Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 93 of 290
Found at i:31255126 original size:3 final size:3
Alignment explanation
Indices: 31255118--31255161 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
31255108 CATGACAATT
31255118 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31255162 CTATAATGCA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31255675 original size:25 final size:25
Alignment explanation
Indices: 31255647--31255696 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
31255637 ATTTGAGCTC
31255647 AACTTGGCTGGATTACACCCCTATA
1 AACTTGGCTGGATTACACCCCTATA
31255672 AACTTGGCTGGATTACACCCCTATA
1 AACTTGGCTGGATTACACCCCTATA
31255697 CAACACCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (25 bp):
AACTTGGCTGGATTACACCCCTATA
Found at i:31256581 original size:45 final size:46
Alignment explanation
Indices: 31256511--31256606 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 46
31256501 CCCTTGATCA
*
31256511 AGTATAGATAATTAATAATAAATACTATCTAATTTAGTTAA-ATTT
1 AGTATAAATAATTAATAATAAATACTATCTAATTTAGTTAATATTT
* *
31256556 AGTATAAATAATTTAA-AATATATACTATGTAATTTAGTTAATTATTT
1 AGTATAAATAA-TTAATAATAAATACTATCTAATTTAGTTAA-TATTT
31256603 AGTA
1 AGTA
31256607 GGTCAAATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 33 0.73
46 4 0.09
47 8 0.18
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (46 bp):
AGTATAAATAATTAATAATAAATACTATCTAATTTAGTTAATATTT
Found at i:31259157 original size:13 final size:13
Alignment explanation
Indices: 31259141--31259165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31259131 AAATTTACAG
31259141 AAGAAAAGAAAAA
1 AAGAAAAGAAAAA
31259154 AAGAAAAGAAAA
1 AAGAAAAGAAAA
31259166 TAGAAAGAGA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAGAAAAGAAAAA
Found at i:31260386 original size:161 final size:163
Alignment explanation
Indices: 31260106--31260415 Score: 491
Period size: 162 Copynumber: 1.9 Consensus size: 163
31260096 ATATTGTATA
* *
31260106 TGAAACATTGAAATTGTACCACATCATCACTTGAAAATTCATATAATTTATATGAATTTTCAAGT
1 TGAAACATTGAAATTGTACCACATCATCACCTAAAAATTCATATAATTTATATGAATTTTCAAGT
* * *
31260171 GATGATGTAGCACAATCTCATAATGTCACGTAATCAAACTTTTATAGTTTTCAAG-TTGGGACTA
66 GATGATGTAGCACAATCTCATAATGCCACATAATCAAACTTTTATAGGTTTCAAGTTTGGGACTA
* *
31260235 AAATTGACTCAGTTGTCAAATTTAAGTGCCATG
131 AAATGGACTCAATTGTCAAATTTAAGTGCCATG
* *
31260268 TGAAACTTTGAAATTGTACCACATCATCACCTAAAAATTCATATATATTT-T-TTAATTTTCAAG
1 TGAAACATTGAAATTGTACCACATCATCACCTAAAAATTCATATA-ATTTATATGAATTTTCAAG
* *
31260331 TGATGATGTTGCACAATCTCATAATGCCACATCATCAAACTTTTATAGGTTTCAAGTTTGGGACT
65 TGATGATGTAGCACAATCTCATAATGCCACATAATCAAACTTTTATAGGTTTCAAGTTTGGGACT
31260396 AAAATGGACTCAATTGTCAA
130 AAAATGGACTCAATTGTCAA
31260416 GTTGATACCT
Statistics
Matches: 135, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
161 62 0.46
162 69 0.51
163 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (163 bp):
TGAAACATTGAAATTGTACCACATCATCACCTAAAAATTCATATAATTTATATGAATTTTCAAGT
GATGATGTAGCACAATCTCATAATGCCACATAATCAAACTTTTATAGGTTTCAAGTTTGGGACTA
AAATGGACTCAATTGTCAAATTTAAGTGCCATG
Found at i:31261236 original size:45 final size:43
Alignment explanation
Indices: 31261149--31261271 Score: 124
Period size: 45 Copynumber: 2.8 Consensus size: 43
31261139 ATTTGCATAT
* ****
31261149 TAAAGCTGCTAGTACTGTGTGGATAAACCACTCATTGGTGCAGA
1 TAAAGCTGCTAATA-TGTGTGGATAAACCACTCAACAATGCAGA
31261193 TAAAAGCTGCTAATATAGTGTGGATAAACCACTCAACAATGCAGA
1 T-AAAGCTGCTAATAT-GTGTGGATAAACCACTCAACAATGCAGA
* *
31261238 TAAA-CTGATCAA-ATGGTATGGATAAACCACTCAA
1 TAAAGCTGCT-AATAT-GTGTGGATAAACCACTCAA
31261272 TGATGTAGAG
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
43 24 0.35
44 7 0.10
45 37 0.54
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (43 bp):
TAAAGCTGCTAATATGTGTGGATAAACCACTCAACAATGCAGA
Found at i:31263319 original size:20 final size:21
Alignment explanation
Indices: 31263278--31263322 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
31263268 ATAATACCTG
31263278 ATTATATTATTTTGATAATTTA
1 ATTATATTATTTTGAT-ATTTA
31263300 ATTAT-TTATTTATGAT-TTTA
1 ATTATATTATTT-TGATATTTA
31263320 ATT
1 ATT
31263323 TCGGTATTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.32
21 6 0.27
22 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
ATTATATTATTTTGATATTTA
Found at i:31263548 original size:21 final size:20
Alignment explanation
Indices: 31263509--31263548 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31263499 ATATAAGATA
*
31263509 TCAAAATTATTAATTAAATG
1 TCAAAATTATTAATCAAATG
*
31263529 TCAAAATTTTATAATCAAAT
1 TCAAAATTAT-TAATCAAAT
31263549 CTAATACACG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (20 bp):
TCAAAATTATTAATCAAATG
Found at i:31269595 original size:16 final size:16
Alignment explanation
Indices: 31269573--31269625 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
31269563 GAAAAATTAT
31269573 ATTTTTCATCCTTCTA
1 ATTTTTCATCCTTCTA
* *
31269589 GTTTTTCTACCCTT-TA
1 ATTTTTC-ATCCTTCTA
*
31269605 ATTTTTCATCCTTCCA
1 ATTTTTCATCCTTCTA
31269621 ATTTT
1 ATTTT
31269626 CTTTTTGCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 20 0.67
17 5 0.17
ACGTcount: A:0.17, C:0.25, G:0.02, T:0.57
Consensus pattern (16 bp):
ATTTTTCATCCTTCTA
Found at i:31275010 original size:18 final size:18
Alignment explanation
Indices: 31274987--31275022 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31274977 TTTTCATACT
31274987 CTTCATCATCTTCTTCTC
1 CTTCATCATCTTCTTCTC
*
31275005 CTTCATCTTCTTCTTCTC
1 CTTCATCATCTTCTTCTC
31275023 AGCATAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.39, G:0.00, T:0.53
Consensus pattern (18 bp):
CTTCATCATCTTCTTCTC
Found at i:31276705 original size:2 final size:2
Alignment explanation
Indices: 31276698--31276735 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
31276688 TCTTTAATTT
31276698 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31276736 CACTGTGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:31285604 original size:88 final size:88
Alignment explanation
Indices: 31285462--31285630 Score: 268
Period size: 88 Copynumber: 1.9 Consensus size: 88
31285452 TGATTTCACA
* *
31285462 CCCTTGCCGTCCAGCCCAAATAACTTTTGGGTCTAATTGCCTTTTATATCCTTTCTCATTAGACT
1 CCCTTGCCGTCCAGCCCAAATAAATTTTGGGTCTAATTGCCTTTTAAATCCTTTCTCATTAGACT
31285527 AATAAGCTATTTAATCTTTCATG
66 AATAAGCTATTTAATCTTTCATG
* *
31285550 CCCTTTCCGTCCAG-CCATAATAAATTTTGGGTCTAATTTCCTTTTAAATCCTTTCTCATTAGAC
1 CCCTTGCCGTCCAGCCCA-AATAAATTTTGGGTCTAATTGCCTTTTAAATCCTTTCTCATTAGAC
**
31285614 TCTTAAGCTATTTAATC
65 TAATAAGCTATTTAATC
31285631 ATTCTAGCAA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
87 3 0.04
88 71 0.96
ACGTcount: A:0.24, C:0.25, G:0.10, T:0.41
Consensus pattern (88 bp):
CCCTTGCCGTCCAGCCCAAATAAATTTTGGGTCTAATTGCCTTTTAAATCCTTTCTCATTAGACT
AATAAGCTATTTAATCTTTCATG
Found at i:31288694 original size:43 final size:43
Alignment explanation
Indices: 31288630--31288718 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
31288620 CACAATCTCA
31288630 AAGACCTGTCTTTCTTTTTTCACAAAC-GAACCAGAGCACCCC
1 AAGACCTGTCTTTCTTTTTTCACAAACAGAACCAGAGCACCCC
*
31288672 AAGNACCTGTCTTTCTTTTTTCACAAACAGAACCGGAGCACCCC
1 AAG-ACCTGTCTTTCTTTTTTCACAAACAGAACCAGAGCACCCC
31288716 AAG
1 AAG
31288719 GTGAATGACT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 3 0.07
43 24 0.55
44 17 0.39
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.25
Consensus pattern (43 bp):
AAGACCTGTCTTTCTTTTTTCACAAACAGAACCAGAGCACCCC
Found at i:31291026 original size:22 final size:23
Alignment explanation
Indices: 31291001--31291046 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
31290991 CAACCAGACC
31291001 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
31291023 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
31291046 A
1 A
31291047 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:31291052 original size:23 final size:23
Alignment explanation
Indices: 31291008--31291052 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31290998 ACCAATTCAA
*
31291008 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
31291031 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
31291053 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:31292491 original size:62 final size:62
Alignment explanation
Indices: 31292420--31292544 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
31292410 TTCATATGCA
*
31292420 ACATTCTCTATAATTCAACTATTATTATTTATAGTTTATTCAAAGTTATCTATTTGAGTCAT
1 ACATTCTCTATAATTCAACTATTATTATTTATAGTTTATTCAAAGCTATCTATTTGAGTCAT
* *
31292482 ACATTCTCTATAATTCAACTATTATTATTTATAGTTTATTCAAAGCTGTCTATTTGATTCAT
1 ACATTCTCTATAATTCAACTATTATTATTTATAGTTTATTCAAAGCTATCTATTTGAGTCAT
31292544 A
1 A
31292545 GTCACTAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.32, C:0.14, G:0.06, T:0.48
Consensus pattern (62 bp):
ACATTCTCTATAATTCAACTATTATTATTTATAGTTTATTCAAAGCTATCTATTTGAGTCAT
Found at i:31293736 original size:73 final size:73
Alignment explanation
Indices: 31293616--31293761 Score: 222
Period size: 73 Copynumber: 2.0 Consensus size: 73
31293606 TTGCAATATT
**
31293616 CCAATTTTGCCCTTAATTTATCAATTTTTCTGCTGATTTCACACCCTTGCCGTCCAGCCCA-AAT
1 CCAATTTTGCCCTTAATTTATCAATTTCCCTGCTGATTTCACACCCTTGCCGTCCAG-CCATAAT
*
31293680 AACTTTTGG
65 AAATTTTGG
** *
31293689 CCAATTTTGCCCTTAATTTATCAATTTCCCTGCTGATTTCATGCCCTTTCCGTCCAGCCATAATA
1 CCAATTTTGCCCTTAATTTATCAATTTCCCTGCTGATTTCACACCCTTGCCGTCCAGCCATAATA
31293754 AATTTTGG
66 AATTTTGG
31293762 GTCTAATTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 3 0.05
73 63 0.95
ACGTcount: A:0.22, C:0.28, G:0.11, T:0.39
Consensus pattern (73 bp):
CCAATTTTGCCCTTAATTTATCAATTTCCCTGCTGATTTCACACCCTTGCCGTCCAGCCATAATA
AATTTTGG
Found at i:31299165 original size:22 final size:23
Alignment explanation
Indices: 31299140--31299185 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
31299130 CAACCAGACC
31299140 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
31299162 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
31299185 A
1 A
31299186 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:31299191 original size:23 final size:23
Alignment explanation
Indices: 31299147--31299191 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31299137 ACCAATTCAA
*
31299147 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
31299170 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
31299192 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:31301585 original size:66 final size:66
Alignment explanation
Indices: 31301502--31301634 Score: 205
Period size: 66 Copynumber: 2.0 Consensus size: 66
31301492 TTCCTGCTGA
*
31301502 TTTCATACCCTTGCCGTCCAACCCA-AATAACGTTTGGGTCAAATTTCCTTTTAAATCCTTTCTC
1 TTTCATACCCTTGCCGTCC-ACCCATAATAAAGTTTGGGTCAAATTTCCTTTTAAATCCTTTCTC
31301566 AT
65 AT
* * * *
31301568 TTTCATGCCCTTGCCGTCCAGCCATAATAAATTTTGGGTCTAATTTCCTTTTAAATCCTTTCTCA
1 TTTCATACCCTTGCCGTCCACCCATAATAAAGTTTGGGTCAAATTTCCTTTTAAATCCTTTCTCA
31301633 T
66 T
31301634 T
1 T
31301635 AGACTCTTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 4 0.07
66 57 0.93
ACGTcount: A:0.23, C:0.27, G:0.10, T:0.41
Consensus pattern (66 bp):
TTTCATACCCTTGCCGTCCACCCATAATAAAGTTTGGGTCAAATTTCCTTTTAAATCCTTTCTCA
T
Found at i:31301745 original size:59 final size:59
Alignment explanation
Indices: 31301648--31301764 Score: 189
Period size: 59 Copynumber: 2.0 Consensus size: 59
31301638 CTCTTAAGCT
* * * *
31301648 ATTTAATTATTCTAGCAACTTTTACACCTATTATAATTTAGTCCTTTTCATTTGATTGG
1 ATTTAATCATTCTAGCAACTTTTACACATATTACAATTTAGTCCTTTTCATTTAATTGG
*
31301707 ATTTAATCATTCTAGCAATTTTTACACATATTACAATTTAGTCCTTTTCATTTAATTG
1 ATTTAATCATTCTAGCAACTTTTACACATATTACAATTTAGTCCTTTTCATTTAATTG
31301765 ACTACCCAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (59 bp):
ATTTAATCATTCTAGCAACTTTTACACATATTACAATTTAGTCCTTTTCATTTAATTGG
Found at i:31303009 original size:25 final size:25
Alignment explanation
Indices: 31302975--31303026 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
31302965 ATTCAAACAG
31302975 GTTCCGTACATACCTGTACCACCTC
1 GTTCCGTACATACCTGTACCACCTC
31303000 GTTCCGTACATACCTGTACCACCTC
1 GTTCCGTACATACCTGTACCACCTC
31303025 GT
1 GT
31303027 ACTAACCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.38, G:0.13, T:0.29
Consensus pattern (25 bp):
GTTCCGTACATACCTGTACCACCTC
Found at i:31304828 original size:13 final size:13
Alignment explanation
Indices: 31304810--31304848 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
31304800 CTGTGTATTC
*
31304810 TTAGTTTAGTTAA
1 TTAGTTTAGATAA
31304823 TTAGTTTAGATAA
1 TTAGTTTAGATAA
31304836 TTAGTTTAGATAA
1 TTAGTTTAGATAA
31304849 AGCAAATCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (13 bp):
TTAGTTTAGATAA
Found at i:31307896 original size:55 final size:55
Alignment explanation
Indices: 31307769--31307899 Score: 172
Period size: 55 Copynumber: 2.4 Consensus size: 55
31307759 TTAAAATTTT
* * *
31307769 AAGTCATTGTTGTACACGGGCAGGCCACACGGGCGTGTGCCATGGTCGTGTCTTA
1 AAGTCAGTGTTGTACACGGGCAGGCCACACGGGCGAGTGCCATGGCCGTGTCTTA
* * * * * *
31307824 AAGTCAGTATCGTACACGGGCAGGTCACATGGGCGAGTGCCATGGCCGTGTGTTG
1 AAGTCAGTGTTGTACACGGGCAGGCCACACGGGCGAGTGCCATGGCCGTGTCTTA
*
31307879 AAGTCAGTGTTGCACACGGGC
1 AAGTCAGTGTTGTACACGGGC
31307900 TAAGGACATG
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (55 bp):
AAGTCAGTGTTGTACACGGGCAGGCCACACGGGCGAGTGCCATGGCCGTGTCTTA
Found at i:31310545 original size:58 final size:58
Alignment explanation
Indices: 31310431--31310548 Score: 148
Period size: 58 Copynumber: 2.0 Consensus size: 58
31310421 AAATTGATAG
*
31310431 CAGGAATGAAGAGTGTAAACTACTCGAACCACCATGACTATTGAAGATCGAAGTAAGT
1 CAGGAATGAAGAGTGTAAACTACTCGAACCACCATGACTATTGAAAATCGAAGTAAGT
* * * * * * *
31310489 CAGGAATGAGGAGTGTCAACTCCTTGAACCACTATGACTA-TGCAAAATTGAGGTAAGT
1 CAGGAATGAAGAGTGTAAACTACTCGAACCACCATGACTATTG-AAAATCGAAGTAAGT
31310547 CA
1 CA
31310549 AGCTTAAACT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 2 0.04
58 49 0.96
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (58 bp):
CAGGAATGAAGAGTGTAAACTACTCGAACCACCATGACTATTGAAAATCGAAGTAAGT
Found at i:31313617 original size:19 final size:19
Alignment explanation
Indices: 31313593--31313630 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31313583 TATTATTCTA
31313593 GAACTTGCTTCGATTATGC
1 GAACTTGCTTCGATTATGC
31313612 GAACTTGCTTCGATTATGC
1 GAACTTGCTTCGATTATGC
31313631 ATGTCAAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
GAACTTGCTTCGATTATGC
Found at i:31315076 original size:21 final size:21
Alignment explanation
Indices: 31315052--31315091 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31315042 AAAACCCTTC
*
31315052 TTAAAATAAAAGAAACCTTAA
1 TTAAAATAAAAAAAACCTTAA
**
31315073 TTAACTTAAAAAAAACCTT
1 TTAAAATAAAAAAAACCTT
31315092 TCAGTTACGA
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:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (21 bp):
TTAAAATAAAAAAAACCTTAA
Found at i:31316094 original size:29 final size:29
Alignment explanation
Indices: 31316028--31316142 Score: 126
Period size: 29 Copynumber: 4.0 Consensus size: 29
31316018 TACATACATG
*
31316028 CATATGGCCCACTAGGCCCAA-TC-TCATT
1 CATATGGCCCATTAGGCCCAATTCAT-ATT
* *
31316056 CATATGGCCCATTTGGCCCAGTTCATATT
1 CATATGGCCCATTAGGCCCAATTCATATT
* * * *
31316085 CTTATGGCCCACTAGACCCAATTCACATT
1 CATATGGCCCATTAGGCCCAATTCATATT
* *
31316114 CATATTGCCCATTAGGCCCAAATCATATT
1 CATATGGCCCATTAGGCCCAATTCATATT
31316143 ATACTCATGC
Statistics
Matches: 70, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
28 18 0.26
29 51 0.73
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (29 bp):
CATATGGCCCATTAGGCCCAATTCATATT
Found at i:31316132 original size:58 final size:57
Alignment explanation
Indices: 31316030--31316142 Score: 163
Period size: 58 Copynumber: 2.0 Consensus size: 57
31316020 CATACATGCA
* * * **
31316030 TATGGCCCACTAGGCCCAATCTCATTCATATGGCCCATTTGGCCCAGTTCATATTCT
1 TATGGCCCACTAGACCCAATCACATTCATATGGCCCATTAGGCCCAAATCATATTCT
*
31316087 TATGGCCCACTAGACCCAATTCACATTCATATTGCCCATTAGGCCCAAATCATATT
1 TATGGCCCACTAGACCCAA-TCACATTCATATGGCCCATTAGGCCCAAATCATATT
31316143 ATACTCATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 18 0.37
58 31 0.63
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (57 bp):
TATGGCCCACTAGACCCAATCACATTCATATGGCCCATTAGGCCCAAATCATATTCT
Found at i:31316352 original size:8 final size:8
Alignment explanation
Indices: 31316339--31316381 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
31316329 GTAGCCCAAC
31316339 TTTTGGCT
1 TTTTGGCT
*
31316347 TTTTGGCA
1 TTTTGGCT
*
31316355 TTTCGGCT
1 TTTTGGCT
*
31316363 TTTTGGCA
1 TTTTGGCT
*
31316371 TTTCGGCT
1 TTTTGGCT
31316379 TTT
1 TTT
31316382 GTCGTTTCAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.05, C:0.16, G:0.23, T:0.56
Consensus pattern (8 bp):
TTTTGGCT
Found at i:31316389 original size:15 final size:16
Alignment explanation
Indices: 31316343--31316381 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
31316333 CCCAACTTTT
31316343 GGCTTTTTGGCATTTC
1 GGCTTTTTGGCATTTC
31316359 GGCTTTTTGGCATTTC
1 GGCTTTTTGGCATTTC
31316375 GGCTTTT
1 GGCTTTT
31316382 GTCGTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.05, C:0.18, G:0.26, T:0.51
Consensus pattern (16 bp):
GGCTTTTTGGCATTTC
Found at i:31324555 original size:12 final size:13
Alignment explanation
Indices: 31324529--31324559 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
31324519 ATGACATATA
31324529 TTCTTAACAAATT
1 TTCTTAACAAATT
31324542 TTCTTAAC-AATT
1 TTCTTAACAAATT
31324554 TTCTTA
1 TTCTTA
31324560 GTAAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (13 bp):
TTCTTAACAAATT
Found at i:31331352 original size:51 final size:51
Alignment explanation
Indices: 31331271--31331371 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
31331261 CATATGACAT
31331271 AACTCCCATCATCATAGCAACATCATCAAAATCATGTCATTCATTCAGGCC
1 AACTCCCATCATCATAGCAACATCATCAAAATCATGTCATTCATTCAGGCC
*
31331322 AACTTCCATCATCATAGCAACATCATCAAAATCATGTCATTCATTCAGGC
1 AACTCCCATCATCATAGCAACATCATCAAAATCATGTCATTCATTCAGGC
31331372 AATGCAACAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.36, C:0.30, G:0.08, T:0.27
Consensus pattern (51 bp):
AACTCCCATCATCATAGCAACATCATCAAAATCATGTCATTCATTCAGGCC
Found at i:31338346 original size:31 final size:31
Alignment explanation
Indices: 31338311--31338383 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
31338301 TACAATTAAT
* *
31338311 AAAAATTAAAATTTTATGTGTATATTT-CAAC
1 AAAAATAAAAATTTAATGTGTATATTTGC-AC
* *
31338342 AAAAATCAAACTTTAATGTGTATATTTGCAC
1 AAAAATAAAAATTTAATGTGTATATTTGCAC
31338373 AAAAATAAAAA
1 AAAAATAAAAA
31338384 AAAAAATTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (31 bp):
AAAAATAAAAATTTAATGTGTATATTTGCAC
Found at i:31339707 original size:17 final size:17
Alignment explanation
Indices: 31339658--31339707 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
31339648 AGAAACATGT
*
31339658 TCTTCGAAGATATGCAA
1 TCTTAGAAGATATGCAA
*
31339675 TCTTAGATATGATATGTAA
1 TCTTAGA-A-GATATGCAA
31339694 TCTTAGAAGATATG
1 TCTTAGAAGATATG
31339708 ATTTTGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 12 0.41
18 2 0.07
19 15 0.52
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (17 bp):
TCTTAGAAGATATGCAA
Found at i:31339707 original size:22 final size:21
Alignment explanation
Indices: 31339679--31339736 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
31339669 ATGCAATCTT
*
31339679 AGATATGATATGTAATCTTAG
1 AGATATGATTTGTAATCTTAG
31339700 AAGATATGATTTTGTAATCTTAG
1 -AGATATGA-TTTGTAATCTTAG
*
31339723 AGATTTGATTTGTA
1 AGATATGATTTGTA
31339737 GATACCCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 6 0.18
22 15 0.45
23 12 0.36
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43
Consensus pattern (21 bp):
AGATATGATTTGTAATCTTAG
Found at i:31344837 original size:17 final size:17
Alignment explanation
Indices: 31344787--31344838 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 17
31344777 TGGAAACATG
*
31344787 ATCTTCGAAGATATGAA
1 ATCTTAGAAGATATGAA
*
31344804 ATCTTAGATATGATATGTA
1 ATCTTAGA-A-GATATGAA
31344823 ATCTTAGAAGATATGA
1 ATCTTAGAAGATATGA
31344839 TTTTGTAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (17 bp):
ATCTTAGAAGATATGAA
Found at i:31344837 original size:22 final size:21
Alignment explanation
Indices: 31344796--31344861 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
31344786 GATCTTCGAA
*
31344796 GATATGAAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
31344815 GATATGTAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
* *
31344837 GATTTTGTAATCTTAGAGATTT
1 GA-TATGTAATCTTAGAGATAT
31344859 GAT
1 GAT
31344862 TTATAGATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.30
21 1 0.03
22 15 0.38
23 12 0.30
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:31344862 original size:22 final size:23
Alignment explanation
Indices: 31344809--31344863 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
31344799 ATGAAATCTT
*
31344809 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTTTGTAATCTTAGA
31344831 AGATATGATTTTGTAATCTTAG-
1 AGATATGATTTTGTAATCTTAGA
*
31344853 AGATTTGATTT
1 AGATATGATTT
31344864 ATAGATACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.44
Consensus pattern (23 bp):
AGATATGATTTTGTAATCTTAGA
Found at i:31348124 original size:12 final size:12
Alignment explanation
Indices: 31348107--31348133 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31348097 ATTCCGAAGT
31348107 ATATATATATAC
1 ATATATATATAC
31348119 ATATATATATAC
1 ATATATATATAC
31348131 ATA
1 ATA
31348134 AGTATGCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:31348645 original size:27 final size:27
Alignment explanation
Indices: 31348614--31348791 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
31348604 TAAATTGTAC
31348614 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
31348641 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * *
31348667 ATGCACTAACTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
31348695 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
31348723 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31348750 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
31348777 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31348792 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:31348755 original size:82 final size:81
Alignment explanation
Indices: 31348615--31348770 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
31348605 AAATTGTACA
* *
31348615 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAACTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAACTGT
31348680 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
** * *
31348696 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAACT
*
31348760 GTGCGAGTTGA
64 GTGCGAATTGA
31348771 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAACTGT
GCGAATTGACCATGCG
Found at i:31348782 original size:82 final size:81
Alignment explanation
Indices: 31348611--31348791 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
31348601 GATTAAATTG
* *
31348611 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
31348676 CTGTGCGAATTGACCA
66 CTGTGCGAATTGACCA
* * ** *
31348692 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* * **
31348756 AAGTGTGCGAGTTGATTA
64 AACTGTGCGAATTGACCA
* *
31348774 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
31348792 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
CTGTGCGAATTGACCA
Found at i:31357348 original size:27 final size:27
Alignment explanation
Indices: 31357317--31357494 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31357307 TAAATTGTAC
31357317 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
31357344 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31357370 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
31357398 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
31357426 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31357453 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
31357480 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31357495 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:31357431 original size:82 final size:81
Alignment explanation
Indices: 31357318--31357473 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31357308 AAATTGTACA
* *
31357318 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
31357382 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
31357399 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
31357464 TGCGAGTTGA
65 TGCGAATTGA
31357474 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:31357485 original size:82 final size:81
Alignment explanation
Indices: 31357314--31357494 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
31357304 GATTAAATTG
* *
31357314 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
31357379 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
31357395 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
31357459 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
31357477 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
31357495 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:31363937 original size:33 final size:34
Alignment explanation
Indices: 31363894--31363973 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
31363884 AGCTGATCTA
* *
31363894 TTATAAGCATATTACTTGTTACTATATTGAACTG
1 TTATAAGCATATTAATTGATACTATATTGAACTG
* * *
31363928 TTA-AAGCATATTAATTGATATTGTATTGAATTG
1 TTATAAGCATATTAATTGATACTATATTGAACTG
31363961 TTATAAGCATATT
1 TTATAAGCATATT
31363974 GATTACTACC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 28 0.70
34 12 0.30
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (34 bp):
TTATAAGCATATTAATTGATACTATATTGAACTG
Found at i:31363988 original size:34 final size:33
Alignment explanation
Indices: 31363898--31363988 Score: 85
Period size: 33 Copynumber: 2.7 Consensus size: 33
31363888 GATCTATTAT
* * **
31363898 AAGCATATTACTTGTTACTATATTGAACTGTTA
1 AAGCATATTAATTGATACCGTATTGAACTGTTA
** *
31363931 AAGCATATTAATTGATATTGTATTGAATTGTTA
1 AAGCATATTAATTGATACCGTATTGAACTGTTA
*
31363964 TAAGCATATTGATT-ACTACCGTATT
1 -AAGCATATTAATTGA-TACCGTATT
31363989 ATTCTATTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
33 29 0.60
34 19 0.40
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (33 bp):
AAGCATATTAATTGATACCGTATTGAACTGTTA
Found at i:31369727 original size:33 final size:34
Alignment explanation
Indices: 31369684--31369763 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
31369674 AGCTGATCTA
* *
31369684 TTATAAGCATATTACTTGTTACTATATTGAACTG
1 TTATAAGCATATTAATTGATACTATATTGAACTG
* * *
31369718 TTA-AAGCATATTAATTGATATTGTATTGAATTG
1 TTATAAGCATATTAATTGATACTATATTGAACTG
31369751 TTATAAGCATATT
1 TTATAAGCATATT
31369764 GATTACTACC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 28 0.70
34 12 0.30
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (34 bp):
TTATAAGCATATTAATTGATACTATATTGAACTG
Found at i:31369778 original size:34 final size:33
Alignment explanation
Indices: 31369688--31369778 Score: 85
Period size: 33 Copynumber: 2.7 Consensus size: 33
31369678 GATCTATTAT
* * **
31369688 AAGCATATTACTTGTTACTATATTGAACTGTTA
1 AAGCATATTAATTGATACCGTATTGAACTGTTA
** *
31369721 AAGCATATTAATTGATATTGTATTGAATTGTTA
1 AAGCATATTAATTGATACCGTATTGAACTGTTA
*
31369754 TAAGCATATTGATT-ACTACCGTATT
1 -AAGCATATTAATTGA-TACCGTATT
31369779 ATTCTATTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
33 29 0.60
34 19 0.40
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (33 bp):
AAGCATATTAATTGATACCGTATTGAACTGTTA
Found at i:31371759 original size:101 final size:101
Alignment explanation
Indices: 31371618--31371812 Score: 295
Period size: 101 Copynumber: 1.9 Consensus size: 101
31371608 TTATTCAAAC
** * *
31371618 GTAAGACCATGGTTGGACCATGGTAGTGTATATATCTAAGA-TCATAGCTAGGCTATGGCATTCT
1 GTAAGACCATGGTTGGACCATGACAGTGTATATATCTAAGACT-ATAGCTACGCTATCGCATTCT
31371682 GATGATAAGACCATAACTAGGTTATGGCACAATGGAT
65 GATGATAAGACCATAACTAGGTTATGGCACAATGGAT
* *
31371719 GTAAGACCCTGGTTGGACCATGACAGTGCT-TATATGTAAGACTATAGCTACGCTATCGCATTCT
1 GTAAGACCATGGTTGGACCATGACAGTG-TATATATCTAAGACTATAGCTACGCTATCGCATTCT
*
31371783 GATGATAAGACCATAACTGGGTTATGGCAC
65 GATGATAAGACCATAACTAGGTTATGGCAC
31371813 TATGAACGTA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
101 83 0.98
102 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (101 bp):
GTAAGACCATGGTTGGACCATGACAGTGTATATATCTAAGACTATAGCTACGCTATCGCATTCTG
ATGATAAGACCATAACTAGGTTATGGCACAATGGAT
Found at i:31371841 original size:101 final size:101
Alignment explanation
Indices: 31371615--31371842 Score: 271
Period size: 101 Copynumber: 2.3 Consensus size: 101
31371605 AAATTATTCA
* ** ** * *
31371615 AACGTAAGACCATGGTTGGACCATGGTAGTG-TATATATCTAAGATCATAGCTAGGCTATGGCAT
1 AACGTAAGACCCTGGAAGGACCATGACAGTGCT-TATATCTAAGATCATAGCTACGCTATCGCAT
31371679 TCTGATGATAAGACCATAACTAGGTTATGGCACAATG
65 TCTGATGATAAGACCATAACTAGGTTATGGCACAATG
* * ** *
31371716 GATGTAAGACCCTGGTTGGACCATGACAGTGCTTATATGTAAGA-CTATAGCTACGCTATCGCAT
1 AACGTAAGACCCTGGAAGGACCATGACAGTGCTTATATCTAAGATC-ATAGCTACGCTATCGCAT
* *
31371780 TCTGATGATAAGACCATAACTGGGTTATGGCACTATG
65 TCTGATGATAAGACCATAACTAGGTTATGGCACAATG
* * *
31371817 AACGTAATACCGTGGAAGGGCCATGA
1 AACGTAAGACCCTGGAAGGACCATGA
31371843 AAATTCATAT
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
100 1 0.01
101 106 0.98
102 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (101 bp):
AACGTAAGACCCTGGAAGGACCATGACAGTGCTTATATCTAAGATCATAGCTACGCTATCGCATT
CTGATGATAAGACCATAACTAGGTTATGGCACAATG
Found at i:31386142 original size:27 final size:27
Alignment explanation
Indices: 31386074--31386174 Score: 85
Period size: 27 Copynumber: 3.7 Consensus size: 27
31386064 TGGAACATAA
* * * * *
31386074 GGGCATAACCATCATTCTACCATATAG
1 GGGCATTACGATCATTTTACCCTACAG
* * *
31386101 GGGTATTATGGTCATTTTACCCTACAG
1 GGGCATTACGATCATTTTACCCTACAG
* *
31386128 GGGCATTACGATCATTTTACACTACAA
1 GGGCATTACGATCATTTTACCCTACAG
* * *
31386155 GGGTATTTCGATAATTTTAC
1 GGGCATTACGATCATTTTAC
31386175 TAATATTGGG
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (27 bp):
GGGCATTACGATCATTTTACCCTACAG
Found at i:31388225 original size:48 final size:48
Alignment explanation
Indices: 31388102--31388234 Score: 203
Period size: 48 Copynumber: 2.8 Consensus size: 48
31388092 TCTCATATTG
* ** *
31388102 ATGCCATGTCCCAGACATGGTCTTACACGAAATCAAATATCGAGGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGAGGCCA
* *
31388150 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATTGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGAGGCCA
*
31388198 ATGCCATGTCCCTGACATGGTCTTACATGGGATCACA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACA
31388235 ATGCCATAGC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 78 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGAGGCCA
Found at i:31388276 original size:37 final size:37
Alignment explanation
Indices: 31388214--31388333 Score: 136
Period size: 37 Copynumber: 3.2 Consensus size: 37
31388204 TGTCCCTGAC
* * * *
31388214 ATGGTCTTACATGGGATCACAATGCCATAGCCCAGTT
1 ATGGTCTTACACGGTATTACGATGCCATAGCCCAGTT
* *
31388251 ATGGTCTTACA-TGTCATTATGATGCCATAGCCCA-TCT
1 ATGGTCTTACACGGT-ATTACGATGCCATAGCCCAGT-T
*
31388288 ATGGTCTTACACGGTATTACGATGCCATAGCCCAGCT
1 ATGGTCTTACACGGTATTACGATGCCATAGCCCAGTT
*
31388325 ATAGTCTTA
1 ATGGTCTTA
31388334 ATTCGTACTC
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
36 2 0.03
37 66 0.94
38 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (37 bp):
ATGGTCTTACACGGTATTACGATGCCATAGCCCAGTT
Found at i:31394005 original size:48 final size:48
Alignment explanation
Indices: 31393953--31394371 Score: 732
Period size: 48 Copynumber: 8.6 Consensus size: 48
31393943 TACCTGGACA
31393953 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
1 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
31394001 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
1 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
31394049 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
1 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
31394097 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
1 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
31394145 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
1 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
*
31394193 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATATATTTC
1 ACATTAGCCATTCGGCTTTACCACATATACATATCTC------ATACATATTTC
* *
31394247 ACATT-GACCATTCGGCTTCACCACATATGCATATCTCATACATATTTC
1 ACATTAG-CCATTCGGCTTTACCACATATACATATCTCATACATATTTC
*
31394295 ACAATAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
1 ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
31394343 ACATTAGCCATTCGGCTTTACCACATATA
1 ACATTAGCCATTCGGCTTTACCACATATA
31394372 TGGATGTTCA
Statistics
Matches: 355, Mismatches: 8, Indels: 16
0.94 0.02 0.04
Matches are distributed among these distances:
48 310 0.87
49 1 0.00
53 1 0.00
54 43 0.12
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.35
Consensus pattern (48 bp):
ACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTC
Found at i:31394477 original size:47 final size:47
Alignment explanation
Indices: 31394341--31394487 Score: 177
Period size: 47 Copynumber: 3.1 Consensus size: 47
31394331 CATACATATT
* * * ** *
31394341 TCACATTAGCCATTCGGCTTTACCACATATATGGATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCA
* * * *
31394388 CCACATTGGCCATTCGGCCTTATCACACATATTCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCA
* **
31394435 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCA
31394482 TCACAT
1 TCACAT
31394488 AAAATCCTAA
Statistics
Matches: 84, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 84 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCA
Found at i:31400684 original size:27 final size:25
Alignment explanation
Indices: 31400654--31400704 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
31400644 CTTTTGAGTT
*
31400654 AATAAATTCTCTTTGAGTTTTTCTTTC
1 AATAAATTATC-TTGAG-TTTTCTTTC
*
31400681 AATAATTTATCTTGAGTTTTCTTT
1 AATAAATTATCTTGAGTTTTCTTT
31400705 TAGAAAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
26 5 0.23
27 9 0.41
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.57
Consensus pattern (25 bp):
AATAAATTATCTTGAGTTTTCTTTC
Found at i:31402566 original size:42 final size:41
Alignment explanation
Indices: 31402517--31402775 Score: 225
Period size: 42 Copynumber: 6.2 Consensus size: 41
31402507 CTAGCACCAC
*
31402517 AGTGCATCATTGGATAAACTGAAGGAAATATACTAGCACATA
1 AGTGCATCATTAGATAAACTGAAGG-AATATACTAGCACATA
* * * *
31402559 AGTGCATCATTAGACAAGCTG-AGACAATTATACTGGCACATA
1 AGTGCATCATTAGATAAACTGAAG-GAA-TATACTAGCACATA
* * ** * *
31402601 AGTGCATCATTGGATGAACCAAAACGATTATACTAGCACATA
1 AGTGCATCATTAGAT-AAACTGAAGGAATATACTAGCACATA
* ** * * **
31402643 AGTGTATCACCAGATGAATTGAATCATATATACTAGCACATA
1 AGTGCATCATTAGATAAACTGAAGGA-ATATACTAGCACATA
* * *
31402685 AGTGCATCATTAGCTAAAATGAAGCGAATATACTGGCACATA
1 AGTGCATCATTAGATAAACTGAAG-GAATATACTAGCACATA
* * *
31402727 AGTGCATCATGAGCTAAACTGAAGCGAATATACTGGCACATA
1 AGTGCATCATTAGATAAACTGAAG-GAATATACTAGCACATA
31402769 AGT-CATC
1 AGTGCATC
31402776 GACTAAACCG
Statistics
Matches: 174, Mismatches: 37, Indels: 13
0.78 0.17 0.06
Matches are distributed among these distances:
41 12 0.07
42 156 0.90
43 5 0.03
44 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (41 bp):
AGTGCATCATTAGATAAACTGAAGGAATATACTAGCACATA
Found at i:31402758 original size:84 final size:83
Alignment explanation
Indices: 31402517--31402775 Score: 265
Period size: 84 Copynumber: 3.1 Consensus size: 83
31402507 CTAGCACCAC
* *
31402517 AGTGCATCATTGGATAAACTGAAG-GAAATATACTAGCACATAAGTGCATCATTAGAC-AAGCTG
1 AGTGCATCATTGGATAAACTGAAGCG-AATATACTAGCACATAAGTGCATCATCAG-CTAAACTG
31402580 -AGACAATTATACTGGCACATA
64 AAG-CAA-TATACTGGCACATA
* ** * * * * * * *
31402601 AGTGCATCATTGGATGAACCAAAACGATTATACTAGCACATAAGTGTATCACCAGATGAATTGAA
1 AGTGCATCATTGGATAAACTGAAGCGAATATACTAGCACATAAGTGCATCATCAGCTAAACTGAA
* *
31402666 TCATATATACTAGCACATA
66 GCA-ATATACTGGCACATA
* * * * *
31402685 AGTGCATCATTAGCTAAAATGAAGCGAATATACTGGCACATAAGTGCATCATGAGCTAAACTGAA
1 AGTGCATCATTGGATAAACTGAAGCGAATATACTAGCACATAAGTGCATCATCAGCTAAACTGAA
31402750 GCGAATATACTGGCACATA
66 GC-AATATACTGGCACATA
31402769 AGT-CATC
1 AGTGCATC
31402776 GACTAAACCG
Statistics
Matches: 139, Mismatches: 31, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
83 4 0.03
84 131 0.94
85 4 0.03
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (83 bp):
AGTGCATCATTGGATAAACTGAAGCGAATATACTAGCACATAAGTGCATCATCAGCTAAACTGAA
GCAATATACTGGCACATA
Found at i:31402759 original size:126 final size:126
Alignment explanation
Indices: 31402544--31402771 Score: 311
Period size: 126 Copynumber: 1.8 Consensus size: 126
31402534 ACTGAAGGAA
**
31402544 ATATACTAGCACATAAGTGCATCATTAGACAAGCTGAGACAATTATACTGGCACATAAGTGCATC
1 ATATACTAGCACATAAGTGCATCATTAGACAAAATGAGACAATTATACTGGCACATAAGTGCATC
* *
31402609 ATTGGATGAACCAAAACGATTATACTAGCACATAAGTGTATCACCAGATGAATTGAATCAT
66 ATTGGATAAACCAAAACGAATATACTAGCACATAAGTGTATCACCAGATGAATTGAATCAT
31402670 ATATACTAGCACATAAGTGCATCATTAG-CTAAAATGA-AGCGAA-TATACTGGCACATAAGTGC
1 ATATACTAGCACATAAGTGCATCATTAGAC-AAAATGAGA-C-AATTATACTGGCACATAAGTGC
* ** * *
31402732 ATCA-TGAGCTAAACTGAAGCGAATATACTGGCACATAAGT
63 ATCATTG-GATAAACCAAAACGAATATACTAGCACATAAGT
31402772 CATCGACTAA
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
125 4 0.04
126 83 0.93
127 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (126 bp):
ATATACTAGCACATAAGTGCATCATTAGACAAAATGAGACAATTATACTGGCACATAAGTGCATC
ATTGGATAAACCAAAACGAATATACTAGCACATAAGTGTATCACCAGATGAATTGAATCAT
Found at i:31404414 original size:27 final size:26
Alignment explanation
Indices: 31404397--31404710 Score: 315
Period size: 27 Copynumber: 11.7 Consensus size: 26
31404387 TTACACTACA
* * *
31404397 AGGGAATTTCGGTAATTTTACACTACA
1 AGGGTATTTCGGTAATTTTACA-AACG
*
31404424 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAA-CG
* *
31404451 AGGGTGTTTTGGTAATTTTACAAAACG
1 AGGGTATTTCGGTAATTTTAC-AAACG
*
31404478 AGGGTATTTTGGTAATTTTACAAACTG
1 AGGGTATTTCGGTAATTTTACAAAC-G
* *
31404505 AGGGTATTTCGATAATTTTACAAATTG
1 AGGGTATTTCGGTAATTTTACAAA-CG
* *
31404532 AAGGTGTTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAA-CG
* *
31404559 AGGGTGTTTCGATAATTTTACAAACCG
1 AGGGTATTTCGGTAATTTTACAAA-CG
* * *
31404586 AGGGTGTTTCAGTAATTTCACAAATCG
1 AGGGTATTTCGGTAATTTTACAAA-CG
* *
31404613 AGGGTATTTCAGTAATTTTACAATCG
1 AGGGTATTTCGGTAATTTTACAAACG
**
31404639 AGGGTATTTCAATAATTTTACAAATC-
1 AGGGTATTTCGGTAATTTTACAAA-CG
*
31404665 AGGGGTATTTCGGTAATTTTACAAATTG
1 A-GGGTATTTCGGTAATTTTACAAA-CG
* *
31404693 AAGGTATTTCAGTAATTT
1 AGGGTATTTCGGTAATTT
31404711 CTCTTTATTA
Statistics
Matches: 248, Mismatches: 32, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
26 30 0.12
27 214 0.86
28 4 0.02
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (26 bp):
AGGGTATTTCGGTAATTTTACAAACG
Found at i:31404497 original size:81 final size:81
Alignment explanation
Indices: 31404397--31404710 Score: 364
Period size: 81 Copynumber: 3.9 Consensus size: 81
31404387 TTACACTACA
* * * *
31404397 AGGGAATTTCGGTAATTTTACACTA-CAAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTT
1 AGGGTATTTCGATAATTTTACA-AACCAAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTC
*
31404461 GGTAATTTTACAAAACG
65 GGTAATTTTACAAATCG
* * ** * *
31404478 AGGGTATTTTGGTAATTTTACAAACTGAGGGTATTTCGATAATTTTACAAATTGAAGGTGTTTCG
1 AGGGTATTTCGATAATTTTACAAACCAAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCG
31404543 GTAATTTTACAAATCG
66 GTAATTTTACAAATCG
* * * * *
31404559 AGGGTGTTTCGATAATTTTACAAACCGAGGGTGTTTC-AGTAATTTCACAAATCGAGGGTATTTC
1 AGGGTATTTCGATAATTTTACAAACCAAGGGTATTTCGA-TAATTTTACAAATCGAGGGTGTTTC
*
31404623 AGTAATTTTAC-AATCG
65 GGTAATTTTACAAATCG
* * * * * * * *
31404639 AGGGTATTTCAATAATTTTACAAATCAGGGGTATTTCGGTAATTTTACAAATTGAAGGTATTTCA
1 AGGGTATTTCGATAATTTTACAAACCAAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCG
31404704 GTAATTT
66 GTAATTT
31404711 CTCTTTATTA
Statistics
Matches: 201, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
80 68 0.34
81 133 0.66
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (81 bp):
AGGGTATTTCGATAATTTTACAAACCAAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCG
GTAATTTTACAAATCG
Found at i:31407358 original size:27 final size:27
Alignment explanation
Indices: 31407327--31407414 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
31407317 ACATGGGCCA
* *
31407327 AAGCCCGTTACAATATCATTTGGGTCC
1 AAGCCCATAACAATATCATTTGGGTCC
31407354 AAGCCCATAACAATATCATTTGGGTCC
1 AAGCCCATAACAATATCATTTGGGTCC
*
31407381 AAGCCCATAACAGA-ATCAATTGGG-CC
1 AAGCCCATAACA-ATATCATTTGGGTCC
*
31407407 TAGCCCAT
1 AAGCCCAT
31407415 CTTAGCCTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
26 9 0.16
27 46 0.82
28 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (27 bp):
AAGCCCATAACAATATCATTTGGGTCC
Found at i:31407986 original size:27 final size:27
Alignment explanation
Indices: 31407941--31408003 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
31407931 GCAAAAGAGG
* * *
31407941 CATTTTACCCTACAGGGGTATATCGGT
1 CATTTTACACTACAAGGGTATATCGAT
* *
31407968 CATTTTACACTATAAGGGTATTTCGAT
1 CATTTTACACTACAAGGGTATATCGAT
*
31407995 AATTTTACA
1 CATTTTACA
31408004 AATCGGGGGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (27 bp):
CATTTTACACTACAAGGGTATATCGAT
Found at i:31408013 original size:27 final size:27
Alignment explanation
Indices: 31407982--31408266 Score: 305
Period size: 27 Copynumber: 10.7 Consensus size: 27
31407972 TTACACTATA
31407982 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * * * *
31408009 GGGGTGTTTCGGTAGTTCTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
31408036 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * *
31408063 AGGGTGTTTTGATAATTTTACAAATCA
1 AGGGTATTTCGATAATTTTACAAATCG
* *
31408090 AGGGTGTTTC-AGTAATTTTACAAATTG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* *
31408117 AGGGTGTTTCGATAATTTCACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
*
31408144 GGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * **
31408171 AGGGTATTT-TAGTAATTTCAC-AATAA
1 AGGGTATTTCGA-TAATTTTACAAATCG
*
31408197 AGGGTATTTCGATAA-TTTACGAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
31408223 GGGGTATTTCGGTAA---TACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
*
31408247 AGGGTATTTCAATAAATTTT
1 AGGGTATTTCGAT-AATTTT
31408267 CTTTATTATG
Statistics
Matches: 213, Mismatches: 36, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
24 18 0.08
25 6 0.03
26 33 0.15
27 154 0.72
28 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.37
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACAAATCG
Found at i:31411551 original size:27 final size:27
Alignment explanation
Indices: 31411463--31411551 Score: 124
Period size: 27 Copynumber: 3.3 Consensus size: 27
31411453 CAAAAGAGTC
* * * * *
31411463 ATTTTACTCTACAGGGGTATGTCGGTC
1 ATTTTACACTACAAGGGTATTTCGATA
*
31411490 ATTTTACATTACAAGGGTATTTCGATA
1 ATTTTACACTACAAGGGTATTTCGATA
31411517 ATTTTACACTACAAGGGTATTTCGATA
1 ATTTTACACTACAAGGGTATTTCGATA
31411544 ATTTTACA
1 ATTTTACA
31411552 AATCGGGCGT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGATA
Found at i:31411602 original size:27 final size:27
Alignment explanation
Indices: 31411477--31411843 Score: 323
Period size: 27 Copynumber: 13.6 Consensus size: 27
31411467 TACTCTACAG
* * * *
31411477 GGGTATGTCGGTCATTTTAC-ATTACAA
1 GGGTATTTCGGTAATTTTACAAAT-CGA
* * *
31411504 GGGTATTTCGATAATTTTAC-ACTACAA
1 GGGTATTTCGGTAATTTTACAAAT-CGA
*
31411531 GGGTATTTCGATAATTTTACAAATCG-
1 GGGTATTTCGGTAATTTTACAAATCGA
* * * *
31411557 GGCGTGTTTTGGTAGTTTTACAAATTGA
1 GG-GTATTTCGGTAATTTTACAAATCGA
* ** * *
31411585 GGGAATTTCAATAATTTTATAAATTGA
1 GGGTATTTCGGTAATTTTACAAATCGA
* * **
31411612 AGGTATTTCAGTAATTTTACAAATTAA
1 GGGTATTTCGGTAATTTTACAAATCGA
*
31411639 GGGTGTTTCGGTAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTACAAATCGA
* *
31411666 GGGTGTTTCGATAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTACAAATCGA
** *
31411693 GGG-AGTTTTTGTAATTTCACAAATC-A
1 GGGTA-TTTCGGTAATTTTACAAATCGA
*
31411719 GGGGTATTTCGGTAATTTTACAAATTGA
1 -GGGTATTTCGGTAATTTTACAAATCGA
* *
31411747 GGGTATTTCAGTAATTTCAC-AATCGA
1 GGGTATTTCGGTAATTTTACAAATCGA
* * *
31411773 GGGTATTTTGATAATTTTACAAATCGG
1 GGGTATTTCGGTAATTTTACAAATCGA
* *
31411800 GGGTATATCGATAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTACAAATCGA
*
31411827 GGGTATTTCAGTAATTT
1 GGGTATTTCGGTAATTT
31411844 CTCTTTATTA
Statistics
Matches: 280, Mismatches: 52, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
26 24 0.09
27 250 0.89
28 6 0.02
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACAAATCGA
Found at i:31427067 original size:49 final size:49
Alignment explanation
Indices: 31427011--31427104 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
31427001 TCTAGAAGGG
31427011 ATAAATAATGATAAGAGTGTAGATAGTGGAAGA-CTAAGTTTAGTAATGT
1 ATAAATAATGATAAGAGTGTAGATAGTGGAAGAGC-AAGTTTAGTAATGT
*
31427060 ATAAATAATGTTAAGAGTGTAGATAGTGGAAGAGCAAGTTTAGTA
1 ATAAATAATGATAAGAGTGTAGATAGTGGAAGAGCAAGTTTAGTA
31427105 TTGCATAGCA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
49 42 0.98
50 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.26, T:0.30
Consensus pattern (49 bp):
ATAAATAATGATAAGAGTGTAGATAGTGGAAGAGCAAGTTTAGTAATGT
Found at i:31427541 original size:35 final size:35
Alignment explanation
Indices: 31427492--31427562 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
31427482 AAAAGATGGC
** *
31427492 AAATGAATTTGATAAGGAAGTGGAACAAGCGTTCT
1 AAATGAATCAGATAAGGAAGTGGAACAAGAGTTCT
*
31427527 AAATGAATCAGATAATGAAGTGGAACAAGAGTTCT
1 AAATGAATCAGATAAGGAAGTGGAACAAGAGTTCT
31427562 A
1 A
31427563 CTCTAGTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (35 bp):
AAATGAATCAGATAAGGAAGTGGAACAAGAGTTCT
Found at i:31434375 original size:29 final size:29
Alignment explanation
Indices: 31434327--31434388 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
31434317 TTAAAATAAA
* * *
31434327 TATATATGTTATATATATTAAATTTAATG
1 TATATATGTAATATATATTAAAATGAATG
31434356 TATATATGTAATA-ATAATTAAAATGAATG
1 TATATATGTAATATAT-ATTAAAATGAATG
31434385 TATA
1 TATA
31434389 ATAAAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (29 bp):
TATATATGTAATATATATTAAAATGAATG
Found at i:31435917 original size:27 final size:27
Alignment explanation
Indices: 31435887--31436064 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
31435877 ATATCGAGTC
* * * *
31435887 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
31435914 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31435941 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
31435969 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
31435996 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
31436023 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31436050 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31436065 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:31436026 original size:82 final size:81
Alignment explanation
Indices: 31435908--31436063 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
31435898 TGCTATATAA
*
31435908 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31435973 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
31435990 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31436054 CACTTAGTGC
65 CACTTAGTGC
31436064 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:31440781 original size:47 final size:46
Alignment explanation
Indices: 31440665--31440795 Score: 165
Period size: 46 Copynumber: 2.8 Consensus size: 46
31440655 ATAATTTCAC
* * * *
31440665 CCATAATGAACTCAGAACGCAACTCCACGAGCTCGGGTGTTCACAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGTTCACAT
* * *
31440711 CCATAATGAACTCGGAACACAACTCAACAAGTTCGGATGCTT-GCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATG-TTCACAT
*
31440757 CCATAAGTGAACTCGGAACGCAACTCAATGAGTTCGGAT
1 CCATAA-TGAACTCGGAACGCAACTCAACGAGTTCGGAT
31440796 CTCAAATTTC
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
46 42 0.58
47 31 0.42
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGTTCACAT
Found at i:31442445 original size:43 final size:43
Alignment explanation
Indices: 31442380--31442494 Score: 162
Period size: 43 Copynumber: 2.7 Consensus size: 43
31442370 GTACCATACG
*
31442380 AATGCCATATCCCAGATATGGTCTTACATGAAA-TCTCGTATC
1 AATGCCATATCCCAGATATGGTCTTACATGAAAGTCTCATATC
* * *
31442422 AATGCCAATATTCCAGCTATGGTCTTACA-CAAAGTCTCATATC
1 AATGCC-ATATCCCAGATATGGTCTTACATGAAAGTCTCATATC
*
31442465 AATGCCATATCCCAAATATGGTCTTACATG
1 AATGCCATATCCCAGATATGGTCTTACATG
31442495 TTATCTTAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
42 28 0.45
43 34 0.55
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.30
Consensus pattern (43 bp):
AATGCCATATCCCAGATATGGTCTTACATGAAAGTCTCATATC
Found at i:31446159 original size:47 final size:46
Alignment explanation
Indices: 31446090--31446265 Score: 191
Period size: 47 Copynumber: 3.8 Consensus size: 46
31446080 TGTAACCCGC
* * *
31446090 CCATAAGCGAACTCCGACTCAACTCAACGAGCTCGGGCGTTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTTCGCAT
*
31446137 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-CT--TTCGCAT
* * *
31446187 CTCA-CA---AACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTTCGCAT
31446230 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
31446266 ATGCTCAACC
Statistics
Matches: 109, Mismatches: 9, Indels: 23
0.77 0.06 0.16
Matches are distributed among these distances:
42 4 0.04
43 5 0.05
44 1 0.01
46 27 0.25
47 60 0.55
49 2 0.02
50 6 0.06
51 4 0.04
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTTCGCAT
Found at i:31446259 original size:93 final size:94
Alignment explanation
Indices: 31446099--31446269 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 94
31446089 CCCATAAGCG
* *
31446099 AACTCCGACTCAACTCAACGAGCTCGGGCGTTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 AACTCCGACTCAACTCAACGAGCTCGGACGATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
31446164 CGAGTTCGGATGCCTAGTTACATCTCACA
66 CGAGTTCGGATGCCTAGTTACATCTCACA
* *
31446193 AACTCGGACTCAACTCAACGAGTTCGGAC-ATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 AACTCCGACTCAACTCAACGAGCTCGGACGATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
31446257 CGAGTTCGGATGC
66 CGAGTTCGGATGC
31446270 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 47 0.64
94 26 0.36
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (94 bp):
AACTCCGACTCAACTCAACGAGCTCGGACGATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCACA
Found at i:31446285 original size:46 final size:44
Alignment explanation
Indices: 31446142--31446285 Score: 132
Period size: 46 Copynumber: 3.1 Consensus size: 44
31446132 CGCATCCATA
31446142 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
** * * *
31446189 CA-CAAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
31446235 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
31446281 AGTGA
1 AGTGA
31446286 CATGTCACTT
Statistics
Matches: 78, Mismatches: 11, Indels: 16
0.74 0.10 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 32 0.41
47 30 0.38
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:31452836 original size:29 final size:29
Alignment explanation
Indices: 31452794--31452910 Score: 191
Period size: 29 Copynumber: 4.1 Consensus size: 29
31452784 GAAAGCATGT
31452794 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
31452823 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
31452852 ATACGAATGTGATTTGGACCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
31452881 ATATGAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
31452909 AT
1 AT
31452911 TTGCATGTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
28 16 0.20
29 66 0.80
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.29
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:31461352 original size:39 final size:40
Alignment explanation
Indices: 31461289--31461364 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
31461279 NNNNNNNNTA
*
31461289 TAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGAAT
1 TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAAT
*
31461328 TAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
31461365 TTATCATCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 24 0.71
40 10 0.29
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAAT
Found at i:31467363 original size:40 final size:40
Alignment explanation
Indices: 31467293--31467498 Score: 245
Period size: 40 Copynumber: 5.2 Consensus size: 40
31467283 CGGGATTCAG
** * *
31467293 CCGGATATAACCACTGGCAC-AAGGCCTTCGGGTCTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
31467332 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC
*
31467372 CCGGATATAGTCGCTAGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
31467412 CCGGA-ATGGAAACTCGCACAAATGCCTTCGGATCTTAGT
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
31467451 CCGGATATAGTCACTAGCATAAAAGCCTTCGGGACTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC
31467491 CCGGATAT
1 CCGGATAT
31467499 CATTCGAATA
Statistics
Matches: 138, Mismatches: 27, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
39 47 0.34
40 91 0.66
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:31467436 original size:79 final size:80
Alignment explanation
Indices: 31467293--31467498 Score: 265
Period size: 79 Copynumber: 2.6 Consensus size: 80
31467283 CGGGATTCAG
** * * ** *
31467293 CCGGATATAACCACTGGCAC-AAGGCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATG
1 CCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATGGAAACTAGCACAAATG
31467357 CCTTCGGGA-CTTAGC
66 CCTTC-GGATCTTAGC
* * *
31467372 CCGGATATAGTCGCTAGCACAAATGCCTTCGGGTCTTAGCCCGGA-ATGGAAACTCGCACAAATG
1 CCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATGGAAACTAGCACAAATG
*
31467436 CCTTCGGATCTTAGT
66 CCTTCGGATCTTAGC
* *
31467451 CCGGATATAGTCACTAGCATAAAAGCCTTCGGGACTTAGCCCGGATAT
1 CCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATAT
31467499 CATTCGAATA
Statistics
Matches: 110, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
78 3 0.03
79 82 0.75
80 25 0.23
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (80 bp):
CCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATGGAAACTAGCACAAATG
CCTTCGGATCTTAGC
Found at i:31479448 original size:43 final size:42
Alignment explanation
Indices: 31479372--31479491 Score: 143
Period size: 42 Copynumber: 2.8 Consensus size: 42
31479362 CACACAGTAC
* * *
31479372 CATACCAATGCCATATCCCAGATATTGTCTTACATGAAA-TCT
1 CATATCAATGCCATATCCCAGATATGGTCTTACA-CAAAGTCT
* * *
31479414 CGTATCAATGCCAATATTCCAGCTATGGTCTTACACAAAGTCT
1 CATATCAATGCC-ATATCCCAGATATGGTCTTACACAAAGTCT
* *
31479457 CATATCAATTCCATATCCCAAATATGGTCTTACAC
1 CATATCAATGCCATATCCCAGATATGGTCTTACAC
31479492 GTTATCTTAG
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 33 0.51
43 32 0.49
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.31
Consensus pattern (42 bp):
CATATCAATGCCATATCCCAGATATGGTCTTACACAAAGTCT
Found at i:31487120 original size:16 final size:16
Alignment explanation
Indices: 31487078--31487120 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
31487068 GTATATCGAC
*
31487078 AAAAGCCAAAATGCCA
1 AAAAGCCGAAATGCCA
*
31487094 AAAAGCCGAAATGCCG
1 AAAAGCCGAAATGCCA
*
31487110 AAAAGCTGAAA
1 AAAAGCCGAAA
31487121 GTTTGGCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.53, C:0.21, G:0.19, T:0.07
Consensus pattern (16 bp):
AAAAGCCGAAATGCCA
Found at i:31487373 original size:29 final size:29
Alignment explanation
Indices: 31487331--31487447 Score: 182
Period size: 29 Copynumber: 4.1 Consensus size: 29
31487321 GAAAGCATGT
31487331 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
31487360 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* * *
31487389 GTACGAATGTGATTTGGGCCTAATGGGCT
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
31487418 ATATGAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
31487446 AT
1 AT
31487448 TTGCATGTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
28 16 0.20
29 64 0.80
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:31490434 original size:93 final size:93
Alignment explanation
Indices: 31490324--31490495 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
31490314 GCCCATAAGT
* * *
31490324 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTAAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
31490389 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
31490417 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
*
31490482 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
31490496 CAAATATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:31490491 original size:46 final size:46
Alignment explanation
Indices: 31490316--31490491 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
31490306 TGTAACCCGC
* *
31490316 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
31490362 CCATAAGTAAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** * *
31490408 ACATCTCTCGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
31490455 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
31490492 TGCCCAAATA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 68 0.64
47 30 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:31494633 original size:21 final size:21
Alignment explanation
Indices: 31494585--31494624 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31494575 CATGATATAA
*
31494585 CATTAATGATAAAATGGCTAT
1 CATTCATGATAAAATGGCTAT
31494606 CATTCATGATAAAATGGCT
1 CATTCATGATAAAATGGCT
31494625 TCCTTTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (21 bp):
CATTCATGATAAAATGGCTAT
Found at i:31501395 original size:39 final size:39
Alignment explanation
Indices: 31501292--31501420 Score: 159
Period size: 40 Copynumber: 3.3 Consensus size: 39
31501282 AAATAGACCG
* * * *
31501292 AACACACCAGACAGAAGCTCATAAGAGCTGATCCAACCAA
1 AACACGCCA-ACAAAAGCTCATAAGAGCTGATCCACCCGA
* *
31501332 AATACGCCAAACAAAAGCTCATAAGAGCTGGTCCACCCGA
1 AACACGCC-AACAAAAGCTCATAAGAGCTGATCCACCCGA
* *
31501372 AACACGCCAACAAAAGCTCATAAGAGCTGATACACTCGA
1 AACACGCCAACAAAAGCTCATAAGAGCTGATCCACCCGA
*
31501411 ATCACGCCAA
1 AACACGCCAA
31501421 ACAGAAAGTA
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 37 0.48
40 39 0.51
41 1 0.01
ACGTcount: A:0.43, C:0.30, G:0.16, T:0.12
Consensus pattern (39 bp):
AACACGCCAACAAAAGCTCATAAGAGCTGATCCACCCGA
Found at i:31511942 original size:39 final size:40
Alignment explanation
Indices: 31511899--31512066 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
31511889 CTCGTTCAAG
* * * *
31511899 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
31511938 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
31511978 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
31512018 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
31512058 TGCCTTCGG
1 TGCCTTCGG
31512067 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:31512050 original size:80 final size:80
Alignment explanation
Indices: 31511934--31512119 Score: 229
Period size: 80 Copynumber: 2.3 Consensus size: 80
31511924 AGTAACTCAT
* * *
31511934 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
31511998 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
31512013 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
31512077 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
31512094 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
31512120 CAGCATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
79 11 0.12
80 72 0.77
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:31512079 original size:40 final size:40
Alignment explanation
Indices: 31511936--31512119 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
31511926 TAACTCATAC
* *
31511936 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
31511976 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
31512016 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
31512056 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
31512097 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
31512120 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 105 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:31513469 original size:76 final size:76
Alignment explanation
Indices: 31513343--31513487 Score: 254
Period size: 76 Copynumber: 1.9 Consensus size: 76
31513333 CACAACCTCT
* * *
31513343 ACCTAGGTCGAATCTTAACTCATCCTCATGTCTCATCACCACCACATCAAACATCAACCAAGAAT
1 ACCTAGGCCGAATCTTAACTCATCCTCATGCCTCATCACCACAACATCAAACATCAACCAAGAAT
31513408 GATGAAACTCC
66 GATGAAACTCC
*
31513419 ACCTAGGCCGAATCTTAACTCATCCTCATGCCTCATCACCACAACATCAAACATCAACCAGGAAT
1 ACCTAGGCCGAATCTTAACTCATCCTCATGCCTCATCACCACAACATCAAACATCAACCAAGAAT
31513484 GATG
66 GATG
31513488 CATCCATGGC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 65 1.00
ACGTcount: A:0.35, C:0.33, G:0.10, T:0.21
Consensus pattern (76 bp):
ACCTAGGCCGAATCTTAACTCATCCTCATGCCTCATCACCACAACATCAAACATCAACCAAGAAT
GATGAAACTCC
Found at i:31515489 original size:43 final size:42
Alignment explanation
Indices: 31515406--31515568 Score: 136
Period size: 43 Copynumber: 3.8 Consensus size: 42
31515396 GGAAAGCTCG
* *
31515406 TACAATGCCAAC-GTCCCAGACATGGTCTTACATGTAATCAAA
1 TACAATGCC-ACTGTCCCAAACATGGTCTTACACGTAATCAAA
* *
31515448 TATCGATGCCACTGTCCCAAACAGGGTCTTACACG-AGATCAAA
1 TA-CAATGCCACTGTCCCAAACATGGTCTTACACGTA-ATCAAA
* * * *
31515491 TACAACGTCAATGTTCCAAACATGGTCTTACACGTAAATCATAA
1 TACAATGCCACTGTCCCAAACATGGTCTTACACGT-AATCA-AA
* * *
31515535 GT-CAATGGCAAC-ATCCCAAACGTGGTCTTACACG
1 -TACAAT-GCCACTGTCCCAAACATGGTCTTACACG
31515569 AAAACACATA
Statistics
Matches: 96, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
42 31 0.32
43 37 0.39
44 25 0.26
45 3 0.03
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (42 bp):
TACAATGCCACTGTCCCAAACATGGTCTTACACGTAATCAAA
Found at i:31517986 original size:43 final size:43
Alignment explanation
Indices: 31517925--31518010 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
31517915 AAGGAAGTGG
31517925 TGTAGGGAAGAGTGGTAGAAGGATTCGGCTATGGAGAAAAGAA
1 TGTAGGGAAGAGTGGTAGAAGGATTCGGCTATGGAGAAAAGAA
* *
31517968 TGTAGGGAAGAGTGGTAGAGGGCTTCGGCTATGGAGAAAAGAA
1 TGTAGGGAAGAGTGGTAGAAGGATTCGGCTATGGAGAAAAGAA
31518011 GAGGAGAAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.35, C:0.06, G:0.41, T:0.19
Consensus pattern (43 bp):
TGTAGGGAAGAGTGGTAGAAGGATTCGGCTATGGAGAAAAGAA
Found at i:31525925 original size:41 final size:41
Alignment explanation
Indices: 31525870--31525952 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
31525860 TAAGGAAGTG
*
31525870 GTGTAGGGGAGAGTGGTAGAAGGATTCAGCTATGGAGAAAA
1 GTGTAGGGAAGAGTGGTAGAAGGATTCAGCTATGGAGAAAA
*
31525911 GTGTAGGGAAGAGTGGTAGAAGGATTCGGCTATGGAGAAAA
1 GTGTAGGGAAGAGTGGTAGAAGGATTCAGCTATGGAGAAAA
31525952 G
1 G
31525953 AAGAGGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.34, C:0.05, G:0.42, T:0.19
Consensus pattern (41 bp):
GTGTAGGGAAGAGTGGTAGAAGGATTCAGCTATGGAGAAAA
Found at i:31540842 original size:46 final size:44
Alignment explanation
Indices: 31540709--31540970 Score: 183
Period size: 46 Copynumber: 5.7 Consensus size: 44
31540699 GTAAGGTGCA
*
31540709 GATGCCATGTCCCAGACATAGTCTTACACTGGC-TCATATCTCAAGTC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTTC--ATCTCAAGTC
* * * * * *
31540756 GATACCATGTCCTAAACATGGTCTTACA-TTGATTCATCTCGTAGTC
1 GAT-GCATGTCCCAGACAT-GTCTTACACTAGCTTCATCTC-AAGTC
* * * *
31540802 GATGCATGTCCCAGACATATCTTACACTAGCTTACGTCTCGAGGC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTT-CATCTCAAGTC
*
31540847 TGATGCATGTACCAGACATGTCTTACACTAGCTCTCATCTCAATGTC
1 -GATGCATGTCCCAGACATGTCTTACACTAGCT-TCATCTCAA-GTC
* **
31540894 GATGCCACGTCCCAGACATGGTCTTACACT-GGATC-TCAT-AATGTGGC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTTCATC-TCAA-GT--C
*
31540941 TGATGCATGTCCCAGACATGACTTACACTA
1 -GATGCATGTCCCAGACATGTCTTACACTA
31540971 TCTCACAAAA
Statistics
Matches: 173, Mismatches: 27, Indels: 30
0.75 0.12 0.13
Matches are distributed among these distances:
44 7 0.04
45 31 0.18
46 66 0.38
47 55 0.32
48 14 0.08
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (44 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTTCATCTCAAGTC
Found at i:31545807 original size:40 final size:41
Alignment explanation
Indices: 31545728--31545809 Score: 148
Period size: 40 Copynumber: 2.0 Consensus size: 41
31545718 GCGAGATTGA
*
31545728 ATAAGATAACATTTAACCAAAGAATTCATGTGTATTTCCCT
1 ATAAGATAACATTTAACCAAAGAATTCATGTGTACTTCCCT
31545769 ATAAGATAACATTTAACC-AAGAATTCATGTGTACTTCCCT
1 ATAAGATAACATTTAACCAAAGAATTCATGTGTACTTCCCT
31545809 A
1 A
31545810 CAAACAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 22 0.55
41 18 0.45
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (41 bp):
ATAAGATAACATTTAACCAAAGAATTCATGTGTACTTCCCT
Found at i:31546669 original size:33 final size:35
Alignment explanation
Indices: 31546627--31546694 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
31546617 TCAGTGACGG
*
31546627 TCTAGTATCAGT-AGGGCCATAGCCCATTACAGTA
1 TCTAGTATCAGTGAGGGCCATAGCCCAATACAGTA
* * *
31546661 TCTA-TATCAGTGTGGGCCTTAGCCTAATACAGTA
1 TCTAGTATCAGTGAGGGCCATAGCCCAATACAGTA
31546695 ACAATAACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (35 bp):
TCTAGTATCAGTGAGGGCCATAGCCCAATACAGTA
Found at i:31546765 original size:22 final size:23
Alignment explanation
Indices: 31546726--31546768 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
31546716 GAAATCCTAC
*
31546726 CCATCCATCCTCTACACTCCACT
1 CCATCCAGCCTCTACACTCCACT
31546749 CCATCCAGCC-CTACACTCCA
1 CCATCCAGCCTCTACACTCCA
31546769 TGTGGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.23, C:0.53, G:0.02, T:0.21
Consensus pattern (23 bp):
CCATCCAGCCTCTACACTCCACT
Found at i:31558078 original size:30 final size:30
Alignment explanation
Indices: 31558023--31558079 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
31558013 CTTTTGAAAA
**
31558023 TATTTACAAAAAGAGGCACTTAATTTTTAT
1 TATTTACAAAAAGAGGCACCAAATTTTTAT
31558053 TATTTACAAAAAGA-GCAACCAAATTTT
1 TATTTACAAAAAGAGGC-ACCAAATTTT
31558080 AAAAATAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (30 bp):
TATTTACAAAAAGAGGCACCAAATTTTTAT
Found at i:31564496 original size:41 final size:41
Alignment explanation
Indices: 31564407--31564543 Score: 107
Period size: 43 Copynumber: 3.2 Consensus size: 41
31564397 TTTGGGATGT
* * * *
31564407 TGGCATCGATATGTGATTACGTATAAGACCATGTCTGGGA-AA
1 TGGCATTG-TATGTGATT-CGTGTAAGACCCTGTCTAGGACAA
* *
31564449 TCGGCATTGTATTTGATTCGTGTAAGACCCTGTCTAGGACAG
1 T-GGCATTGTATGTGATTCGTGTAAGACCCTGTCTAGGACAA
* * * *
31564491 TGGCATCGATATGTGATAGCATGTAAGACCAC-GTCTAGGACAT
1 TGGCATTG-TATGTGAT-TCGTGTAAGACC-CTGTCTAGGACAA
*
31564534 TGACATTGTA
1 TGGCATTGTA
31564544 CGATATATGT
Statistics
Matches: 77, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
41 24 0.31
42 20 0.26
43 32 0.42
44 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (41 bp):
TGGCATTGTATGTGATTCGTGTAAGACCCTGTCTAGGACAA
Found at i:31566871 original size:40 final size:40
Alignment explanation
Indices: 31566773--31567035 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
31566763 TCCTCGTTCA
* * * * *
31566773 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
31566812 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
31566852 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
31566892 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
31566932 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
31566972 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
31567012 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
31567036 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:31567044 original size:41 final size:41
Alignment explanation
Indices: 31566967--31567044 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
31566957 TTAGTATCTC
* * *
31566967 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
31567008 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
31567045 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:31574006 original size:15 final size:15
Alignment explanation
Indices: 31573986--31574016 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31573976 AAATATGAAA
31573986 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
31574001 GATATGTTTTGTATT
1 GATATGTTTTGGATT
31574016 G
1 G
31574017 GAATTTTTGA
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:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:31577871 original size:29 final size:29
Alignment explanation
Indices: 31577770--31577885 Score: 121
Period size: 29 Copynumber: 4.1 Consensus size: 29
31577760 ATACATGCAC
* *
31577770 ATGGCCCACTAGGCCCAA-TCTTATTCAA
1 ATGGCCCACTAGGCCCAATTCATATTCAT
* *
31577798 ATGGCCCATCT-GGCCCAGTTCATATTCTT
1 ATGGCCCA-CTAGGCCCAATTCATATTCAT
* *
31577827 ATGGCCCACTACGCCCAATTCACATTCAT
1 ATGGCCCACTAGGCCCAATTCATATTCAT
* * *
31577856 ATGGCCTATTAGGCCCAAATCATATT-AT
1 ATGGCCCACTAGGCCCAATTCATATTCAT
31577884 AT
1 AT
31577886 TCATGCTCAC
Statistics
Matches: 72, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
28 20 0.28
29 52 0.72
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (29 bp):
ATGGCCCACTAGGCCCAATTCATATTCAT
Found at i:31577879 original size:58 final size:57
Alignment explanation
Indices: 31577770--31577881 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 57
31577760 ATACATGCAC
* ** **
31577770 ATGGCCCACTAGGCCCAATCTTATTCAAATGGCCCATCTGGCCCAGTTCATATTCTT
1 ATGGCCCACTACGCCCAATCACATTCAAATGGCCCATCTGGCCCAAATCATATTCTT
* *
31577827 ATGGCCCACTACGCCCAATTCACATTCATATGGCCTAT-TAGGCCCAAATCATATT
1 ATGGCCCACTACGCCCAA-TCACATTCAAATGGCCCATCT-GGCCCAAATCATATT
31577882 ATATTCATGC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
57 18 0.39
58 28 0.61
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (57 bp):
ATGGCCCACTACGCCCAATCACATTCAAATGGCCCATCTGGCCCAAATCATATTCTT
Found at i:31578571 original size:25 final size:25
Alignment explanation
Indices: 31578537--31578589 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
31578527 TAGAAAGAGT
31578537 AAGGGACAATATTCAATACTTAGCA
1 AAGGGACAATATTCAATACTTAGCA
*
31578562 AAGGGACAATATTCGATACTTAGCA
1 AAGGGACAATATTCAATACTTAGCA
31578587 AAG
1 AAG
31578590 AAACCGATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (25 bp):
AAGGGACAATATTCAATACTTAGCA
Found at i:31579088 original size:95 final size:95
Alignment explanation
Indices: 31578925--31579116 Score: 366
Period size: 95 Copynumber: 2.0 Consensus size: 95
31578915 AATTTTCCCA
*
31578925 TGCCCAATTCCCCATTCGGCTCCATCACTTCTCCCTTCTCATCTCCTCGTTTTTCTCCCTGATAA
1 TGCCCAATTCCCCATTCGACTCCATCACTTCTCCCTTCTCATCTCCTCGTTTTTCTCCCTGATAA
31578990 CCTCTTGATCCTTTCCTTAATTTTCTCTCC
66 CCTCTTGATCCTTTCCTTAATTTTCTCTCC
*
31579020 TGCCCAATTCCCCATTCGACTCCATCACTTCTCCCTTCTCATCTCCTTGTTTTTCTCCCTGATAA
1 TGCCCAATTCCCCATTCGACTCCATCACTTCTCCCTTCTCATCTCCTCGTTTTTCTCCCTGATAA
31579085 CCTCTTGATCCTTTCCTTAATTTTCTCTCC
66 CCTCTTGATCCTTTCCTTAATTTTCTCTCC
31579115 TG
1 TG
31579117 AACACTTCCT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.13, C:0.39, G:0.06, T:0.42
Consensus pattern (95 bp):
TGCCCAATTCCCCATTCGACTCCATCACTTCTCCCTTCTCATCTCCTCGTTTTTCTCCCTGATAA
CCTCTTGATCCTTTCCTTAATTTTCTCTCC
Found at i:31583972 original size:40 final size:40
Alignment explanation
Indices: 31583917--31584064 Score: 251
Period size: 40 Copynumber: 3.7 Consensus size: 40
31583907 GAGCATTGGA
31583917 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
31583957 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
31583997 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
31584037 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
31584065 ATGTGTTTGC
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 101 1.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.20
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:31585718 original size:84 final size:84
Alignment explanation
Indices: 31585617--31585774 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 84
31585607 ATATGTGTTC
* * * ** * *
31585617 TCGTGTAAGACCATGTCTGGGA-CGTTCGCATCGATATGTGATTATGTGTAAGACCATGTCTGGG
1 TCGTGTAAGACCATGTCTAGGATAG-TCGCATCGATATGTGATAACATGTAAGACCACGTCTAGG
31585681 ACATTGGCATCATATTTGAT
65 ACATTGGCATCATATTTGAT
* * *
31585701 TCGTGTAAGACCCTGTCTAGGATAGTGGCATCGATATGTGATAACATGTAAGACCACGTTTAGGA
1 TCGTGTAAGACCATGTCTAGGATAGTCGCATCGATATGTGATAACATGTAAGACCACGTCTAGGA
31585766 CATTGGCAT
66 CATTGGCAT
31585775 TGTACGATAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
84 62 0.98
85 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (84 bp):
TCGTGTAAGACCATGTCTAGGATAGTCGCATCGATATGTGATAACATGTAAGACCACGTCTAGGA
CATTGGCATCATATTTGAT
Found at i:31585765 original size:43 final size:42
Alignment explanation
Indices: 31585618--31585774 Score: 156
Period size: 43 Copynumber: 3.7 Consensus size: 42
31585608 TATGTGTTCT
* * * *
31585618 CGTGTAAGACCATGTCTGGGACGTTCGCATCGATATGTGATTA
1 CGTGTAAGACCACGTCTAGGACATTGGCATCGATATGTGA-TA
* * * * *
31585661 TGTGTAAGACCATGTCTGGGACATTGGCATC-ATATTTGATT
1 CGTGTAAGACCACGTCTAGGACATTGGCATCGATATGTGATA
* *
31585702 CGTGTAAGACC-CTGTCTAGGATAGTGGCATCGATATGTGATAA
1 CGTGTAAGACCAC-GTCTAGGACATTGGCATCGATATGTGAT-A
* *
31585745 CATGTAAGACCACGTTTAGGACATTGGCAT
1 CGTGTAAGACCACGTCTAGGACATTGGCAT
31585775 TGTACGATAT
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
41 26 0.28
42 15 0.16
43 52 0.55
44 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTAGGACATTGGCATCGATATGTGATA
Found at i:31586800 original size:31 final size:31
Alignment explanation
Indices: 31586762--31586821 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
31586752 GTTTTTCTTT
31586762 GTGAATGGTTTATTAATTTGGTTTAGTAACG
1 GTGAATGGTTTATTAATTTGGTTTAGTAACG
31586793 GTGAATGGTTTATTAATTTGGTTTAGTAA
1 GTGAATGGTTTATTAATTTGGTTTAGTAA
31586822 TGGAGTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.47
Consensus pattern (31 bp):
GTGAATGGTTTATTAATTTGGTTTAGTAACG
Found at i:31589497 original size:42 final size:43
Alignment explanation
Indices: 31589313--31589649 Score: 457
Period size: 43 Copynumber: 7.9 Consensus size: 43
31589303 TTATATAGAA
*
31589313 AAACGCAGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
** *
31589356 AAACGCCAATATAGAACAT-ACCCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTATAGAACATGA-CCTTTAGCGGCGCTTTTCCCAC
* **
31589399 AAACGCCGCTATAGAACATGACCTTTAGAGGCATTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
31589442 AAACGTCGCTATAGAACATGACCTTTAGTGGTGCTTTT-CCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
31589484 AAACGCCGCTATAGAATAAGACCTTTAGTGGCGCTTTTACCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* *
31589527 AAACGCCGCTATAGAACATGACCTTTAACGGCGC-TCTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
**
31589569 AAACGCCGCTATAGAACATGACCTTTAATGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* *
31589612 AAACGCCACTATAGAACA-GACCTTTAACGGCGCTTTTC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTC
31589650 TTAAAAATGC
Statistics
Matches: 263, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
42 97 0.37
43 165 0.63
44 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:31589531 original size:85 final size:85
Alignment explanation
Indices: 31589313--31589649 Score: 462
Period size: 85 Copynumber: 4.0 Consensus size: 85
31589303 TTATATAGAA
* * *
31589313 AAACGCAGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCAATATAGAACAT-AC
1 AAACGCCGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTATAGAACATGA-
*
31589377 CCTTTAGCGGCACTTTTCCCAC
65 CCTTTAGCGGCGCTTTT-CCAC
* ** * *
31589399 AAACGCCGCTATAGAACATGACCTTTAGAGGCATTTTTCCCACAAACGTCGCTATAGAACATGAC
1 AAACGCCGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTATAGAACATGAC
* *
31589464 CTTTAGTGGTGCTTTTCCAC
66 CTTTAGCGGCGCTTTTCCAC
* * * *
31589484 AAACGCCGCTATAGAATAAGACCTTTAGTGGCGCTTTTACCACAAACGCCGCTATAGAACATGAC
1 AAACGCCGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTATAGAACATGAC
* * *
31589549 CTTTAACGGCGCTCTCCCAC
66 CTTTAGCGGCGCTTTTCCAC
*
31589569 AAACGCCGCTATAGAACATGACCTTTAATGGCGCTTTTCCCACAAACGCCACTATAGAACA-GAC
1 AAACGCCGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTATAGAACATGAC
*
31589633 CTTTAACGGCGCTTTTC
66 CTTTAGCGGCGCTTTTC
31589650 TTAAAAATGC
Statistics
Matches: 221, Mismatches: 29, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
84 18 0.08
85 133 0.60
86 69 0.31
87 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (85 bp):
AAACGCCGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTATAGAACATGAC
CTTTAGCGGCGCTTTTCCAC
Found at i:31595099 original size:7 final size:7
Alignment explanation
Indices: 31595087--31595179 Score: 89
Period size: 7 Copynumber: 13.1 Consensus size: 7
31595077 ACTAATTAAT
31595087 CTAAACC
1 CTAAACC
31595094 CTAAACCC
1 CTAAA-CC
*
31595102 CTAACCC
1 CTAAACC
31595109 CTAAACC
1 CTAAACC
31595116 CTAAACC
1 CTAAACC
31595123 CTAAA-C
1 CTAAACC
* **
31595129 ATAAAAT
1 CTAAACC
*
31595136 ATAAACC
1 CTAAACC
*
31595143 CTAACCC
1 CTAAACC
*
31595150 CTAACCC
1 CTAAACC
31595157 CTAAACCC
1 CTAAA-CC
31595165 CTAAACC
1 CTAAACC
*
31595172 TTAAACC
1 CTAAACC
31595179 C
1 C
31595180 CAACCCTTAA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
6 5 0.07
7 54 0.75
8 13 0.18
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAAACC
Found at i:31595189 original size:14 final size:15
Alignment explanation
Indices: 31595145--31595191 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
31595135 TATAAACCCT
*
31595145 AACCCCTAACCCCTA
1 AACCCCTAACCCTTA
*
31595160 AACCCCTAAACCTTA
1 AACCCCTAACCCTTA
31595175 AACCCC-AACCCTTA
1 AACCCCTAACCCTTA
31595189 AAC
1 AAC
31595192 AATAATTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.38, C:0.47, G:0.00, T:0.15
Consensus pattern (15 bp):
AACCCCTAACCCTTA
Found at i:31595366 original size:7 final size:7
Alignment explanation
Indices: 31595354--31595426 Score: 67
Period size: 7 Copynumber: 10.4 Consensus size: 7
31595344 ACTAATTAAT
31595354 CTAAACC
1 CTAAACC
31595361 CTAAACCC
1 CTAAA-CC
*
31595369 CTAACCC
1 CTAAACC
31595376 CTAAACC
1 CTAAACC
31595383 CTAAACC
1 CTAAACC
31595390 CTAAA-C
1 CTAAACC
* **
31595396 ATAAAAT
1 CTAAACC
*
31595403 ATAAACC
1 CTAAACC
*
31595410 CTAACCC
1 CTAAACC
*
31595417 CTAACCC
1 CTAAACC
31595424 CTA
1 CTA
31595427 TAGTATTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.09
7 45 0.80
8 6 0.11
ACGTcount: A:0.42, C:0.41, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAAACC
Found at i:31600048 original size:15 final size:15
Alignment explanation
Indices: 31600009--31600088 Score: 74
Period size: 15 Copynumber: 5.4 Consensus size: 15
31599999 GTATCTTGGG
* *
31600009 TTTCTTTATCCTAGA
1 TTTCTTTATTCTGGA
*
31600024 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
31600039 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
31600054 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
* *
31600069 TTTATTTATTC-GGT
1 TTTCTTTATTCTGGA
31600083 TTTCTT
1 TTTCTT
31600089 GTTATCTTTG
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
14 9 0.17
15 41 0.79
16 2 0.04
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:31600069 original size:30 final size:30
Alignment explanation
Indices: 31600000--31600087 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 30
31599990 CGTAGTATCG
* * * * *
31600000 TATCTTGGGTTTCTTTATCCTAGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
31600030 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
* *
31600060 TATCTTGGATTTATTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
31600088 TGTTATCTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 8 0.17
30 39 0.81
31 1 0.02
ACGTcount: A:0.12, C:0.16, G:0.15, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Done.