Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 4 of 135
Found at i:1147613 original size:59 final size:57
Alignment explanation
Indices: 1147535--1147807 Score: 200
Period size: 59 Copynumber: 4.7 Consensus size: 57
1147525 ACTTTTAAAG
* *
1147535 ATTATATTTTAACCCCGAAACTTCCAAAAATTACATTTTAACCTC-AAAATATCCCAAA
1 ATTACATTTTAACCTCGAAACTTCCAAAAATTACATTTTAACC-CGAAAAT-TCCCAAA
* * *
1147593 ATTACCATTTTGACCTCGAAACTTCTAAAAATTACATTTTAACCCCGAAACTT-CCAAA
1 ATTA-CATTTTAACCTCGAAACTTCCAAAAATTACATTTTAA-CCCGAAAATTCCCAAA
* * * * * **
1147651 ATTAAAATTTTAACCTTGAAATTTTCC-AAAATTACCATTTTGACCCTAAAATTTCTAAAA
1 ATT-ACATTTTAACCTCGAAA-CTTCCAAAAATTA-CATTTTAACCCGAAAA-TTCCCAAA
* * * * * *
1147711 ATTACATTTTTGACC-CTAAAACTTCCAAAAATTACATTTT-GCCCCAAACTTCCAAAA
1 ATTACA-TTTTAACCTC-GAAACTTCCAAAAATTACATTTTAACCCGAAAATTCCCAAA
* * *
1147768 ATTGCATTTTAACC-CTAAAACTTTC-AAAATTACCATTTTA
1 ATTACATTTTAACCTC-GAAACTTCCAAAAATTA-CATTTTA
1147808 CCCCCAAACA
Statistics
Matches: 175, Mismatches: 27, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
55 7 0.04
56 23 0.13
57 12 0.07
58 44 0.25
59 60 0.34
60 29 0.17
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.34
Consensus pattern (57 bp):
ATTACATTTTAACCTCGAAACTTCCAAAAATTACATTTTAACCCGAAAATTCCCAAA
Found at i:1147632 original size:88 final size:87
Alignment explanation
Indices: 1147513--1147825 Score: 325
Period size: 88 Copynumber: 3.6 Consensus size: 87
1147503 AAAATTTCAT
* * * *
1147513 TTTTAACCCT-AAACTTTTAAAGATTATATTTTAACCCCGAAACTTCCAAAAATTACATTTTAAC
1 TTTTGACCCTAAAACTTCTAAAAATTACATTTTAACCCCGAAACTTCCAAAAATTACATTTTAAC
1147577 CTCAAAATATCCCAAAATTACCA
66 CTCAAAAT-TCCCAAAATTACCA
* *
1147600 TTTTGA-CCTCGAAACTTCTAAAAATTACATTTTAACCCCGAAACTTCC-AAAATTAAAATTTTA
1 TTTTGACCCT-AAAACTTCTAAAAATTACATTTTAACCCCGAAACTTCCAAAAATT-ACATTTTA
* * *
1147663 ACCTTGAAATTTTCCAAAATTACCA
64 ACC-TCAAAATTCCCAAAATTACCA
* * ** *
1147688 TTTTGACCCTAAAATTTCTAAAAATTACATTTTTGACCCTAAAACTTCCAAAAATTACATTTT-G
1 TTTTGACCCTAAAACTTCTAAAAATTACA-TTTTAACCCCGAAACTTCCAAAAATTACATTTTAA
* * * *
1147752 CCCCAAACTTCCAAAAATT-GCA
65 CCTCAAAATTCCCAAAATTACCA
* * * *
1147774 TTTTAACCCTAAAACTT-TCAAAATTACCATTTT-ACCCCCAAACATCCAAAAA
1 TTTTGACCCTAAAACTTCTAAAAATTA-CATTTTAACCCCGAAACTTCCAAAAA
1147826 CCCCAATTTT
Statistics
Matches: 191, Mismatches: 27, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
84 16 0.08
85 12 0.06
86 22 0.12
87 23 0.12
88 82 0.43
89 30 0.16
90 6 0.03
ACGTcount: A:0.40, C:0.24, G:0.03, T:0.33
Consensus pattern (87 bp):
TTTTGACCCTAAAACTTCTAAAAATTACATTTTAACCCCGAAACTTCCAAAAATTACATTTTAAC
CTCAAAATTCCCAAAATTACCA
Found at i:1151957 original size:34 final size:34
Alignment explanation
Indices: 1151919--1151992 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
1151909 ATTGAATCAA
*
1151919 TCAATCTCCAAACTTGAGCTTAATTTTTTTTAGT
1 TCAATCTCCAAACTTGAGCTTAAATTTTTTTAGT
*
1151953 TCAATCTCTAAACTTGAGCTTAAATTTTTTTAGT
1 TCAATCTCCAAACTTGAGCTTAAATTTTTTTAGT
*
1151987 TTAATC
1 TCAATC
1151993 ATTACTGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.47
Consensus pattern (34 bp):
TCAATCTCCAAACTTGAGCTTAAATTTTTTTAGT
Found at i:1152125 original size:2 final size:2
Alignment explanation
Indices: 1152120--1152147 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1152110 AAAACAAATA
1152120 AT 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 AT
1152148 GAAATCTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1154458 original size:17 final size:17
Alignment explanation
Indices: 1154428--1154528 Score: 96
Period size: 17 Copynumber: 5.9 Consensus size: 17
1154418 AGTCCCAATT
* *
1154428 TTTAATTTTTAATTTAC
1 TTTAAATTTAAATTTAC
* * *
1154445 TTTAAGTTTGAATTTAT
1 TTTAAATTTAAATTTAC
1154462 TTTAAATTTAAATTTA-
1 TTTAAATTTAAATTTAC
* * *
1154478 TTGTGAGTTTAAGTTTAC
1 TT-TAAATTTAAATTTAC
*
1154496 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAC
*
1154513 TTTAAATTAAAATTTA
1 TTTAAATTTAAATTTA
1154529 ATTTTAAAAG
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
16 2 0.03
17 65 0.94
18 2 0.03
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTAAATTTAAATTTAC
Found at i:1154473 original size:6 final size:6
Alignment explanation
Indices: 1154462--1154536 Score: 50
Period size: 6 Copynumber: 13.0 Consensus size: 6
1154452 TTGAATTTAT
* * * *
1154462 TTTAAA TTTAAA TTT--A TTGTGAG TTTAAG TTT-AC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
1154508 TTT-AT TTTAAA TTAAAA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1154537 AGTCCAAATA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
4 3 0.06
5 9 0.17
6 40 0.74
7 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:1156216 original size:30 final size:29
Alignment explanation
Indices: 1156165--1156275 Score: 125
Period size: 30 Copynumber: 3.8 Consensus size: 29
1156155 CAGATCCTTG
* *
1156165 AACTATCTAAAAATCATATTTTGGCCCCCA
1 AACTTTCTAAAAATCACATTTT-GCCCCCA
* * *
1156195 AAC-TTCTCAAAAATTACATTTTAACCCTCA
1 AACTTTCT-AAAAATCACATTTT-GCCCCCA
* *
1156225 AACTTTCTAATAATCACATTTTGACCCCA
1 AACTTTCTAAAAATCACATTTTGCCCCCA
1156254 AACTTTCTAAAAATCACATTTT
1 AACTTTCTAAAAATCACATTTT
1156276 TACCCTCAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
29 28 0.42
30 35 0.52
31 4 0.06
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
AACTTTCTAAAAATCACATTTTGCCCCCA
Found at i:1156259 original size:29 final size:30
Alignment explanation
Indices: 1156165--1156397 Score: 178
Period size: 29 Copynumber: 7.9 Consensus size: 30
1156155 CAGATCCTTG
* * * *
1156165 AACTATCTAAAAATCATATTTTGGCCCCCA
1 AACTTTCTAAAAATCACATTTTGACCCTCA
* *
1156195 AAC-TTCTCAAAAATTACATTTTAACCCTCA
1 AACTTTCT-AAAAATCACATTTTGACCCTCA
*
1156225 AACTTTCTAATAATCACATTTTGACCC-CA
1 AACTTTCTAAAAATCACATTTTGACCCTCA
*
1156254 AACTTTCTAAAAATCACATTTTTACCCTCA
1 AACTTTCTAAAAATCACATTTTGACCCTCA
* * *
1156284 AA-TTTCAAAAAATTC-CATTTTAACCC-AA
1 AACTTTCTAAAAA-TCACATTTTGACCCTCA
* * * *
1156312 AATTTTCCAAAAATTACCATTTT-ACCCTTA
1 AACTTTCTAAAAATCA-CATTTTGACCCTCA
* * *
1156342 AATTTTC-AAAAATTC-CATTTTTAACCTCA
1 AACTTTCTAAAAA-TCACATTTTGACCCTCA
* *
1156371 AATTTTCCAAAAATTC-CATTTTGACCC
1 AACTTTCTAAAAA-TCACATTTTGACCC
1156398 CGATTTTTCC
Statistics
Matches: 170, Mismatches: 22, Indels: 22
0.79 0.10 0.10
Matches are distributed among these distances:
28 10 0.06
29 79 0.46
30 77 0.45
31 4 0.02
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.36
Consensus pattern (30 bp):
AACTTTCTAAAAATCACATTTTGACCCTCA
Found at i:1156267 original size:59 final size:58
Alignment explanation
Indices: 1156190--1156397 Score: 217
Period size: 59 Copynumber: 3.5 Consensus size: 58
1156180 ATATTTTGGC
* *
1156190 CCCCAAAC-TTCTCAAAAATTACATTTTAACCCTCAAACTTTCTAATAA-TCACATTTTGA
1 CCCCAAACTTTC-CAAAAATTACATTTT-ACCCTCAAACTTTCTAAAAATTC-CATTTTAA
* * *
1156249 CCCCAAACTTTCTAAAAATCACATTTTTACCCTCAAA-TTTCAAAAAATTCCATTTTAA
1 CCCCAAACTTTCCAAAAATTACA-TTTTACCCTCAAACTTTCTAAAAATTCCATTTTAA
* * * *
1156307 CCCAAAATTTTCCAAAAATTACCATTTTACCCTTAAATTTTC-AAAAATTCCATTTTTAA
1 CCCCAAACTTTCCAAAAATTA-CATTTTACCCTCAAACTTTCTAAAAATTCCA-TTTTAA
* * *
1156366 CCTCAAATTTTCCAAAAATTCCATTTTGACCC
1 CCCCAAACTTTCCAAAAATTACATTTT-ACCC
1156398 CGATTTTTCC
Statistics
Matches: 129, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
58 60 0.47
59 62 0.48
60 7 0.05
ACGTcount: A:0.38, C:0.26, G:0.01, T:0.36
Consensus pattern (58 bp):
CCCCAAACTTTCCAAAAATTACATTTTACCCTCAAACTTTCTAAAAATTCCATTTTAA
Found at i:1156332 original size:30 final size:31
Alignment explanation
Indices: 1156202--1156423 Score: 182
Period size: 29 Copynumber: 7.5 Consensus size: 31
1156192 CCAAACTTCT
*
1156202 CAAAAATTA-CATTTTAACCCTCAAACTTTC
1 CAAAAATTACCATTTTAACCCTCAAATTTTC
* * * * *
1156232 TAATAATCA-CATTTTGACCC-CAAACTTTC
1 CAAAAATTACCATTTTAACCCTCAAATTTTC
* * *
1156261 TAAAAATCA-CATTTTTACCCTCAAA-TTTC
1 CAAAAATTACCATTTTAACCCTCAAATTTTC
* *
1156290 AAAAAATT-CCATTTTAACCC-AAAATTTTC
1 CAAAAATTACCATTTTAACCCTCAAATTTTC
*
1156319 CAAAAATTACCATTTT-ACCCTTAAATTTT-
1 CAAAAATTACCATTTTAACCCTCAAATTTTC
1156348 CAAAAATT-CCATTTTTAA-CCTCAAATTTTC
1 CAAAAATTACCA-TTTTAACCCTCAAATTTTC
* * *
1156378 CAAAAATT-CCATTTTGACCC-CGATTTTTC
1 CAAAAATTACCATTTTAACCCTCAAATTTTC
* * *
1156407 CAAGAAGTGCCATTTTA
1 CAAAAATTACCATTTTA
1156424 CCCCCGAATG
Statistics
Matches: 163, Mismatches: 19, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
28 6 0.04
29 102 0.63
30 55 0.34
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (31 bp):
CAAAAATTACCATTTTAACCCTCAAATTTTC
Found at i:1156441 original size:88 final size:86
Alignment explanation
Indices: 1156261--1156451 Score: 222
Period size: 88 Copynumber: 2.2 Consensus size: 86
1156251 CCAAACTTTC
*
1156261 TAAAAA-TCACATTTTTACCCTCAAATTTCAAAAAATTCCATTTTAACCCAAAATTTTCCAAAAA
1 TAAAAATTC-CATTTTTAACCTCAAATTTCAAAAAATTCCATTTTAACCCAAAATTTTCCAAAAA
* ** *
1156325 TTACCATTTTACCCTTAAATTT
65 GTACCATTTTACCCCCAAATTA
* * ** * *
1156347 TCAAAAATTCCATTTTTAACCTCAAATTTTCCAAAAATTCCATTTTGACCCCGATTTTTCCAAGA
1 T-AAAAATTCCATTTTTAACCTCAAA-TTTCAAAAAATTCCATTTTAACCCAAAATTTTCCAAAA
* *
1156412 AGTGCCATTTTACCCCCGAATGTA
64 AGTACCATTTTACCCCCAAAT-TA
1156436 TAAAAATTCCATTTTT
1 TAAAAATTCCATTTTT
1156452 GCCCTCGAGC
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
86 1 0.01
87 20 0.23
88 65 0.74
89 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (86 bp):
TAAAAATTCCATTTTTAACCTCAAATTTCAAAAAATTCCATTTTAACCCAAAATTTTCCAAAAAG
TACCATTTTACCCCCAAATTA
Found at i:1156480 original size:29 final size:29
Alignment explanation
Indices: 1156316--1156560 Score: 117
Period size: 29 Copynumber: 8.4 Consensus size: 29
1156306 ACCCAAAATT
** **
1156316 TTCCAAAAATTACCATTTTACCCTTAAAT
1 TTCCAAAAATTACCATTTTACCCTCGAGC
* * * **
1156345 TTTCAAAAATT-CCATTTTTAACCTCAAATT
1 TTCCAAAAATTACCA-TTTTACCCTC-GAGC
**
1156375 TTCCAAAAATT-CCATTTTGACCC-CGATTT
1 TTCCAAAAATTACCATTTT-ACCCTCGA-GC
* * * * *
1156404 TTCCAAGAAGTGCCATTTTACCCCCGA-A
1 TTCCAAAAATTACCATTTTACCCTCGAGC
** *
1156432 TGTATAAAAATT-CCATTTTTGCCCTCGAGC
1 T-TCCAAAAATTACCA-TTTTACCCTCGAGC
* * *
1156462 TTCCAAAAGTTACCATTTTATCCTCGAAC
1 TTCCAAAAATTACCATTTTACCCTCGAGC
* * *
1156491 ATCCAAAAATTACTATTTTTACCCCCGAG-
1 TTCCAAAAATTACCA-TTTTACCCTCGAGC
*
1156520 TGTCCAAAAATTACCATTTTACCC-CTGAAC
1 T-TCCAAAAATTACCATTTTACCCTC-GAGC
*
1156550 CTCCAAAAATT
1 TTCCAAAAATT
1156561 GCCGTTTTGC
Statistics
Matches: 169, Mismatches: 33, Indels: 28
0.73 0.14 0.12
Matches are distributed among these distances:
28 9 0.05
29 104 0.62
30 56 0.33
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.34
Consensus pattern (29 bp):
TTCCAAAAATTACCATTTTACCCTCGAGC
Found at i:1156534 original size:59 final size:58
Alignment explanation
Indices: 1156376--1156560 Score: 160
Period size: 59 Copynumber: 3.2 Consensus size: 58
1156366 CCTCAAATTT
* ** * * * * **
1156376 TCCAAAAATTCCATTTTGA-CCCCGATTTTTCCAAGAAGTGCCATTTTACCCCCGAATG
1 TCCAAAAATTCCATTTTTACCCCCGA-GCTTCCAAAAATTACCATTTTACCCCTGAACA
** * * * *
1156434 TATAAAAATTCCATTTTTGCCCTCGAGCTTCCAAAAGTTACCATTTTA-TCCTCGAACA
1 TCCAAAAATTCCATTTTTACCCCCGAGCTTCCAAAAATTACCATTTTACCCCT-GAACA
* *
1156492 TCCAAAAATTACTATTTTTACCCCCGAG-TGTCCAAAAATTACCATTTTACCCCTGAACC
1 TCCAAAAATT-CCATTTTTACCCCCGAGCT-TCCAAAAATTACCATTTTACCCCTGAACA
1156551 TCCAAAAATT
1 TCCAAAAATT
1156561 GCCGTTTTGC
Statistics
Matches: 99, Mismatches: 23, Indels: 9
0.76 0.18 0.07
Matches are distributed among these distances:
57 2 0.02
58 43 0.43
59 51 0.52
60 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTTACCCCCGAGCTTCCAAAAATTACCATTTTACCCCTGAACA
Found at i:1156587 original size:29 final size:29
Alignment explanation
Indices: 1156437--1156588 Score: 110
Period size: 29 Copynumber: 5.2 Consensus size: 29
1156427 CCGAATGTAT
** * *
1156437 AAAAATT-CCATTTTTGCCCTCGAGCTTCC
1 AAAAATTACCATTTTACCCCT-GAACATCC
* *
1156466 AAAAGTTACCATTTTA-TCCTCGAACATCC
1 AAAAATTACCATTTTACCCCT-GAACATCC
* * ***
1156495 AAAAATTACTATTTTTACCCCCGAGTGTCC
1 AAAAATTACCA-TTTTACCCCTGAACATCC
*
1156525 AAAAATTACCATTTTACCCCTGAACCTCC
1 AAAAATTACCATTTTACCCCTGAACATCC
* * * *
1156554 AAAAATTGCCGTTTTGCCCCTGAGCATCC
1 AAAAATTACCATTTTACCCCTGAACATCC
*
1156583 TAAAAT
1 AAAAAT
1156589 CGCATTTTTG
Statistics
Matches: 97, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
29 68 0.70
30 27 0.28
31 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.31
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCTGAACATCC
Found at i:1156915 original size:97 final size:97
Alignment explanation
Indices: 1156808--1157001 Score: 309
Period size: 97 Copynumber: 2.0 Consensus size: 97
1156798 TAAACTTTTA
* *
1156808 AAATCGAGGCAATATTCCTTTATTTC-GAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGA
1 AAATCAAGGCAATATTCCTTTATCTCTG-GTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGA
* *
1156872 TTTTTCTTCAAATCGGAATAATCGAATACCCTT
65 CTTTTCTTCAAATCGAAATAATCGAATACCCTT
* * *
1156905 AAATCAAGGCAATGTTTCTTTATCTCTGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAC
1 AAATCAAGGCAATATTCCTTTATCTCTGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAC
1156970 TTTTCTTCAAATCGAAATAATCGAATACCCTT
66 TTTTCTTCAAATCGAAATAATCGAATACCCTT
1157002 TTCAAAGGTT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
97 88 0.99
98 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (97 bp):
AAATCAAGGCAATATTCCTTTATCTCTGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAC
TTTTCTTCAAATCGAAATAATCGAATACCCTT
Found at i:1157596 original size:28 final size:29
Alignment explanation
Indices: 1157538--1157596 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
1157528 TTAATTTTTA
* **
1157538 AAAATTTAGTGTTTTATTTTTCAGATTTT
1 AAAATTTAGTATTTTATTTTTCAGAAATT
1157567 AAAATTTAG-ATTTTATATTTTC-GAAATT
1 AAAATTTAGTATTTTAT-TTTTCAGAAATT
1157595 AA
1 AA
1157597 TCCTAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (29 bp):
AAAATTTAGTATTTTATTTTTCAGAAATT
Found at i:1167385 original size:3 final size:3
Alignment explanation
Indices: 1167377--1167411 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
1167367 GCTTGAAAAA
*
1167377 TGT TGT TGT TGCT TGT TGC TGT TGT TGT TGT TGT T
1 TGT TGT TGT TG-T TGT TGT TGT TGT TGT TGT TGT T
1167412 CGAGTCTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.06, G:0.31, T:0.63
Consensus pattern (3 bp):
TGT
Found at i:1169620 original size:26 final size:24
Alignment explanation
Indices: 1169589--1169636 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
1169579 ATTTGTTTTA
*
1169589 ATATTTTTAAATGTATTTGATATATC
1 ATATTTTAAAAT-TATTT-ATATATC
1169615 ATATTTTAAAATTATTTATATA
1 ATATTTTAAAATTATTTATATA
1169637 ATAAAACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
ATATTTTAAAATTATTTATATATC
Found at i:1171065 original size:5 final size:5
Alignment explanation
Indices: 1171055--1171079 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1171045 AAAGACTTGG
1171055 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
1171080 AATATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:1171165 original size:14 final size:14
Alignment explanation
Indices: 1171142--1171171 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1171132 TTGTATTTAA
*
1171142 TTTATGTTTATCTT
1 TTTATATTTATCTT
1171156 TTTATATTTATCTT
1 TTTATATTTATCTT
1171170 TT
1 TT
1171172 AGAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTATATTTATCTT
Found at i:1171963 original size:15 final size:16
Alignment explanation
Indices: 1171943--1171972 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1171933 CTTCCCTATT
1171943 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
1171958 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
1171973 TTTTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:1171964 original size:22 final size:22
Alignment explanation
Indices: 1171938--1171981 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1171928 TTCGACTTCC
1171938 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
1171960 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
1171982 TTGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.70
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:1173558 original size:21 final size:21
Alignment explanation
Indices: 1173534--1173583 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1173524 GAATTTCAGC
*
1173534 AGCAATCTATAGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
*
1173555 AGCAAACTATGGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
*
1173576 AGAAAACT
1 AGCAAACT
1173584 GAGGCATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (21 bp):
AGCAAACTATAGATTTTCAAA
Found at i:1177600 original size:6 final size:6
Alignment explanation
Indices: 1177589--1177614 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1177579 GGCAACTCGA
1177589 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
1177615 TATCTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:1177622 original size:12 final size:11
Alignment explanation
Indices: 1177594--1177647 Score: 58
Period size: 12 Copynumber: 4.8 Consensus size: 11
1177584 CTCGATTATT
*
1177594 TTTATTTTTATT
1 TTTATTTTT-TA
1177606 TTTATTTTTTA
1 TTTATTTTTTA
1177617 TCTTA--TTTTA
1 T-TTATTTTTTA
1177627 TTTATTTATTTA
1 TTTATTT-TTTA
1177639 TTTATTTTT
1 TTTATTTTT
1177648 GTCCAGGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
9 3 0.08
10 6 0.16
11 5 0.14
12 23 0.62
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:1177632 original size:4 final size:4
Alignment explanation
Indices: 1177606--1177645 Score: 55
Period size: 4 Copynumber: 9.8 Consensus size: 4
1177596 TATTTTTATT
1177606 TTTA TTT- TTTA TCTTA TTTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA T-TTA -TTTA TTTA TTTA TTTA TTTA TTT
1177646 TTGTCCAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
4 23 0.70
5 6 0.18
6 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1179183 original size:19 final size:19
Alignment explanation
Indices: 1179161--1179205 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1179151 TTATATTAGG
1179161 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
1179180 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
1179199 ATTTAAT
1 ATTTAAT
1179206 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:1180023 original size:15 final size:16
Alignment explanation
Indices: 1180005--1180034 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1179995 CTTCCCTATT
1180005 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
1180020 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
1180035 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:1180027 original size:22 final size:22
Alignment explanation
Indices: 1180000--1180060 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
1179990 TTCGACTTCC
1180000 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
1180022 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
* *
1180044 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTACTTTT
1180061 CCTTAGATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:1180050 original size:21 final size:22
Alignment explanation
Indices: 1180014--1180060 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1180004 TTTCTATTTC
*
1180014 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
1180036 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
1180057 TTTT
1 TTTT
1180061 CCTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:1185913 original size:26 final size:27
Alignment explanation
Indices: 1185884--1185953 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 27
1185874 TAAGATGACT
1185884 ATATAAAAAAT-TTCAATAAATAAAA-A
1 ATATAAAAAATATTCAAT-AATAAAATA
* *
1185910 ATATATAAAATTATTCAATATTAAAATA
1 ATATA-AAAAATATTCAATAATAAAATA
1185938 ATATAATATAAATATT
1 ATATAA-A-AAATATT
1185954 TTTTAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 5 0.14
27 12 0.33
28 13 0.36
29 6 0.17
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (27 bp):
ATATAAAAAATATTCAATAATAAAATA
Found at i:1185964 original size:31 final size:30
Alignment explanation
Indices: 1185905--1185970 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
1185895 TTCAATAAAT
1185905 AAAAA-AT-ATATAAAATTATTCAATATTA
1 AAAAATATAATATAAAATTATTCAATATTA
* *
1185933 AAATAATATAATATAAATATTTTTTAA-ATTA
1 AAA-AATATAATATAAA-ATTATTCAATATTA
1185964 AAAAATA
1 AAAAATA
1185971 ATATGAGCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 3 0.09
29 2 0.06
30 6 0.19
31 14 0.44
32 7 0.22
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
AAAAATATAATATAAAATTATTCAATATTA
Found at i:1189020 original size:25 final size:25
Alignment explanation
Indices: 1188985--1189032 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1188975 AAGCTATGAA
*
1188985 TAATTATAAATAT-TATGTAAAAAT
1 TAATTATAAATATATATCTAAAAAT
1189009 TAATTAATAAATATATATCTAAAA
1 TAATT-ATAAATATATATCTAAAA
1189033 GTCTACTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 8 0.38
26 8 0.38
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
TAATTATAAATATATATCTAAAAAT
Found at i:1195590 original size:3 final size:3
Alignment explanation
Indices: 1195582--1195617 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1195572 TCACAATCTT
1195582 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1195618 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1195699 original size:7 final size:7
Alignment explanation
Indices: 1195687--1195723 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1195677 AAGGGATCCT
1195687 CACATTG
1 CACATTG
1195694 CACATTG
1 CACATTG
*
1195701 CACTTTG
1 CACATTG
*
1195708 CACTTTG
1 CACATTG
1195715 CACATTG
1 CACATTG
1195722 CA
1 CA
1195724 AATATCAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (7 bp):
CACATTG
Found at i:1200040 original size:29 final size:30
Alignment explanation
Indices: 1200006--1200063 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1199996 TTTTTCAAAT
*
1200006 GATTAAAATAAAATTTTATCATTT-TTAAG
1 GATTAAAATAAAATTTTATAATTTATTAAG
* *
1200035 GATTAAAGTATAATTTTATAATTTATTAA
1 GATTAAAATAAAATTTTATAATTTATTAA
1200064 TTTATAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (30 bp):
GATTAAAATAAAATTTTATAATTTATTAAG
Found at i:1203224 original size:48 final size:48
Alignment explanation
Indices: 1203151--1203464 Score: 153
Period size: 48 Copynumber: 6.7 Consensus size: 48
1203141 ATCCCCTCCT
* * * * * *
1203151 CCGCCTTATGAGTATAAGTCACCACCGCCGCCTTCTCCTTCTCCACCG
1 CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTCTCCACCA
* *
1203199 CCGCCTTATGTGTATAAATCTCCACCACCACCTTCACCTTCTCCTCCA
1 CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTCTCCACCA
* * * * * * **
1203247 CCTCCATATGTGTACAAGTCTCCTCCACCA-C--CACCTAAGCAT-GAGGA
1 CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCT--TC-TCCACCA
** ** * **** *
1203294 GAAGCCTTATGAATACAAGTCTCCACCACCA-C--CACC-TAAGGA-GA
1 -CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTCTCCACCA
* * * * * * *
1203338 -AGCCTTATGAGTACAAGTCTCCACCACCTCCATCGCCTTCTCCTCCA
1 CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTCTCCACCA
* * * * * *
1203385 CCTCCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCA
1 CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTCTCCACCA
* *
1203433 CCTCCTTATGTGTACAAGTCTCCACCACCACC
1 CCGCCTTATGTGTATAAGTCTCCACCACCACC
1203465 ACCAAAGCAT
Statistics
Matches: 210, Mismatches: 45, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
42 27 0.13
43 1 0.00
44 2 0.01
45 10 0.05
46 1 0.00
47 4 0.02
48 165 0.79
ACGTcount: A:0.24, C:0.41, G:0.11, T:0.24
Consensus pattern (48 bp):
CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTCTCCACCA
Found at i:1203318 original size:45 final size:42
Alignment explanation
Indices: 1203269--1203365 Score: 140
Period size: 42 Copynumber: 2.2 Consensus size: 42
1203259 TACAAGTCTC
*
1203269 CTCCACCACCACCTAAGCATGAGGAGAAGCCTTATGAATACAAGT
1 CTCCACCACCACC--A-CATAAGGAGAAGCCTTATGAATACAAGT
* *
1203314 CTCCACCACCACCACCTAAGGAGAAGCCTTATGAGTACAAGT
1 CTCCACCACCACCACATAAGGAGAAGCCTTATGAATACAAGT
1203356 CTCCACCACC
1 CTCCACCACC
1203366 TCCATCGCCT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
42 35 0.71
43 1 0.02
45 13 0.27
ACGTcount: A:0.33, C:0.35, G:0.15, T:0.16
Consensus pattern (42 bp):
CTCCACCACCACCACATAAGGAGAAGCCTTATGAATACAAGT
Found at i:1203336 original size:42 final size:43
Alignment explanation
Indices: 1203253--1203596 Score: 197
Period size: 48 Copynumber: 7.5 Consensus size: 43
1203243 TCCACCTCCA
* * *
1203253 TATGTGTACAAGTCTCCTCCACCACCACCTAAGCATGAGGAGAAGCCT
1 TATGAGTACAAGTCTCCACCACCACCACCT-----TAAGGAGAAGCCT
*
1203301 TATGAATACAAGTCTCCACCACCACCACC-TAAGGAGAAGCCT
1 TATGAGTACAAGTCTCCACCACCACCACCTTAAGGAGAAGCCT
* ****** **
1203343 TATGAGTACAAGTCTCCACCACCTCCATCGCCTTCTCCTCCACCTCCT
1 TATGAGTACAAGTCTCCACCACCACCA---CCTT-AAGGAGA-AGCCT
* * **** * **
1203391 TATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACCTCCT
1 TATGAGTACAAGTCTCCACCA---CCACCACCTTAAGGA-GA-AGCCT
* * *
1203439 TATGTGTACAAGTCTCCACCACCACCACCAAAGCATGAGGAGAAGCCT
1 TATGAGTACAAGTCTCCACCACCACCA-C----CTTAAGGAGAAGCCT
* * *
1203487 TATGAATACAAGTCTCCACCACCACCGCC-AAAGGAGAAGCCT
1 TATGAGTACAAGTCTCCACCACCACCACCTTAAGGAGAAGCCT
** *
1203529 TATGAGTACAAGTCTCCACCACCACCACCACCGAAGGAGAAACCT
1 TATGAGTACAAGTCTCCACCACCACCA-C-CTTAAGGAGAAGCCT
1203574 TATGAGTACAAGTCTCCACCACC
1 TATGAGTACAAGTCTCCACCACC
1203597 TCCTTATGAG
Statistics
Matches: 237, Mismatches: 41, Indels: 39
0.75 0.13 0.12
Matches are distributed among these distances:
42 73 0.31
43 2 0.01
44 1 0.00
45 41 0.17
46 2 0.01
47 3 0.01
48 107 0.45
49 1 0.00
50 3 0.01
51 4 0.02
ACGTcount: A:0.30, C:0.37, G:0.14, T:0.19
Consensus pattern (43 bp):
TATGAGTACAAGTCTCCACCACCACCACCTTAAGGAGAAGCCT
Found at i:1203414 original size:27 final size:26
Alignment explanation
Indices: 1203376--1203461 Score: 74
Period size: 27 Copynumber: 3.4 Consensus size: 26
1203366 TCCATCGCCT
*
1203376 TCTCCTCCACCTCCTTATGAGTACAAA
1 TCTCCACCACCTCCTTATG-GTACAAA
* **
1203403 TCTCCACCACCTCC--AT--CAC-CT
1 TCTCCACCACCTCCTTATGGTACAAA
*
1203424 TCTCCACCACCTCCTTATGTGTACAAG
1 TCTCCACCACCTCCTTATG-GTACAAA
1203451 TCTCCACCACC
1 TCTCCACCACC
1203462 ACCACCAAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
21 14 0.30
22 2 0.04
23 2 0.04
25 2 0.04
26 2 0.04
27 24 0.52
ACGTcount: A:0.22, C:0.45, G:0.06, T:0.27
Consensus pattern (26 bp):
TCTCCACCACCTCCTTATGGTACAAA
Found at i:1203467 original size:186 final size:186
Alignment explanation
Indices: 1203153--1203551 Score: 627
Period size: 186 Copynumber: 2.1 Consensus size: 186
1203143 CCCCTCCTCC
* * * * * * * *
1203153 GCCTTATGAGTATAAGTCACCACCGCCGCCTTCTCCTTCTCCACCGCCGCCTTATGTGTATAAAT
1 GCCTTATGAGTACAAGTCTCCACCACCGCCATCGCCTTCTCCACCACCGCCTTATGAGTACAAAT
* * * *
1203218 CTCCACCACCACCTTCACCTTCTCCTCCACCTCCATATGTGTACAAGTCTCCTCCACCACCACCT
66 CTCCACCACCACCATCACCTTCTCCACCACCTCCATATGTGTACAAGTCTCCACCACCACCACCA
*
1203283 AAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCTAAGGAGAA
131 AAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
* * *
1203339 GCCTTATGAGTACAAGTCTCCACCACCTCCATCGCCTTCTCCTCCACCTCCTTATGAGTACAAAT
1 GCCTTATGAGTACAAGTCTCCACCACCGCCATCGCCTTCTCCACCACCGCCTTATGAGTACAAAT
* *
1203404 CTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTACAAGTCTCCACCACCACCACCA
66 CTCCACCACCACCATCACCTTCTCCACCACCTCCATATGTGTACAAGTCTCCACCACCACCACCA
*
1203469 AAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCGCCAAAGGAGAA
131 AAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
1203525 GCCTTATGAGTACAAGTCTCCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACC
1203552 ACCACCACCG
Statistics
Matches: 194, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
186 194 1.00
ACGTcount: A:0.27, C:0.39, G:0.13, T:0.22
Consensus pattern (186 bp):
GCCTTATGAGTACAAGTCTCCACCACCGCCATCGCCTTCTCCACCACCGCCTTATGAGTACAAAT
CTCCACCACCACCATCACCTTCTCCACCACCTCCATATGTGTACAAGTCTCCACCACCACCACCA
AAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
Found at i:1203488 original size:48 final size:44
Alignment explanation
Indices: 1203436--1203596 Score: 218
Period size: 42 Copynumber: 3.6 Consensus size: 44
1203426 TCCACCACCT
*
1203436 CCTTATGTGTACAAGTCTCCACCACCACCACCAAAGCATGAGGAGAAG
1 CCTTATGAGTACAAGTCTCCACCACCACCACC-AAG-A--AGGAGAAG
* *
1203484 CCTTATGAATACAAGTCTCCACCACCACCGCC-A-AAGGAGAAG
1 CCTTATGAGTACAAGTCTCCACCACCACCACCAAGAAGGAGAAG
* *
1203526 CCTTATGAGTACAAGTCTCCACCACCACCACCACCGAAGGAGAAA
1 CCTTATGAGTACAAGTCTCCACCACCACCACCA-AGAAGGAGAAG
1203571 CCTTATGAGTACAAGTCTCCACCACC
1 CCTTATGAGTACAAGTCTCCACCACC
1203597 TCCTTATGAG
Statistics
Matches: 103, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
42 38 0.37
44 1 0.01
45 34 0.33
46 1 0.01
48 29 0.28
ACGTcount: A:0.34, C:0.34, G:0.16, T:0.16
Consensus pattern (44 bp):
CCTTATGAGTACAAGTCTCCACCACCACCACCAAGAAGGAGAAG
Found at i:1203551 original size:45 final size:45
Alignment explanation
Indices: 1203436--1203596 Score: 204
Period size: 45 Copynumber: 3.6 Consensus size: 45
1203426 TCCACCACCT
* *
1203436 CCTTATGTGTACAAGTCTCCACCACCACCACCAAAG-CATGAGGAGAAG
1 CCTTATGAGTACAAGTCTCCACCACCACCACC---GCCA-AAGGAGAAG
*
1203484 CCTTATGAATACAAGTCT---CCACCACCACCGCCAAAGGAGAAG
1 CCTTATGAGTACAAGTCTCCACCACCACCACCGCCAAAGGAGAAG
* * *
1203526 CCTTATGAGTACAAGTCTCCACCACCACCACCACCGAAGGAGAAA
1 CCTTATGAGTACAAGTCTCCACCACCACCACCGCCAAAGGAGAAG
1203571 CCTTATGAGTACAAGTCTCCACCACC
1 CCTTATGAGTACAAGTCTCCACCACC
1203597 TCCTTATGAG
Statistics
Matches: 102, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
42 26 0.25
43 2 0.02
45 58 0.57
48 16 0.16
ACGTcount: A:0.34, C:0.34, G:0.16, T:0.16
Consensus pattern (45 bp):
CCTTATGAGTACAAGTCTCCACCACCACCACCGCCAAAGGAGAAG
Found at i:1203605 original size:27 final size:26
Alignment explanation
Indices: 1203571--1203671 Score: 104
Period size: 27 Copynumber: 4.0 Consensus size: 26
1203561 GAAGGAGAAA
1203571 CCTTATGAGTACAAGTCTCCACCACCT
1 CCTTAT-AGTACAAGTCTCCACCACCT
*
1203598 CCTTATGAGTACAAATCTCCACCACCT
1 CCTTAT-AGTACAAGTCTCCACCACCT
* **
1203625 CC--AT--CAC-CTTCTCCACCACCT
1 CCTTATAGTACAAGTCTCCACCACCT
1203646 CCTTATATGTACAAGTCTCCACCACC
1 CCTTATA-GTACAAGTCTCCACCACC
1203672 ACCACCAAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
21 14 0.23
22 2 0.03
23 2 0.03
25 2 0.03
26 2 0.03
27 39 0.64
ACGTcount: A:0.26, C:0.42, G:0.07, T:0.26
Consensus pattern (26 bp):
CCTTATAGTACAAGTCTCCACCACCT
Found at i:1203610 original size:210 final size:212
Alignment explanation
Indices: 1203376--1203809 Score: 773
Period size: 210 Copynumber: 2.1 Consensus size: 212
1203366 TCCATCGCCT
*
1203376 TCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTA
1 TCTCCACCACCTCCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTA
*
1203441 TGTGTACAAGTCTCCACCACCACCACCAAAGCATGAGGAGAAGCCTTATGAATACAAG-T-CTCC
66 TATGTACAAGTCTCCACCACCACCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGCTCCTCC
* * *
1203504 ACCACCACCGCCAAAGGAGAAGCCTTATGAGTACAAGTCTCCACCACCACCACCACCGAAGGAGA
131 ACCACCACCACCAAAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCACCAAAGGAGA
*
1203569 AACCTTATGAGTACAAG
196 AACCTTATGAATACAAG
1203586 TCTCCACCACCTCCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTA
1 TCTCCACCACCTCCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTA
1203651 TATGTACAAGTCTCCACCACCACCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCTC
66 TATGTACAAGTCTCCACCACCACCACCAAAGCATGAGGAGAAGCCTTATGAATACAAG-CTCCTC
*
1203716 CACCACCACCACCAAAGGAGAAGCCTTATGAATACAAGTCTCCTCCACCACCACCACCAAAGGAG
130 CACCACCACCACCAAAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCACCAAAGGAG
*
1203781 AAGCCTTATGAATACAAG
195 AAACCTTATGAATACAAG
1203799 TCTCCACCACC
1 TCTCCACCACC
1203810 ACCACCAAAG
Statistics
Matches: 213, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
210 121 0.57
212 1 0.00
213 91 0.43
ACGTcount: A:0.31, C:0.38, G:0.12, T:0.19
Consensus pattern (212 bp):
TCTCCACCACCTCCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTA
TATGTACAAGTCTCCACCACCACCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGCTCCTCC
ACCACCACCACCAAAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCACCAAAGGAGA
AACCTTATGAATACAAG
Found at i:1203735 original size:45 final size:45
Alignment explanation
Indices: 1203655--1203816 Score: 261
Period size: 45 Copynumber: 3.5 Consensus size: 45
1203645 TCCTTATATG
* *
1203655 TACAAGTCTCCACCACCACCACCAAAGCATGAGGAGAAGCCTTATGAA
1 TACAAGTCTCCACCACCACCACC--ACCA-AAGGAGAAGCCTTATGAA
*
1203703 TACAAGTCTCCTCCACCACCACCACCAAAGGAGAAGCCTTATGAA
1 TACAAGTCTCCACCACCACCACCACCAAAGGAGAAGCCTTATGAA
*
1203748 TACAAGTCTCCTCCACCACCACCACCAAAGGAGAAGCCTTATGAA
1 TACAAGTCTCCACCACCACCACCACCAAAGGAGAAGCCTTATGAA
1203793 TACAAGTCTCCACCACCACCACCA
1 TACAAGTCTCCACCACCACCACCA
1203817 AAGCATGAAG
Statistics
Matches: 110, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
45 85 0.77
46 3 0.03
48 22 0.20
ACGTcount: A:0.36, C:0.36, G:0.13, T:0.15
Consensus pattern (45 bp):
TACAAGTCTCCACCACCACCACCACCAAAGGAGAAGCCTTATGAA
Found at i:1204016 original size:96 final size:96
Alignment explanation
Indices: 1203835--1204052 Score: 292
Period size: 96 Copynumber: 2.3 Consensus size: 96
1203825 AGAACAACCA
* * * * * *
1203835 CCATACTACTACAAGTCACCTCCTCCTCCATCTCCATCACCACCTCCTCCGTACTATTACAAGTC
1 CCATACTACTACAAGTCTCCTCCACCTCCATCACCATCACCACCACCACCGTACTACTACAAGTC
* * *
1203900 CCCACCGCCGCCTTCACCATCACCACCACCT
66 CCCACCACCGCCATCACCATCACCACCACCC
* *
1203931 CCATACTACTACAAGTCTCCTCCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAGTC
1 CCATACTACTACAAGTCTCCTCCACCTCCATCACCATCACCACCACCACCGTACTACTACAAGTC
* * *
1203996 CCCACCACCTCCATCTCCATCACCACCTCCC
66 CCCACCACCGCCATCACCATCACCACCACCC
* *
1204027 CCATACTACTACAAATCTCCACCACC
1 CCATACTACTACAAGTCTCCTCCACC
1204053 ACCACCAAAG
Statistics
Matches: 106, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 106 1.00
ACGTcount: A:0.25, C:0.51, G:0.03, T:0.21
Consensus pattern (96 bp):
CCATACTACTACAAGTCTCCTCCACCTCCATCACCATCACCACCACCACCGTACTACTACAAGTC
CCCACCACCGCCATCACCATCACCACCACCC
Found at i:1204101 original size:24 final size:24
Alignment explanation
Indices: 1204074--1204152 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
1204064 ATGAAGAACA
1204074 ACCACCATACTACTACAAGTCTCC
1 ACCACCATACTACTACAAGTCTCC
* *
1204098 ACCACCA-CCT-CCACATTACGTCT-C
1 ACCACCATACTACTACA--A-GTCTCC
*
1204122 ACCACCATACTACTACAAATCTCC
1 ACCACCATACTACTACAAGTCTCC
1204146 ACCACCA
1 ACCACCA
1204153 CCAGTGAAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
22 4 0.09
23 5 0.11
24 25 0.57
25 6 0.14
26 4 0.09
ACGTcount: A:0.33, C:0.46, G:0.03, T:0.19
Consensus pattern (24 bp):
ACCACCATACTACTACAAGTCTCC
Found at i:1204104 original size:27 final size:27
Alignment explanation
Indices: 1204074--1204155 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
1204064 ATGAAGAACA
1204074 ACCACCATACTACTACAAGTCTCCACC
1 ACCACCATACTACTACAAGTCTCCACC
*
1204101 ACCACC-TCCAC-ATTAC--GTCT----C
1 ACCACCAT--ACTACTACAAGTCTCCACC
*
1204122 ACCACCATACTACTACAAATCTCCACC
1 ACCACCATACTACTACAAGTCTCCACC
1204149 ACCACCA
1 ACCACCA
1204156 GTGAAGTCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 20
0.65 0.05 0.31
Matches are distributed among these distances:
20 2 0.05
21 11 0.26
22 1 0.02
23 3 0.07
25 4 0.10
26 1 0.02
27 18 0.43
28 2 0.05
ACGTcount: A:0.33, C:0.46, G:0.02, T:0.18
Consensus pattern (27 bp):
ACCACCATACTACTACAAGTCTCCACC
Found at i:1204126 original size:48 final size:49
Alignment explanation
Indices: 1203793--1204155 Score: 256
Period size: 48 Copynumber: 7.4 Consensus size: 49
1203783 GCCTTATGAA
* * * *
1203793 TACAAGTCTCCACCACCACCA-CCAAAGCATGAAGAACAACCACCATACTAC
1 TACAAGTCTCCACCACCACCATCC--ACCATCACG-ACCACCACCATACTAC
* * * * * * * * * *
1203844 TACAAGTCACCTCCTCCTCCAT-CTCCATCACCACCTCCTCCGTACTAT
1 TACAAGTCTCCACCACCACCATCCACCATCACGACCACCACCATACTAC
* * * * * *
1203892 TACAAGTCCCCACCGCCGCC-TTCACCATCACCACCACCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCCACCATCACGACCACCACCATACTAC
* * * * *
1203940 TACAAGTCTCCTCCACCTCCAT-CACCCTCACCACCACCACCTTACTAC
1 TACAAGTCTCCACCACCACCATCCACCATCACGACCACCACCATACTAC
* * * * * *
1203988 TACAAGTCCCCACCACCTCCAT-CTCCATCACCACCTCCCCCATACTAC
1 TACAAGTCTCCACCACCACCATCCACCATCACGACCACCACCATACTAC
* * * * *
1204036 TACAAATCTCCACCACCACCA-CCAAAGCATGAAGAACAACCACCATACTAC
1 TACAAGTCTCCACCACCACCATCC--ACCATCACG-ACCACCACCATACTAC
* *
1204087 TACAAGTCTCCACCACCACC-TCCA-CATTACGTCTCACCACCATACTAC
1 TACAAGTCTCCACCACCACCATCCACCATCACGAC-CACCACCATACTAC
*
1204135 TACAAATCTCCACCACCACCA
1 TACAAGTCTCCACCACCACCA
1204156 GTGAAGTCTC
Statistics
Matches: 249, Mismatches: 53, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
47 2 0.01
48 185 0.74
49 6 0.02
50 4 0.02
51 52 0.21
ACGTcount: A:0.31, C:0.47, G:0.04, T:0.18
Consensus pattern (49 bp):
TACAAGTCTCCACCACCACCATCCACCATCACGACCACCACCATACTAC
Found at i:1205234 original size:36 final size:36
Alignment explanation
Indices: 1205187--1205266 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 36
1205177 GTACTACTAT
*
1205187 AAGTCTCCACCTCCACCGACTC-CC-ACTTATGTTTAC
1 AAGTCACCACCTCCACC-AC-CACCAACTTATGTTTAC
1205223 AAGTCACCACCTCCACCACCACCAACTTATGTTTAC
1 AAGTCACCACCTCCACCACCACCAACTTATGTTTAC
1205259 AAGTCACC
1 AAGTCACC
1205267 TCCACCTCCT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
34 1 0.02
35 4 0.10
36 36 0.88
ACGTcount: A:0.28, C:0.41, G:0.07, T:0.24
Consensus pattern (36 bp):
AAGTCACCACCTCCACCACCACCAACTTATGTTTAC
Found at i:1205375 original size:150 final size:150
Alignment explanation
Indices: 1205178--1205752 Score: 954
Period size: 150 Copynumber: 3.8 Consensus size: 150
1205168 GCCACCACCG
* *
1205178 TACTACTATAAGTCTCCACCTCCACCGACTCCCACTTATGTTTACAAGTCACCACCTCCACCACC
1 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCACCTCCACCATC
* *
1205243 ACCAACTTATGTTTACAAGTCACCTCCACCTCCTGTGTACTACTACAAGTCTCCACCACCACCAA
66 GCCAACTTATGTTTACAAGTCACCTCCACCTCCCGTGTACTACTACAAGTCTCCACCACCACCAA
1205308 AGCATGAGGAGCAGCCCCCA
131 AGCATGAGGAGCAGCCCCCA
1205328 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCACCTCCACCATC
1 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCACCTCCACCATC
* * *
1205393 GCCGACTTATGTTTACAAGTCACCTCCACCTCCCGTGTACTACTATAAGTCTCCACCACCTCCAA
66 GCCAACTTATGTTTACAAGTCACCTCCACCTCCCGTGTACTACTACAAGTCTCCACCACCACCAA
1205458 AGCATGAGGAGCAGCCCCCA
131 AGCATGAGGAGCAGCCCCCA
* * ** *
1205478 TACTACTATAAATCTCCACCACCGTCGGCTCCCATTTATGTTTACAAGTCACCACCTCCACCATC
1 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCACCTCCACCATC
* *
1205543 GCCGAA-ATATATTTACAAGTCACCTCCACCTCCCGTGTACTACTACAAGTCTCCACCACCACCA
66 GCC-AACTTATGTTTACAAGTCACCTCCACCTCCCGTGTACTACTACAAGTCTCCACCACCACCA
1205607 AAGCATGAGGAGCAGCCCCCA
130 AAGCATGAGGAGCAGCCCCCA
1205628 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCACCTCCACCATC
1 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCACCTCCACCATC
** * * * *
1205693 GCCGGCTTATGTTTACAAGTCACCTCCACCACCTGTGTACTACTACAAATCACCACCACC
66 GCCAACTTATGTTTACAAGTCACCTCCACCTCCCGTGTACTACTACAAGTCTCCACCACC
1205753 TCCCACGTAT
Statistics
Matches: 393, Mismatches: 30, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
150 392 1.00
151 1 0.00
ACGTcount: A:0.27, C:0.39, G:0.11, T:0.23
Consensus pattern (150 bp):
TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCACCTCCACCATC
GCCAACTTATGTTTACAAGTCACCTCCACCTCCCGTGTACTACTACAAGTCTCCACCACCACCAA
AGCATGAGGAGCAGCCCCCA
Found at i:1205384 original size:36 final size:36
Alignment explanation
Indices: 1205337--1205416 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
1205327 ATACTACTAT
* * *
1205337 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* *
1205373 AAGTCACCACCTCCACCATCGCCGACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
1205409 AAGTCACC
1 AAGTCACC
1205417 TCCACCTCCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.24, C:0.40, G:0.11, T:0.25
Consensus pattern (36 bp):
AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
Found at i:1205684 original size:36 final size:36
Alignment explanation
Indices: 1205637--1205725 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 36
1205627 ATACTACTAT
* * *
1205637 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* **
1205673 AAGTCACCACCTCCACCATCGCCGGCTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* *
1205709 AAGTCACCTCCACCACC
1 AAGTCACCACCTCCACC
1205726 TGTGTACTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.22, C:0.43, G:0.11, T:0.24
Consensus pattern (36 bp):
AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
Found at i:1205860 original size:48 final size:47
Alignment explanation
Indices: 1205808--1207084 Score: 632
Period size: 48 Copynumber: 26.6 Consensus size: 47
1205798 GCAGCCCCCG
*
1205808 TACTATTACAAGTCCCCACCACCACCAGTTCAC-TCTCCATCACCACCA
1 TACTACTACAAGTCCCCACCACCACCA--TCACATCTCCATCACCACCA
* **** * *
1205856 TACTACTACAAGTCCCCACCACCACCGA-AACATGAAGAGCAGCCCCCA
1 TACTACTACAAGTCCCCACCACCACC-ATCACATCTCCATCA-CCACCA
* * * * *
1205904 TACTACTACAAATCTCCTCCTCCACCATCGCCATCTCC-TCCACCACCA
1 TACTACTACAAGTCCCCACCACCACCATC-ACATCTCCAT-CACCACCA
* * * ** ** *
1205952 TACTACTACAAATCCCCACCACCACCA-AAGCATGTAGAGAAGCCCCCA
1 TACTACTACAAGTCCCCACCACCACCATCA-CATCTCCATCA-CCACCA
* * * * *
1206000 TACTACTACAAATCTCCTCCACCACCATCGCCATCTCC-TCCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATC-ACATCTCCAT-CACCACCA
* * * * *
1206048 TACTACTACAAGTCTCCACCACCACCATCTCCATCACCACCCCCACCA
1 TACTACTACAAGTCCCCACCACCACCATC-ACATCTCCATCACCACCA
* * * *
1206096 TACTATTACAAATCACCC-CCACCACCATCGCCATCTCC-TCTTCCACCA
1 TACTACTACAAGTC-CCCACCACCACCATC-ACATCTCCATC-ACCACCA
* * ** ** *
1206144 TACTACTACAAGTCCCCACCACCACCGA-AACATGTAGAAGAGCCCCCA
1 TACTACTACAAGTCCCCACCACCACC-ATCACATCTCCATCA-CCACCA
* * *
1206192 TACTACTACAAATCTCCC-CCACCACCATCGCCATCTCC-TCCTCCACCA
1 TACTACTACAAGTC-CCCACCACCACCATC-ACATCTCCAT-CACCACCA
* * * *
1206240 TACTATTACAAGTCCCCACCACCACCTGTC-CATTCCCCACCACCACCA
1 TACTACTACAAGTCCCCACCACCACC-ATCACA-TCTCCATCACCACCA
* * * *
1206288 TACTACTACAAGTCTCCACCACCACCAGTC-CACTCCCCACCCCCACCA
1 TACTACTACAAGTCCCCACCACCACCA-TCACA-TCTCCATCACCACCA
** * ** **
1206336 TACTACTACAAGTCCCCACCACCACCAAAACATGTAGAGGAGCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACATCTCCATCA-CCACCA
* *
1206384 TACTACTACAAATCTCCC-CCACCACCATCGCCATCTCC-TCCACCACCA
1 TACTACTACAAGTC-CCCACCACCACCATC-ACATCTCCAT-CACCACCA
* * *
1206432 TACTATTACAAGTCCCCACCACCACCAGTC-CATTCCCCACCACCACCA
1 TACTACTACAAGTCCCCACCACCACCA-TCACA-TCTCCATCACCACCA
* * * * *
1206480 TACTACTACAAATCTCCTCCGCCACCATCACCATCTCC-TCCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCA-CATCTCCAT-CACCACCA
* * * * * * *
1206528 TACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATC-ACATCTCCATCACCACCA
* ** * ** ** *
1206576 TACTATTACAAGTCCCCACCACCACCAAAACATGTAGAGGAGCCCCCA
1 TACTACTACAAGTCCCCACCACCACCATCACATCTCCATCA-CCACCA
* * * *
1206624 TAC-ATCTACAAATCTCCTCCACCACCATCACCATCTCC-TCCTCCACCA
1 TACTA-CTACAAGTCCCCACCACCACCATCA-CATCTCCAT-CACCACCA
* * * *
1206672 TATTATTACAAGTCCCCGCCACCACCAGTC-CATTCTCCACCACCACCA
1 TACTACTACAAGTCCCCACCACCACCA-TCACA-TCTCCATCACCACCA
* * * * *
1206720 TACTATTACAAGTCCCCTCCTCCACCATCGCCATCTCC-TCCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATC-ACATCTCCAT-CACCACCA
* * * * * *
1206768 TACTACTACAAATCCCCACCACCACCATCTCCTTCACCACCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATC-ACATCTCCATCACCACCA
* * * * * * *
1206816 TACTACTACAAATCACCACCACCTCCAGTGAAAGCTCCAACACCTACC-
1 TACTACTACAAGTCCCCACCACCACCA-TCACATCTCCATCACC-ACCA
* * * * * *
1206864 TACCACTACAACTCCCCTCCTCCACCATCACCATCTTCTCCTC-CC-CCC
1 TACTACTACAAGTCCCCACCACCACCATCA-CATC-TC-CATCACCACCA
* * * * *
1206912 TACTACTACAAATCACCC-CCACCCCCAATGA-AGGCTCCAGCACCTACC-
1 TACTACTACAAGTC-CCCACCACCACC-ATCACA-TCTCCATCACC-ACCA
* * * * * * *
1206960 TACCACTACAACTCTCCTCCTCCACCATCACCATCTCC-TCCTCCCCCA
1 TACTACTACAAGTCCCCACCACCACCATCA-CATCTCCAT-CACCACCA
* *
1207008 TACTACTACAAATCTCCC-CCACCACCAGTC-CACTCTCCACCACCACCA
1 TACTACTACAAGTC-CCCACCACCACCA-TCACA-TCTCCATCACCACCA
* * * *
1207056 TACTACTACAAATCTCCACCTCCTCCATC
1 TACTACTACAAGTCCCCACCACCACCATC
1207085 TCCCTCACCA
Statistics
Matches: 930, Mismatches: 223, Indels: 153
0.71 0.17 0.12
Matches are distributed among these distances:
46 4 0.00
47 63 0.07
48 797 0.86
49 64 0.07
50 2 0.00
ACGTcount: A:0.29, C:0.48, G:0.05, T:0.19
Consensus pattern (47 bp):
TACTACTACAAGTCCCCACCACCACCATCACATCTCCATCACCACCA
Found at i:1205865 original size:96 final size:94
Alignment explanation
Indices: 1205765--1206553 Score: 792
Period size: 96 Copynumber: 8.2 Consensus size: 94
1205755 CCACGTATAT
* * * *
1205765 CTACAAGTCTCCACCACCACCAAAGCATGTAGAGCAGCCCCCGTACTATTACAAGTCCCCACCAC
1 CTACAAGTCCCCACCACCACCAAA-CATGTAGAGCAGCCCCCATACTACTACAAATCCCC-CCAC
*
1205830 CACCA--GTTCACTCTCCAT-CACCACCATACTA
64 CACCATCG-CCA-TCTCC-TCCACCACCATACTA
* * *
1205861 CTACAAGTCCCCACCACCACCGAAACATGAAGAGCAGCCCCCATACTACTACAAATCTCCTCCTC
1 CTACAAGTCCCCACCACCACC-AAACATGTAGAGCAGCCCCCATACTACTACAAATC-CCCCCAC
1205926 CACCATCGCCATCTCCTCCACCACCATACTA
64 CACCATCGCCATCTCCTCCACCACCATACTA
* * *
1205957 CTACAAATCCCCACCACCACCAAAGCATGTAGAGAAGCCCCCATACTACTACAAATCTCCTCCAC
1 CTACAAGTCCCCACCACCACCAAA-CATGTAGAGCAGCCCCCATACTACTACAAATC-CCCCCAC
*
1206022 CACCATCGCCATCTCCTCCTCCACCATACTA
64 CACCATCGCCATCTCCTCCACCACCATACTA
* * ** * * * *
1206053 CTACAAGTCTCCACCACCACC-ATC-TCCATCACCACCCCCACCATACTATTACAAATCACCCCC
1 CTACAAGTCCCCACCACCACCAAACATGTA-GAGCA-GCCC-CCATACTACTACAAATC-CCCCC
**
1206116 ACCACCATCGCCATCTCCTCTTCCACCATACTA
62 ACCACCATCGCCATCTCCTCCACCACCATACTA
1206149 CTACAAGTCCCCACCACCACCGAAACATGTAGAAG-AGCCCCCATACTACTACAAATCTCCCCCA
1 CTACAAGTCCCCACCACCACC-AAACATGTAG-AGCAGCCCCCATACTACTACAAATC-CCCCCA
*
1206213 CCACCATCGCCATCTCCTCCTCCACCATACTA
63 CCACCATCGCCATCTCCTCCACCACCATACTA
* *** ** * * * *
1206245 TTACAAGTCCCCACCACCACCTGTCCAT-TCCCCACCA-CCACCATACTACTACAAGTCTCCACC
1 CTACAAGTCCCCACCACCACC-AAACATGT--AGAGCAGCCCCCATACTACTACAAATC-CCCCC
* * *
1206308 ACCACCA--GTCCACTCCCCACCCCCACCATACTA
62 ACCACCATCG-CCA-TCTCCTCCACCACCATACTA
* *
1206341 CTACAAGTCCCCACCACCACCAAAACATGTAGAGGAGCCACCATACTACTACAAATCTCCCCCAC
1 CTACAAGTCCCCACCACCACC-AAACATGTAGAGCAGCCCCCATACTACTACAAATC-CCCCCAC
1206406 CACCATCGCCATCTCCTCCACCACCATACTA
64 CACCATCGCCATCTCCTCCACCACCATACTA
* ** ** * * *
1206437 TTACAAGTCCCCACCACCACCAGTCCAT-TCCCCACCA-CCACCATACTACTACAAATCTCCTCC
1 CTACAAGTCCCCACCACCACCA-AACATGT--AGAGCAGCCCCCATACTACTACAAATC-CCCCC
* * *
1206500 GCCACCATCACCATCTCCTCCTCCACCATACTA
62 ACCACCATCGCCATCTCCTCCACCACCATACTA
*
1206533 CTACAAGTCTCCACCACCACC
1 CTACAAGTCCCCACCACCACC
1206554 TTCTCCCTCA
Statistics
Matches: 591, Mismatches: 77, Indels: 50
0.82 0.11 0.07
Matches are distributed among these distances:
93 2 0.00
94 4 0.01
95 16 0.03
96 544 0.92
97 17 0.03
98 5 0.01
99 3 0.01
ACGTcount: A:0.30, C:0.47, G:0.06, T:0.17
Consensus pattern (94 bp):
CTACAAGTCCCCACCACCACCAAACATGTAGAGCAGCCCCCATACTACTACAAATCCCCCCACCA
CCATCGCCATCTCCTCCACCACCATACTA
Found at i:1205998 original size:192 final size:190
Alignment explanation
Indices: 1205765--1206553 Score: 986
Period size: 192 Copynumber: 4.1 Consensus size: 190
1205755 CCACGTATAT
* * * * *
1205765 CTACAAGTCTCCACCACCACCAAAGCATGTAGAGCAGCCCCCGTACTATTACAAGTC-CCCACCA
1 CTACAAGTCCCCACCACCACCAAAGCATGTAGAGAAGCCCCCATACTACTACAAATCTCCC-CCA
* * *
1205829 CCACCA--GTTCACTCTCCAT-CACCACCATACTACTACAAGTCCCCACCACCACCGAAACA-TG
65 CCACCATCG-CCA-TCTCC-TCCACCACCATACTACTACAAGTCCCCACCACCACC--ACCATTC
** * * * *
1205890 AAGAGCAGCCCCCATACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCATAC
125 ACCACCA-CCACCATACTACTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCATAC
1205955 TA
189 TA
* *
1205957 CTACAAATCCCCACCACCACCAAAGCATGTAGAGAAGCCCCCATACTACTACAAATCTCCTCCAC
1 CTACAAGTCCCCACCACCACCAAAGCATGTAGAGAAGCCCCCATACTACTACAAATCTCCCCCAC
* *
1206022 CACCATCGCCATCTCCTCCTCCACCATACTACTACAAGTCTCCACCACCACCATCTCCA-TCACC
66 CACCATCGCCATCTCCTCCACCACCATACTACTACAAGTCCCCACCACCACCA---CCATTCACC
* * * * *
1206086 ACCCCCACCATACTATTACAAATCACCCCCACCACCATCGCCATCTCCTCTTCCACCATACTA
128 ACCACCACCATACTACTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCATACTA
1206149 CTACAAGTCCCCACCACCACCGAAA-CATGTAGA-AGAGCCCCCATACTACTACAAATCTCCCCC
1 CTACAAGTCCCCACCACCACC-AAAGCATGTAGAGA-AGCCCCCATACTACTACAAATCTCCCCC
* * * *
1206212 ACCACCATCGCCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCTGTCCATTCCC
64 ACCACCATCGCCATCTCCTCCACCACCATACTACTACAAGTCCCCACCACCACC--ACCATTCAC
* * * * *
1206277 CACCACCACCATACTACTACAAGTCTCCACCACCACCA--GTCCACTCCCCACCCCCACCATACT
127 CACCACCACCATACTACTACAAATCTCCTCCACCACCATCG-CCA-TCTCCTCCTCCACCATACT
1206340 A
190 A
* * *
1206341 CTACAAGTCCCCACCACCACCAAAACATGTAGAGGAGCCACCATACTACTACAAATCTCCCCCAC
1 CTACAAGTCCCCACCACCACCAAAGCATGTAGAGAAGCCCCCATACTACTACAAATCTCCCCCAC
* *
1206406 CACCATCGCCATCTCCTCCACCACCATACTATTACAAGTCCCCACCACCACCAGTCCATTCCCCA
66 CACCATCGCCATCTCCTCCACCACCATACTACTACAAGTCCCCACCACCACCA--CCATTCACCA
* *
1206471 CCACCACCATACTACTACAAATCTCCTCCGCCACCATCACCATCTCCTCCTCCACCATACTA
129 CCACCACCATACTACTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCATACTA
*
1206533 CTACAAGTCTCCACCACCACC
1 CTACAAGTCCCCACCACCACC
1206554 TTCTCCCTCA
Statistics
Matches: 527, Mismatches: 50, Indels: 40
0.85 0.08 0.06
Matches are distributed among these distances:
190 2 0.00
191 11 0.02
192 497 0.94
193 16 0.03
194 1 0.00
ACGTcount: A:0.30, C:0.47, G:0.06, T:0.17
Consensus pattern (190 bp):
CTACAAGTCCCCACCACCACCAAAGCATGTAGAGAAGCCCCCATACTACTACAAATCTCCCCCAC
CACCATCGCCATCTCCTCCACCACCATACTACTACAAGTCCCCACCACCACCACCATTCACCACC
ACCACCATACTACTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCATACTA
Found at i:1206073 original size:240 final size:239
Alignment explanation
Indices: 1205808--1207075 Score: 1178
Period size: 240 Copynumber: 5.3 Consensus size: 239
1205798 GCAGCCCCCG
* * * * *
1205808 TACTATTACAAGTCCCCACCACCACCAGT-TCACTCTCCATCACCACCATACTACTACAAGTCCC
1 TACTACTACAAGTCTCCACCACCACCAGTCTCACTCACCACCACCACCATACTACTACAAATCCC
* * * *
1205872 CACCACCACCGAAACATGAAGAGCAGCCCCCATACTACTACAAATCTCCTCCTCCACCATCGCCA
66 CACCACCACCAAAACATGCAGAGCAGCCACCATACTACTACAAATCTCCTCCACCACCATCGCCA
* * ** ** *
1205937 TCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCAAAGCATGTAGAGAAGCCCCCATA
131 TCTCCTCCACCACCATACTACTACAAATCCCC-CCACCACCAATGCATCTCCACCA-CCACCATA
1206002 CTACTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCA
194 CTACTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCA
* *
1206048 TACTACTACAAGTCTCCACCACCACCA-TCTC-CATCACCACCCCCACCATACTATTACAAATCA
1 TACTACTACAAGTCTCCACCACCACCAGTCTCAC-TCACCACCACCACCATACTACTACAAATC-
*** **** ** * *
1206111 CCC-CCACCACCATCGCCAT-CTCCTCTTCCACCATACTACTAC-AA-GTCC-CCACCACCACCG
64 CCCACCACCACCA-AAACATGCAGAGCAGCCACCATACTACTACAAATCTCCTCCACCACCATCG
* * ***** * * *
1206171 AAACATGTAGAAGAGCCCCCATACTACTACAAATCTCCCCCACCACC-ATCGCCATCTCCTCCTC
128 --CCATCTCCTCCA-CCACCATACTACTACAAATC-CCCCCACCACCAAT-G-CATCTCCACCAC
* * * * * * *
1206235 CACCATACTATTACAAGTCCCCACCACCACC-T-GTCCATTCCCCACCACCACCA
187 CACCATACTACTACAAATCTCCTCCACCACCATCG-CCA-TCTCCTCCTCCACCA
* * *
1206288 TACTACTACAAGTCTCCACCACCACCAGTC-CACTCCCCACCCCCACCATACTACTACAAGTCCC
1 TACTACTACAAGTCTCCACCACCACCAGTCTCACTCACCACCACCACCATACTACTACAAATCCC
* * *
1206352 CACCACCACCAAAACATGTAGAGGAGCCACCATACTACTACAAATCTCCCCCACCACCATCGCCA
66 CACCACCACCAAAACATGCAGAGCAGCCACCATACTACTACAAATCTCCTCCACCACCATCGCCA
* * * * *
1206417 TCTCCTCCACCACCATACTATTACAAGTCCCCACCACCACCAGTCCATTCCCCACCACCACCATA
131 TCTCCTCCACCACCATACTACTACAAATCCCC-CCACCACCAATGCA-TCTCCACCACCACCATA
* *
1206482 CTACTACAAATCTCCTCCGCCACCATCACCATCTCCTCCTCCACCA
194 CTACTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCA
* * * * *
1206528 TACTACTACAAGTCTCCACCACCACC-TTCTCCCTCACCACCTCCACCATACTATTACAAGTCCC
1 TACTACTACAAGTCTCCACCACCACCAGTCTCACTCACCACCACCACCATACTACTACAAATCCC
* * * *
1206592 CACCACCACCAAAACATGTAGAGGAGCCCCCATAC-ATCTACAAATCTCCTCCACCACCATCACC
66 CACCACCACCAAAACATGCAGAGCAGCCACCATACTA-CTACAAATCTCCTCCACCACCATCGCC
* * * * * *
1206656 ATCTCCTCCTCCACCATATTATTACAAGTCCCCGCCACCACCAGTCCATTCTCCACCACCACCAT
130 ATCTCCTCCACCACCATACTACTACAAATCCCC-CCACCACCAATGCA-TCTCCACCACCACCAT
* * * *
1206721 ACTATTACAAGTCCCCTCCTCCACCATCGCCATCTCCTCCTCCACCA
193 ACTACTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCA
* * * *
1206768 TACTACTACAAATCCCCACCACCACCA-TCTC-CTTCACCACCTCCACCATACTACTACAAATCA
1 TACTACTACAAGTCTCCACCACCACCAGTCTCAC-TCACCACCACCACCATACTACTACAAATCC
* * * * * *
1206831 CCACCACCTCCAGTGAAAGC-TCCA-A-CA-CCTACC-TACCACTACAACTCCCCTCCTCCACCA
65 CCACCACCACCA---AAA-CATGCAGAGCAGCC-ACCATACTACTACAAATCTCCTCCACCACCA
* * * * * * * * *
1206891 TCACCATCTTCTCCTCCCCCCTACTACTACAAATCACCCCCACCCCCAATGAAGGCTCCAGCACC
125 TCGCCATCTCCTCCACCACCATACTACTACAAATC-CCCCCACCACCAATGCA-TCTCCACCACC
* * * * *
1206956 TACC-TACCACTACAACTCTCCTCCTCCACCATCACCATCTCCTCCTCCCCCA
188 -ACCATACTACTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCA
* * * *
1207008 TACTACTACAAATCTCCCCCACCACCAGTC-CACTCTCCACCACCACCATACTACTACAAATCTC
1 TACTACTACAAGTCTCCACCACCACCAGTCTCACTCACCACCACCACCATACTACTACAAATCCC
1207072 CACC
66 CACC
1207076 TCCTCCATCT
Statistics
Matches: 850, Mismatches: 140, Indels: 76
0.80 0.13 0.07
Matches are distributed among these distances:
237 10 0.01
238 4 0.00
239 29 0.03
240 745 0.88
241 41 0.05
242 4 0.00
243 16 0.02
244 1 0.00
ACGTcount: A:0.29, C:0.48, G:0.05, T:0.19
Consensus pattern (239 bp):
TACTACTACAAGTCTCCACCACCACCAGTCTCACTCACCACCACCACCATACTACTACAAATCCC
CACCACCACCAAAACATGCAGAGCAGCCACCATACTACTACAAATCTCCTCCACCACCATCGCCA
TCTCCTCCACCACCATACTACTACAAATCCCCCCACCACCAATGCATCTCCACCACCACCATACT
ACTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCA
Found at i:1206327 original size:21 final size:21
Alignment explanation
Indices: 1206252--1206335 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 21
1206242 CTATTACAAG
* *
1206252 TCCCCACCACCACCTGTCCAT
1 TCCCCACCACCACCAGTCCAC
1206273 TCCCCACCACCACCA-TACTACTAC
1 TCCCCACCACCACCAGT-C--C-AC
*
1206297 AAGTCTCCACCACCACCAGTCCAC
1 ---TCCCCACCACCACCAGTCCAC
*
1206321 TCCCCACCCCCACCA
1 TCCCCACCACCACCA
1206336 TACTACTACA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
20 1 0.02
21 28 0.56
23 1 0.02
24 3 0.06
25 1 0.02
27 15 0.30
28 1 0.02
ACGTcount: A:0.25, C:0.57, G:0.04, T:0.14
Consensus pattern (21 bp):
TCCCCACCACCACCAGTCCAC
Found at i:1206568 original size:96 final size:96
Alignment explanation
Indices: 1205850--1207112 Score: 805
Period size: 96 Copynumber: 13.2 Consensus size: 96
1205840 CTCTCCATCA
** * * ** * *
1205850 CCACCATACTACTACAAGTCCCCACCACCACC-GAAACATGAAGAGCAGCCCCCATACTACTACA
1 CCACCATACTACTACAAGTCCCCACCACCACCTTCACCATCACCACCA-CCACCATACTACTACA
* * *
1205914 AATCTCCTCCTCCACCATCGCCATCTCCTCCA
65 AATCTCCTCCACCACCATCACCATCTCCTCCT
* ** * * * ** *
1205946 CCACCATACTACTACAAATCCCCACCACCACC-AAAGCATGTA-GAGAAGCCCCCATACTACTAC
1 CCACCATACTACTACAAGTCCCCACCACCACCTTCACCAT-CACCACCA-CCACCATACTACTAC
*
1206009 AAATCTCCTCCACCACCATCGCCATCTCCTCCT
64 AAATCTCCTCCACCACCATCACCATCTCCTCCT
* * * * *
1206042 CCACCATACTACTACAAGTCTCCACCACCACCATCTCCATCACCACCCCCACCATACTATTACAA
1 CCACCATACTACTACAAGTCCCCACCACCACCTTCACCATCACCACCACCACCATACTACTACAA
* * * *
1206107 ATCACCCCCACCACCATCGCCATCTCCTCTT
66 ATCTCCTCCACCACCATCACCATCTCCTCCT
** * * * ** *
1206138 CCACCATACTACTACAAGTCCCCACCACCACC-GAAACATGTA-GAAGAGCCCCCATACTACTAC
1 CCACCATACTACTACAAGTCCCCACCACCACCTTCACCAT-CACCACCA-CCACCATACTACTAC
* *
1206201 AAATCTCCCCCACCACCATCGCCATCTCCTCCT
64 AAATCTCCTCCACCACCATCACCATCTCCTCCT
* *
1206234 CCACCATACTATTACAAGTCCCCACCACCACCTGT--CCATTCCCCACCACCACCATACTACTAC
1 CCACCATACTACTACAAGTCCCCACCACCACCT-TCACCA-TCACCACCACCACCATACTACTAC
* * * * *
1206297 AAGTCTCCACCACCACCAGT--CCACTCCCCACCC
64 AAATCTCCTCCACCACCA-TCACCA-TCTCCTCCT
** * * * **
1206330 CCACCATACTACTACAAGTCCCCACCACCACC-AAAACATGTA-GAGGAGCCACCATACTACTAC
1 CCACCATACTACTACAAGTCCCCACCACCACCTTCACCAT-CACCACCA-CCACCATACTACTAC
* * *
1206393 AAATCTCCCCCACCACCATCGCCATCTCCTCCA
64 AAATCTCCTCCACCACCATCACCATCTCCTCCT
* * *
1206426 CCACCATACTATTACAAGTCCCCACCACCACCAGT--CCATTCCCCACCACCACCATACTACTAC
1 CCACCATACTACTACAAGTCCCCACCACCACC-TTCACCA-TCACCACCACCACCATACTACTAC
*
1206489 AAATCTCCTCCGCCACCATCACCATCTCCTCCT
64 AAATCTCCTCCACCACCATCACCATCTCCTCCT
* * * * *
1206522 CCACCATACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCATACTATTACAA
1 CCACCATACTACTACAAGTCCCCACCACCACCTTCACCATCACCACCACCACCATACTACTACAA
* * * * * * ******
1206587 GTCCCCACCACCACCA-AAACATGTAGAGGAG
66 ATCTCCTCCACCACCATCACCATCT-CCTCCT
* * * * * * * * * *
1206618 CCCCCATAC-ATCTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATATTATTACA
1 CCACCATACTA-CTACAAGTCCCCACCACCACCTTCACCATCACCACCACCACCATACTACTACA
* * * * *
1206682 AGTCCCCGCCACCACCAGT--CCATTCTCCACCA
65 AATCTCCTCCACCACCA-TCACCA-TCTCCTCCT
* * * * * * * *
1206714 CCACCATACTATTACAAGTCCCCTCCTCCACCATCGCCATCTCCTCCTCCACCATACTACTACAA
1 CCACCATACTACTACAAGTCCCCACCACCACCTTCACCATCACCACCACCACCATACTACTACAA
* * * * * *
1206779 ATCCCCACCACCACCATCTCCTTCACCACCT
66 ATCTCCTCCACCACCATCACCATCTCCTCCT
* * * * * * * * * *
1206810 CCACCATACTACTACAAATCACCACCACCTCCAGTGA-AAGCTCCAACACCTACC-TACCACTAC
1 CCACCATACTACTACAAGTCCCCACCACCACC-TTCACCATCACCACCACC-ACCATACTACTAC
* * * *
1206873 AACTCCCCTCCTCCACCATCACCATCTTCTCCT
64 AAATCTCCTCCACCACCATCACCATCTCCTCCT
* * * * * * * * * *
1206906 CCCCCCTACTACTACAAATCACCC-CCACCCCCAATGA--AGGCTCCAGCACCTACC-TACCACT
1 CCACCATACTACTACAAGTC-CCCACCACCACC-TTCACCA-TCACCACCACC-ACCATACTACT
* *
1206967 ACAACTCTCCTCCTCCACCATCACCATCTCCTCCT
62 ACAAATCTCCTCCACCACCATCACCATCTCCTCCT
* * * *
1207002 CCCCCATACTACTACAAATCTCCC-CCACCACCAGT--CCACTCTCCACCACCACCATACTACTA
1 CCACCATACTACTACAAGTC-CCCACCACCACC-TTCACCA-TCACCACCACCACCATACTACTA
* * * * * * *
1207064 CAAATCTCCACCTCCTCCATCTCCCTCACCACCT
63 CAAATCTCCTCCACCACCATCACCATCTCCTCCT
*
1207098 CCTCCATACTACTAC
1 CCACCATACTACTAC
1207113 CACTCACCTC
Statistics
Matches: 955, Mismatches: 174, Indels: 76
0.79 0.14 0.06
Matches are distributed among these distances:
95 23 0.02
96 904 0.95
97 28 0.03
ACGTcount: A:0.28, C:0.48, G:0.04, T:0.19
Consensus pattern (96 bp):
CCACCATACTACTACAAGTCCCCACCACCACCTTCACCATCACCACCACCACCATACTACTACAA
ATCTCCTCCACCACCATCACCATCTCCTCCT
Found at i:1206576 original size:192 final size:192
Alignment explanation
Indices: 1205901--1207112 Score: 939
Period size: 192 Copynumber: 6.3 Consensus size: 192
1205891 AGAGCAGCCC
* * *
1205901 CCATACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCATACTACTACAAATC
1 CCATACTACTACAAATCTCCTCCTCCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
* * ** * *
1205966 CCCACCACCACC-AAAGCATGTAGAGAAGC-CC-CCATACTACTACAAATCTCCTCCACCACCAT
66 CCCACCACCACCAAAACCA--TACACCACCTCCACCATACTACTACAAATCTCCCCCACCACCAT
* * * * *
1206028 CGCCATCTCCTCCTCCACCATACTACTACAAGTCTCCACCACCACCATCTCCATCACCACCCCCA
129 CGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCA-GTCCATCTCCACCACCA
* * * * * *
1206093 CCATACTATTACAAATCACCCCCACCACCATCGCCATCTCCTCTTCCACCATACTACTACAAGTC
1 CCATACTACTACAAATCTCCTCCTCCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
* * ** *
1206158 CCCACCACCACCGAAA-CATGTAGAAGAGC-CC-CCATACTACTACAAATCTCCCCCACCACCAT
66 CCCACCACCACCAAAACCA--TACACCACCTCCACCATACTACTACAAATCTCCCCCACCACCAT
* * * *
1206220 CGCCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCTGTCCATTCCCCACCACCA
129 CGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGTCCA-TCTCCACCACCA
* * * * * *
1206285 CCATACTACTACAAGTCTCCACCACCACCAGT--CCACTCCCCACCCCCACCATACTACTACAAG
1 CCATACTACTACAAATCTCCTCCTCCACCA-TCACCA-TCTCCTCCTCCACCATACTACTACAAG
* ** *
1206348 TCCCCACCACCACCAAAA-CATGTAGAGGA--GCCACCATACTACTACAAATCTCCCCCACCACC
64 TCCCCACCACCACCAAAACCA--TACACCACCTCCACCATACTACTACAAATCTCCCCCACCACC
* * * *
1206410 ATCGCCATCTCCTCCACCACCATACTATTACAAGTCCCCACCACCACCAGTCCATTCCCCACCAC
127 ATCGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGTCCA-TCTCCACCAC
1206475 CA
191 CA
*
1206477 CCATACTACTACAAATCTCCTCCGCCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
1 CCATACTACTACAAATCTCCTCCTCCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
* **** * * * *
1206542 TCCACCACCACCTTCTCCCT-CACCACCTCCACCATACTATTACAAGTC-CCCACCACCACCA-A
66 CCCACCACCACCAAAACCATACACCACCTCCACCATACTACTACAAATCTCCC-CCACCACCATC
** * ****** * * * * *
1206604 AACATGTAGAGGAGCCCCCATAC-ATCTACAAATCTCCTCCACCACCA-TCACCATCTCCTCCTC
130 GCCATCT-CCTCCTCCACCATACTA-CTACAAATCCCCACCACCACCAGT--CCATCTCCACCAC
1206667 CA
191 CA
* * * * * * * * *
1206669 CCATATTATTACAAGTCCCCGCCACCACCAGT--CCATTCTCCACCACCACCATACTATTACAAG
1 CCATACTACTACAAATCTCCTCCTCCACCA-TCACCA-TCTCCTCCTCCACCATACTACTACAAG
* * *** * *
1206732 TCCCCTCCTCCACCATCGCCAT-CTCCTCCTCCACCATACTACTACAAATC-CCCACCACCACCA
64 TCCCCACCACCACCAAAACCATACACCACCTCCACCATACTACTACAAATCTCCC-CCACCACCA
* * * * * * ** * *
1206795 TCTCCTTCACCACCTCCACCATACTACTACAAATCACCACCACCTCCAGTGAAAGCTCCAACACC
128 TCGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGT-CCATCTCCACCACC
1206860 TA
192 -A
* * * * * * *
1206862 CC-TACCACTACAACTCCCCTCCTCCACCATCACCATCTTCTCCTCCCCCCTACTACTACAAATC
1 CCATACTACTACAAATCTCCTCCTCCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
* * * * * * * *
1206926 ACCC-CCACCCCCAATGAAGGC-TCCAGCACCT--ACC-TACCACTACAACTCTCCTCCTCCACC
66 -CCCACCACCACCAA--AA-CCATACACCACCTCCACCATACTACTACAAATCTCCCCCACCACC
* *
1206986 ATCACCATCTCCTCCTCCCCCATACTACTACAAATCTCCC-CCACCACCAGTCCACTCTCCACCA
127 ATCGCCATCTCCTCCTCCACCATACTACTACAAATC-CCCACCACCACCAGTCCA-TCTCCACCA
1207050 CCA
190 CCA
* * * * * * *
1207053 CCATACTACTACAAATCTCCACCTCCTCCATCTCCCTCACCACCTCCTCCATACTACTAC
1 CCATACTACTACAAATCTCCTCCTCCACCATCACCATCTCCTCCTCCACCATACTACTAC
1207113 CACTCACCTC
Statistics
Matches: 832, Mismatches: 155, Indels: 66
0.79 0.15 0.06
Matches are distributed among these distances:
190 2 0.00
191 28 0.03
192 763 0.92
193 32 0.04
194 1 0.00
195 6 0.01
ACGTcount: A:0.28, C:0.49, G:0.04, T:0.19
Consensus pattern (192 bp):
CCATACTACTACAAATCTCCTCCTCCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC
CCCACCACCACCAAAACCATACACCACCTCCACCATACTACTACAAATCTCCCCCACCACCATCG
CCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGTCCATCTCCACCACCA
Found at i:1206769 original size:144 final size:141
Alignment explanation
Indices: 1205808--1207112 Score: 870
Period size: 144 Copynumber: 9.1 Consensus size: 141
1205798 GCAGCCCCCG
* * * *
1205808 TACTATTACAAGTCCCCACCACCACCAGTTCACTCTCCATCACCACCATACTACTACAAGTCCCC
1 TACTACTACAAATCCCCACCACCACCAGTCCA-TCTCCACCACCACCATACTACTACAAGTCCCC
** **** ** * * * *
1205873 ACCACCACCGAAACATGAAGAGCAGCCCCCATACTACTACAAATCTCCTCCTCCACCATCGCCAT
65 ACCACCACC-AGCCATCTCCA-CCTCCACCATACTACTACAAATCTCCACCACCACCATCACCAT
*
1205938 CTCCTCCACCACCA
128 CTCCTCCTCCACCA
*** * ** ** * * *
1205952 TACTACTACAAATCCCCACCACCACCAAAGCATGTAGAGAAGCCCCCATACTACTACAAATCTCC
1 TACTACTACAAATCCCCACCACCACCAGTCCATCTCCACCA-CCACCATACTACTACAAGTCCCC
* * * *
1206017 TCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAGTCTCCACCACCACCATCTCCAT
65 ACCACCACCA--GCCATCTCCACCTCCACCATACTACTACAAATCTCCACCACCACCATCACCAT
* * *
1206082 CACCACCCCCACCA
128 CTCCTCCTCCACCA
* * **
1206096 TACTATTACAAATCACCC-CCACCACCA-TCGCCATCTCCTCTTCCACCATACTACTACAAGTCC
1 TACTACTACAAATC-CCCACCACCACCAGT--CCATCTCCACCACCACCATACTACTACAAGTCC
** * ** *** * * *
1206159 CCACCACCACCGAAACATGTAGAAGAGCCCCCATACTACTACAAATCTCCCCCACCACCATCGCC
63 CCACCACCACC-AGCCATCT-CCACCTCCACCATACTACTACAAATCTCCACCACCACCATCACC
1206224 ATCTCCTCCTCCACCA
126 ATCTCCTCCTCCACCA
* * * * *
1206240 TACTATTACAAGTCCCCACCACCACCTGTCCATTCCCCACCACCACCATACTACTACAAGTCTCC
1 TACTACTACAAATCCCCACCACCACCAGTCCA-TCTCCACCACCACCATACTACTACAAGTCCCC
* * * * * *
1206305 ACCACCACCAGTCCACTCCCCACCCCCACCATACTACTACAAGTCCCCACCACCACCA-AAACAT
65 ACCACCACCAG-CCA-TCTCCACCTCCACCATACTACTACAAATCTCCACCACCACCATCACCAT
* ******
1206369 GTAGAGGAGCCACCA
128 CT-CCTCCTCCACCA
* *
1206384 TACTACTACAAATCTCCC-CCACCACCA-TCGCCATCTCCTCCACCACCATACTATTACAAGTCC
1 TACTACTACAAATC-CCCACCACCACCAGT--CCATCTCCACCACCACCATACTACTACAAGTCC
* * * *
1206447 CCACCACCACCAGTCCATTCCCCACCACCACCATACTACTACAAATCTCCTCCGCCACCATCACC
63 CCACCACCACCAG-CCA-TCTCCACCTCCACCATACTACTACAAATCTCCACCACCACCATCACC
1206512 ATCTCCTCCTCCACCA
126 ATCTCCTCCTCCACCA
* * ** * * * *
1206528 TACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCATACTATTACAAGTCCCC
1 TACTACTACAAATCCCCACCACCACC-AGTCCATCTCCACCACCACCATACTACTACAAGTCCCC
** * ** *** * *
1206593 ACCACCACCAAAACATGTAGAGGAGCCCCCATAC-ATCTACAAATCTCCTCCACCACCATCACCA
65 ACCACCACC-AGCCATCTCCA-CCTCCACCATACTA-CTACAAATCTCCACCACCACCATCACCA
1206657 TCTCCTCCTCCACCA
127 TCTCCTCCTCCACCA
* * * * *
1206672 TATTATTACAAGTCCCCGCCACCACCAGTCCATTCTCCACCACCACCATACTATTACAAGTCCCC
1 TACTACTACAAATCCCCACCACCACCAGTCCA-TCTCCACCACCACCATACTACTACAAGTCCCC
* * * * * *
1206737 TCCTCCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCATCTCCTT
65 ACCACCACCA--GCCATCTCCACCTCCACCATACTACTACAAATCTCCACCACCACCATCACCAT
* *
1206802 CACCACCTCCACCA
128 CTCCTCCTCCACCA
* * ** * * * *
1206816 TACTACTACAAATCACCACCACCTCCAGTGAAAGCTCCAACACCTACC-TACCACTACAACTCCC
1 TACTACTACAAATCCCCACCACCACCAGT-CCATCTCCACCACC-ACCATACTACTACAAGTCCC
* * * * * * * * * * *
1206880 CTCCTCCACCATCACCATCTTCTCCTCCCCCCTACTACTACAAATCACCCCCACCCCCAATGA--
64 CACCACCACCA--GCCATCTCCACCTCCACCATACTACTACAAATCTCCACCACCACC-ATCACC
* ** *
1206943 AGGCTCCAGCACCTACC-
126 A-TCTCCTCCTCC-ACCA
* * * * * * * * *
1206960 TACCACTACAACTCTCCTCCTCCACCA-TCACCATCTCCTCCTCCCCCATACTACTACAAATCTC
1 TACTACTACAAATCCCCACCACCACCAGT--CCATCTCCACCACCACCATACTACTACAAGTC-C
* * * *
1207024 CC-CCACCACCAGTCCACTCTCCACCACCACCATACTACTACAAATCTCCACCTCCTCCATCTCC
63 CCACCACCACCAG-CCA-TCTCCACCTCCACCATACTACTACAAATCTCCACCACCACCATCACC
* * * *
1207088 CTCACCACCTCCTCCA
126 ATCTCCTCCTCCACCA
1207104 TACTACTAC
1 TACTACTAC
1207113 CACTCACCTC
Statistics
Matches: 899, Mismatches: 221, Indels: 82
0.75 0.18 0.07
Matches are distributed among these distances:
143 40 0.04
144 816 0.91
145 42 0.05
146 1 0.00
ACGTcount: A:0.28, C:0.48, G:0.04, T:0.19
Consensus pattern (141 bp):
TACTACTACAAATCCCCACCACCACCAGTCCATCTCCACCACCACCATACTACTACAAGTCCCCA
CCACCACCAGCCATCTCCACCTCCACCATACTACTACAAATCTCCACCACCACCATCACCATCTC
CTCCTCCACCA
Found at i:1207118 original size:27 final size:27
Alignment explanation
Indices: 1207037--1207120 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
1207027 CACCACCAGT
* * *
1207037 CCACTCTCCACCACCACCATACTACTA
1 CCACTCACCACCTCCTCCATACTACTA
* * *
1207064 CAAATCTCCACCTCCTCC--A-T-CT-
1 CCACTCACCACCTCCTCCATACTACTA
1207086 CC-CTCACCACCTCCTCCATACTACTA
1 CCACTCACCACCTCCTCCATACTACTA
1207112 CCACTCACC
1 CCACTCACC
1207121 TCCCCCACCA
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
21 13 0.30
22 1 0.02
23 3 0.07
24 2 0.05
25 3 0.07
26 2 0.05
27 20 0.45
ACGTcount: A:0.25, C:0.54, G:0.00, T:0.21
Consensus pattern (27 bp):
CCACTCACCACCTCCTCCATACTACTA
Found at i:1210365 original size:27 final size:27
Alignment explanation
Indices: 1210311--1210365 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1210301 GCTAATGTTA
* *
1210311 ATAAATTTAACTATTATAATAAATATT
1 ATAAAATTAACTATTATAAGAAATATT
*
1210338 ATAAAATTAATTATTATAGAGAAA-ATT
1 ATAAAATTAACTATTATA-AGAAATATT
1210365 A
1 A
1210366 ATTGTACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (27 bp):
ATAAAATTAACTATTATAAGAAATATT
Found at i:1210742 original size:15 final size:15
Alignment explanation
Indices: 1210722--1210752 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1210712 CCATCTTTTC
*
1210722 TATGTTTGGTTTTAA
1 TATGTTTGGTTGTAA
1210737 TATGTTTGGTTGTAA
1 TATGTTTGGTTGTAA
1210752 T
1 T
1210753 TGTAATACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (15 bp):
TATGTTTGGTTGTAA
Found at i:1219533 original size:55 final size:55
Alignment explanation
Indices: 1219473--1219614 Score: 144
Period size: 55 Copynumber: 2.5 Consensus size: 55
1219463 TTAATATAAT
* * *
1219473 ATTTGGTACATGAATTTGACATTTTTTTTAAATTGGTATTTAAAAC-TTT-GACTTA
1 ATTTGGTAC-TGAACTTGACATTTTTTCTAAATTGGTACTT-AAACTTTTGGACTTA
* * * *
1219528 ATTTGGTATCTGAACTTGATATTTTTCCTGATTTGGTACTTAAACTTTTTTTGGACTTA
1 ATTTGGTA-CTGAACTTGACATTTTTTCTAAATTGGTACTTAAAC---TTTTGGACTTA
1219587 ATTTGGTACTTGAACTTGACATTTTTTC
1 ATTTGGTAC-TGAACTTGACATTTTTTC
1219615 CTAATTTCGT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
54 4 0.06
55 32 0.45
56 1 0.01
58 4 0.06
59 30 0.42
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (55 bp):
ATTTGGTACTGAACTTGACATTTTTTCTAAATTGGTACTTAAACTTTTGGACTTA
Found at i:1219637 original size:59 final size:59
Alignment explanation
Indices: 1219522--1219639 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 59
1219512 TTAAAACTTT
* * * *
1219522 GACTTAATTTGGTATCTGAACTTGATATTTTTCCTGATTTGGTACTTAAACTTTTTTTG
1 GACTTAATTTGGTATCTGAACTTGACATTTTTCCTAATTTCGTACCTAAACTTTTTTTG
**
1219581 GACTTAATTTGGTA-CTTGAACTTGACATTTTTTCCTAATTTCGTACCTATTCTTTTTTT
1 GACTTAATTTGGTATC-TGAACTTGACA-TTTTTCCTAATTTCGTACCTAAACTTTTTTT
1219640 TTAATTCAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 1 0.02
59 24 0.47
60 26 0.51
ACGTcount: A:0.21, C:0.14, G:0.13, T:0.52
Consensus pattern (59 bp):
GACTTAATTTGGTATCTGAACTTGACATTTTTCCTAATTTCGTACCTAAACTTTTTTTG
Found at i:1219918 original size:26 final size:26
Alignment explanation
Indices: 1219856--1219918 Score: 63
Period size: 30 Copynumber: 2.3 Consensus size: 26
1219846 ATTGGACCCC
**
1219856 AAAAAGTTTAAGTACCAACTTAAAAA
1 AAAAAGTTTAAGTACCAAAATAAAAA
*
1219882 AAATGTCAAGTTTAGGTACCAAAATAAAAA
1 AAA----AAGTTTAAGTACCAAAATAAAAA
1219912 AAAAAGT
1 AAAAAGT
1219919 ATCAAGTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
26 7 0.23
30 23 0.77
ACGTcount: A:0.57, C:0.10, G:0.11, T:0.22
Consensus pattern (26 bp):
AAAAAGTTTAAGTACCAAAATAAAAA
Found at i:1226463 original size:3 final size:3
Alignment explanation
Indices: 1226455--1226480 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1226445 CCTGGGGCTT
1226455 CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CT
1226481 ACCAATAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:1228004 original size:33 final size:33
Alignment explanation
Indices: 1227944--1228006 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1227934 GTCAACAGGC
* **
1227944 ACAGTCAAGTGCTAATATGTACAGCCAACCGAT
1 ACAGCCAAGTGCTAATACATACAGCCAACCGAT
* *
1227977 ACAGCCAAGTGCTAATCCATACGGCCAACC
1 ACAGCCAAGTGCTAATACATACAGCCAACC
1228007 TGCACAGCCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.17
Consensus pattern (33 bp):
ACAGCCAAGTGCTAATACATACAGCCAACCGAT
Found at i:1228014 original size:33 final size:32
Alignment explanation
Indices: 1227942--1228024 Score: 76
Period size: 33 Copynumber: 2.5 Consensus size: 32
1227932 TGGTCAACAG
* **
1227942 GCACAGTCAAGTGCTAATATGTACAGCCAACC
1 GCACAGCCAAGTGCTAATACATACAGCCAACC
* * *
1227974 GATACAGCCAAGTGCTAATCCATACGGCCAACC
1 G-CACAGCCAAGTGCTAATACATACAGCCAACC
**
1228007 TGCACAGCCTGGTGCTAA
1 -GCACAGCCAAGTGCTAA
1228025 CGCATATGAC
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
32 1 0.03
33 38 0.95
34 1 0.03
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.18
Consensus pattern (32 bp):
GCACAGCCAAGTGCTAATACATACAGCCAACC
Found at i:1240221 original size:28 final size:28
Alignment explanation
Indices: 1240169--1240222 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1240159 TTTAAAGCAT
* * **
1240169 GATTGAAATATTTTAAATTCGAAAAACA
1 GATTGAAAAATTTTAAAATAAAAAAACA
1240197 GATTGAAAAATTTTAAAATAAAAAAA
1 GATTGAAAAATTTTAAAATAAAAAAA
1240223 TAGGCTTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (28 bp):
GATTGAAAAATTTTAAAATAAAAAAACA
Found at i:1247791 original size:33 final size:33
Alignment explanation
Indices: 1247754--1247817 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1247744 AGTTAACGTT
1247754 TAATTCACTGAT-TGCAGCATAAAAAAGTGATTG
1 TAATT-ACTGATATGCAGCATAAAAAAGTGATTG
* * *
1247787 TAATTAGTGTTATGCAGTATAAAAAAGTGAT
1 TAATTACTGATATGCAGCATAAAAAAGTGAT
1247818 CCAGAGCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.33
Consensus pattern (33 bp):
TAATTACTGATATGCAGCATAAAAAAGTGATTG
Found at i:1248500 original size:21 final size:21
Alignment explanation
Indices: 1248475--1248519 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1248465 GCTTCCCTCA
* *
1248475 CTTGCCTCGTTGTTGCCTTTG
1 CTTGCCTCGTTGCTGCCTCTG
*
1248496 CTTGCCTTGTTGCTGCCTCTG
1 CTTGCCTCGTTGCTGCCTCTG
1248517 CTT
1 CTT
1248520 TAAGTTGTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.31, G:0.22, T:0.47
Consensus pattern (21 bp):
CTTGCCTCGTTGCTGCCTCTG
Found at i:1250460 original size:10 final size:10
Alignment explanation
Indices: 1250445--1250493 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
1250435 GTTGTTTTTT
1250445 ATAATTAAAA
1 ATAATTAAAA
1250455 ATAATTAAATA
1 ATAATTAAA-A
* *
1250466 TTTAATTAAAC
1 -ATAATTAAAA
*
1250477 ATAATTAAAT
1 ATAATTAAAA
1250487 ATAATTA
1 ATAATTA
1250494 TTTAATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 8 0.24
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
ATAATTAAAA
Found at i:1250524 original size:22 final size:22
Alignment explanation
Indices: 1250446--1250558 Score: 101
Period size: 22 Copynumber: 5.3 Consensus size: 22
1250436 TTGTTTTTTA
*
1250446 TAATTAAAAATAATTAAATATT
1 TAATTAAATATAATTAAATATT
*
1250468 TAATTAAACATAATTAAATA--
1 TAATTAAATATAATTAAATATT
*
1250488 TAATT--ATTTAATTAAATATT
1 TAATTAAATATAATTAAATATT
* *
1250508 TAATTAAATAGAATTAAATAAT
1 TAATTAAATATAATTAAATATT
* ***
1250530 TAAATCTTTCA-AATTAAATATT
1 TAATTAAAT-ATAATTAAATATT
1250552 TAATTAA
1 TAATTAA
1250559 CTAATATTGT
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
18 11 0.15
20 10 0.14
22 50 0.69
23 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (22 bp):
TAATTAAATATAATTAAATATT
Found at i:1250586 original size:76 final size:74
Alignment explanation
Indices: 1250496--1250675 Score: 256
Period size: 76 Copynumber: 2.4 Consensus size: 74
1250486 TATAATTATT
*
1250496 TAATTAAATATTTAATTAAATAGAATTAAATAATTAAATCTTTCAAATTAAATATTTAATTAACT
1 TAATT-AATATTTAATTAAATA-AATTAAATAATTAAATCTTTCAAATTAAAGATTTAATTAACT
1250561 AATATTGTTTA
64 AATATTGTTTA
* * *
1250572 TAATTAACTATTTAATTAAACATAATTAAATAATTAAATCTTTTAAATTAAAGATTTAATTAATT
1 TAATTAA-TATTTAATTAAATA-AATTAAATAATTAAATCTTTCAAATTAAAGATTTAATTAACT
*
1250637 GATATTGTTTA
64 AATATTGTTTA
*
1250648 TAATTAA-ATATAATTAAAT-AATTAAATA
1 TAATTAATATTTAATTAAATAAATTAAATA
1250676 TAATTATTTA
Statistics
Matches: 95, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
72 9 0.09
74 10 0.11
75 2 0.02
76 74 0.78
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (74 bp):
TAATTAATATTTAATTAAATAAATTAAATAATTAAATCTTTCAAATTAAAGATTTAATTAACTAA
TATTGTTTA
Found at i:1250591 original size:44 final size:42
Alignment explanation
Indices: 1250456--1250558 Score: 138
Period size: 40 Copynumber: 2.5 Consensus size: 42
1250446 TAATTAAAAA
* * *
1250456 TAATTAAATATTTAATTAAACATAATTAAAT-A-TAATTATT
1 TAATTAAATATTTAATTAAATAGAATTAAATAATTAAATATT
*
1250496 TAATTAAATATTTAATTAAATAGAATTAAATAATTAAATCTT
1 TAATTAAATATTTAATTAAATAGAATTAAATAATTAAATATT
1250538 TCAAATTAAATATTTAATTAA
1 T--AATTAAATATTTAATTAA
1250559 CTAATATTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
40 29 0.53
41 1 0.02
42 7 0.13
44 18 0.33
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (42 bp):
TAATTAAATATTTAATTAAATAGAATTAAATAATTAAATATT
Found at i:1250661 original size:10 final size:10
Alignment explanation
Indices: 1250646--1250694 Score: 61
Period size: 10 Copynumber: 5.3 Consensus size: 10
1250636 TGATATTGTT
1250646 TATAATTAAA
1 TATAATTAAA
1250656 TATAATT-AA
1 TATAATTAAA
1250665 -ATAATTAAA
1 TATAATTAAA
1250674 TATAATT--A
1 TATAATTAAA
*
1250682 TTTAATTAAA
1 TATAATTAAA
1250692 TAT
1 TAT
1250695 TTATTCATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
8 13 0.39
9 4 0.12
10 16 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TATAATTAAA
Found at i:1250670 original size:18 final size:18
Alignment explanation
Indices: 1250647--1250694 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1250637 GATATTGTTT
1250647 ATAATTAAATATAATTAA
1 ATAATTAAATATAATTAA
*
1250665 ATAATTAAATATAATTAT
1 ATAATTAAATATAATTAA
*
1250683 TTAATTAAATAT
1 ATAATTAAATAT
1250695 TTATTCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATTAAATATAATTAA
Found at i:1255325 original size:12 final size:12
Alignment explanation
Indices: 1255308--1255338 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1255298 CATAGCTTGA
*
1255308 AATGCTTAGGGT
1 AATGCTTAGGAT
1255320 AATGCTTAGGAT
1 AATGCTTAGGAT
1255332 AATGCTT
1 AATGCTT
1255339 GAAAAGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.35
Consensus pattern (12 bp):
AATGCTTAGGAT
Found at i:1263884 original size:28 final size:29
Alignment explanation
Indices: 1263830--1263885 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
1263820 AATTTGATTC
* *
1263830 TTAAAAATGATAATTTTTTTATTTAATAT
1 TTAAAAATGATAATATTTTTATATAATAT
1263859 TTAAAAAT-AT-ATATTTTTATCATAATA
1 TTAAAAATGATAATATTTTTAT-ATAATA
1263886 AAAATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.38
28 7 0.29
29 8 0.33
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
TTAAAAATGATAATATTTTTATATAATAT
Found at i:1265040 original size:23 final size:22
Alignment explanation
Indices: 1265021--1265067 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1265011 TTAGCTTGTT
1265021 TTATTAATTTTGTTTGGCTTTTA
1 TTATT-ATTTTGTTTGGCTTTTA
* *
1265044 TTATTCTTTTGTTTGACTTTTA
1 TTATTATTTTGTTTGGCTTTTA
1265066 TT
1 TT
1265068 TTTGAACGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.15, C:0.06, G:0.11, T:0.68
Consensus pattern (22 bp):
TTATTATTTTGTTTGGCTTTTA
Found at i:1265418 original size:33 final size:33
Alignment explanation
Indices: 1265380--1265479 Score: 200
Period size: 33 Copynumber: 3.0 Consensus size: 33
1265370 TGTTAAACTC
1265380 TACCAAAAATAAGTTAAAAAACAATAAACTATT
1 TACCAAAAATAAGTTAAAAAACAATAAACTATT
1265413 TACCAAAAATAAGTTAAAAAACAATAAACTATT
1 TACCAAAAATAAGTTAAAAAACAATAAACTATT
1265446 TACCAAAAATAAGTTAAAAAACAATAAACTATT
1 TACCAAAAATAAGTTAAAAAACAATAAACTATT
1265479 T
1 T
1265480 CAGAATATAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.60, C:0.12, G:0.03, T:0.25
Consensus pattern (33 bp):
TACCAAAAATAAGTTAAAAAACAATAAACTATT
Found at i:1276312 original size:14 final size:14
Alignment explanation
Indices: 1276293--1276320 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1276283 ACATTTTTGA
1276293 AGTGAAAATCGCAT
1 AGTGAAAATCGCAT
1276307 AGTGAAAATCGCAT
1 AGTGAAAATCGCAT
1276321 CATCATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AGTGAAAATCGCAT
Found at i:1277500 original size:19 final size:19
Alignment explanation
Indices: 1277476--1277523 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1277466 AAAATTTATA
1277476 ATTAAATTATTTTAAAAAT
1 ATTAAATTATTTTAAAAAT
1277495 ATTAAATTATTTTAAAAAT
1 ATTAAATTATTTTAAAAAT
1277514 ATTAAATTAT
1 ATTAAATTAT
1277524 GATTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTAAATTATTTTAAAAAT
Found at i:1277502 original size:24 final size:23
Alignment explanation
Indices: 1277464--1277522 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 23
1277454 ATAAATATAA
1277464 TTAAAAT-TTATAATTAAATTATT
1 TTAAAATATTA-AATTAAATTATT
1277487 TTAAAA-A-T--ATTAAATTATT
1 TTAAAATATTAAATTAAATTATT
1277506 TTAAAAATATTAAATTA
1 TT-AAAATATTAAATTA
1277523 TGATTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 1 0.03
22 2 0.07
23 6 0.20
24 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAAAATATTAAATTAAATTATT
Found at i:1278836 original size:28 final size:28
Alignment explanation
Indices: 1278804--1278862 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
1278794 ATCTTCAAAT
*
1278804 AGAGGTAAAACTTGTAACTTCTGTAAGA
1 AGAGGTAAAACTTGTAACTTCTGCAAGA
1278832 AGAGGTAAAACTTGTAACTTCTGCAAGA
1 AGAGGTAAAACTTGTAACTTCTGCAAGA
1278860 AGA
1 AGA
1278863 AAAGGCACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (28 bp):
AGAGGTAAAACTTGTAACTTCTGCAAGA
Found at i:1279584 original size:399 final size:399
Alignment explanation
Indices: 1278846--1279644 Score: 1400
Period size: 399 Copynumber: 2.0 Consensus size: 399
1278836 GTAAAACTTG
*
1278846 TAACTTCTGCAAGAAGAAAAGGCACATTAAAAAAAAGAGCTACAAGTTACAAAATAAGATCAAAA
1 TAACTTCTACAAGAAGAAAAGGCACATTAAAAAAAAGAGCTACAAGTTACAAAATAAGATCAAAA
1278911 AGGAGGCAGAGAATCAAAAGGGAAAAAAACTAGAACAATCTGGTGAAGTTGATGTAGTAGAAGAC
66 AGGAGGCAGAGAATCAAAAGGGAAAAAAACTAGAACAATCTGGTGAAGTTGATGTAGTAGAAGAC
*
1278976 TACAGTGATGGTGAACTCCTACTTGCTTCTGTCGATAATTCTAAAGTGAGCGAGGAGTGGATCCT
131 TACAGTGATGGTGAACTCCTACTTGCTTCTGTCGATAATTCTAAAATGAGCGAGGAGTGGATCCT
* *
1279041 CGATTCTGGTTGCACCTTTCATATGAGTCCCAATCGGGATTGGTTTACAACATATGAAGTTGTGT
196 CGATTCTGATTGCACCTTCCATATGAGTCCCAATCGGGATTGGTTTACAACATATGAAGTTGTGT
* * *
1279106 CTGAAGGTGTTGTTTTGATGGGAAATAATGCTTCATGTAAAATCGCAGGTGTTGGCACAATCAAA
261 CTGAAGGTGTTATTTTGATGGGAAATAATGCTTCATGTAAAATCACAGGTGTTGGCACAATAAAA
**
1279171 ATAAAGATGTTTGATGGGGTCGTTAGAACTCTTAGTGGCGTGCGACATGTACCAGAATTGACATG
326 ATAAAGATGTTTGATAAGGTCGTTAGAACTCTTAGTGGCGTGCGACATGTACCAGAATTGACATG
1279236 AAATTTGAT
391 AAATTTGAT
* * * * *
1279245 TAACTTCTATAAGAAGAAAGGGCACATTAAGAAAGAGTGCTACAAGTTACAAAATAAGATCAAAA
1 TAACTTCTACAAGAAGAAAAGGCACATTAAAAAAAAGAGCTACAAGTTACAAAATAAGATCAAAA
* * * *
1279310 GGGAGGCAGAGAATCAAAAGGGAAAACAACTAGAATAATTTGGTGAAGTTGATGTAGTAGAAGAC
66 AGGAGGCAGAGAATCAAAAGGGAAAAAAACTAGAACAATCTGGTGAAGTTGATGTAGTAGAAGAC
*
1279375 TACAGTGATGGTGAACTCCTACTTGCTTCTGTCGATAATTTTAAAATGAGCGAGGAGTGGATCCT
131 TACAGTGATGGTGAACTCCTACTTGCTTCTGTCGATAATTCTAAAATGAGCGAGGAGTGGATCCT
1279440 CGATTCTGATTGCACCTTCCATATGAGTCCCAATCGGGATTGGTTTACAACATATGAAGTTGTGT
196 CGATTCTGATTGCACCTTCCATATGAGTCCCAATCGGGATTGGTTTACAACATATGAAGTTGTGT
* *
1279505 TTGGAGGTGTTATTTTGATGGGAAATAATGCTTCATGTAAAATCACAGGTGTTGGCACAATAAAA
261 CTGAAGGTGTTATTTTGATGGGAAATAATGCTTCATGTAAAATCACAGGTGTTGGCACAATAAAA
1279570 ATAAAGATGTTTGATAAGGTCGTTAGAACTCTTAGTGGCGTGCGACATGTACCAGAATTGACATG
326 ATAAAGATGTTTGATAAGGTCGTTAGAACTCTTAGTGGCGTGCGACATGTACCAGAATTGACATG
*
1279635 GAATTTGAT
391 AAATTTGAT
1279644 T
1 T
1279645 TCGTTGAGTA
Statistics
Matches: 378, Mismatches: 22, Indels: 0
0.94 0.05 0.00
Matches are distributed among these distances:
399 378 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (399 bp):
TAACTTCTACAAGAAGAAAAGGCACATTAAAAAAAAGAGCTACAAGTTACAAAATAAGATCAAAA
AGGAGGCAGAGAATCAAAAGGGAAAAAAACTAGAACAATCTGGTGAAGTTGATGTAGTAGAAGAC
TACAGTGATGGTGAACTCCTACTTGCTTCTGTCGATAATTCTAAAATGAGCGAGGAGTGGATCCT
CGATTCTGATTGCACCTTCCATATGAGTCCCAATCGGGATTGGTTTACAACATATGAAGTTGTGT
CTGAAGGTGTTATTTTGATGGGAAATAATGCTTCATGTAAAATCACAGGTGTTGGCACAATAAAA
ATAAAGATGTTTGATAAGGTCGTTAGAACTCTTAGTGGCGTGCGACATGTACCAGAATTGACATG
AAATTTGAT
Found at i:1284820 original size:21 final size:22
Alignment explanation
Indices: 1284796--1284836 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1284786 TTGGTCCAGT
*
1284796 TTGTTTTTTTAGT-TTGTTTAG
1 TTGTATTTTTAGTCTTGTTTAG
1284817 TTGTATTTTTAGTCTTGTTT
1 TTGTATTTTTAGTCTTGTTT
1284837 CATTAGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.10, C:0.02, G:0.17, T:0.71
Consensus pattern (22 bp):
TTGTATTTTTAGTCTTGTTTAG
Found at i:1300712 original size:58 final size:58
Alignment explanation
Indices: 1300636--1300776 Score: 205
Period size: 58 Copynumber: 2.4 Consensus size: 58
1300626 CATGATTATC
*
1300636 TATGAATTATCCTAGGACATTATCGGTGGA-AATAATAAATTGAAGAAAGTTAACTTGAA
1 TATG-ATTATCCTAGGACATTATCGGT-GACAATAATAAATTGAAGAAAATTAACTTGAA
*
1300695 TAT-ACTTATCCTAGGACATTATCGGTGACAATAATAAATTGAGGAAAATTAACTTGAA
1 TATGA-TTATCCTAGGACATTATCGGTGACAATAATAAATTGAAGAAAATTAACTTGAA
*
1300753 TGTGGATTATCCTAGGACATTATC
1 TAT-GATTATCCTAGGACATTATC
1300777 TGAGGATTTT
Statistics
Matches: 75, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
57 3 0.04
58 50 0.67
59 21 0.28
60 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (58 bp):
TATGATTATCCTAGGACATTATCGGTGACAATAATAAATTGAAGAAAATTAACTTGAA
Found at i:1302024 original size:22 final size:22
Alignment explanation
Indices: 1301999--1302059 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
1301989 TAAAAATGAT
* **
1301999 AAATTTTTATTTAATATTTTAA
1 AAATTATTATTTAATATAATAA
1302021 AAATATATT-TTT-ATCATAATAA
1 AAAT-TATTATTTAAT-ATAATAA
1302043 AAATTATTATTTAATAT
1 AAATTATTATTTAATAT
1302060 CGATTCCTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 6 0.19
22 21 0.66
23 5 0.16
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
AAATTATTATTTAATATAATAA
Found at i:1305714 original size:25 final size:25
Alignment explanation
Indices: 1305680--1305749 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
1305670 AGATTTGACC
1305680 CTTGACCTTTCACCTACTAAAAACT
1 CTTGACCTTTCACCTACTAAAAACT
1305705 CTTGACCTTTCACCTACTAAAAACT
1 CTTGACCTTTCACCTACTAAAAACT
*
1305730 CTTGATCTTTCACCTACTAA
1 CTTGACCTTTCACCTACTAA
1305750 CTTCTAAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.30, C:0.31, G:0.04, T:0.34
Consensus pattern (25 bp):
CTTGACCTTTCACCTACTAAAAACT
Found at i:1310062 original size:25 final size:25
Alignment explanation
Indices: 1310034--1310097 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
1310024 GACCCTTGGT
1310034 CTTTCACCTACTAAAAACTCTTGAC
1 CTTTCACCTACTAAAAACTCTTGAC
*
1310059 CTTTCACCTACTAAAAACTCTTGAT
1 CTTTCACCTACTAAAAACTCTTGAC
1310084 CTTTCACCTACTAA
1 CTTTCACCTACTAA
1310098 CTTCTAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.34
Consensus pattern (25 bp):
CTTTCACCTACTAAAAACTCTTGAC
Found at i:1317799 original size:79 final size:79
Alignment explanation
Indices: 1317697--1317862 Score: 233
Period size: 79 Copynumber: 2.1 Consensus size: 79
1317687 AGGTGTGACT
* * *
1317697 CAAAGCTCGCAGTTCGCAAAAGAGCTTGCACCAAGGAAACAAGAAAATCACCAAGCAAGGGGAAT
1 CAAAGCTCGCAATTCGCAAAAGAGCTCGCAACAAGGAAACAAGAAAATCACCAAGCAAGGGGAAT
1317762 GTTATGAGTATTCA
66 GTTATGAGTATTCA
* * * * * * *
1317776 CAAAGCTCGCAATTCGTAGAAGAGCTCGTAACAGGGAGACAAGAAAGTCACCAAGCAGGGGGAAT
1 CAAAGCTCGCAATTCGCAAAAGAGCTCGCAACAAGGAAACAAGAAAATCACCAAGCAAGGGGAAT
1317841 GTTATGAGTATTCA
66 GTTATGAGTATTCA
*
1317855 CAGAGCTC
1 CAAAGCTC
1317863 ATGGTTCTCA
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (79 bp):
CAAAGCTCGCAATTCGCAAAAGAGCTCGCAACAAGGAAACAAGAAAATCACCAAGCAAGGGGAAT
GTTATGAGTATTCA
Found at i:1321939 original size:6 final size:6
Alignment explanation
Indices: 1321930--1321954 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1321920 TTTTATATTT
1321930 AGAGGC AGAGGC AGAGGC AGAGGC A
1 AGAGGC AGAGGC AGAGGC AGAGGC A
1321955 AAGGGTCGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.48, T:0.00
Consensus pattern (6 bp):
AGAGGC
Found at i:1329138 original size:6 final size:6
Alignment explanation
Indices: 1329127--1329163 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1329117 TTTGATATTT
1329127 AGAGGC AGAGGC AGAGGC AGAGGC AGAGGC AGAGGC A
1 AGAGGC AGAGGC AGAGGC AGAGGC AGAGGC AGAGGC A
1329164 AAGGATCGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.49, T:0.00
Consensus pattern (6 bp):
AGAGGC
Found at i:1343678 original size:13 final size:13
Alignment explanation
Indices: 1343660--1343684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1343650 CATCCATACA
1343660 CTAAATTTTTATT
1 CTAAATTTTTATT
1343673 CTAAATTTTTAT
1 CTAAATTTTTAT
1343685 GTAATTTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
CTAAATTTTTATT
Found at i:1353945 original size:27 final size:27
Alignment explanation
Indices: 1353907--1353963 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
1353897 AGGCTCCAAC
*
1353907 CAATCCCTTTGGTGCCATCCTTAAGGT
1 CAATCCCTTTGGTGCCATCCTTAAAGT
1353934 CAATCCCTTTGGTGCCATCCTTAAAGT
1 CAATCCCTTTGGTGCCATCCTTAAAGT
1353961 CAA
1 CAA
1353964 CTCTTTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.32
Consensus pattern (27 bp):
CAATCCCTTTGGTGCCATCCTTAAAGT
Found at i:1355440 original size:6 final size:6
Alignment explanation
Indices: 1355429--1355466 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
1355419 TTAAATCTAT
1355429 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TT
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TT
1355467 TTTAAATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TTAAAA
Found at i:1368900 original size:29 final size:31
Alignment explanation
Indices: 1368841--1368917 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 31
1368831 TGCTTGTTTA
* * *
1368841 ATCTTTAATTTTATAAATATAATGATAATTT
1 ATCTATAATATTATATATATAATGATAATTT
*
1368872 -T-TATAATATTATATATATATAT-ATTATTT
1 ATCTATAATATTATATATATA-ATGATAATTT
*
1368901 ATCTAT-ATATTAAATAT
1 ATCTATAATATTATATAT
1368918 CTTTTTTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 21 0.55
30 14 0.37
31 3 0.08
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (31 bp):
ATCTATAATATTATATATATAATGATAATTT
Found at i:1368918 original size:15 final size:15
Alignment explanation
Indices: 1368877--1368919 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1368867 AATTTTTATA
*
1368877 ATATTATATATATAT
1 ATATTATATATCTAT
*
1368892 ATATTATTTATCTAT
1 ATATTATATATCTAT
*
1368907 ATATTAAATATCT
1 ATATTATATATCT
1368920 TTTTTATATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTATATATCTAT
Found at i:1368946 original size:22 final size:23
Alignment explanation
Indices: 1368921--1368963 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1368911 TAAATATCTT
1368921 TTTTATATCT-TA-GTTATATTTC
1 TTTTATAT-TATATGTTATATTTC
1368943 TTTTATATTATATGTTATATT
1 TTTTATATTATATGTTATATT
1368964 GATTATTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.05
22 10 0.53
23 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (23 bp):
TTTTATATTATATGTTATATTTC
Found at i:1374922 original size:6 final size:6
Alignment explanation
Indices: 1374913--1374944 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1374903 GGCTCCAGTG
1374913 CCAGCA CCAGCA CCAGCA CCAGCA CCAGCA CC
1 CCAGCA CCAGCA CCAGCA CCAGCA CCAGCA CC
1374945 GGAGACTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
CCAGCA
Found at i:1376158 original size:21 final size:21
Alignment explanation
Indices: 1376134--1376173 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1376124 GAAATAAAAA
*
1376134 TATTTAATATTATTATATTAT
1 TATTCAATATTATTATATTAT
* *
1376155 TATTCAATTTTTTTATATT
1 TATTCAATATTATTATATT
1376174 TTAAATTCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTCAATATTATTATATTAT
Found at i:1379751 original size:13 final size:14
Alignment explanation
Indices: 1379728--1379760 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1379718 ACATTATTAA
*
1379728 ATTTGTTTCAATTT
1 ATTTTTTTCAATTT
1379742 -TTTTTTTCAATTT
1 ATTTTTTTCAATTT
1379755 ATTTTT
1 ATTTTT
1379761 GATACGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (14 bp):
ATTTTTTTCAATTT
Found at i:1380844 original size:137 final size:135
Alignment explanation
Indices: 1380691--1381010 Score: 437
Period size: 137 Copynumber: 2.3 Consensus size: 135
1380681 AATATTTTTT
1380691 AAAAATATAATTAATATATAAATTTATTTCATACAAAATATTAATGATATATATTTTACCGAATT
1 AAAAATATAATTAATATATAAATTTA-TTCATACAAAATATTAATG-TATATATTTTACCGAATT
* * ** *
1380756 TATTAATATAAATAATTGTATTAATTAATTTCGGTCAGAATAT-AAAAGACATAAAAATTAATAT
64 TATTAATATAAACAATTATATTAATTAATTTCAATCAAAATATAAAAAG-CATAAAAATTAATAT
***
1380820 TCTT-TTGA
128 T-TTAAAAA
* *
1380828 AAAAATATAATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTACTGAATT
1 AAAAATATAATTAATATATAAATTT-ATTCATACAAAATATTAA-TGTATATATTTTACCGAATT
* *
1380893 TATTAATATAAACAGTTATATTAATTAATTTCAATCAAAATATAAAAAGCATGAAAATTAATATT
64 TATTAATATAAACAATTATATTAATTAATTTCAATCAAAATATAAAAAGCATAAAAATTAATATT
1380958 TTAAAAAA
129 TT-AAAAA
*
1380966 AAAAATATAATTAATATATGAAATTGATTCATACAAAATATTAAT
1 AAAAATATAATTAATATAT-AAATTTATTCATACAAAATATTAAT
1381011 TGTTAAACGA
Statistics
Matches: 163, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
136 2 0.01
137 111 0.68
138 46 0.28
139 4 0.02
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (135 bp):
AAAAATATAATTAATATATAAATTTATTCATACAAAATATTAATGTATATATTTTACCGAATTTA
TTAATATAAACAATTATATTAATTAATTTCAATCAAAATATAAAAAGCATAAAAATTAATATTTT
AAAAA
Found at i:1383238 original size:13 final size:13
Alignment explanation
Indices: 1383222--1383248 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1383212 AAAAAAGGGG
1383222 AAAAAAAAGGAAA
1 AAAAAAAAGGAAA
1383235 AAAAAAAAGGAAA
1 AAAAAAAAGGAAA
1383248 A
1 A
1383249 TTCTTGGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGGAAA
Found at i:1391700 original size:16 final size:16
Alignment explanation
Indices: 1391675--1391705 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1391665 GAATCCAACT
*
1391675 TAAAATAACCCTAACA
1 TAAAACAACCCTAACA
1391691 TAAAACAACCCTAAC
1 TAAAACAACCCTAAC
1391706 CCAAAATGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (16 bp):
TAAAACAACCCTAACA
Found at i:1393825 original size:21 final size:21
Alignment explanation
Indices: 1393799--1393839 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1393789 CAACAAAAGG
1393799 AAAAAGAGTTAGCGACGAAAC
1 AAAAAGAGTTAGCGACGAAAC
* *
1393820 AAAAAGATTTGGCGACGAAA
1 AAAAAGAGTTAGCGACGAAA
1393840 GATATTACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.12, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGTTAGCGACGAAAC
Found at i:1398289 original size:25 final size:24
Alignment explanation
Indices: 1398239--1398314 Score: 102
Period size: 25 Copynumber: 3.2 Consensus size: 24
1398229 CAACAAAAAT
* *
1398239 AAAATTTAATCT-AAAAAAAAGGG
1 AAAATCTAATCTAAAAAAAAAGAG
1398262 AAAATCTAATCTAAAAAGAAAAGAG
1 AAAATCTAATCTAAAAA-AAAAGAG
1398287 AAAATCTAATCTAAAAATAAAA-AG
1 AAAATCTAATCTAAAAA-AAAAGAG
1398311 AAAA
1 AAAA
1398315 AAAAACTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
23 11 0.23
24 10 0.21
25 27 0.56
ACGTcount: A:0.66, C:0.07, G:0.09, T:0.18
Consensus pattern (24 bp):
AAAATCTAATCTAAAAAAAAAGAG
Found at i:1412326 original size:57 final size:57
Alignment explanation
Indices: 1412257--1412367 Score: 222
Period size: 57 Copynumber: 1.9 Consensus size: 57
1412247 TAGGGTTTGA
1412257 ACTTTTTTTTATCTAAGTTAGTATTTAATATTTCCTTGAAAATTCTAAAATTCATGT
1 ACTTTTTTTTATCTAAGTTAGTATTTAATATTTCCTTGAAAATTCTAAAATTCATGT
1412314 ACTTTTTTTTATCTAAGTTAGTATTTAATATTTCCTTGAAAATTCTAAAATTCA
1 ACTTTTTTTTATCTAAGTTAGTATTTAATATTTCCTTGAAAATTCTAAAATTCA
1412368 AGTCTTAACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.50
Consensus pattern (57 bp):
ACTTTTTTTTATCTAAGTTAGTATTTAATATTTCCTTGAAAATTCTAAAATTCATGT
Found at i:1421972 original size:2 final size:2
Alignment explanation
Indices: 1421967--1421998 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1421957 ATGCATATTA
1421967 AT AT AT 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 AT AT AT
1421999 CATAAATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1422266 original size:22 final size:21
Alignment explanation
Indices: 1422237--1422307 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
1422227 AATTAAAAAA
1422237 TTTTATTGTTTTTCTTGCT-TT
1 TTTTATTGTTTTTC-TGCTATT
*
1422258 TTTTAATTGTTTTGCTGCTATTT
1 TTTT-ATTGTTTTTCTGCTA-TT
* *
1422281 TTTTGTTGTTTTTC-ACTATT
1 TTTTATTGTTTTTCTGCTATT
1422301 TTGTTAT
1 TT-TTAT
1422308 CATTTCATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.10
21 14 0.34
22 17 0.41
23 6 0.15
ACGTcount: A:0.10, C:0.08, G:0.11, T:0.70
Consensus pattern (21 bp):
TTTTATTGTTTTTCTGCTATT
Found at i:1422344 original size:11 final size:11
Alignment explanation
Indices: 1422297--1422344 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
1422287 TGTTTTTCAC
1422297 TATTTTGTTAT
1 TATTTTGTTAT
* **
1422308 CATTTCATTAT
1 TATTTTGTTAT
* *
1422319 TATATTGTTAC
1 TATTTTGTTAT
1422330 TATTTTGTTAT
1 TATTTTGTTAT
1422341 TATT
1 TATT
1422345 ATTTAGATAT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (11 bp):
TATTTTGTTAT
Found at i:1423732 original size:19 final size:20
Alignment explanation
Indices: 1423694--1423732 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1423684 ATTTATGGTT
*
1423694 CATTTCTAATTATTTAATAA
1 CATTTCTAATAATTTAATAA
*
1423714 CATTTC-AATAATTTTATAA
1 CATTTCTAATAATTTAATAA
1423733 TGTCATTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (20 bp):
CATTTCTAATAATTTAATAA
Found at i:1427451 original size:15 final size:15
Alignment explanation
Indices: 1427433--1427465 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1427423 TTTTAATTCA
1427433 ATAT-TTAATAATTTT
1 ATATATTAA-AATTTT
1427448 ATATATTAAAATTTT
1 ATATATTAAAATTTT
1427463 ATA
1 ATA
1427466 GAAAGTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATATTAAAATTTT
Found at i:1427571 original size:17 final size:16
Alignment explanation
Indices: 1427542--1427576 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1427532 TTTTATGTGT
*
1427542 TATAAATTATATAATA
1 TATAAAATATATAATA
1427558 TATAAAATAGTATAATA
1 TATAAAATA-TATAATA
1427575 TA
1 TA
1427577 AAATATTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
TATAAAATATATAATA
Found at i:1435988 original size:3 final size:3
Alignment explanation
Indices: 1435980--1436023 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1435970 TACGGTTCCT
1435980 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1436024 TATATATCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1442035 original size:80 final size:80
Alignment explanation
Indices: 1441899--1442050 Score: 209
Period size: 80 Copynumber: 1.9 Consensus size: 80
1441889 ATAATTTCCA
* * * *
1441899 TCAATTCATGGCACCCGGTGCCTAGCAGTTAAATCGCAATAAGTGAATCCAGCTCTAGTTGGATT
1 TCAATTCATAGCACCCAGTGCCTAGCAGATAAATCGCAATAAGTGAATCCAACTCTAGTTGGATT
1441964 AACCAACAAAGTCCG
66 AACCAACAAAGTCCG
** *
1441979 TCAATTCATAGCACCCAGTGCCTAGTGGATAAA-CAGCAATAAGTG-AGCTCAACTCTAGTTGGA
1 TCAATTCATAGCACCCAGTGCCTAGCAGATAAATC-GCAATAAGTGAATC-CAACTCTAGTTGGA
1442042 TTAACCAAC
64 TTAACCAAC
1442051 GATTTGAGCC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
79 3 0.05
80 60 0.95
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (80 bp):
TCAATTCATAGCACCCAGTGCCTAGCAGATAAATCGCAATAAGTGAATCCAACTCTAGTTGGATT
AACCAACAAAGTCCG
Done.