 1238589--1238625 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1238579 TGCAGATGAT
1238589 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
1238608 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
1238626 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:1239812 original size:19 final size:17
Alignment explanation
Indices: 1239790--1239834 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
1239780 TGAAACAAAT
1239790 ATAAAAAAAATGAAATTGA
1 ATAAAAAAAAT-AAA-TGA
1239809 ATAAAATAAAATAAATGA
1 ATAAAA-AAAATAAATGA
*
1239827 AGAAAAAA
1 ATAAAAAA
1239835 TATATATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.08
18 8 0.33
19 9 0.38
20 5 0.21
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (17 bp):
ATAAAAAAAATAAATGA
Found at i:1239941 original size:22 final size:20
Alignment explanation
Indices: 1239916--1239974 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 20
1239906 AACTAAAAAC
1239916 ATAATGAAAATA-AATAAATAGT
1 ATAAT-AAAATATAA-AAATA-T
1239938 ATAAATAAAATATAAAAATAT
1 AT-AATAAAATATAAAAATAT
1239959 AT-A-AAAATATAAAAAT
1 ATAATAAAATATAAAAAT
1239975 GTATTTATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
18 13 0.37
19 1 0.03
21 3 0.09
22 13 0.37
23 5 0.14
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (20 bp):
ATAATAAAATATAAAAATAT
Found at i:1239962 original size:10 final size:10
Alignment explanation
Indices: 1239931--1239973 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
1239921 GAAAATAAAT
1239931 AAATAGTATAA
1 AAATA-TATAA
*
1239942 ATAAAATATAA
1 A-AATATATAA
1239953 AAATATATAA
1 AAATATATAA
1239963 AAATATA-AA
1 AAATATATAA
1239972 AA
1 AA
1239974 TGTATTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 4 0.14
10 15 0.52
11 7 0.24
12 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (10 bp):
AAATATATAA
Found at i:1256474 original size:25 final size:26
Alignment explanation
Indices: 1256423--1256484 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 26
1256413 AACTGAAATT
* *
1256423 AAAT-AAATAAAAAGTAAATGACATA
1 AAATAAAATATAAAGTAAAGGACATA
*
1256448 AATTAAAATATAAAGTAAAGGAC-TA
1 AAATAAAATATAAAGTAAAGGACATA
1256473 AAATAAAATATA
1 AAATAAAATATA
1256485 TCAGAAGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 16 0.50
26 16 0.50
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.23
Consensus pattern (26 bp):
AAATAAAATATAAAGTAAAGGACATA
Found at i:1258523 original size:123 final size:122
Alignment explanation
Indices: 1258101--1258826 Score: 876
Period size: 123 Copynumber: 5.9 Consensus size: 122
1258091 GGTGTTGATT
* * * * **
1258101 TATCTCCTTCTGTGATAGAATCAAGCAGTATGTTGAACAAGTTCTTCTCATTATGAACTTCTT-T
1 TATCTCCTTCTGCGATAGAATCAAGCA-AAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT
* * * * *
1258165 T--TCTTCGGATGAGTTCTTCTCATTATGAACTCTTTCATTGAAAATG-T--TGAT-C-C
65 TCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC--TGGAAATGTTGATGATGCTC
** * * * * ** *
1258218 -ATCTCCTTCTGTAATGGAATCTAGTAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTAT
1 TATCTCCTTCTGCGATAGAATCAAGCAAAAG-TTGAATAAGTTCTTCAGATTATGAACTTCTTCT
* * * * *
1258282 TCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGATGTTTGTTC
65 TCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTGATG-ATGCTC
* *
1258341 TATCTCCTTCTGCGATAGAGTCAAACAAAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT
1 TATCTCCTTCTGCGATAGAATCAAGC-AAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT
* * * *
1258406 TCCTCTTCATATGAGTTCTTCTTATTATGAACTCTTTCTGGAAATGTTGATGATGTTC
65 TCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTGATGATGCTC
* * *
1258464 TATCTCCTTCTGCGATAGAGTCGAGCAAAAGTTTGAATAAGTTCTTCAGATTATGAACTTTTTTC
1 TATCTCCTTCTGCGATAGAATCAAGCAAAAG-TTGAATAAGTTCTTCAGATTATGAAC-TTCTTC
** * *
1258529 TTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTACAAATGTTGATGTTACTC
64 TTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTGATGATGCTC
* * *
1258588 TATCTCCTTCTACGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT
1 TATCTCCTTCTGCGATAGAATCAAGCAAAA-GTTGAATAAGTTCTTCAGATTATGAACTTCTTCT
* *
1258653 TTCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTGATGCTGCTC
65 TCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTGATGATGCTC
* *
1258711 TATCTCCTTATGTGATAGAATCAAGCAAAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT
1 TATCTCCTTCTGCGATAGAATCAAGC-AAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT
* *
1258776 TCATCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAAAGTTGAT
65 TCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTGAT
1258827 CCCTCGAGTG
Statistics
Matches: 540, Mismatches: 53, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
115 2 0.00
116 53 0.10
117 9 0.02
118 1 0.00
119 33 0.06
120 2 0.00
121 1 0.00
122 5 0.01
123 218 0.40
124 210 0.39
125 6 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (122 bp):
TATCTCCTTCTGCGATAGAATCAAGCAAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTT
CCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTGATGATGCTC
Found at i:1258597 original size:247 final size:244
Alignment explanation
Indices: 1258101--1258814 Score: 913
Period size: 247 Copynumber: 2.9 Consensus size: 244
1258091 GGTGTTGATT
* * ** * * **
1258101 TATCTCCTTCTGTGATAGAATCAAGCAGTATGTTGAACAAGTTCTTCTCATTATGAACTTCTT-T
1 TATCTCCTTCTGCGATAGAGTCAAGCAAAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT
* * * *
1258165 T-TCTTCGGATGAGTTCTTCTCATTATGAACTCTTTCATTGAAAATG-T--TGA--TCCATCTCC
66 TCTCTTCAGATGAGTTCTTCTTATTATGAACTCTTTC--TGGAAATGTTGATGATGTCTATCTCC
* * * * * ** * *
1258224 TTCTGTAATGGAATCTAGTAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTATTCTTCTT
129 TTCTGTGATAGAATCAAGCAAAAG-TTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCATCTT
* * ** **
1258289 CAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGATGTTTGTTC
193 CAGATGAGTTCTTCTTATTACGAACTCCTTCTACAAATGTTGATGTTTACTC
*
1258341 TATCTCCTTCTGCGATAGAGTCAAACAAAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT
1 TATCTCCTTCTGCGATAGAGTCAAGCAAAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT
*
1258406 TCCTCTTCATATGAGTTCTTCTTATTATGAACTCTTTCTGGAAATGTTGATGATGTTCTATCTCC
66 T-CTCTTCAGATGAGTTCTTCTTATTATGAACTCTTTCTGGAAATGTTGATGATG-TCTATCTCC
* * * * *
1258471 TTCTGCGATAGAGTCGAGCAAAAGTTTGAATAAGTTCTTCAGATTATGAACTTTTTTCTTCCTCT
129 TTCTGTGATAGAATCAAGCAAAAG-TTGAATAAGTTCTTCAGATTATGAAC-TTCTTCTTCATCT
1258536 TCAGATGAGTTCTTCTTATTACGAACTCCTTCTACAAATGTTGATG-TTACTC
192 TCAGATGAGTTCTTCTTATTACGAACTCCTTCTACAAATGTTGATGTTTACTC
* * *
1258588 TATCTCCTTCTACGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT
1 TATCTCCTTCTGCGATAGAGTCAAGCAAAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTC-
* * *
1258653 TTCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTGATGCTGCTCTATCTCC
65 TTCTCTTCAGATGAGTTCTTCTTATTATGAACTCTTTCTGGAAATGTTGATGATG-TCTATCTCC
*
1258718 TTATGTGATAGAATCAAGCAAAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCATCTT
129 TTCTGTGATAGAATCAAGC-AAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCATCTT
1258783 CAGATGAGTTCTTCTTATTACGAACTCCTTCT
193 CAGATGAGTTCTTCTTATTACGAACTCCTTCT
1258815 GGAAAAGTTG
Statistics
Matches: 414, Mismatches: 48, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
240 54 0.13
241 9 0.02
242 1 0.00
243 32 0.08
244 3 0.01
246 44 0.11
247 212 0.51
248 59 0.14
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (244 bp):
TATCTCCTTCTGCGATAGAGTCAAGCAAAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCT
TCTCTTCAGATGAGTTCTTCTTATTATGAACTCTTTCTGGAAATGTTGATGATGTCTATCTCCTT
CTGTGATAGAATCAAGCAAAAGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCATCTTCAG
ATGAGTTCTTCTTATTACGAACTCCTTCTACAAATGTTGATGTTTACTC
Found at i:1261555 original size:14 final size:14
Alignment explanation
Indices: 1261536--1261574 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1261526 TCTTATTTTT
1261536 TCTTTTCTTTTTCA
1 TCTTTTCTTTTTCA
*
1261550 TCTTTT-TTTTTCT
1 TCTTTTCTTTTTCA
*
1261563 TTTTTTCTTTTT
1 TCTTTTCTTTTT
1261575 TTCTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (14 bp):
TCTTTTCTTTTTCA
Found at i:1261565 original size:8 final size:8
Alignment explanation
Indices: 1261516--1261586 Score: 72
Period size: 8 Copynumber: 8.6 Consensus size: 8
1261506 CTTGATTCAA
1261516 TTTCTTTT
1 TTTCTTTT
* *
1261524 CTTCTTAT
1 TTTCTTTT
*
1261532 TTT-TTCT
1 TTTCTTTT
1261539 TTTCTTTT
1 TTTCTTTT
*
1261547 TCATCTTTTTT
1 T--T-TCTTTT
1261558 TTTCTTTT
1 TTTCTTTT
1261566 TTTCTTTT
1 TTTCTTTT
1261574 TTTCTTTT
1 TTTCTTTT
1261582 TTTCT
1 TTTCT
1261587 GATGAATGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
7 6 0.12
8 38 0.73
9 1 0.02
10 1 0.02
11 6 0.12
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTCTTTT
Found at i:1261581 original size:24 final size:24
Alignment explanation
Indices: 1261516--1261586 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 24
1261506 CTTGATTCAA
* *
1261516 TTTCTTTTCTTCTTATTTT-TTCT
1 TTTCTTTTTTTCTTTTTTTCTTCT
* *
1261539 TTTCTTTTTCATCTTTTTTTTTCTTTT
1 TTTCTTTTT--T-TCTTTTTTTCTTCT
1261566 TTTCTTTTTTTCTTTTTTTCT
1 TTTCTTTTTTTCTTTTTTTCT
1261587 GATGAATGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 8 0.21
24 10 0.26
25 2 0.05
26 7 0.18
27 12 0.31
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTCTTTTTTTCTTTTTTTCTTCT
Found at i:1266406 original size:25 final size:26
Alignment explanation
Indices: 1266355--1266416 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
1266345 AACTGAAATT
*
1266355 AAAT-AAATAAAAAGTAAATGACATA
1 AAATAAAATATAAAGTAAATGACATA
*
1266380 AAGTAAAATATAAAGTAAATGAC-TA
1 AAATAAAATATAAAGTAAATGACATA
1266405 AAATAAAATATA
1 AAATAAAATATA
1266417 TCAGAGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 16 0.48
26 17 0.52
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.23
Consensus pattern (26 bp):
AAATAAAATATAAAGTAAATGACATA
Found at i:1266489 original size:45 final size:45
Alignment explanation
Indices: 1266396--1266489 Score: 102
Period size: 45 Copynumber: 2.1 Consensus size: 45
1266386 AATATAAAGT
* * * *
1266396 AAATGACTAAAATAAAATATATCAGAGGATTAAAAGATAGAATTA
1 AAATGACTAAAATAAAATATAGCAGAGGATCAAAAGAAAGAATAA
* *
1266441 AAATGACTAAAATATAATA-AGCATG-GAGATCAAAAGAAATAATAA
1 AAATGACTAAAATAAAATATAGCA-GAG-GATCAAAAGAAAGAATAA
1266486 AAAT
1 AAAT
1266490 AACAGTGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
44 4 0.10
45 37 0.90
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (45 bp):
AAATGACTAAAATAAAATATAGCAGAGGATCAAAAGAAAGAATAA
Found at i:1269844 original size:18 final size:18
Alignment explanation
Indices: 1269818--1269857 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1269808 AATATACATC
*
1269818 TTAATTTAAATTCAAATA
1 TTAAATTAAATTCAAATA
*
1269836 TTAAATTAAATTCACATA
1 TTAAATTAAATTCAAATA
1269854 TTAA
1 TTAA
1269858 TTTTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAATTAAATTCAAATA
Found at i:1270055 original size:29 final size:28
Alignment explanation
Indices: 1269992--1270072 Score: 81
Period size: 30 Copynumber: 2.8 Consensus size: 28
1269982 ACTCAACTTT
* *
1269992 AAAATATATTTTGTTTGTATCTTAAATTAT
1 AAAATATATTTTATTT-TATC-TAAATTAA
*
1270022 TAAATATATTTTATTTTATCTAAATTCAA
1 AAAATATATTTTATTTTATCTAAATT-AA
* *
1270051 AAAATATGTGTTATTCTTATCT
1 AAAATATATTTTATT-TTATCT
1270073 TTATTTTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
28 6 0.14
29 17 0.40
30 20 0.47
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (28 bp):
AAAATATATTTTATTTTATCTAAATTAA
Found at i:1270089 original size:19 final size:19
Alignment explanation
Indices: 1270061--1270097 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1270051 AAAATATGTG
*
1270061 TTATTCTTATCTTTATTTT
1 TTATTCTTATCTTAATTTT
*
1270080 TTATTTTTATCTTAATTT
1 TTATTCTTATCTTAATTT
1270098 AAATGTATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATTCTTATCTTAATTTT
Found at i:1280064 original size:33 final size:32
Alignment explanation
Indices: 1280026--1280090 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 32
1280016 ATAAGATCCA
1280026 ACTCAAGGCTACTTTAGAATAAGTTTTAATGAT
1 ACTCAAGGCTACTTTAGAATAAG-TTTAATGAT
*
1280059 ACTCAAGGCTACTTTAGAATCAGTTTAATGAT
1 ACTCAAGGCTACTTTAGAATAAGTTTAATGAT
1280091 TGGCTCAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 9 0.29
33 22 0.71
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (32 bp):
ACTCAAGGCTACTTTAGAATAAGTTTAATGAT
Found at i:1281343 original size:123 final size:124
Alignment explanation
Indices: 1281134--1281365 Score: 288
Period size: 123 Copynumber: 1.9 Consensus size: 124
1281124 AACATTTTTC
* * *
1281134 CTTCACCAGATCTGTTCTTCTAATTTATTGGGACTTTCTTTTTGGTGGAGGCAAGGCCATTAAAC
1 CTTCACCAGATATGTTCTTCTAATTTATTGGGACTTTCTTTTTGGTGGAAGCAAGACCATTAAAC
* * ** * * *
1281199 TTTGAGCTCCCGGGTATAATCTGAAGT-CTCTCTTGGGCAAGAAAGCTAAACACTTAACT
66 TTCGAACTCCCGAATACAATCT-AAATCCGCTCTTGGGCAAGAAAGCTAAACACTTAACT
* * * *
1281258 CTTC-CCAGATATTTTCTTCTCATTTATTGGGACTTTCTTTTTTGTGGAAGCAAGACCATTAAGC
1 CTTCACCAGATATGTTCTTCTAATTTATTGGGACTTTCTTTTTGGTGGAAGCAAGACCATTAAAC
** *
1281322 TTCGAACTTTCGAATGCAATCTAAATCCGCTCTTGGGCAAGAAA
66 TTCGAACTCCCGAATACAATCTAAATCCGCTCTTGGGCAAGAAA
1281366 ACATTCTATT
Statistics
Matches: 90, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
122 3 0.03
123 83 0.92
124 4 0.04
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (124 bp):
CTTCACCAGATATGTTCTTCTAATTTATTGGGACTTTCTTTTTGGTGGAAGCAAGACCATTAAAC
TTCGAACTCCCGAATACAATCTAAATCCGCTCTTGGGCAAGAAAGCTAAACACTTAACT
Found at i:1283358 original size:2 final size:2
Alignment explanation
Indices: 1283351--1283385 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1283341 CATAATATTG
1283351 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1283386 TAACTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1283405 original size:21 final size:22
Alignment explanation
Indices: 1283372--1283439 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 22
1283362 ATATATATAT
* *
1283372 ATATATATATATATTAACTTAAA
1 ATATAT-TTTATATTAATTTAAA
1283395 ATAT-TTTTATATTAATTTATTAA
1 ATATATTTTATATTAATTTA--AA
1283418 ATATATTTTATTATTAATTTAA
1 ATATATTTTA-TATTAATTTAA
1283440 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 12 0.31
22 1 0.03
23 11 0.28
24 5 0.13
25 10 0.26
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATATTTTATATTAATTTAAA
Found at i:1283423 original size:25 final size:24
Alignment explanation
Indices: 1283390--1283438 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
1283380 ATATATTAAC
1283390 TTAAAATATTTT-TATATTAATTTA
1 TTAAAATATTTTAT-TATTAATTTA
1283414 TTAAATATATTTTATTATTAATTTA
1 TTAAA-ATATTTTATTATTAATTTA
1283439 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.22
25 17 0.74
26 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTAAAATATTTTATTATTAATTTA
Found at i:1290147 original size:36 final size:36
Alignment explanation
Indices: 1290096--1290318 Score: 313
Period size: 36 Copynumber: 6.2 Consensus size: 36
1290086 AAAAATAAAC
* *
1290096 ACTTGAATCGAAAGTGCCTATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* * * *
1290132 ATTTGAATCAGAAGTGTCGATGCTTTCTTCCGTTC-
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* *
1290167 ACTTGAATCGGAAGTGTCAATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* *
1290203 ACTTGAATCGGAAGTACCGATGCTTCCTTTCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* * *
1290239 ATTTGAATCGGAAGTGCCAATGCTTCCCTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
1290275 ACTTGAATCGGAAGTGCCGATGCTTCCCTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
1290311 ACTTGAAT
1 ACTTGAAT
1290319 TGATGCAAAC
Statistics
Matches: 165, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
35 31 0.19
36 134 0.81
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.33
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
Found at i:1297611 original size:98 final size:100
Alignment explanation
Indices: 1297440--1297639 Score: 287
Period size: 98 Copynumber: 2.0 Consensus size: 100
1297430 TAACTTCAAC
* *
1297440 TTTTTTTAAGCATACTTTAAGGGGAGTCATCTCATCACACTACCATCCCACACTCTAAATGAAAG
1 TTTTTTTAAGCATAC-TTAAGGGGAGTCAACTCATCACACTACCATCACACACTCTAAATGAAAG
*
1297505 GGAGCATACCTTCTA-CCCAAGCTACTCAAGTAGAG
65 GGAGCATACCTTCCACCCCAAGCTACTCAAGTAGAG
* * * *
1297540 TTTTTTTAAGCATA-TTAAGGGGTGTCAACTCATCACACTACCATCACACATTCTAAGTGAAATG
1 TTTTTTTAAGCATACTTAAGGGGAGTCAACTCATCACACTACCATCACACACTCTAAATGAAAGG
* * *
1297604 GAGCATACCTTCCACCCCGAGCTAGTCAGGTAGAG
66 GAGCATACCTTCCACCCCAAGCTACTCAAGTAGAG
1297639 T
1 T
1297640 CATCATGTGA
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
98 57 0.64
99 18 0.20
100 14 0.16
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (100 bp):
TTTTTTTAAGCATACTTAAGGGGAGTCAACTCATCACACTACCATCACACACTCTAAATGAAAGG
GAGCATACCTTCCACCCCAAGCTACTCAAGTAGAG
Found at i:1303333 original size:15 final size:15
Alignment explanation
Indices: 1303313--1303345 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1303303 TGCTTCATCA
1303313 GCTAATCATCTTTAT
1 GCTAATCATCTTTAT
1303328 GCTAATCATCTTTAT
1 GCTAATCATCTTTAT
1303343 GCT
1 GCT
1303346 TTCTACAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.45
Consensus pattern (15 bp):
GCTAATCATCTTTAT
Found at i:1306575 original size:14 final size:15
Alignment explanation
Indices: 1306556--1306584 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1306546 TGAAAGTTTA
1306556 TAAAAAT-ATAAAAT
1 TAAAAATAATAAAAT
1306570 TAAAAATAATAAAAT
1 TAAAAATAATAAAAT
1306585 AATATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAAAATAATAAAAT
Found at i:1307098 original size:101 final size:101
Alignment explanation
Indices: 1306921--1307123 Score: 361
Period size: 101 Copynumber: 2.0 Consensus size: 101
1306911 AATGCATTAT
* *
1306921 ATGGAATTCAACTCGAAATCATTGATTAAATATAATATTATTTTTTAAAGATTCTAGATTTAAAT
1 ATGGAATTCAACTCGAAATCAGTGATTAAATATAATATTATTTTTTAAAGATTCTAGATTTAAAC
1306986 AATTATATTTATATATATGTACGTTATTAATAATTG
66 AATTATATTTATATATATGTACGTTATTAATAATTG
* *
1307022 ATGGAATTCAACTCGAATTCAGTGATTAAATATAATATTATTTTTTTAAGATTCTAGATTTAAAC
1 ATGGAATTCAACTCGAAATCAGTGATTAAATATAATATTATTTTTTAAAGATTCTAGATTTAAAC
*
1307087 AATTATTTTTATATATATGTACGTTATTAATAATTG
66 AATTATATTTATATATATGTACGTTATTAATAATTG
1307123 A
1 A
1307124 AAAAATTCTG
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 97 1.00
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (101 bp):
ATGGAATTCAACTCGAAATCAGTGATTAAATATAATATTATTTTTTAAAGATTCTAGATTTAAAC
AATTATATTTATATATATGTACGTTATTAATAATTG
Found at i:1308643 original size:4 final size:4
Alignment explanation
Indices: 1308634--1308664 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
1308624 TTGCACTTTC
1308634 ATTT ATTT ATTT ATTT ATTTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT A-TTT ATTT ATTT AT
1308665 GTATATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:1313330 original size:95 final size:95
Alignment explanation
Indices: 1313155--1313416 Score: 337
Period size: 95 Copynumber: 2.7 Consensus size: 95
1313145 TATAATATTA
* * *
1313155 TATATATATATAATAAAGCTTGAGTTGTCCCCTCTAAAGCAATTGGTTAAACTCCCCGGCTTTAT
1 TATA-ATATACAATAAAGCTTGAGTTGT-CCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
* ** *
1313220 GGATAAGATTCAGCTAGCCTGATAAAGGTGAT
64 GGATAAAATTCAGCTAGCCTGATAAAGACGAC
*
1313252 TATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGCTTTATGG
1 TATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
*
1313317 ATAAAATTTAGCTAGCCTGATAAAGACGAC
66 ATAAAATTCAGCTAGCCTGATAAAGACGAC
* * * * *
1313347 TATAATAT-CTATACAATGATATTAAGATGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTT
1 TATAATATACAATA-AA-G--CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTT
1313411 ATGGAT
62 ATGGAT
1313417 TCAGCTAGCC
Statistics
Matches: 146, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
94 4 0.03
95 70 0.48
96 23 0.16
97 4 0.03
98 45 0.31
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (95 bp):
TATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
ATAAAATTCAGCTAGCCTGATAAAGACGAC
Found at i:1314548 original size:36 final size:36
Alignment explanation
Indices: 1314508--1314854 Score: 182
Period size: 36 Copynumber: 9.6 Consensus size: 36
1314498 ATTTGTCTCA
*
1314508 CTTGAGACTATTTTACTTGAAAGAAGATTTATTTCC
1 CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
* * * * *
1314544 CTTGAGATTGTTATT-CTT-AAA-ACAGACCTTGTCTCG
1 CTTGAGACTGTT-TTACTTGAAAGA-AGA-TTTATTTCC
1314580 CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
1 CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
* * * * * *
1314616 CTTGAGATTGTCATT-CTT-AAA-ACAGACCTTGTCTCA
1 CTTGAGACTGT-TTTACTTGAAAGA-AGA-TTTATTTCC
1314652 CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
1 CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
** * * * * * *
1314688 CTCAAGATTATTTTTCTT-AAA-ATATACTT-TGTCGC
1 CTTGAGACTGTTTTACTTGAAAGA-AGATTTATTTC-C
*
1314723 ACTTGAGACTGTTTTACTCGAAAGAAGATTTATTTCC
1 -CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
** * * * * *
1314760 CTCAAGATTGTTTTTCTTAAAACAAGATTT-TGTCTCT
1 CTTGAGACTGTTTTACTTGAAAGAAGATTTAT-T-TCC
* *
1314797 CTTGAGA-TAGTTTTCCTTGAAACAA-ATTT-TGTCTCC
1 CTTGAGACT-GTTTTACTTGAAAGAAGATTTAT-T-TCC
*
1314833 CTTGAGACAGTTTCT-CTTGAAA
1 CTTGAGACTGTTT-TACTTGAAA
1314855 CATAAACATT
Statistics
Matches: 234, Mismatches: 54, Indels: 46
0.70 0.16 0.14
Matches are distributed among these distances:
34 6 0.03
35 25 0.11
36 151 0.65
37 46 0.20
38 6 0.03
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (36 bp):
CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
Found at i:1314594 original size:72 final size:72
Alignment explanation
Indices: 1314500--1314839 Score: 443
Period size: 72 Copynumber: 4.7 Consensus size: 72
1314490 TGCAAATGAT
*
1314500 TTGTCTCACTTGAGACTATTTTACTTGAAAGAAGATTTATTTCCCTTGAGATTGTTATTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTTGAGATTGTTATTCTTAAA
1314565 ACAGACC
66 ACAGACC
* *
1314572 TTGTCTCGCTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTTGAGATTGTCATTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTTGAGATTGTTATTCTTAAA
1314637 ACAGACC
66 ACAGACC
** * *
1314644 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTATTTTTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTTGAGATTGTTATTCTTAAA
* * *
1314709 ATATACT
66 ACAGACC
* * ** *
1314716 TTGTCGCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTTGAGATTGTTATTCTTAAA
**
1314781 ACAAGATT
66 AC-AGACC
* * *
1314789 TTGTCTCTCTTGAGA-TAGTTTTCCTTGAAACAA-ATTT-TGTCTCCCTTGAGA
1 TTGTCTCACTTGAGACT-GTTTTACTTGAAAGAAGATTTAT-T-TCCCTTGAGA
1314840 CAGTTTCTCT
Statistics
Matches: 239, Mismatches: 25, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
71 1 0.00
72 201 0.84
73 37 0.15
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (72 bp):
TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTTGAGATTGTTATTCTTAAA
ACAGACC
Found at i:1314926 original size:36 final size:34
Alignment explanation
Indices: 1314876--1315057 Score: 110
Period size: 36 Copynumber: 5.3 Consensus size: 34
1314866 AAAATATTTC
** * *
1314876 CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTT
1 CCTTGAAACAAATTTT-TCTCCCTTGAGACAG-TTT
1314912 CCTTGAAACAAATTTTTCTCCCTTGAGACAGTTT
1 CCTTGAAACAAATTTTTCTCCCTTGAGACAGTTT
* * *
1314946 CTCTTGAAACATAA-------ACATTGAAAACA-TTT
1 C-CTTGAAACA-AATTTTTCTCCCTTG-AGACAGTTT
* ** * *
1314975 CCCTTTAAATGAATTTTGTCTCTCTTGAGATAGTTT
1 -CCTTGAAACAAATTTT-TCTCCCTTGAGACAGTTT
1315011 CCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTT
1 -CCTTGAAACAAATTTT-TCTCCCTTGAGACAGTTT
1315047 CTCTTGAAACA
1 C-CTTGAAACA
1315058 TAAACTTTGA
Statistics
Matches: 112, Mismatches: 20, Indels: 28
0.70 0.12 0.17
Matches are distributed among these distances:
28 2 0.02
29 13 0.12
30 5 0.04
34 4 0.04
35 26 0.23
36 62 0.55
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (34 bp):
CCTTGAAACAAATTTTTCTCCCTTGAGACAGTTT
Found at i:1314975 original size:100 final size:101
Alignment explanation
Indices: 1314786--1315367 Score: 540
Period size: 101 Copynumber: 5.7 Consensus size: 101
1314776 TTAAAACAAG
1314786 ATTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
1 ATTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
* *
1314851 GAAACATAAACATTAAAAATATTTCCCTTGAAATGA
66 GAAACATAAACATTGAAAACATTTCCCTTGAAATGA
1314887 ATTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTT-TCTCCCTTGAGACAGTTTCTCTT
1 ATTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
*
1314951 GAAACATAAACATTGAAAACATTTCCCTTTAAATGA
66 GAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
1314987 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
1 ATTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
* **
1315052 GAAACATAAACTTTGAAAACAGTTTCCCTTGAAAACA
66 GAAACATAAACATTGAAAACA-TTTCCCTTGAAATGA
** * * *
1315089 A-----AATCT-TTGA-ATATGTTTTACATT-AAATAAATTTTGTCTCCCTTGAGACAGTTTCTT
1 ATTTTGTCTCTCTTGAGATA-GTTTT-CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTC
** *** * * * * **
1315146 TTGAAAGTTTTGTCTCTCTTAAGACAGTTTCTCTTGAAACAA
64 TTGAAA-CATAAAC-AT-TGAAAACA-TTTCCCTTGAAATGA
* * * **
1315188 ATTTTGTTTTCGTCTCTCTTGAGACAATTTTCCTTGAAACAAATTTTGTTTCTTTTGAGACAGTT
1 A-----TTTT-GTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
* * * ** ** *
1315253 TCCCTTGAAACA-AAATCTTTGAATATGTTT-TATATTAAACT-A
60 TCTCTTGAAACATAAA-CATTGAAAACATTTCCCT-TGAAA-TGA
* * * ** *
1315295 ATTTCGTCTCCCTTGAGACAGTTTCTTTTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTC
1 ATTTTGTCTCTCTTGAGATAGTTT-TCCTTGAAACAAA-TTTTGTCTCCCTTGAGACAGTTTCTC
1315360 TTGAAACA
64 TTGAAACA
1315368 CCAACCTTTG
Statistics
Matches: 398, Mismatches: 57, Indels: 50
0.79 0.11 0.10
Matches are distributed among these distances:
95 3 0.01
96 45 0.11
97 8 0.02
98 1 0.00
99 20 0.05
100 96 0.24
101 101 0.25
102 27 0.07
103 31 0.08
106 2 0.01
107 9 0.02
108 4 0.01
109 1 0.00
110 7 0.02
111 41 0.10
112 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (101 bp):
ATTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
GAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:1315074 original size:30 final size:31
Alignment explanation
Indices: 1315040--1315099 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
1315030 CTCCCTTGAG
*
1315040 ACAGTTTCTCTTG-AAACATAAA-CTTTGAAA
1 ACAGTTTCCCTTGAAAACA-AAATCTTTGAAA
1315070 ACAGTTTCCCTTGAAAACAAAATCTTTGAA
1 ACAGTTTCCCTTGAAAACAAAATCTTTGAA
1315100 TATGTTTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (31 bp):
ACAGTTTCCCTTGAAAACAAAATCTTTGAAA
Found at i:1315171 original size:33 final size:33
Alignment explanation
Indices: 1315120--1315184 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1315110 ATTAAATAAA
* *
1315120 TTTTGTCTCCCTTGAGACAGTTTCTTTTGAAAG
1 TTTTGTCTCCCTTAAGACAGTTTCTCTTGAAAG
*
1315153 TTTTGTCTCTCTTAAGACAGTTTCTCTTGAAA
1 TTTTGTCTCCCTTAAGACAGTTTCTCTTGAAA
1315185 CAAATTTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.46
Consensus pattern (33 bp):
TTTTGTCTCCCTTAAGACAGTTTCTCTTGAAAG
Found at i:1315193 original size:201 final size:198
Alignment explanation
Indices: 1314769--1315275 Score: 522
Period size: 201 Copynumber: 2.5 Consensus size: 198
1314759 CCTCAAGATT
*
1314769 GTTTTTCTTAAAACAAGATTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTTGTCTCCC
1 GTTTCTCTTAAAACAA-ATTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTTGTCTCCC
* * * ** **
1314834 TTGAGACAGTTTCTCTTGAAACATAAACATTAAAAATATTTCCCTTGAAATGAATTTTGTCTCTC
65 TTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACATTTCCCTTGAAAACAA---T-AATCTC
*
1314899 TTGAGATAGTTTTCCTTGAAACAAATTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACAT
126 TTGAGATAGTTTTCATTGAAACAAATTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACAT
1314964 TGAAAACA
191 TGAAAACA
* * ** *
1314972 -TTTCCCTTTAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCT
1 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTTGTCTCCCT
1315036 TGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACAGTTTCCCTTGAAAACAA-AATCT-TTGA
66 TGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACA-TTTCCCTTGAAAACAATAATCTCTTGA
* * ** *** *
1315099 -ATATGTTTTACATT-AAATAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGAAAGTTTTGTCTC
130 GATA-GTTTT-CATTGAAACAAATTTT-TCTCCCTTGAGACAGTTTCTCTTGAAA-CATAAAC-A
* *
1315162 TCTTAAGACA
190 T-TGAAAACA
* * *
1315172 GTTTCTCTTGAAACAAATTTTGTTTTCGTCTCTCTTGAGACAATTTTCCTTGAAACAAATTTTGT
1 GTTTCTCTTAAAACAAA-----TTTT-GTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTTGT
* ** *
1315237 TTCTTTTGAGACAGTTTCCCTTGAAACA-AAATCTTTGAA
60 CTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CTTTGAA
1315276 TATGTTTTAT
Statistics
Matches: 254, Mismatches: 35, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
195 3 0.01
196 19 0.07
197 32 0.13
198 2 0.01
199 1 0.00
200 6 0.02
201 94 0.37
202 24 0.09
206 7 0.03
207 66 0.26
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (198 bp):
GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACATTTCCCTTGAAAACAATAATCTCTTGAG
ATAGTTTTCATTGAAACAAATTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
ACA
Found at i:1315206 original size:42 final size:41
Alignment explanation
Indices: 1315152--1315238 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 41
1315142 TCTTTTGAAA
*
1315152 GTTTTGTCTCTCTTAAGAC-AGTTTCTCTTGAAACAAATTTT
1 GTTTTGTCTCTCTTAAGACAATTTTC-CTTGAAACAAATTTT
*
1315193 GTTTTCGTCTCTCTTGAGACAATTTTCCTTGAAACAAATTTT
1 GTTTT-GTCTCTCTTAAGACAATTTTCCTTGAAACAAATTTT
1315235 GTTT
1 GTTT
1315239 CTTTTGAGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
41 5 0.12
42 32 0.76
43 5 0.12
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (41 bp):
GTTTTGTCTCTCTTAAGACAATTTTCCTTGAAACAAATTTT
Found at i:1315259 original size:36 final size:36
Alignment explanation
Indices: 1315153--1315266 Score: 120
Period size: 36 Copynumber: 3.0 Consensus size: 36
1315143 CTTTTGAAAG
* * * *
1315153 TTTTGTCTCTCTTAAGACAGTTTCTCTTGAAACAAA
1 TTTTGTTTCTTTTGAGACAGTTTCCCTTGAAACAAA
* *
1315189 TTTTGTTTTCGTCTCTCTTGAGACAATTTTCCTTGAAACAAA
1 TTTTG--TT--TCT-T-TTGAGACAGTTTCCCTTGAAACAAA
1315231 TTTTGTTTCTTTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTTTCTTTTGAGACAGTTTCCCTTGAAACAAA
1315267 ATCTTTGAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
36 28 0.44
37 1 0.02
38 4 0.06
40 5 0.08
42 26 0.41
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.44
Consensus pattern (36 bp):
TTTTGTTTCTTTTGAGACAGTTTCCCTTGAAACAAA
Found at i:1315431 original size:67 final size:66
Alignment explanation
Indices: 1315323--1315468 Score: 195
Period size: 67 Copynumber: 2.2 Consensus size: 66
1315313 CAGTTTCTTT
* * * ** *
1315323 TTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAACCTTTGAATCTGTTTC
1 TTGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAAAAAAAACCTTTGAA-ATGTTTC
1315388 TC
65 TC
1315390 TTGAAACAAAATTTTGTCTC-CTTGGAGACAATTTCTCTTGAAAAAAAAACCTTTGAAATGTTTC
1 TTGAAACAAAATTTTGTCTCTCTT-GAGACAATTTCTCTTGAAAAAAAAACCTTTGAAATGTTTC
1315454 TC
65 TC
1315456 TTGGAACACAAAA
1 TT-GAA-ACAAAA
1315469 AGAAAACCTT
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
66 13 0.19
67 51 0.73
68 6 0.09
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (66 bp):
TTGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAAAAAAAACCTTTGAAATGTTTCT
C
Found at i:1315476 original size:36 final size:36
Alignment explanation
Indices: 1315430--1315538 Score: 175
Period size: 37 Copynumber: 3.0 Consensus size: 36
1315420 ATTTCTCTTG
*
1315430 AAAAA-AAAACCTTTGAAATGTTTCTCTTGGAACAC
1 AAAAAGAAAACCTTTGAAATGTTTCTCTTGAAACAC
*
1315465 AAAAAGAAAACCTTTGAAATTGTTTCTCTTGAAACAA
1 AAAAAGAAAACCTTTGAAA-TGTTTCTCTTGAAACAC
1315502 AAAAAGAAAACCTTTGAACATGTTTCTCTTGAAACAC
1 AAAAAGAAAACCTTTGAA-ATGTTTCTCTTGAAACAC
1315539 CAAACCTTTG
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 5 0.07
36 13 0.19
37 49 0.72
38 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (36 bp):
AAAAAGAAAACCTTTGAAATGTTTCTCTTGAAACAC
Found at i:1317359 original size:20 final size:20
Alignment explanation
Indices: 1317336--1317373 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1317326 TTTTATTTTC
*
1317336 ATTCTTATTTCCTTTATTTG
1 ATTCTTATTTACTTTATTTG
*
1317356 ATTCTTTTTTACTTTATT
1 ATTCTTATTTACTTTATT
1317374 CATTTTTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.13, G:0.03, T:0.68
Consensus pattern (20 bp):
ATTCTTATTTACTTTATTTG
Found at i:1329241 original size:3 final size:3
Alignment explanation
Indices: 1329230--1329273 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
1329220 TTTTTTATCG
*
1329230 TTA TT- TTA TTA TTA TTA TTA TT- TTA TTA TTA TTTA TTA TGA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
1329274 AATTTTTGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1329250 original size:17 final size:18
Alignment explanation
Indices: 1329230--1329268 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
1329220 TTTTTTATCG
1329230 TTATTTTATTATTA-TTA
1 TTATTTTATTATTATTTA
1329247 TTATTTTATTATTATTTA
1 TTATTTTATTATTATTTA
1329265 TTAT
1 TTAT
1329269 GATTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATTTTATTATTATTTA
Found at i:1333057 original size:31 final size:32
Alignment explanation
Indices: 1333016--1333077 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1333006 ATTTTACATG
1333016 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
*
1333047 TACTGACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1333078 CATTTTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.13, C:0.15, G:0.11, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:1336366 original size:4 final size:4
Alignment explanation
Indices: 1336357--1336390 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1336347 AAAAGTATAC
1336357 ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1336391 GATACATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
4 26 0.93
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1336381 original size:22 final size:21
Alignment explanation
Indices: 1336353--1336398 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
1336343 CGAGAAAAGT
1336353 ATACACATACATACATACATAC
1 ATACACATACATACAT-CATAC
*
1336375 ATACACATACATACATGATAC
1 ATACACATACATACATCATAC
1336396 ATA
1 ATA
1336399 AAATTTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (21 bp):
ATACACATACATACATCATAC
Found at i:1337143 original size:34 final size:35
Alignment explanation
Indices: 1337059--1337154 Score: 115
Period size: 35 Copynumber: 2.7 Consensus size: 35
1337049 CGTTTTCCTC
* *
1337059 AAAACAAACTTTGTCTCGCTTGAGACAATTTCTCTA
1 AAAAC-AATTTTGTCTCGCTTGAGACAATATCTCTA
** *
1337095 AAAACAATTTTGTCTCATTTGAGACTATATCT-TA
1 AAAACAATTTTGTCTCGCTTGAGACAATATCTCTA
1337129 AAGAA-AATTTTGTCTCGCTTGAGACA
1 AA-AACAATTTTGTCTCGCTTGAGACA
1337155 TCATTTTATC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
34 22 0.43
35 24 0.47
36 5 0.10
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (35 bp):
AAAACAATTTTGTCTCGCTTGAGACAATATCTCTA
Found at i:1337524 original size:30 final size:30
Alignment explanation
Indices: 1337483--1337551 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
1337473 GACAATTTTG
1337483 TGAAA-AAAAATCTTTGAGATTGTTTCTTT
1 TGAAACAAAAATCTTTGAGATTGTTTCTTT
*
1337512 TGAAACAAAAATCTTTGAGTTTGTTTCTTT
1 TGAAACAAAAATCTTTGAGATTGTTTCTTT
*
1337542 GGAAACAAAA
1 TGAAACAAAA
1337552 TTTGTCTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
29 5 0.14
30 32 0.86
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (30 bp):
TGAAACAAAAATCTTTGAGATTGTTTCTTT
Found at i:1337841 original size:120 final size:120
Alignment explanation
Indices: 1337703--1337927 Score: 278
Period size: 120 Copynumber: 1.9 Consensus size: 120
1337693 TTAACAAAAT
* * *
1337703 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTCTCTCTT-GAGACAGTTTCTAATGAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTAATGAAAA
*
1337766 ACTAA-CTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGTGATC
64 A-AAATC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
* ** **
1337823 CATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
* * *
1337888 AATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
66 AATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTC
1337928 TCAAGACAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
119 30 0.34
120 55 0.62
121 4 0.04
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (120 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
AATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
Found at i:1337904 original size:65 final size:64
Alignment explanation
Indices: 1337824--1337949 Score: 198
Period size: 65 Copynumber: 2.0 Consensus size: 64
1337814 GATGTGATCC
* *
1337824 ATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAAA
* * *
1337889 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCAAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
1337950 TACCCACCTT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
64 20 0.36
65 36 0.64
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (64 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAAA
Found at i:1337986 original size:40 final size:39
Alignment explanation
Indices: 1337931--1338009 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 39
1337921 TTGTCTCTCA
1337931 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACC-TTGAGATCGTTT
1337971 AGACAACTTCTTTTGAAAATACCCACCTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACCTTGAGATCGTTT
1338010 CTATTAAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
39 12 0.31
40 27 0.69
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (39 bp):
AGACAACTTCTTTTGAAAATACCCACCTTGAGATCGTTT
Found at i:1338636 original size:28 final size:28
Alignment explanation
Indices: 1338605--1338685 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
1338595 GAAACACGTT
1338605 ATCTTTGAG-CTTGTTT-TTCTTGAAACAA
1 ATCTTTGAGTC-TGTTTCTT-TTGAAACAA
1338633 ATCTTTGAGTCTGTTTCTTTTGAAACAA
1 ATCTTTGAGTCTGTTTCTTTTGAAACAA
* * *
1338661 ATCTTTGAATCGGTTTCTCTTGAAA
1 ATCTTTGAGTCTGTTTCTTTTGAAA
1338686 TCATAACTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
28 45 0.94
29 3 0.06
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.46
Consensus pattern (28 bp):
ATCTTTGAGTCTGTTTCTTTTGAAACAA
Found at i:1338847 original size:43 final size:43
Alignment explanation
Indices: 1338699--1338991 Score: 200
Period size: 40 Copynumber: 6.8 Consensus size: 43
1338689 TAACTCCTAA
* * * * *
1338699 AGATGGCCAGCTGTCCTCATCACATAGGAACTGTGTCATTCC-T
1 AGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGTCA-CCCTT
* * * *
1338742 -CA-A-CCAGCTGTCCTCATCACATAGGAACCGTGTCATTCC-T
1 AGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGTCA-CCCTT
* *
1338782 -CA-A-CCAGACC-TCCTCATCACGTAGGAGCCGTGTCACCCTT
1 AGATAGCCAG-CCGTCCTCATCACGTAGGAACCGTGTCACCCTT
*
1338822 AGATAGCCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCACTCCT
1 AGATAGCCAGCCGTCCTCATCACGTAGGAACC--G-TGTCACC-CT--T
* *
1338871 AAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGCCATCCC-T
1 --AGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGTCA-CCCTT
* * *
1338916 CG--A-CCAGACC-TCCTCATCACGTAGGAGCCGTGTCACCCTA
1 AGATAGCCAG-CCGTCCTCATCACGTAGGAACCGTGTCACCCTT
* *
1338956 AGATAACCAGTCGTCCTCATCACGTAGGAACCGTGT
1 AGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGT
1338992 TATCACCTTT
Statistics
Matches: 208, Mismatches: 21, Indels: 42
0.77 0.08 0.15
Matches are distributed among these distances:
39 5 0.02
40 95 0.46
41 4 0.02
42 6 0.03
43 49 0.24
45 2 0.01
46 6 0.03
47 2 0.01
48 4 0.02
49 4 0.02
51 31 0.15
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.22
Consensus pattern (43 bp):
AGATAGCCAGCCGTCCTCATCACGTAGGAACCGTGTCACCCTT
Found at i:1338985 original size:134 final size:134
Alignment explanation
Indices: 1338745--1338998 Score: 427
Period size: 134 Copynumber: 1.9 Consensus size: 134
1338735 CATTCCTCAA
* * *
1338745 CCAGCTGTCCTCATCACATAGGAACCGTGTCATTCCTCAACCAGACCTCCTCATCACGTAGGAGC
1 CCAGCCGTCCTCATCACATAGGAACCGTGCCATCCCTCAACCAGACCTCCTCATCACGTAGGAGC
* *
1338810 CGTGTCACCCTTAGATAGCCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCACTCCTAAAG
66 CGTGTCACCCTAAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCACTCCTAAAG
1338875 ATGG
131 ATGG
* *
1338879 CCAGCCGTCCTCATCACGTAGGAACCGTGCCATCCCTCGACCAGACCTCCTCATCACGTAGGAGC
1 CCAGCCGTCCTCATCACATAGGAACCGTGCCATCCCTCAACCAGACCTCCTCATCACGTAGGAGC
* *
1338944 CGTGTCACCCTAAGATAACCAGTCGTCCTCATCACGTAGGAACCGTGTTATCACC
66 CGTGTCACCCTAAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACC
1338999 TTTAGATGGC
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
134 111 1.00
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (134 bp):
CCAGCCGTCCTCATCACATAGGAACCGTGCCATCCCTCAACCAGACCTCCTCATCACGTAGGAGC
CGTGTCACCCTAAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCACTCCTAAAG
ATGG
Found at i:1339122 original size:43 final size:40
Alignment explanation
Indices: 1339011--1339122 Score: 109
Period size: 43 Copynumber: 2.7 Consensus size: 40
1339001 TAGATGGCCA
1339011 AGAACTCTTCATCATGTATGAGTAGTGTCATCCCTCGACC
1 AGAACTCTTCATCATGTATGAGTAGTGTCATCCCTCGACC
** * * * *
1339051 AGATTTCTTCATCACGTAGGAATTGTGTCA-CCCTTAGACGACC
1 AGAACTCTTCATCATGTATGAGTAGTGTCATCCC-T---CGACC
* *
1339094 CGAACTCTTCATCATGTATGAGCAGTGTC
1 AGAACTCTTCATCATGTATGAGTAGTGTC
1339123 GCCCCCACCA
Statistics
Matches: 54, Mismatches: 14, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
39 3 0.06
40 25 0.46
43 26 0.48
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (40 bp):
AGAACTCTTCATCATGTATGAGTAGTGTCATCCCTCGACC
Found at i:1339294 original size:3 final size:3
Alignment explanation
Indices: 1339283--1339332 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
1339273 TTTTTTATCG
1339283 TTA TT- TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
1339327 TTA TTA
1 TTA TTA
1339333 AATTTTTGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1339303 original size:23 final size:24
Alignment explanation
Indices: 1339277--1339332 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
1339267 CGGGTTTTTT
*
1339277 TTATCGTTATTTTATTATTA-TTA
1 TTATCATTATTTTATTATTATTTA
*
1339300 TTATTATTATTTTATTATTATTTA
1 TTATCATTATTTTATTATTATTTA
*
1339324 TTATTATTA
1 TTATCATTA
1339333 AATTTTTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 18 0.60
24 12 0.40
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (24 bp):
TTATCATTATTTTATTATTATTTA
Found at i:1339339 original size:27 final size:23
Alignment explanation
Indices: 1339283--1339332 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 23
1339273 TTTTTTATCG
1339283 TTATTTTATTATTATTATTATTA
1 TTATTTTATTATTATTATTATTA
1339306 TTATTTTATTATTATTTATTATTA
1 TTATTTTATTATTA-TTATTATTA
1339330 TTA
1 TTA
1339333 AATTTTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATTTTATTATTATTATTATTA
Found at i:1342494 original size:3 final size:3
Alignment explanation
Indices: 1342486--1342532 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1342476 TGTCCAGTTG
1342486 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1342533 AATTGAGTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1347983 original size:20 final size:20
Alignment explanation
Indices: 1347958--1348011 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1347948 TAAATGACTA
1347958 GGGGTATCGGTACCGATAAG
1 GGGGTATCGGTACCGATAAG
* *
1347978 GGGGTATCGATACCTATAAG
1 GGGGTATCGGTACCGATAAG
*
1347998 GGGGTATCAGTACC
1 GGGGTATCGGTACC
1348012 CATAGAGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.17, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGTATCGGTACCGATAAG
Found at i:1350234 original size:13 final size:13
Alignment explanation
Indices: 1350212--1350254 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
1350202 TCCTAATGGG
1350212 CAAT-TTTGAAAA
1 CAATGTTTGAAAA
*
1350224 CTATGTTTGAAAA
1 CAATGTTTGAAAA
1350237 CAATGTTTGAAAA
1 CAATGTTTGAAAA
1350250 TCAAT
1 -CAAT
1350255 ATCTAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 3 0.11
13 20 0.74
14 4 0.15
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:1350290 original size:19 final size:21
Alignment explanation
Indices: 1350266--1350307 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
1350256 TCTAGTTTTC
1350266 AAAACAAC-ATATT-AAATCA
1 AAAACAACAATATTAAAATCA
*
1350285 AAAACAACAATTTTAAAATCA
1 AAAACAACAATATTAAAATCA
1350306 AA
1 AA
1350308 TTTTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAACAACAATATTAAAATCA
Found at i:1350761 original size:23 final size:22
Alignment explanation
Indices: 1350709--1350787 Score: 90
Period size: 21 Copynumber: 3.6 Consensus size: 22
1350699 AGAACCCGAT
* * *
1350709 GGGGTATCGGTAC-CCTTATAG
1 GGGGTATCGATACACATTAAAG
1350730 GGGTGTATCGATACACATTTAAAG
1 GGG-GTATCGATACACA-TTAAAG
*
1350754 GGGGTATCGATACACATTGAA-
1 GGGGTATCGATACACATTAAAG
1350775 GGGGTATCGATAC
1 GGGGTATCGATAC
1350788 CTGGTGCACA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
21 16 0.31
22 13 0.25
23 14 0.27
24 8 0.16
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (22 bp):
GGGGTATCGATACACATTAAAG
Found at i:1353798 original size:5 final size:5
Alignment explanation
Indices: 1353782--1353864 Score: 50
Period size: 5 Copynumber: 17.0 Consensus size: 5
1353772 TGAAATAAAG
* * * *
1353782 AAAAT AATAT AAAAT -AAAG AAAAT -AAAT -GAAT AAAAAT AAATT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT
* *
1353830 AAAGT AAAGAT AAAA- ATGAAT AAAAT -AAAT AAAAT
1 AAAAT AAA-AT AAAAT A-AAAT AAAAT AAAAT AAAAT
1353865 GAAGAAAGAT
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
4 15 0.25
5 36 0.61
6 8 0.14
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:1353842 original size:11 final size:10
Alignment explanation
Indices: 1353774--1353843 Score: 56
Period size: 10 Copynumber: 6.7 Consensus size: 10
1353764 AAAATGAATG
1353774 AAATAAAG-A
1 AAATAAAGTA
1353783 AAATAATA-TA
1 AAATAA-AGTA
1353793 AAATAAAG-A
1 AAATAAAGTA
1353802 AAATAAATGAATAA
1 AAATAAA-G--T-A
*
1353816 AAATAAATTA
1 AAATAAAGTA
1353826 AAATAAAGTA
1 AAATAAAGTA
1353836 AAGATAAA
1 AA-ATAAA
1353844 AATGAATAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
9 15 0.30
10 21 0.42
11 6 0.12
14 8 0.16
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (10 bp):
AAATAAAGTA
Found at i:1353860 original size:9 final size:9
Alignment explanation
Indices: 1353730--1353864 Score: 80
Period size: 9 Copynumber: 14.6 Consensus size: 9
1353720 AATGTGTTAG
*
1353730 AAAAAAAAT
1 AAAATAAAT
1353739 GAAAATAAAT
1 -AAAATAAAT
*
1353749 --AATAAAG
1 AAAATAAAT
*
1353756 AAAATACA-
1 AAAATAAAT
*
1353764 AAAATGAAT
1 AAAATAAAT
* *
1353773 GAAATAAAG
1 AAAATAAAT
1353782 AAAATAATAT
1 AAAATAA-AT
*
1353792 AAAATAAAG
1 AAAATAAAT
1353801 AAAATAAAT
1 AAAATAAAT
1353810 GAATAA-AAAT
1 -AA-AATAAAT
*
1353820 AAATTAAAAT
1 AAAAT-AAAT
*
1353830 AAAGTAAAGAT
1 AAAAT-AA-AT
*
1353841 AAAAATGAAT
1 -AAAATAAAT
1353851 AAAATAAAT
1 AAAATAAAT
1353860 AAAAT
1 AAAAT
1353865 GAAGAAAGAT
Statistics
Matches: 98, Mismatches: 17, Indels: 21
0.72 0.12 0.15
Matches are distributed among these distances:
7 6 0.06
8 7 0.07
9 41 0.42
10 35 0.36
11 5 0.05
12 4 0.04
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (9 bp):
AAAATAAAT
Found at i:1353997 original size:17 final size:18
Alignment explanation
Indices: 1353972--1354033 Score: 65
Period size: 17 Copynumber: 3.4 Consensus size: 18
1353962 AAAGATAAAG
*
1353972 TAGAGAAAAAATAAAAAA
1 TAGAAAAAAAATAAAAAA
1353990 TA-AAAAAATAA-AAAAAA
1 TAGAAAAAA-AATAAAAAA
*
1354007 TAGAAAAATAATAATAATAA
1 TAGAAAAAAAATAA-AA-AA
1354027 TAGAAAA
1 TAGAAAA
1354034 TAGAAAACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 15 0.41
18 11 0.30
19 2 0.05
20 9 0.24
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (18 bp):
TAGAAAAAAAATAAAAAA
Found at i:1354014 original size:20 final size:20
Alignment explanation
Indices: 1353991--1354033 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1353981 AATAAAAAAT
1353991 AAAAAAATAAAAAAAATAGA
1 AAAAAAATAAAAAAAATAGA
* * *
1354011 AAAATAATAATAATAATAGA
1 AAAAAAATAAAAAAAATAGA
1354031 AAA
1 AAA
1354034 TAGAAAACCA
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:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (20 bp):
AAAAAAATAAAAAAAATAGA
Found at i:1354132 original size:2 final size:2
Alignment explanation
Indices: 1354087--1354112 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1354077 GAAATATAAT
1354087 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
1354113 CTAATGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1354138 original size:14 final size:14
Alignment explanation
Indices: 1354119--1354166 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1354109 TATACTAATG
1354119 ATAAAATATATATA
1 ATAAAATATATATA
*
1354133 ATAAAAT-TAATAAA
1 ATAAAATAT-ATATA
**
1354147 ATGTAATATATATA
1 ATAAAATATATATA
1354161 ATAAAA
1 ATAAAA
1354167 ATAAGAAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
ATAAAATATATATA
Done.