Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008953.1 Hibiscus syriacus cultivar Beakdansim tig00112281_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2822058
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 15
Found at i:1237499 original size:20 final size:20
Alignment explanation
Indices: 1237471--1237510 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1237461 TATAATACTT
1237471 ATTTATTATTATTATTATTA
1 ATTTATTATTATTATTATTA
*
1237491 ATTTTTTATTATTATTATTA
1 ATTTATTATTATTATTATTA
1237511 TTAAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTATTATTATTATTATTA
Found at i:1237502 original size:23 final size:24
Alignment explanation
Indices: 1237472--1237528 Score: 98
Period size: 23 Copynumber: 2.4 Consensus size: 24
1237462 ATAATACTTA
1237472 TTTATTATTATTATTATT-AATTT
1 TTTATTATTATTATTATTAAATTT
1237495 TTTATTATTATTATTATTAAATTT
1 TTTATTATTATTATTATTAAATTT
1237519 TTTATATATT
1 TTTAT-TATT
1237529 TTTTCAGGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 18 0.56
24 10 0.31
25 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTATTATTATTATTATTAAATTT
Found at i:1238939 original size:23 final size:23
Alignment explanation
Indices: 1238913--1238975 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
1238903 TTAATTTGTT
1238913 TTTTCATTTGATTTATTATT-TGA
1 TTTTC-TTTGATTTATTATTATGA
* *
1238936 TTTT-TTTTATTTTCATTATTATGT
1 TTTTCTTTGA-TTT-ATTATTATGA
1238960 TTTTCTTTGATTTATT
1 TTTTCTTTGATTTATT
1238976 TAATATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
21 4 0.12
22 3 0.09
23 13 0.39
24 9 0.27
25 4 0.12
ACGTcount: A:0.17, C:0.05, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTTCTTTGATTTATTATTATGA
Found at i:1243301 original size:116 final size:116
Alignment explanation
Indices: 1243142--1243456 Score: 501
Period size: 116 Copynumber: 2.7 Consensus size: 116
1243132 TAATACAAGC
* * *
1243142 TTGGATTTCAACTTCACGACGAATGATATTCAAGTCAAGGCTCAACTTCACAAAGAAAGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAAAGAAAGGGCCAT
*
1243207 CCACGGTTTCAACTTCACGACGAAAGGAATCGTGTTCACCAGCAACATTCA
66 CCACGGTTTCAACTTCACGACGAAAGGAATCGTGCTCACCAGCAACATTCA
1243258 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAAA-AAATGGGCCA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAAAGAAA-GGGCCA
*
1243322 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCA
65 TCCACGGTTTCAACTTCACGACGAAAGGAATCGTGCTCACCAGCAACATTCA
*
1243374 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAATTTCA-AAACG-AAGAGGCC
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAAA-GAAAG-GGCC
** *
1243437 ATCCACTATTTCAATTTCAC
64 ATCCACGGTTTCAACTTCAC
1243457 AAAGAATGAT
Statistics
Matches: 186, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
115 7 0.04
116 179 0.96
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (116 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAAAGAAAGGGCCAT
CCACGGTTTCAACTTCACGACGAAAGGAATCGTGCTCACCAGCAACATTCA
Found at i:1243710 original size:36 final size:35
Alignment explanation
Indices: 1243663--1243770 Score: 144
Period size: 36 Copynumber: 3.0 Consensus size: 35
1243653 CAAAATAAAG
1243663 TTTTGTCTCTCTTGAGACAGTTCTTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTT-TTCTTGAAACAAA
* *
1243699 TTTTGTTTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTT-TCTTGAAACAAA
* * *
1243735 TTTTATCTCTCTTAAGATAGTTTTCATTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTTC-TTGAAACAAA
1243771 ATATTTGAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
35 2 0.03
36 61 0.97
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.43
Consensus pattern (35 bp):
TTTTGTCTCTCTTGAGACAGTTTTCTTGAAACAAA
Found at i:1243911 original size:73 final size:73
Alignment explanation
Indices: 1243805--1243941 Score: 238
Period size: 73 Copynumber: 1.9 Consensus size: 73
1243795 ACAAATTCCG
** * *
1243805 TCTCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAT
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAT
1243870 TTTTTTTA
66 TTTTTTTA
1243878 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1243942 CACAAAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (73 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAT
TTTTTTTA
Found at i:1243939 original size:37 final size:37
Alignment explanation
Indices: 1243785--1243943 Score: 198
Period size: 37 Copynumber: 4.4 Consensus size: 37
1243775 TTGAATATGT
**
1243785 TTTC-CTTGAAACAAA-TTCCGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
* * *
1243820 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
**** *
1243857 TTTCTCTTGAAA-TTTTTTTTATCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
*
1243893 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1243930 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
1243944 CAAAAAAACA
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
35 4 0.04
36 39 0.38
37 60 0.58
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
Found at i:1243995 original size:37 final size:35
Alignment explanation
Indices: 1243929--1244022 Score: 145
Period size: 37 Copynumber: 2.7 Consensus size: 35
1243919 TCTTGAGACA
1243929 GTTTCTCTTGAAACAC-AAAAAAACATTTGAAATC
1 GTTTCTCTTGAAACACAAAAAAAACATTTGAAATC
* *
1243963 GTTTCTCTTGAAACACCAAAAAAAACCCTTTGAAATT
1 GTTTCTCTTGAAACA-CAAAAAAAA-CATTTGAAATC
1244000 GTTTCTCTTGAAACACAAAAAAA
1 GTTTCTCTTGAAACACAAAAAAA
1244023 TGTTTCACTT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
34 15 0.27
35 1 0.02
36 15 0.27
37 24 0.44
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.29
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAACATTTGAAATC
Found at i:1244186 original size:83 final size:84
Alignment explanation
Indices: 1244038--1244209 Score: 204
Period size: 83 Copynumber: 2.1 Consensus size: 84
1244028 CACTTGAAAC
* * * * **
1244038 ACAAAGACCTTCGAGTTTGACTACACTCAGCTTCGAGGGCACATCATTTGTAGCATAACTCAAGG
1 ACAAAGACCCTCAAGTTCGACTACACACAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGG
* *
1244103 CTAGAAGGGTTATCTGCCA
66 CAAGAAGGGTTATATGCCA
* * * *
1244122 ACAAAGACCCTCAAGTTCGATTACACACAGC-TCTGA-GGCGCATCATTTACAGCATAGCTTAAG
1 ACAAAGACCCTCAAGTTCGACTACACACAGCTTC-GAGGGCACATCATTTACAGCATAACTCAAG
*
1244185 GCAAGAAGGGTTATATGTCA
65 GCAAGAAGGGTTATATGCCA
1244205 ACAAA
1 ACAAA
1244210 ATTATCGAGT
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
83 46 0.62
84 28 0.38
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (84 bp):
ACAAAGACCCTCAAGTTCGACTACACACAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGG
CAAGAAGGGTTATATGCCA
Found at i:1244563 original size:3 final size:3
Alignment explanation
Indices: 1244555--1244596 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
1244545 TAATACTTAT
1244555 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
1244597 ATTTTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1244600 original size:22 final size:22
Alignment explanation
Indices: 1244551--1244596 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1244541 TATATAATAC
1244551 TTATTTATTATTATTATTATTA
1 TTATTTATTATTATTATTATTA
1244573 TTATTTATTATTATT-TTATTA
1 TTATTTATTATTATTATTATTA
1244594 TTA
1 TTA
1244597 ATTTTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTTATTATTATTATTATTA
Found at i:1244606 original size:12 final size:11
Alignment explanation
Indices: 1244554--1244615 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 11
1244544 ATAATACTTA
1244554 TTTATTATTATT
1 TTTATTATT-TT
*
1244566 ATTATTATTATT
1 TTTATTATT-TT
1244578 TATTATTATTTT
1 T-TTATTATTTT
*
1244590 ATTATTAATTTT
1 TTTATT-ATTTT
1244602 TTTATATATTTT
1 TTTAT-TATTTT
1244614 TT
1 TT
1244616 CAGGCCCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
11 5 0.12
12 29 0.67
13 9 0.21
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTATTATTTT
Found at i:1246034 original size:21 final size:21
Alignment explanation
Indices: 1245997--1246036 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1245987 AATTTGTTTA
*
1245997 TTCATTTATTATTTTATTTTT
1 TTCATTTATTATATTATTTTT
1246018 TTCATTTGATT-TATTATTT
1 TTCATTT-ATTATATTATTT
1246037 GATTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (21 bp):
TTCATTTATTATATTATTTTT
Found at i:1246034 original size:26 final size:25
Alignment explanation
Indices: 1245982--1246049 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 25
1245972 AATTTACTTG
* * *
1245982 TATTTAATTTGTTTA-TTCATTTAT
1 TATTTGATTTTTTTATTTGATTTAT
*
1246006 TATTTTATTTTTTTCATTTGATTTAT
1 TATTTGATTTTTTT-ATTTGATTTAT
1246032 TATTTGATTTTTTTATTT
1 TATTTGATTTTTTTATTT
1246050 TCATTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 12 0.32
25 5 0.13
26 21 0.55
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.72
Consensus pattern (25 bp):
TATTTGATTTTTTTATTTGATTTAT
Found at i:1246056 original size:25 final size:26
Alignment explanation
Indices: 1245997--1246059 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
1245987 AATTTGTTTA
*
1245997 TTCATTTATTATTTTATTTTTTTCAT
1 TTCATTTATTATTTGATTTTTTTCAT
*
1246023 TTGATTTATTATTTGATTTTTTT-ATT
1 TTCATTTATTATTTGATTTTTTTCA-T
1246049 TTCA-TTATTAT
1 TTCATTTATTAT
1246060 GTTTTTCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.24
26 25 0.76
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (26 bp):
TTCATTTATTATTTGATTTTTTTCAT
Found at i:1246074 original size:25 final size:24
Alignment explanation
Indices: 1246005--1246074 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 24
1245995 TATTCATTTA
*
1246005 TTATT-TTATTTTTTTCATTTGA-T
1 TTATTATTATGTTTTTC-TTTGATT
*
1246028 TTATTATT-TGATTTT-TTT-ATT
1 TTATTATTATGTTTTTCTTTGATT
1246049 TTCATTATTATGTTTTTCTTTGATT
1 TT-ATTATTATGTTTTTCTTTGATT
1246074 T
1 T
1246075 ATTTAATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
20 1 0.03
21 6 0.16
22 6 0.16
23 16 0.42
24 5 0.13
25 4 0.11
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (24 bp):
TTATTATTATGTTTTTCTTTGATT
Found at i:1250582 original size:35 final size:35
Alignment explanation
Indices: 1250476--1250843 Score: 152
Period size: 36 Copynumber: 10.2 Consensus size: 35
1250466 GTGTTTTTAT
* * *
1250476 TATAGTTTGTAAAAATGTTTTTGACAAA-ATATAATA
1 TATAGTTTTTAAAAATATTTTT-A-AAATATATATTA
* * *
1250512 TATAATTTTCAGAAAATGATTTTCGAAAATTTATATATTA
1 TATAGTTTTTA-AAAAT-ATTTT-TAAAA--TATATATTA
*
1250552 TATAGTTTTTGAAAATATTTTTAAAATATATATAATA
1 TATAGTTTTTAAAAATATTTTTAAAATATATAT--TA
* * *
1250589 TATAG-TTTTGAAAACATTTTGAAAACGT-TATATATA
1 TATAGTTTTTAAAAATATTTTTAAAA--TATATAT-TA
* ** *
1250625 TATAGTTTTTAAACAT-TTTGAAAACATATATAGTA
1 TATAGTTTTTAAAAATATTTTTAAA-ATATATATTA
* * * *
1250660 TATAGTTTTAAAAACATTTTTTGTGAAATTATATAATA
1 TATAGTTTTTAAAA-ATATTTT-T-AAAATATATATTA
*
1250698 TATAG-TTTTAAAAACATTTTTTGAAAACT-TATA-TA
1 TATAGTTTTTAAAAATA-TTTTT-AAAA-TATATATTA
** * * *
1250733 -ATA-TTTTT-AAAACGTTTTGAAAACTATGTAATA
1 TATAGTTTTTAAAAATATTTTTAAAA-TATATATTA
** * * * *
1250766 TATAG-TTTT-GGATTTTTTTTTAAGTATA-A-TA
1 TATAGTTTTTAAAAATATTTTTAAAATATATATTA
1250797 TATAGTTTTCTAAAACATATTTTTGAAATATATATATTA
1 TATAGTTTT-TAAAA-ATATTTTT-AAA-ATATATATTA
1250836 TATAGTTT
1 TATAGTTT
1250844 ATATCATATT
Statistics
Matches: 254, Mismatches: 46, Indels: 61
0.70 0.13 0.17
Matches are distributed among these distances:
31 13 0.05
32 11 0.04
33 11 0.04
34 22 0.09
35 30 0.12
36 58 0.23
37 51 0.20
38 25 0.10
39 18 0.07
40 15 0.06
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.46
Consensus pattern (35 bp):
TATAGTTTTTAAAAATATTTTTAAAATATATATTA
Found at i:1250608 original size:36 final size:35
Alignment explanation
Indices: 1250504--1250775 Score: 225
Period size: 38 Copynumber: 7.5 Consensus size: 35
1250494 TTTTGACAAA
* *
1250504 ATATAATATATAATTTTCAGAAAATGATTTTCGAAAATTT
1 ATATAATATATAGTTTT--GAAAA-CATTTT-GAAAA-TT
* * *
1250544 ATATATTATATAGTTTTTGAAAATATTTTTAAAATAT
1 ATATAATATATAG-TTTTGAAAACATTTTGAAAAT-T
1250581 ATATAATATATAGTTTTGAAAACATTTTGAAAACGTT
1 ATATAATATATAGTTTTGAAAACATTTTGAAAA--TT
* *
1250618 ATAT-ATATATAGTTTT-TAAACATTTTGAAAACAT
1 ATATAATATATAGTTTTGAAAACATTTTGAAAA-TT
* * *
1250652 ATATAGTATATAGTTTTAAAAACATTTTTTGTGAAATT
1 ATATAATATATAGTTTTGAAAACA--TTTTG-AAAATT
*
1250690 ATATAATATATAGTTTTAAAAACATTTTTTGAAAACTT
1 ATATAATATATAGTTTTGAAAACA--TTTTGAAAA-TT
* *
1250728 ATAT-A-ATAT--TTTT-AAAACGTTTTGAAAACT
1 ATATAATATATAGTTTTGAAAACATTTTGAAAATT
*
1250758 ATGTAATATATAGTTTTG
1 ATATAATATATAGTTTTG
1250776 GATTTTTTTT
Statistics
Matches: 198, Mismatches: 19, Indels: 35
0.79 0.08 0.14
Matches are distributed among these distances:
30 4 0.02
31 10 0.05
32 4 0.02
33 5 0.03
34 13 0.07
35 25 0.13
36 40 0.20
37 26 0.13
38 48 0.24
39 8 0.04
40 11 0.06
41 4 0.02
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (35 bp):
ATATAATATATAGTTTTGAAAACATTTTGAAAATT
Found at i:1256876 original size:23 final size:23
Alignment explanation
Indices: 1256846--1256906 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
1256836 ATATTTGGTA
1256846 AACTCTTACAAATTTGGTTTAGG
1 AACTCTTACAAATTTGGTTTAGG
1256869 AACTCTTACAAATTTGGTTTAGG
1 AACTCTTACAAATTTGGTTTAGG
*
1256892 AACTTTTACAAATTT
1 AACTCTTACAAATTT
1256907 CGTAAACTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (23 bp):
AACTCTTACAAATTTGGTTTAGG
Found at i:1256939 original size:19 final size:19
Alignment explanation
Indices: 1256817--1256940 Score: 90
Period size: 19 Copynumber: 6.1 Consensus size: 19
1256807 GTTTTAGATT
1256817 TATTGTGGTAAACT-TGTACA
1 TATT-TGGTAAACTCT-TACA
1256837 TATTTGGTAAACTCTTACA
1 TATTTGGTAAACTCTTACA
*
1256856 AATTTGGTTTAGGAACTCTTACA
1 TATTTGG--TA--AACTCTTACA
* *
1256879 AATTTGGTTTAGGAACTTTTACA
1 TATTTGG--TA--AACTCTTACA
* *
1256902 AATTTCGTAAACT-TGTACA
1 TATTTGGTAAACTCT-TACA
1256921 TATTTGGTAAACTCTTACA
1 TATTTGGTAAACTCTTACA
1256940 T
1 T
1256941 TCTTAGATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 15
0.82 0.04 0.13
Matches are distributed among these distances:
18 1 0.01
19 43 0.47
20 6 0.07
21 4 0.04
23 38 0.41
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (19 bp):
TATTTGGTAAACTCTTACA
Found at i:1257541 original size:32 final size:31
Alignment explanation
Indices: 1257505--1257578 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
1257495 ATCCGAACCA
1257505 ACGGGGATGGAGAATAACTGAAATCTTCACTC
1 ACGGGGATGG-GAATAACTGAAATCTTCACTC
1257537 AC-GGGATAGGGAATAACTGAAATCTTCACTC
1 ACGGGGAT-GGGAATAACTGAAATCTTCACTC
1257568 ACGGGGATGGG
1 ACGGGGATGGG
1257579 GATGGGGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
31 31 0.77
32 9 0.22
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.20
Consensus pattern (31 bp):
ACGGGGATGGGAATAACTGAAATCTTCACTC
Found at i:1259382 original size:50 final size:50
Alignment explanation
Indices: 1259279--1259433 Score: 184
Period size: 50 Copynumber: 3.0 Consensus size: 50
1259269 TAGATGCAAC
1259279 TATTAGTGTCCTACTTTAACACTAACTCTAGAATCCTACTTTGTAAATAAGATAAT
1 TATTAGTGTCCTACTTT-A-A--AA-T-TAGAATCCTACTTTGTAAATAAGATAAT
* *
1259335 TATTAGTGTCCTACTTTAAAATTAGAATCCTATTTTGTAGATAAGATAAT
1 TATTAGTGTCCTACTTTAAAATTAGAATCCTACTTTGTAAATAAGATAAT
* * * * * *
1259385 TATTAGTATCCTACTTTAACACTAGAATACTACTTTATAAATAAAATAA
1 TATTAGTGTCCTACTTTAAAATTAGAATCCTACTTTGTAAATAAGATAA
1259434 CCTCTAGTCT
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
50 67 0.75
51 1 0.01
52 2 0.02
54 1 0.01
55 1 0.01
56 17 0.19
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (50 bp):
TATTAGTGTCCTACTTTAAAATTAGAATCCTACTTTGTAAATAAGATAAT
Found at i:1267318 original size:137 final size:138
Alignment explanation
Indices: 1267072--1267347 Score: 545
Period size: 137 Copynumber: 2.0 Consensus size: 138
1267062 ACATTCACCT
1267072 CTCAGTCTCTTTCGCTCGCACGCTCTCTCGATTGGTTTTTTTCTTCAATTTTCCGCCATGTAAAA
1 CTCAGTCTCTTTCGCTCGCACGCTCTCTCGATTGGTTTTTTTCTTCAATTTTCCGCCATGTAAAA
1267137 TTGTAAACCCAAGCAGTGCTCTGTCTTTCAACTTTTTATTTACAAAGAAAAAATTGA-GAAGAAT
66 TTGTAAACCCAAGCAGTGCTCTGTCTTTCAACTTTTTATTTACAAAGAAAAAATTGAGGAAGAAT
1267201 TGCTGGAA
131 TGCTGGAA
1267209 CTCAGTCTCTTTCGCTCGCACGCTCTCTCGATTGGTTTTTTTCTTCAATTTTCCGCCATGTAAAA
1 CTCAGTCTCTTTCGCTCGCACGCTCTCTCGATTGGTTTTTTTCTTCAATTTTCCGCCATGTAAAA
1267274 TTGTAAACCCAAGCAGTGCTCTGTCTTTCAACTTTTTATTTACAAAGAAAAAATTGAGGAAGAAT
66 TTGTAAACCCAAGCAGTGCTCTGTCTTTCAACTTTTTATTTACAAAGAAAAAATTGAGGAAGAAT
1267339 TGCTGGAA
131 TGCTGGAA
1267347 C
1 C
1267348 GCAACACTGA
Statistics
Matches: 138, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
137 122 0.88
138 16 0.12
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (138 bp):
CTCAGTCTCTTTCGCTCGCACGCTCTCTCGATTGGTTTTTTTCTTCAATTTTCCGCCATGTAAAA
TTGTAAACCCAAGCAGTGCTCTGTCTTTCAACTTTTTATTTACAAAGAAAAAATTGAGGAAGAAT
TGCTGGAA
Found at i:1267630 original size:202 final size:202
Alignment explanation
Indices: 1267284--1267689 Score: 812
Period size: 202 Copynumber: 2.0 Consensus size: 202
1267274 TTGTAAACCC
1267284 AAGCAGTGCTCTGTCTTTCAACTTTTTATTTACAAAGAAAAAATTGAGGAAGAATTGCTGGAACG
1 AAGCAGTGCTCTGTCTTTCAACTTTTTATTTACAAAGAAAAAATTGAGGAAGAATTGCTGGAACG
1267349 CAACACTGATTGTATTTATTTCTTAGCCTCTCCCCTCACATGCAAGAAGTTATTTATTTTCTCTT
66 CAACACTGATTGTATTTATTTCTTAGCCTCTCCCCTCACATGCAAGAAGTTATTTATTTTCTCTT
1267414 TTGGGCTATCCGGAAGTAAGCTTTTCCTTTTTCGCACTTTCCCATTTTCAGCTCACATTATATTT
131 TTGGGCTATCCGGAAGTAAGCTTTTCCTTTTTCGCACTTTCCCATTTTCAGCTCACATTATATTT
1267479 TTTGTTG
196 TTTGTTG
1267486 AAGCAGTGCTCTGTCTTTCAACTTTTTATTTACAAAGAAAAAATTGAGGAAGAATTGCTGGAACG
1 AAGCAGTGCTCTGTCTTTCAACTTTTTATTTACAAAGAAAAAATTGAGGAAGAATTGCTGGAACG
1267551 CAACACTGATTGTATTTATTTCTTAGCCTCTCCCCTCACATGCAAGAAGTTATTTATTTTCTCTT
66 CAACACTGATTGTATTTATTTCTTAGCCTCTCCCCTCACATGCAAGAAGTTATTTATTTTCTCTT
1267616 TTGGGCTATCCGGAAGTAAGCTTTTCCTTTTTCGCACTTTCCCATTTTCAGCTCACATTATATTT
131 TTGGGCTATCCGGAAGTAAGCTTTTCCTTTTTCGCACTTTCCCATTTTCAGCTCACATTATATTT
1267681 TTTGTTG
196 TTTGTTG
1267688 AA
1 AA
1267690 ATTTTTATGT
Statistics
Matches: 204, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 204 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (202 bp):
AAGCAGTGCTCTGTCTTTCAACTTTTTATTTACAAAGAAAAAATTGAGGAAGAATTGCTGGAACG
CAACACTGATTGTATTTATTTCTTAGCCTCTCCCCTCACATGCAAGAAGTTATTTATTTTCTCTT
TTGGGCTATCCGGAAGTAAGCTTTTCCTTTTTCGCACTTTCCCATTTTCAGCTCACATTATATTT
TTTGTTG
Found at i:1293937 original size:512 final size:512
Alignment explanation
Indices: 1292973--1293997 Score: 2032
Period size: 512 Copynumber: 2.0 Consensus size: 512
1292963 GAAAACAAAG
1292973 ATATGAACATAAAATGTAAAACATAGAATATGCATGAAATATACTAAGTATAAGATGAATGGAAC
1 ATATGAACATAAAATGTAAAACATAGAATATGCATGAAATATACTAAGTATAAGATGAATGGAAC
1293038 TATGCTAATCATGAAACATATACTAAGGCATATAAAGATCATGCTTAATATGCTATAACATGGAT
66 TATGCTAATCATGAAACATATACTAAGGCATATAAAGATCATGCTTAATATGCTATAACATGGAT
*
1293103 ACAAAGCCTAGCACAAGTTCATGTCATGTGTGATAGAATAGGTCAAGAAATCTAAGAAGAAGGTA
131 ACAAAGCCTAGCACAAGTTCATGTCATGTGTAATAGAATAGGTCAAGAAATCTAAGAAGAAGGTA
1293168 GTAAACTCCTTGGTCCTTGATGATATCCACGCTTGAAGAAACTAGAATGAACAGTAGAAGGTGCA
196 GTAAACTCCTTGGTCCTTGATGATATCCACGCTTGAAGAAACTAGAATGAACAGTAGAAGGTGCA
1293233 GAAGTAGGATCACATCAAACTTCATTAAAAATCTCTTCGTAACTCAATCAAGCCTAAACCCAATT
261 GAAGTAGGATCACATCAAACTTCATTAAAAATCTCTTCGTAACTCAATCAAGCCTAAACCCAATT
1293298 AAGATAGCATAAAGAAAAAAATACTCAAAATTATATTAACTATCCCCAACATACCGAAATATACA
326 AAGATAGCATAAAGAAAAAAATACTCAAAATTATATTAACTATCCCCAACATACCGAAATATACA
1293363 ATTGTTCATTACATATGTCACCAAACAATTCTCTGGATATAACAAACCAAAATGAAAAAAAGTCT
391 ATTGTTCATTACATATGTCACCAAACAATTCTCTGGATATAACAAACCAAAATGAAAAAAAGTCT
*
1293428 AGCTGCATAACCCCATCATGATTCATTCTAATAATCCAAAAGGCTCAACTCATAGGC
456 AGCTGCATAACCCCATCACGATTCATTCTAATAATCCAAAAGGCTCAACTCATAGGC
1293485 ATATGAACATAAAATGTAAAACATAGAATATGCATGAAATATACTAAGTATAAGATGAATGGAAC
1 ATATGAACATAAAATGTAAAACATAGAATATGCATGAAATATACTAAGTATAAGATGAATGGAAC
1293550 TATGCTAATCATGAAACATATACTAAGGCATATAAAGATCATGCTTAATATGCTATAACATGGAT
66 TATGCTAATCATGAAACATATACTAAGGCATATAAAGATCATGCTTAATATGCTATAACATGGAT
1293615 ACAAAGCCTAGCACAAGTTCATGTCATGTGTAATAGAATAGGTCAAGAAATCTAAGAAGAAGGTA
131 ACAAAGCCTAGCACAAGTTCATGTCATGTGTAATAGAATAGGTCAAGAAATCTAAGAAGAAGGTA
1293680 GTAAACTCCTTGGTCCTTGATGATATCCACGCTTGAAGAAACTAGAATGAACAGTAGAAGGTGCA
196 GTAAACTCCTTGGTCCTTGATGATATCCACGCTTGAAGAAACTAGAATGAACAGTAGAAGGTGCA
1293745 GAAGTAGGATCACATCAAACTTCATTAAAAATCTCTTCGTAACTCAATCAAGCCTAAACCCAATT
261 GAAGTAGGATCACATCAAACTTCATTAAAAATCTCTTCGTAACTCAATCAAGCCTAAACCCAATT
1293810 AAGATAGCATAAAGAAAAAAATACTCAAAATTATATTAACTATCCCCAACATACCGAAATATACA
326 AAGATAGCATAAAGAAAAAAATACTCAAAATTATATTAACTATCCCCAACATACCGAAATATACA
1293875 ATTGTTCATTACATATGTCACCAAACAATTCTCTGGATATAACAAACCAAAATGAAAAAAAGTCT
391 ATTGTTCATTACATATGTCACCAAACAATTCTCTGGATATAACAAACCAAAATGAAAAAAAGTCT
1293940 AGCTGCATAACCCCATCACGATTCATTCTAATAATCCAAAAGGCTCAACTCATAGGC
456 AGCTGCATAACCCCATCACGATTCATTCTAATAATCCAAAAGGCTCAACTCATAGGC
1293997 A
1 A
1293998 ATCCATTAAA
Statistics
Matches: 511, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
512 511 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (512 bp):
ATATGAACATAAAATGTAAAACATAGAATATGCATGAAATATACTAAGTATAAGATGAATGGAAC
TATGCTAATCATGAAACATATACTAAGGCATATAAAGATCATGCTTAATATGCTATAACATGGAT
ACAAAGCCTAGCACAAGTTCATGTCATGTGTAATAGAATAGGTCAAGAAATCTAAGAAGAAGGTA
GTAAACTCCTTGGTCCTTGATGATATCCACGCTTGAAGAAACTAGAATGAACAGTAGAAGGTGCA
GAAGTAGGATCACATCAAACTTCATTAAAAATCTCTTCGTAACTCAATCAAGCCTAAACCCAATT
AAGATAGCATAAAGAAAAAAATACTCAAAATTATATTAACTATCCCCAACATACCGAAATATACA
ATTGTTCATTACATATGTCACCAAACAATTCTCTGGATATAACAAACCAAAATGAAAAAAAGTCT
AGCTGCATAACCCCATCACGATTCATTCTAATAATCCAAAAGGCTCAACTCATAGGC
Found at i:1299983 original size:17 final size:17
Alignment explanation
Indices: 1299963--1300003 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1299953 TTTGTAAAGA
1299963 AATTAAAGAAGAA-AAAT
1 AATTAAAGAA-AATAAAT
1299980 AATTAAAGAAAATAAAT
1 AATTAAAGAAAATAAAT
*
1299997 AACTAAA
1 AATTAAA
1300004 AAATCAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (17 bp):
AATTAAAGAAAATAAAT
Found at i:1309659 original size:31 final size:31
Alignment explanation
Indices: 1309623--1309698 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
1309613 GTTTTGAATA
** * * *
1309623 AAAATATTGATTTAATCCTTAAATTTTAGAT
1 AAAATATCAATTTAATCCATAAAATTCAGAT
*
1309654 AAAATATCAATTTAATTCATAAAATTCAGAT
1 AAAATATCAATTTAATCCATAAAATTCAGAT
*
1309685 AAAATATAAATTTA
1 AAAATATCAATTTA
1309699 GTTATTGAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (31 bp):
AAAATATCAATTTAATCCATAAAATTCAGAT
Found at i:1311344 original size:10 final size:11
Alignment explanation
Indices: 1311331--1311360 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1311321 CTCATCTTTA
1311331 TTCATTTCT-C
1 TTCATTTCTCC
1311341 TTCATTTCTCC
1 TTCATTTCTCC
1311352 TTCATTTCT
1 TTCATTTCT
1311361 TCTCCATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.10, C:0.30, G:0.00, T:0.60
Consensus pattern (11 bp):
TTCATTTCTCC
Found at i:1311368 original size:11 final size:11
Alignment explanation
Indices: 1311331--1311368 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1311321 CTCATCTTTA
1311331 TTCATTTC-TC
1 TTCATTTCTTC
*
1311341 TTCATTTCTCC
1 TTCATTTCTTC
1311352 TTCATTTCTTC
1 TTCATTTCTTC
*
1311363 TCCATT
1 TTCATT
1311369 CACCGTTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.11, C:0.32, G:0.00, T:0.58
Consensus pattern (11 bp):
TTCATTTCTTC
Found at i:1312979 original size:45 final size:45
Alignment explanation
Indices: 1312919--1313058 Score: 147
Period size: 45 Copynumber: 3.1 Consensus size: 45
1312909 CCTAAGGTAC
* * * **
1312919 TGGGAGGCGTCGATGCTATGTAACCGGGACCTCGTCTGAGATACT
1 TGGGAGGTGCCGATGCTATGTGACCCAGACCTCGTCTGAGATACT
** *
1312964 TGTTAGGTGCCGATGCTAAGTGACCCAGACCTCGGT-TGAGATACT
1 TGGGAGGTGCCGATGCTATGTGACCCAGACCTC-GTCTGAGATACT
* ** **
1313009 TGGGAGGTGCTGATGCTATGTGACCTTGACCTCACCTGAGATACT
1 TGGGAGGTGCCGATGCTATGTGACCCAGACCTCGTCTGAGATACT
1313054 TGGGA
1 TGGGA
1313059 AATATTGATG
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
45 75 0.97
46 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.26
Consensus pattern (45 bp):
TGGGAGGTGCCGATGCTATGTGACCCAGACCTCGTCTGAGATACT
Found at i:1315677 original size:31 final size:31
Alignment explanation
Indices: 1315608--1315677 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
1315598 ATGGATTTAG
* *
1315608 TCAGTGACCAAATTATAAGATTTTACAAAGT
1 TCAGTGACCAAAGTATAAGATTTTACAAAGC
**
1315639 TTGGTGACCAAAGTATAA-ACTTTTGA-AAAGC
1 TCAGTGACCAAAGTATAAGA-TTTT-ACAAAGC
1315670 TCAGTGAC
1 TCAGTGAC
1315678 TAAAATGGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
30 1 0.03
31 29 0.94
32 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (31 bp):
TCAGTGACCAAAGTATAAGATTTTACAAAGC
Found at i:1316788 original size:24 final size:24
Alignment explanation
Indices: 1316756--1316814 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
1316746 ACATAGGTAG
1316756 TGTATCGATACACCAGTGAAGGGA
1 TGTATCGATACACCAGTGAAGGGA
1316780 TGTATCGATACACCAGTGAAGGGA
1 TGTATCGATACACCAGTGAAGGGA
1316804 TGTATCGATAC
1 TGTATCGATAC
1316815 CCTATAGTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (24 bp):
TGTATCGATACACCAGTGAAGGGA
Found at i:1317432 original size:22 final size:22
Alignment explanation
Indices: 1317407--1317456 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
1317397 AGGTCTATGA
1317407 AGCTATAGGAAAATGTTATGGG
1 AGCTATAGGAAAATGTTATGGG
1317429 AGCTATAGGAAAATGTTATGGG
1 AGCTATAGGAAAATGTTATGGG
1317451 AGCTAT
1 AGCTAT
1317457 GTGATGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.28
Consensus pattern (22 bp):
AGCTATAGGAAAATGTTATGGG
Found at i:1318036 original size:31 final size:31
Alignment explanation
Indices: 1317998--1318119 Score: 156
Period size: 31 Copynumber: 4.0 Consensus size: 31
1317988 GAGTCGAGGG
* *
1317998 TTACCTATATTCTGCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1318029 TTACCTATGTTCTTCGGGTCATATGGATTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1318060 TTACCTATGTTCTTC-GGATATATGGATTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* * *
1318090 TTACCTAGGTTCTTCAGGACCTATGGACTG
1 TTACCTATGTTCTTCGGGACATATGGACTG
1318120 GTCATTCGGG
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
30 27 0.34
31 53 0.66
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1318115 original size:61 final size:62
Alignment explanation
Indices: 1317998--1318116 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 62
1317988 GAGTCGAGGG
* * *
1317998 TTACCTATATTCTGCGGGACATATGGACTGTTTACCTATGTTCTTCGGGTCATATGGATTGT
1 TTACCTATATTCTGCGGGACATATGGACTGTTTACCTAGGTTCTTCAGGACATATGGATTGT
* * * * *
1318060 TTACCTATGTTCTTC-GGATATATGGATTGTTTACCTAGGTTCTTCAGGACCTATGGA
1 TTACCTATATTCTGCGGGACATATGGACTGTTTACCTAGGTTCTTCAGGACATATGGA
1318117 CTGGTCATTC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
61 36 0.73
62 13 0.27
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (62 bp):
TTACCTATATTCTGCGGGACATATGGACTGTTTACCTAGGTTCTTCAGGACATATGGATTGT
Found at i:1318357 original size:12 final size:12
Alignment explanation
Indices: 1318342--1318380 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1318332 GATATTGATA
1318342 ATGATAGAGATC
1 ATGATAGAGATC
*
1318354 ATGATA-ATGATA
1 ATGATAGA-GATC
1318366 ATGATAGAGATC
1 ATGATAGAGATC
1318378 ATG
1 ATG
1318381 CTAATGATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 1 0.04
12 21 0.91
13 1 0.04
ACGTcount: A:0.44, C:0.05, G:0.23, T:0.28
Consensus pattern (12 bp):
ATGATAGAGATC
Found at i:1318358 original size:24 final size:24
Alignment explanation
Indices: 1318331--1318388 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
1318321 ACACTGTATG
*
1318331 TGATATTGATAATGATAGAGATCA
1 TGATAATGATAATGATAGAGATCA
1318355 TGATAATGATAATGATAGAGATCA
1 TGATAATGATAATGATAGAGATCA
*
1318379 TGCTAATGAT
1 TGATAATGAT
1318389 GATATATGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (24 bp):
TGATAATGATAATGATAGAGATCA
Found at i:1320625 original size:45 final size:45
Alignment explanation
Indices: 1320521--1320625 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
1320511 GTGAGGTCAA
* ** **
1320521 GGTCACATAGCATCAGCACCTCCCAAGTATCTCAACCGAGGTCTG
1 GGTCACATAGCATCGGCACCTAACAAGTATCTCAACCGAGGTCCC
*
1320566 GGTCACTTAGCATCGGCACCTAACAAGTATCTCAGA-CGAGGTCCC
1 GGTCACATAGCATCGGCACCTAACAAGTATCTCA-ACCGAGGTCCC
*
1320611 GGTTACATAGCATCG
1 GGTCACATAGCATCG
1320626 ACGCCTCCCA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 50 0.98
46 1 0.02
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (45 bp):
GGTCACATAGCATCGGCACCTAACAAGTATCTCAACCGAGGTCCC
Found at i:1322228 original size:10 final size:11
Alignment explanation
Indices: 1322203--1322232 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
1322193 TGAATGGAGA
1322203 AGAAATGAAGG
1 AGAAATGAAGG
1322214 AGAAATGAA-G
1 AGAAATGAAGG
1322224 AGAAATGAA
1 AGAAATGAA
1322233 TAAAGATGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.10
Consensus pattern (11 bp):
AGAAATGAAGG
Found at i:1324603 original size:13 final size:13
Alignment explanation
Indices: 1324563--1324613 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 13
1324553 ATTTATGATT
1324563 AAATAATAATAATTA
1 AAAT-ATAA-AATTA
1324578 AATATATTAAAA-TA
1 AA-ATA-TAAAATTA
1324592 AACATATAAAATTA
1 AA-ATATAAAATTA
1324606 AAATATAA
1 AAATATAA
1324614 CTAAATAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 11 0.34
14 11 0.34
15 5 0.16
16 5 0.16
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATATAAAATTA
Found at i:1324642 original size:27 final size:25
Alignment explanation
Indices: 1324599--1324660 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
1324589 ATAAACATAT
* *
1324599 AAAATTAAAATATAACTAAATAATGA
1 AAAAATAAAATAAAACTAAAT-ATGA
* * *
1324625 ATAAATAAAATTAAAACTATATATTA
1 AAAAATAAAA-TAAAACTAAATATGA
1324651 AAAAATAAAA
1 AAAAATAAAA
1324661 CTTGTAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
26 20 0.69
27 9 0.31
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAAATAAAATAAAACTAAATATGA
Found at i:1326560 original size:113 final size:113
Alignment explanation
Indices: 1326353--1326916 Score: 816
Period size: 113 Copynumber: 5.0 Consensus size: 113
1326343 TGCGATAGAG
*
1326353 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTT-TTCTTCC-TCTTCAGATAAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* ** **
1326416 TCTTATTATGAACT-T-CGTCTAGAAAAT-TTGATCGGTCGAGTGATGAAT
66 TCTCATTATGAACTCTAC--CT-GGCAATGTTGATCCATCGAGTGATGAAT
* * * * *
1326464 TCAAGCAAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATAAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
1326529 TCTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAGTGATGAAT
66 TCTCATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAAT
* * *
1326577 TCGAGCAAAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTAT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
1326642 TCTCATTATGAACTCTACCTGGC-ATGTTGATCCATCGAATGATGAAT
66 TCTCATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAAT
* * *
1326689 TTGAGCAAAAGGTTGAACAGGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGGTGAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * *
1326754 TCTCATTATGAACTCTACCTGGCAATATTGATTCATCAAATGATGAAT
66 TCTCATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAAT
* * *
1326802 TTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTTAGATGAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
1326867 TCTCATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGGAT
66 TCTCATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAAT
1326915 TC
1 TC
1326917 AAATCTTTGC
Statistics
Matches: 408, Mismatches: 39, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
111 36 0.09
112 115 0.28
113 255 0.62
114 1 0.00
115 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (113 bp):
TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAAT
Found at i:1326716 original size:225 final size:225
Alignment explanation
Indices: 1326353--1326918 Score: 836
Period size: 225 Copynumber: 2.5 Consensus size: 225
1326343 TGCGATAGAG
* *
1326353 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTT-TTCTTCC-TCTTCAGATAAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCT
* ** **
1326416 TCTTATTATGAACT-T-CGTCTAGAAAAT-TTGATCGGTCGAGTGATGAATTCAAGCAAAAGGTT
66 TCTCATTATGAACTCTAC--CT-G-GCATGTTGATCCATCGAGTGATGAATTCAAGCAAAAGGTT
* *
1326478 GAACAAATTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACT
127 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACT
* *
1326543 CTACCTGGCAATGTTGATCCATCAAGTGATGAAT
192 CTACCTGGCAATATTGATCCATCAAATGATGAAT
* *
1326577 TCGAGCAAAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTAT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCT
* **
1326642 TCTCATTATGAACTCTACCTGGCATGTTGATCCATCGAATGATGAATTTGAGCAAAAGGTTGAAC
66 TCTCATTATGAACTCTACCTGGCATGTTGATCCATCGAGTGATGAATTCAAGCAAAAGGTTGAAC
** * *
1326707 AGGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGGTGAGTTCTTCTCATTATGAACTCTAC
131 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTAC
*
1326772 CTGGCAATATTGATTCATCAAATGATGAAT
196 CTGGCAATATTGATCCATCAAATGATGAAT
* *
1326802 TTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTTAGATGAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCT
*
1326867 TCTCATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGGATTCAA
66 TCTCATTATGAACTCTACCTGGC-ATGTTGATCCATCGAGTGATGAATTCAA
1326919 ATCTTTGCTA
Statistics
Matches: 307, Mismatches: 29, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
224 41 0.13
225 212 0.69
226 52 0.17
227 1 0.00
228 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (225 bp):
TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCT
TCTCATTATGAACTCTACCTGGCATGTTGATCCATCGAGTGATGAATTCAAGCAAAAGGTTGAAC
AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTAC
CTGGCAATATTGATCCATCAAATGATGAAT
Found at i:1327325 original size:22 final size:22
Alignment explanation
Indices: 1327284--1327325 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1327274 TTCGAAAAGA
* *
1327284 GAATCTATCATCATTGAAGAGG
1 GAATCTATCAGCATTAAAGAGG
*
1327306 GAATCTATCAGCTTTAAAGA
1 GAATCTATCAGCATTAAAGA
1327326 ATGTAGATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (22 bp):
GAATCTATCAGCATTAAAGAGG
Found at i:1327790 original size:54 final size:54
Alignment explanation
Indices: 1327690--1327908 Score: 155
Period size: 54 Copynumber: 3.9 Consensus size: 54
1327680 AGAATAACTG
* * * * *
1327690 GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGTTTCTGCCCAGAT
1 GTTCATAAAATATTTGACAACACATTCATCTTTTCATGTGGCTTCTGCCCAGAT
* *
1327744 GTTCATAAAATATTTGACAACACATTCCTCTTTTCCAT-TGGCTTCTGCCCGGAT
1 GTTCATAAAATATTTGACAACACATTCATCTTTT-CATGTGGCTTCTGCCCAGAT
* * * *
1327798 -TTCTGGTCAGGGAAGCTCTTTCATAGGACAACACA-TCATC---TCATGTGGTTTCTGCCCAGA
1 GTTC--AT-A---AA-AT-ATT--T--GACAACACATTCATCTTTTCATGTGGCTTCTGCCCAGA
1327858 T
54 T
*
1327859 GTTCATAAAATATTTGACAACACATTCCTCTTTTCCAT-TGGCTTCTGCCC
1 GTTCATAAAATATTTGACAACACATTCATCTTTT-CATGTGGCTTCTGCCC
1327909 GGATTTCTGG
Statistics
Matches: 127, Mismatches: 18, Indels: 40
0.69 0.10 0.22
Matches are distributed among these distances:
50 9 0.07
51 4 0.03
52 1 0.01
53 3 0.02
54 57 0.45
55 8 0.06
56 3 0.02
59 3 0.02
60 5 0.04
61 17 0.13
62 3 0.02
63 1 0.01
64 4 0.03
65 9 0.07
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.35
Consensus pattern (54 bp):
GTTCATAAAATATTTGACAACACATTCATCTTTTCATGTGGCTTCTGCCCAGAT
Found at i:1327849 original size:115 final size:115
Alignment explanation
Indices: 1327716--1327938 Score: 446
Period size: 115 Copynumber: 1.9 Consensus size: 115
1327706 ACAACACATT
1327716 CATCATCTCATGTGGTTTCTGCCCAGATGTTCATAAAATATTTGACAACACATTCCTCTTTTCCA
1 CATCATCTCATGTGGTTTCTGCCCAGATGTTCATAAAATATTTGACAACACATTCCTCTTTTCCA
1327781 TTGGCTTCTGCCCGGATTTCTGGTCAGGGAAGCTCTTTCATAGGACAACA
66 TTGGCTTCTGCCCGGATTTCTGGTCAGGGAAGCTCTTTCATAGGACAACA
1327831 CATCATCTCATGTGGTTTCTGCCCAGATGTTCATAAAATATTTGACAACACATTCCTCTTTTCCA
1 CATCATCTCATGTGGTTTCTGCCCAGATGTTCATAAAATATTTGACAACACATTCCTCTTTTCCA
1327896 TTGGCTTCTGCCCGGATTTCTGGTCAGGGAAGCTCTTTCATAG
66 TTGGCTTCTGCCCGGATTTCTGGTCAGGGAAGCTCTTTCATAG
1327939 TGTTCAGAAC
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 108 1.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (115 bp):
CATCATCTCATGTGGTTTCTGCCCAGATGTTCATAAAATATTTGACAACACATTCCTCTTTTCCA
TTGGCTTCTGCCCGGATTTCTGGTCAGGGAAGCTCTTTCATAGGACAACA
Found at i:1337529 original size:2 final size:2
Alignment explanation
Indices: 1337522--1337556 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1337512 TAAATATTAT
*
1337522 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1337557 TTATGATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1338657 original size:8 final size:9
Alignment explanation
Indices: 1338635--1338674 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
1338625 ACAAAACACG
1338635 TAAAAATAA
1 TAAAAATAA
1338644 TAAAAATAA
1 TAAAAATAA
1338653 TAAAAATAA
1 TAAAAATAA
*
1338662 -ACAAAATGA
1 TA-AAAATAA
1338671 TAAA
1 TAAA
1338675 TGTTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 1 0.04
9 26 0.93
10 1 0.04
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (9 bp):
TAAAAATAA
Found at i:1338811 original size:33 final size:34
Alignment explanation
Indices: 1338774--1338850 Score: 81
Period size: 33 Copynumber: 2.4 Consensus size: 34
1338764 ATGTGTACAT
* *
1338774 ATAAAGTAGTAT-TTACTAAAAAAAATAA-AAAAA
1 ATAAAGTA-TATAATACTAAAAAAAACAATAAAAA
**
1338807 ATAAA-TATATAATACTAAGTAAAACAATAAAAA
1 ATAAAGTATATAATACTAAAAAAAACAATAAAAA
1338840 ATAAAG-ATATA
1 ATAAAGTATATA
1338851 CATGATATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
31 3 0.08
32 14 0.38
33 20 0.54
ACGTcount: A:0.66, C:0.04, G:0.05, T:0.25
Consensus pattern (34 bp):
ATAAAGTATATAATACTAAAAAAAACAATAAAAA
Found at i:1338823 original size:32 final size:33
Alignment explanation
Indices: 1338787--1338850 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
1338777 AAGTAGTATT
* *
1338787 TACTAAAAAAAATAA-AAAAAATAAATATATAA
1 TACTAAAAAAAACAATAAAAAATAAAGATATAA
**
1338819 TACTAAGTAAAACAATAAAAAATAAAGATATA
1 TACTAAAAAAAACAATAAAAAATAAAGATATA
1338851 CATGATATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (33 bp):
TACTAAAAAAAACAATAAAAAATAAAGATATAA
Found at i:1339070 original size:13 final size:14
Alignment explanation
Indices: 1339025--1339081 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 14
1339015 ATCTTTACAT
*
1339025 ATATATATATATATA
1 ATATA-ATATAAATA
* *
1339040 ATGATAAGATATAT-
1 AT-ATAATATAAATA
1339054 ATATAATA-AAATA
1 ATATAATATAAATA
1339067 ATATAATATAAATA
1 ATATAATATAAATA
1339081 A
1 A
1339082 AAAAAGAGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
12 3 0.08
13 13 0.36
14 8 0.22
15 9 0.25
16 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
ATATAATATAAATA
Found at i:1339070 original size:19 final size:18
Alignment explanation
Indices: 1339029--1339085 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
1339019 TTACATATAT
* *
1339029 ATATATATATAATGATAAG
1 ATATATATATAAT-AAAAA
1339048 ATATATATATAATAAAATA
1 ATATATATATAATAAAA-A
1339067 ATATA-ATATAAATAAAAA
1 ATATATATAT-AATAAAAA
1339085 A
1 A
1339086 AGAGGAATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 9 0.26
19 25 0.74
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
ATATATATATAATAAAAA
Found at i:1340417 original size:36 final size:36
Alignment explanation
Indices: 1340368--1340477 Score: 116
Period size: 36 Copynumber: 3.1 Consensus size: 36
1340358 AAAGATTGAA
*
1340368 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * *
1340404 GTTTCAAGAGAAACTGTCTCAAGAGATATAAAA--A
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * * * *
1340438 CTTCCAAAAGAAACTGTCTCAAGGGAGACGAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
1340474 GTTT
1 GTTT
1340478 AACGTAAAAC
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
34 25 0.44
36 32 0.56
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:1340537 original size:29 final size:30
Alignment explanation
Indices: 1340491--1340548 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1340481 GTAAAACATA
* *
1340491 TTCAAAGATTTTGTTTCAA-ATGAAACTGTT
1 TTCAAAGATTATGCTTCAAGA-GAAACTGTT
1340521 TTCAAAG-TTATGCTTCAAGAGAAACTGT
1 TTCAAAGATTATGCTTCAAGAGAAACTGT
1340549 CTCAAGGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (30 bp):
TTCAAAGATTATGCTTCAAGAGAAACTGTT
Found at i:1340607 original size:99 final size:100
Alignment explanation
Indices: 1340504--1340761 Score: 303
Period size: 99 Copynumber: 2.6 Consensus size: 100
1340494 AAAGATTTTG
*
1340504 TTTCAAATGAAACTGTTTTCAAAG-TTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TT
1 TTTCAAAGGAAA-TGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* *
1340567 GGTTTCAAGGGAAACTATCTCATGAGTGACAAAACA
65 GGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACA
* * * *
1340603 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAAGGAAATGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
*
1340668 GTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAA--CA
* * * * * * * *
1340705 TCT-AAGGGTAATGTTTTCAATGTTT-T-TTTC-AGAGAAACTATCTCTAGAGAGACAAAA
1 TTTCAAAGGAAATGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1340762 CTTAGTTCAA
Statistics
Matches: 142, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
98 34 0.24
99 50 0.35
100 33 0.23
101 21 0.15
102 4 0.03
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (100 bp):
TTTCAAAGGAAATGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAACA
Found at i:1340688 original size:37 final size:37
Alignment explanation
Indices: 1340630--1340702 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
1340620 TCAATGTTTA
* *
1340630 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
1340667 TGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
1340703 CATCTAAGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:1340796 original size:148 final size:151
Alignment explanation
Indices: 1340619--1340912 Score: 443
Period size: 148 Copynumber: 2.0 Consensus size: 151
1340609 GGGAAATGTT
* * * *
1340619 TTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTA
1 TTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTGGTTTCAAGGGAAACTA
* *
1340684 TCTCAAGAGAGACAAAATTCATCT-AAGGGTAATGTTTTCAATGTTT-T-TTTC-AGAGAAACTA
65 TCTCAAGAGAGACAAAATACATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTA
*
1340745 TCTCTAGAGAGACAAAACTTAG
130 TCTCAAGAGAGACAAAACTTAG
1340767 TTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTGGTTTCAAGGGAAACTAT
1 TTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTGGTTTCAAGGGAAACTAT
* * * *
1340832 CTCATGAGTGACAAAATACATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGT
66 CTCAAGAGAGACAAAATACATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTAT
*
1340897 CTCAAGGGAGACAAAA
131 CTCAAGAGAGACAAAA
1340913 TTTTGTTTCA
Statistics
Matches: 130, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
147 37 0.28
148 64 0.49
149 1 0.01
150 4 0.03
151 24 0.18
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (151 bp):
TTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTGGTTTCAAGGGAAACTAT
CTCAAGAGAGACAAAATACATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTAT
CTCAAGAGAGACAAAACTTAG
Found at i:1340821 original size:36 final size:35
Alignment explanation
Indices: 1340781--1340951 Score: 104
Period size: 36 Copynumber: 4.9 Consensus size: 35
1340771 AAGTTTATGC
* *
1340781 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTGGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATT-GT
* * * **
1340817 TTCAAGGGAAACTATCTCATGAGTGACAAAATACAT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAAT-TGT
* * ***
1340853 TTCAAGGGAAA-TGTTTTC-A-A-TG--TTTA-TGT
1 TTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTGT
* *
1340882 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TTGT
* *
1340919 TTCAAGGGAACCTATCTCAAGAGAGACAAAATT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1340952 CATCTAAAGG
Statistics
Matches: 98, Mismatches: 26, Indels: 23
0.67 0.18 0.16
Matches are distributed among these distances:
29 14 0.14
30 3 0.03
31 1 0.01
32 1 0.01
33 2 0.02
34 2 0.02
35 3 0.03
36 42 0.43
37 30 0.31
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (35 bp):
TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTGT
Found at i:1340937 original size:37 final size:37
Alignment explanation
Indices: 1340879--1340951 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
1340869 TCAATGTTTA
* *
1340879 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
1340916 TGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
1340952 CATCTAAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:1340973 original size:102 final size:101
Alignment explanation
Indices: 1340767--1341128 Score: 366
Period size: 102 Copynumber: 3.6 Consensus size: 101
1340757 CAAAACTTAG
* *
1340767 TTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTGGTTTCAAGGGAAACTAT
1 TTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTGGTTTCAAGGGAAACTAT
* * * *
1340832 CTCATGAGTGACAAAATACATTTCAAGGGAAATGTT
66 CTCAAGAGAGACAAAATACATCTAAAGGGAAATGTT
* *
1340868 TTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTA
1 TTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTGGTTTCAAGGGAAACTA
* *
1340933 TCTCAAGAGAGACAAAATTCATCTAAAGGGTAATGTT
65 TCTCAAGAGAGACAAAATACATCTAAAGGGAAATGTT
* * * * * * ** * *
1340970 TTCAATGTTTATTTTTCAAGAGAAACTATCTCTAGAGAGACAAAACTTAGTTCCAAAAGAAAATG
1 TTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTGGTTTCAAGGGAAACTA
* * *** * * ****
1341035 TCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAA
65 TCTCAAGAGAGACAAAATACATCTAAAGGGAAATGTT
* * * **
1341072 TTCAAAGATTT-TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGG
1 TTCAATG-TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTGGTTTCAAGG
1341129 TAAATGTTTC
Statistics
Matches: 218, Mismatches: 41, Indels: 4
0.83 0.16 0.02
Matches are distributed among these distances:
101 50 0.23
102 165 0.76
103 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (101 bp):
TTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTGGTTTCAAGGGAAACTAT
CTCAAGAGAGACAAAATACATCTAAAGGGAAATGTT
Found at i:1341103 original size:167 final size:167
Alignment explanation
Indices: 1340908--1341431 Score: 856
Period size: 167 Copynumber: 3.1 Consensus size: 167
1340898 TCAAGGGAGA
* * * *
1340908 CAAA-ATTTTGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCATCTAAAGGGTAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGTAATGTTTT
* *
1340972 CAATGTTTATTTTTCAAGAGAAACTATCTCTAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
1341037 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
131 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
1341074 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAA-GGTAAATG-TT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGT-AATGTTT
*
1341137 TCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAAATGT
65 TCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGT
* *
1341202 CTCAAGGGAGACGAAATTTGTTTCAAGGGAAATAGATT
130 CTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
*
1341240 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGTAATGTTTT
* *
1341305 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTCCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
* * *
1341370 TCAAGGGAGACGAAATTAGTTTCAATGAAAACAAATT
131 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
* * *
1341407 TAAATATTTTGTTTCAAGGGAAACT
1 CAAAGATTTTGTTTCAAGAGAAACT
1341432 TGGAAAATGT
Statistics
Matches: 333, Mismatches: 21, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
166 164 0.49
167 169 0.51
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (167 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGTAATGTTTT
CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
Found at i:1341181 original size:166 final size:167
Alignment explanation
Indices: 1340908--1341431 Score: 856
Period size: 166 Copynumber: 3.1 Consensus size: 167
1340898 TCAAGGGAGA
* * * *
1340908 CAAA-ATTTTGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCATCTAAAGGGT-AATGTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAA-GGTAAATGTTT
* *
1340971 TCAATGTTTATTTTTCAAGAGAAACTATCTCTAGAGAGACAAAACTTAGTTCCAAAAGAAAATGT
65 TCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGT
1341036 CTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
130 CTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
1341074 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGTAAATG-TTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGTAAATGTTTT
*
1341138 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
* *
1341203 TCAAGGGAGACGAAATTTGTTTCAAGGGAAATAGATT
131 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
*
1341240 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGTAAATGTTTT
* *
1341305 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTCCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
* * *
1341370 TCAAGGGAGACGAAATTAGTTTCAATGAAAACAAATT
131 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
* * *
1341407 TAAATATTTTGTTTCAAGGGAAACT
1 CAAAGATTTTGTTTCAAGAGAAACT
1341432 TGGAAAATGT
Statistics
Matches: 334, Mismatches: 21, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
166 167 0.50
167 167 0.50
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (167 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGTAAATGTTTT
CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
TCAAGGGAGACGAAATTTGTTTCAAGGGAAACAAATT
Found at i:1341205 original size:37 final size:36
Alignment explanation
Indices: 1341148--1341227 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 36
1341138 CAATGTTTAT
* *
1341148 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA
1 GTTTCAAAAGAAAATATCTCAAGAGAGACAAAA-TTA
* * * *
1341185 GTTTCAAAAGAAAATGTCTCAAGGGAGACGAAATTT
1 GTTTCAAAAGAAAATATCTCAAGAGAGACAAAATTA
1341221 GTTTCAA
1 GTTTCAA
1341228 GGGAAATAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 9 0.24
37 28 0.76
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (36 bp):
GTTTCAAAAGAAAATATCTCAAGAGAGACAAAATTA
Found at i:1341280 original size:102 final size:101
Alignment explanation
Indices: 1341084--1341282 Score: 283
Period size: 101 Copynumber: 2.0 Consensus size: 101
1341074 CAAAGATTTT
* * * * *
1341084 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGTAAATGTTTCAATGTTTATG
1 GTTTCAAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGATTCAAAGTTTATG
1341149 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA
66 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA
* * * **
1341185 GTTTCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATAGATTCAAAGATTT-
1 GTTTCAAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAAT-GATTCAAAG-TTTA
1341249 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
64 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
1341283 TTCATTTCAA
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
101 42 0.49
102 41 0.48
103 3 0.03
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (101 bp):
GTTTCAAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGATTCAAAGTTTATG
TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA
Found at i:1341291 original size:65 final size:65
Alignment explanation
Indices: 1341185--1341349 Score: 217
Period size: 65 Copynumber: 2.5 Consensus size: 65
1341175 ACAAAACTTA
* * * * **
1341185 GTTTCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATAG-ATTCAAAGATTT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCATTTCAAGGGAAAT-GTATTCAAAG-TTT
1341249 -T
64 AT
* * *
1341250 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGTATTCAAAGTTTAT
1341315 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATT
1341350 TAGTTCCAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
64 4 0.05
65 84 0.95
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (65 bp):
GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGTATTCAAAGTTTAT
Found at i:1341719 original size:104 final size:101
Alignment explanation
Indices: 1341579--1341857 Score: 324
Period size: 104 Copynumber: 2.7 Consensus size: 101
1341569 TGTATTGTTC
* * **
1341579 CGAGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCT---TCGTGAAGTTGAAATTGGCTCT-GAAATGGGAAATTGTTTGTTGACA
* * *
1341644 GCCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTTTACTGTCT
62 ACCAGCCGCCCCTTCGCTGTGAAGTTGA-CTTGTACTGTCT
** *
1341685 CGAGTCCAATATCCTTCGATGAAGTTGAAATTGGCTCCAAAATTGGGATATTGTTTGTTGACAAC
1 CGAGTCCAATATCCTTCG-TGAAGTTGAAATTGGCTCTGAAA-TGGGAAATTGTTTGTTGACAAC
* * * **
1341750 TAGCCGTCCCTTCGTTGTGAAGTTGACTTGTGTTGTCT
64 CAGCCGCCCCTTCGCTGTGAAGTTGACTTGTACTGTCT
1341788 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTC---GTGAAGTTGAAATTGGCTCTGAAAT-GGGAAATTGTTTGTTGACA
1341853 ACCAG
62 ACCAG
1341858 GTATCCCTTC
Statistics
Matches: 148, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
103 31 0.21
104 58 0.39
105 43 0.29
106 16 0.11
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (101 bp):
CGAGTCCAATATCCTTCGTGAAGTTGAAATTGGCTCTGAAATGGGAAATTGTTTGTTGACAACCA
GCCGCCCCTTCGCTGTGAAGTTGACTTGTACTGTCT
Found at i:1341851 original size:105 final size:104
Alignment explanation
Indices: 1341579--1341898 Score: 374
Period size: 105 Copynumber: 3.0 Consensus size: 104
1341569 TGTATTGTTC
* * * **
1341579 CGAGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTCTGGAA-CTAAGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGT-GTGAAGTTGAAATTGGCTCTGAAATC-GGGAAATTGTTTGTTGAC
* * * * * **
1341643 AGCCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTTTACTGTCT
64 AACCAGCCGTCCCTTCGTTGTGAAGTTGA-CTTGTGTTGTCT
* ** * *
1341685 CGAGTCCAATATCCTTCG-ATGAAGTTGAAATTGGCTCCAAAATTGGGATATTGTTTGTTGACAA
1 CGAGTCCAATATCCTTCGTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTGTTGACAA
*
1341749 CTAGCCGTCCCTTCGTTGTGAAGTTGACTTGTGTTGTCT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGACTTGTGTTGTCT
1341788 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTGTTGACA
*** * *
1341853 ACCAGGTATCCCTTCGTTGTGGAGTTGAACTTGGGTTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTG-ACTTGTGTTGTCT
1341894 CGAGT
1 CGAGT
1341899 GGCACGATAT
Statistics
Matches: 181, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
103 27 0.15
104 58 0.32
105 62 0.34
106 34 0.19
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (104 bp):
CGAGTCCAATATCCTTCGTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGACTTGTGTTGTCT
Found at i:1343709 original size:12 final size:12
Alignment explanation
Indices: 1343694--1343740 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
1343684 TTTTCTTCAA
*
1343694 TTTTCCTTTGTT
1 TTTTCCTTTTTT
1343706 TTTT-CTTTTTT
1 TTTTCCTTTTTT
1343717 ATTTT-CTTTTTT
1 -TTTTCCTTTTTT
*
1343729 TTTTTCTTTTTT
1 TTTTCCTTTTTT
1343741 CTCTTTTGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 10 0.31
12 22 0.69
ACGTcount: A:0.02, C:0.11, G:0.02, T:0.85
Consensus pattern (12 bp):
TTTTCCTTTTTT
Found at i:1343709 original size:24 final size:22
Alignment explanation
Indices: 1343680--1343736 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
1343670 GCATCTTGTC
1343680 TTTTTTTTCTTCAATTTTCCTTT
1 TTTTTTTTCTTCAATTTT-CTTT
**
1343703 GTTTTTTCTT-TTTTATTTTCTTT
1 -TTTTTT-TTCTTCAATTTTCTTT
1343726 TTTTTTTTCTT
1 TTTTTTTTCTT
1343737 TTTTCTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 2 0.07
22 8 0.28
23 4 0.14
24 13 0.45
25 2 0.07
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTTTTTTCTTCAATTTTCTTT
Found at i:1343737 original size:24 final size:24
Alignment explanation
Indices: 1343693--1343740 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1343683 TTTTTCTTCA
1343693 ATTTTCCTTTGTTTTTTCTTTTTT
1 ATTTTCCTTTGTTTTTTCTTTTTT
* *
1343717 ATTTTCTTTTTTTTTTTCTTTTTT
1 ATTTTCCTTTGTTTTTTCTTTTTT
1343741 CTCTTTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.04, C:0.10, G:0.02, T:0.83
Consensus pattern (24 bp):
ATTTTCCTTTGTTTTTTCTTTTTT
Found at i:1346917 original size:18 final size:17
Alignment explanation
Indices: 1346890--1346936 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
1346880 AATTAATGGA
1346890 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
*
1346907 GTAAAAGAAATTAAAAAG
1 GTAAAA-AAATAAAAAAG
1346925 G-AATAAAAATAA
1 GTAA-AAAAATAA
1346937 GGTGTACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:1347070 original size:16 final size:17
Alignment explanation
Indices: 1347036--1347093 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 17
1347026 TGATATTAAG
1347036 AAAA-AAAATAATAGAA
1 AAAATAAAATAATAGAA
*
1347052 AAAATAAAATAA-AGTA
1 AAAATAAAATAATAGAA
*
1347068 AAAATATAATATATA-AA
1 AAAATAAAATA-ATAGAA
*
1347085 TAAATAAAA
1 AAAATAAAA
1347094 ACAAAAATAG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
16 17 0.50
17 16 0.47
18 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAATAAAATAATAGAA
Found at i:1347124 original size:32 final size:34
Alignment explanation
Indices: 1347082--1347151 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 34
1347072 TATAATATAT
1347082 AAATAAATAAAAAC-A-AAAATAGAATATTAAGA
1 AAATAAATAAAAACGATAAAATAGAATATTAAGA
* *
1347114 AAATATATAAAAACGTATAAAATATAATATTAAGA
1 AAATAAATAAAAACG-ATAAAATAGAATATTAAGA
1347149 AAA
1 AAA
1347152 ACAATATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 13 0.39
34 1 0.03
35 19 0.58
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.23
Consensus pattern (34 bp):
AAATAAATAAAAACGATAAAATAGAATATTAAGA
Found at i:1347196 original size:2 final size:2
Alignment explanation
Indices: 1347189--1347229 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
1347179 TTAATACATC
*
1347189 TA TA TA TA TA TA TA TA TA -A TGA TA -A GA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
1347230 ATAAAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1347247 original size:21 final size:21
Alignment explanation
Indices: 1347192--1347256 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 21
1347182 ATACATCTAT
*
1347192 ATATATATATATATAATGATAAG
1 ATATATATATATATAAT-A-AAA
1347215 ATATATATATATATAATAAAA
1 ATATATATATATATAATAAAA
1347236 ATA-ATATA-ATATAAATAAAA
1 ATATATATATATAT-AATAAAA
1347256 A
1 A
1347257 AAGGAATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 4 0.10
20 13 0.32
21 5 0.12
22 1 0.03
23 17 0.43
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
ATATATATATATATAATAAAA
Found at i:1347247 original size:23 final size:23
Alignment explanation
Indices: 1347192--1347288 Score: 71
Period size: 23 Copynumber: 4.3 Consensus size: 23
1347182 ATACATCTAT
*
1347192 ATATATATATATATAATGATAAGAT-
1 ATATA-ATATATATAAT-A-AAAATA
1347217 ATAT-ATATATATAATAAAAATA
1 ATATAATATATATAATAAAAATA
* *
1347239 ATATAATATAAATAA-AAAAAGGA
1 ATATAATATATATAATAAAAA-TA
* *
1347262 ATATAGTAAATA-AAT-AAAA-A
1 ATATAATATATATAATAAAAATA
1347282 ATATAAT
1 ATATAAT
1347289 TAAATATATA
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
20 7 0.11
21 4 0.07
22 16 0.26
23 30 0.49
25 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (23 bp):
ATATAATATATATAATAAAAATA
Found at i:1347257 original size:21 final size:20
Alignment explanation
Indices: 1347217--1347294 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 20
1347207 ATGATAAGAT
*
1347217 ATATATATATATAATAAAAATA
1 ATATA-ATATA-AATAAAAAAA
1347239 ATATAATATAAATAAAAAAA
1 ATATAATATAAATAAAAAAA
1347259 GGA-AT-ATAGTAAATAAATAAAAA
1 --ATATAATA-TAAAT-AA-AAAAA
1347282 ATATAAT-TAAATA
1 ATATAATATAAATA
1347295 TATATATATA
Statistics
Matches: 48, Mismatches: 1, Indels: 16
0.74 0.02 0.25
Matches are distributed among these distances:
20 13 0.27
21 18 0.38
22 10 0.21
23 7 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
ATATAATATAAATAAAAAAA
Found at i:1353810 original size:18 final size:18
Alignment explanation
Indices: 1353774--1353809 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
1353764 TGCTGTGTTC
1353774 TCTTTCTCTGTTTTTTTT
1 TCTTTCTCTGTTTTTTTT
1353792 TCTTT-TCTGTTTTTTTT
1 TCTTTCTCTGTTTTTTTT
1353809 T
1 T
1353810 TTTGTCGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.81
Consensus pattern (18 bp):
TCTTTCTCTGTTTTTTTT
Found at i:1354086 original size:27 final size:27
Alignment explanation
Indices: 1354050--1354140 Score: 173
Period size: 27 Copynumber: 3.4 Consensus size: 27
1354040 GCAGTGAGGC
*
1354050 GGCGGCTGGGATTCTTGAAGCATCAGA
1 GGCGGCTGGGATTCTGGAAGCATCAGA
1354077 GGCGGCTGGGATTCTGGAAGCATCAGA
1 GGCGGCTGGGATTCTGGAAGCATCAGA
1354104 GGCGGCTGGGATTCTGGAAGCATCAGA
1 GGCGGCTGGGATTCTGGAAGCATCAGA
1354131 GGCGGCTGGG
1 GGCGGCTGGG
1354141 GGTGGCTAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.20, C:0.19, G:0.43, T:0.19
Consensus pattern (27 bp):
GGCGGCTGGGATTCTGGAAGCATCAGA
Found at i:1354266 original size:3 final size:3
Alignment explanation
Indices: 1354258--1354369 Score: 127
Period size: 3 Copynumber: 36.7 Consensus size: 3
1354248 TTATTTATTA
* * *
1354258 AAT AAT AAT AAT ATAT AAT ATT GAT AAT AAT AAT AAAT AAT GAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* *
1354305 AAT AAT AAT AAT TAT AAT AAAT AAT AAT ACT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
1354350 TTT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
1354370 ATTTAAATGA
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
2 2 0.02
3 80 0.88
4 9 0.10
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:1355481 original size:113 final size:112
Alignment explanation
Indices: 1354996--1355699 Score: 871
Period size: 113 Copynumber: 6.2 Consensus size: 112
1354986 ATCTCCTTCT
* * *
1354996 GTGATAGAATT-ATGCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCA
1 GTGAT-GAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
1355060 GATGAGTTCTTCTCATTATGAACT-T-CTCTGGAAAAGCTGCTCCATCAA
65 GATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAAA-CTGATCCATCAA
* ** *
1355108 GTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTTATTATGAAC-TCTTCTTCCTTCTTCAG
1 GTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* ** * *
1355172 ATGAGTTCTTCTTATTATGAAC-CTTTTCTGGCAAAAATAATCCATCAA
66 ATGAGTTCTTCTCATTATGAACTC-TACCTGG-AAAACTGATCCATCAA
1355220 GTGATGAATTC-AGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 GTGATGAATTCAAG-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
1355284 GATGACGAGTTCTTCTCATTATGAACT-T-CTCTGGCAACAA-TAATCCATCAA
65 GAT---GAGTTCTTCTCATTATGAACTCTAC-CTGG-AA-AACTGATCCATCAA
* *
1355335 GTGATGAATTCAAACAAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
1 GTGATGAATTCAAGC-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* *
1355400 GATGAGTTCTTCTCATTATGAACTCTACCTGGAAAGGCTGATCCAGCAA
65 GATGAGTTCTTCTCATTATGAACTCTACCTGGAAA-ACTGATCCATCAA
* * *
1355449 ATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 GTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* *
1355514 ATGAGTTCTTCTCATTATGAACTCGAACTGGAAATACTGAAT-CATCGAA
66 ATGAGTTCTTCTCATTATGAACTCTACCTGGAAA-ACTG-ATCCATC-AA
*
1355563 -TGATGAATTCAAGCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 GTGATGAATTCAAGC-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* *
1355626 GATGAGTTCTTCTCATTATGAACTCGAACTGGAAATACTGAAT-CATCGAA
65 GATGAGTTCTTCTCATTATGAACTCTACCTGGAAA-ACTG-ATCCATC-AA
1355676 -TGATGAATTCAAGCGAAAA-GTTGA
1 GTGATGAATTCAAGC-AAAAGGTTGA
1355700 TCCATCATAT
Statistics
Matches: 538, Mismatches: 32, Indels: 43
0.88 0.05 0.07
Matches are distributed among these distances:
111 44 0.08
112 94 0.17
113 262 0.49
114 33 0.06
115 32 0.06
116 73 0.14
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (112 bp):
GTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTCTACCTGGAAAACTGATCCATCAA
Found at i:1355641 original size:226 final size:224
Alignment explanation
Indices: 1355010--1355686 Score: 881
Period size: 229 Copynumber: 3.0 Consensus size: 224
1355000 TAGAATTATG
* *
1355010 CAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * **
1355075 TTATGAACTTCTCTGGAAAAGCTG-CTCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTTCTCTGGAAAA-CTGAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAAT
* * **
1355139 TCTTCTTATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC-CTTTTCTG
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC-TAACTG
* *
1355202 GCAAAAATAATCCATCAAGTGATGAATTCAGA
194 G-AAAAATAATCCAGCAAATGATGAATTCAGA
1355234 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
*
1355299 TCATTATGAACTTCTCTGGCAACAA-T-AATCCATCAAGTGATGAATTCAAACAAAAAGGTTGAA
63 TCATTATGAACTTCTCTGG-AA-AACTGAATCCATCAAGTGATGAATTCAAGC-AAAAGGTTGAA
*
1355362 CAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTA
125 CAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTA
* ** * *
1355427 CCTGGAAAGGCTGATCCAGCAAATGATGGATTCA-A
190 ACTGGAAA-AATAATCCAGCAAATGATGAATTCAGA
*
1355462 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 -CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1355527 ATTATGAAC-TCGAACTGGAAATACTGAAT-CATCGAA-TGATGAATTCAAGCGAAAA-GTTGAA
65 ATTATGAACTTC--TCTGGAAA-ACTGAATCCATC-AAGTGATGAATTCAAGC-AAAAGGTTGAA
* *
1355588 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGA
125 CAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTA
* * *
1355653 ACTGGAAATACTGAAT-CATCGAATGATGAATTCA
190 ACTGGAAA-AAT-AATCCAGCAAATGATGAATTCA
1355687 AGCGAAAAGT
Statistics
Matches: 403, Mismatches: 32, Indels: 34
0.86 0.07 0.07
Matches are distributed among these distances:
224 51 0.13
225 3 0.01
226 115 0.29
227 76 0.19
228 41 0.10
229 116 0.29
230 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (224 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTCTCTGGAAAACTGAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGA
AAAATAATCCAGCAAATGATGAATTCAGA
Found at i:1356144 original size:22 final size:22
Alignment explanation
Indices: 1356119--1356173 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1356109 CATAAAGTTT
*
1356119 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
1356141 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1356163 TCATCTTTGAA
1 TCATCTTTGAA
1356174 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1356666 original size:54 final size:53
Alignment explanation
Indices: 1356542--1356742 Score: 241
Period size: 54 Copynumber: 3.8 Consensus size: 53
1356532 CACTGGTTCA
* * *
1356542 TAAAACATTTGACAATACATTCAT-CTTTTCCTGTGGTTTCTG-TC-GAG-ATG
1 TAAAACATTTGACAACACATTCATCCTTTT-CTGTGGCTTCTGCTCAGAGTTTG
*
1356592 TAAAACACTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
1 TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGA-GTTTG
* * **
1356646 TAAAACATTTGACAACACATTCATCC-TTTCTTGTGGTTTTTGCTCAGACGTTCA
1 TAAAACATTTGACAACACATTCATCCTTTTC-TGTGGCTTCTGCTCAGA-GTTTG
* *
1356700 TAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGC
1 TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGC
1356743 CAAGATTTCT
Statistics
Matches: 130, Mismatches: 14, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
50 33 0.25
51 7 0.05
52 2 0.02
53 5 0.04
54 79 0.61
55 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (53 bp):
TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAGTTTG
Found at i:1356739 original size:108 final size:104
Alignment explanation
Indices: 1356542--1356742 Score: 287
Period size: 104 Copynumber: 1.9 Consensus size: 104
1356532 CACTGGTTCA
* * *
1356542 TAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTGTCGAGATGTAAAACACTTGACAA
1 TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTCGAGACGTAAAACACTTGACAA
1356607 CACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
66 CACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
* * **
1356646 TAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTTTGCTC-AGACGTTCATAAAGCGTTT
1 TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTG-TCGAGACG-T-A-AAA-CACTT
1356710 GACAACACATTCATCCTTTTCTGTGGCTTCTGC
61 GACAACACATTCATCCTTTTCTGTGGCTTCTGC
1356743 CAAGATTTCT
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
104 42 0.49
105 3 0.04
106 1 0.01
107 3 0.04
108 36 0.42
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (104 bp):
TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTCGAGACGTAAAACACTTGACAA
CACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
Found at i:1358051 original size:104 final size:104
Alignment explanation
Indices: 1357871--1358070 Score: 319
Period size: 104 Copynumber: 1.9 Consensus size: 104
1357861 ATTCCTACCG
* * * *
1357871 AACCAGATCAGATAACTCAAAGAATACTTCCAGAAAATGCTATTGAGTATCCTTATTTTTACTAT
1 AACCAAATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGAGCATCCTTATTTCTACTAT
* *
1357936 GAGCAAATTCATCTTCCAAATTCAATGATTGTTCTGTCC
66 GAGCAAATTCATCTTCAAAATCCAATGATTGTTCTGTCC
* *
1357975 AACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACTAT
1 AACCAAATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGAGCATCCTTATTTCTACTAT
*
1358040 GAGCAAATTCATCTTTAAAATCCAATGATTG
66 GAGCAAATTCATCTTCAAAATCCAATGATTG
1358071 GTTTTTGGGG
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 87 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.32
Consensus pattern (104 bp):
AACCAAATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGAGCATCCTTATTTCTACTAT
GAGCAAATTCATCTTCAAAATCCAATGATTGTTCTGTCC
Found at i:1358190 original size:84 final size:84
Alignment explanation
Indices: 1358090--1358645 Score: 951
Period size: 84 Copynumber: 6.7 Consensus size: 84
1358080 GTTCATACCA
* * * * *
1358090 AACCAGATTAGATAACTCAAAGAACATTTCCAAAAGATGCTATTGAACACATTATTCTTCTAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
* *
1358155 TCAATGATTAGTCTTGTTC
66 TCAATGATTGGTCTTGTCC
*
1358174 AACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCACATTATTCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1358239 TCAATGATTGGTCTTGTCC
66 TCAATGATTGGTCTTGTCC
1358258 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1358323 TCAATGATTGGT-TCTGTCC
66 TCAATGATTGGTCT-TGTCC
*
1358342 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTA-T-ATCC-AAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1358404 TCAATGATTGGT-TCTGTCC
66 TCAATGATTGGTCT-TGTCC
*
1358423 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGATCACATTATTCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1358488 TCAATGATTGGTCTTGTCC
66 TCAATGATTGGTCTTGTCC
1358507 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
* *
1358572 TCAATGATTAGTCTTGTTC
66 TCAATGATTGGTCTTGTCC
1358591 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTAT
1358646 ATTTGTTCCA
Statistics
Matches: 454, Mismatches: 13, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
81 75 0.17
82 4 0.01
83 5 0.01
84 369 0.81
85 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (84 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
TCAATGATTGGTCTTGTCC
Found at i:1358531 original size:249 final size:251
Alignment explanation
Indices: 1358090--1358647 Score: 955
Period size: 249 Copynumber: 2.2 Consensus size: 251
1358080 GTTCATACCA
* * * *
1358090 AACCAGATTAGATAACTCAAAGAACATTTCCAAAAGATGCTATTGAACACATTAT-TCTTCTAAA
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATATC-TC-AAA
*
1358154 TTCAATGATTAGTCTTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTG
64 TTCAATGATTAGTCTTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTG
1358219 AGCACATTATTCTTCCAAATTCAATGATTGGTCTTGTCCAACCAGATCAGATAACTCAAAGAACA
129 AGCACATTATTCTTCCAAATTCAATGATTGGTCTTGTCCAACCAGATCAGATAACTCAAAGAACA
*
1358284 CTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAATTCAATGATTGGT-TCTGTCC
194 CTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAATTCAATGATTAGTCT-TGTCC
1358342 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATATC-C-AATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATATCTCAAATT
* *
1358405 CAATGATTGGT-TCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
66 CAATGATTAGTCT-TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGA
*
1358469 TCACATTATTCTTCCAAATTCAATGATTGGTCTTGTCCAACCAGATCAGATAACTCAAAGAACAC
130 GCACATTATTCTTCCAAATTCAATGATTGGTCTTGTCCAACCAGATCAGATAACTCAAAGAACAC
*
1358534 TTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAATTCAATGATTAGTCTTGTTC
195 TTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAATTCAATGATTAGTCTTGTCC
1358591 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATAT
1358648 TTGTTCCAGT
Statistics
Matches: 293, Mismatches: 10, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
248 1 0.00
249 237 0.81
250 1 0.00
251 1 0.00
252 51 0.17
253 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (251 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATATCTCAAATT
CAATGATTAGTCTTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAG
CACATTATTCTTCCAAATTCAATGATTGGTCTTGTCCAACCAGATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTGAGCACATTATTCTTCCAAATTCAATGATTAGTCTTGTCC
Found at i:1362159 original size:1 final size:1
Alignment explanation
Indices: 1362153--1362184 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
1362143 TCAGGAATGG
1362153 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1362185 GTTTAGACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1363511 original size:14 final size:14
Alignment explanation
Indices: 1363492--1363531 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1363482 GCAAAGATGC
1363492 CAAATGTAAATATG
1 CAAATGTAAATATG
*
1363506 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
1363520 TAAATGTAAATA
1 CAAATGTAAATA
1363532 CAAACGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.28
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:1364976 original size:13 final size:15
Alignment explanation
Indices: 1364954--1364990 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1364944 TTTGACATAA
1364954 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
1364966 AAATAAAATACTTGC
1 AAATAAAATACTTGC
1364981 AAATAAAATA
1 AAATAAAATA
1364991 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:1366860 original size:17 final size:17
Alignment explanation
Indices: 1366826--1366858 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1366816 TGCTGTGTTC
1366826 TCTTTCTCTGTTTTTTT
1 TCTTTCTCTGTTTTTTT
1366843 TCTTTCT-T-TTTTTTT
1 TCTTTCTCTGTTTTTTT
1366858 T
1 T
1366859 TTTGTCGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (17 bp):
TCTTTCTCTGTTTTTTT
Found at i:1367135 original size:27 final size:27
Alignment explanation
Indices: 1367099--1367189 Score: 173
Period size: 27 Copynumber: 3.4 Consensus size: 27
1367089 GCAGTGAGGC
*
1367099 GGCGGCTGGGATTCTTGAAGCATCAGA
1 GGCGGCTGGGATTCTGGAAGCATCAGA
1367126 GGCGGCTGGGATTCTGGAAGCATCAGA
1 GGCGGCTGGGATTCTGGAAGCATCAGA
1367153 GGCGGCTGGGATTCTGGAAGCATCAGA
1 GGCGGCTGGGATTCTGGAAGCATCAGA
1367180 GGCGGCTGGG
1 GGCGGCTGGG
1367190 GGTGGCTAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.20, C:0.19, G:0.43, T:0.19
Consensus pattern (27 bp):
GGCGGCTGGGATTCTGGAAGCATCAGA
Found at i:1367314 original size:3 final size:3
Alignment explanation
Indices: 1367306--1367405 Score: 137
Period size: 3 Copynumber: 32.7 Consensus size: 3
1367296 TTATTTATTA
* * *
1367306 AAT AAT AAT AAT ATAT AAT ATT GAT AAT AAT AAT AAAT AAT GAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
**
1367353 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1367401 AAT AA
1 AAT AA
1367406 ATTTAAATGA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
3 79 0.93
4 6 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1370272 original size:73 final size:73
Alignment explanation
Indices: 1370107--1370381 Score: 281
Period size: 74 Copynumber: 3.7 Consensus size: 73
1370097 AAAAAATATA
* * *
1370107 TAATATATGAAATCATTATAATATTTGTTTTCCGACTTGTTTCCTTAATTTAAGCTATAATGGTT
1 TAATATATGAAATCATTATAATATTTGTTTCCCCACTTGTTTCCTTAATTTAAGCTATAGTGGTT
1370172 TAGTTTTT
66 TAGTTTTT
* * * *
1370180 TAAATATATGGAGTCATTATATTATTTGTTTCCCCACATGTTTCCTTAATTTAAGCTATAGTGGT
1 T-AATATATGAAATCATTATAATATTTGTTTCCCCACTTGTTTCCTTAATTTAAGCTATAGTGGT
1370245 TTAGTTTTT
65 TTAGTTTTT
* * * * *
1370254 TAATATATGGAATTATTATAATATTTATTTCTCCAC---TTTCCCTAATTTAAGC-A-ACGTTTG
1 TAATATATGAAATCATTATAATATTTGTTTCCCCACTTGTTTCCTTAATTTAAGCTATA-G--T-
**
1370314 GTGTTTAGCTATTAA
62 G-GTTTAG-T-TTTT
* * *
1370329 TAATATATATAAATTATTATAGTATTTGTTTCCCCACTTGTTTCCTTAATTTA
1 TAATATAT-GAAATCATTATAATATTTGTTTCCCCACTTGTTTCCTTAATTTA
1370382 TTGCTTTGAA
Statistics
Matches: 169, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
68 1 0.01
69 2 0.01
70 15 0.09
71 1 0.01
72 1 0.01
73 37 0.22
74 67 0.40
75 10 0.06
76 23 0.14
79 12 0.07
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.49
Consensus pattern (73 bp):
TAATATATGAAATCATTATAATATTTGTTTCCCCACTTGTTTCCTTAATTTAAGCTATAGTGGTT
TAGTTTTT
Found at i:1375883 original size:37 final size:37
Alignment explanation
Indices: 1375833--1375904 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
1375823 ATGACATTCG
*
1375833 ATATTTTGTGTCATGTTGTATACTTCTATCCTTCCAT
1 ATATTTTGTGTCATGTGGTATACTTCTATCCTTCCAT
1375870 ATATTTTGTGTCATGTGGTATACTTCTATCCTTCC
1 ATATTTTGTGTCATGTGGTATACTTCTATCCTTCC
1375905 CTACTCCATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.18, C:0.19, G:0.12, T:0.50
Consensus pattern (37 bp):
ATATTTTGTGTCATGTGGTATACTTCTATCCTTCCAT
Found at i:1378700 original size:19 final size:19
Alignment explanation
Indices: 1378676--1378726 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1378666 ATCTAGCTGA
*
1378676 GTTGACTGTTGACCAGGTC
1 GTTGACTGTTGACCAGGCC
1378695 GTTGACTGTTGACCAGGCC
1 GTTGACTGTTGACCAGGCC
1378714 GTTGACTGTTGAC
1 GTTGACTGTTGAC
1378727 TTTGACCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (19 bp):
GTTGACTGTTGACCAGGCC
Found at i:1378766 original size:17 final size:18
Alignment explanation
Indices: 1378734--1378768 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1378724 GACTTTGACC
*
1378734 AAAAAGTCAATTTTTTAT
1 AAAAAGTCAATGTTTTAT
1378752 AAAAAGTC-ATGTTTTAT
1 AAAAAGTCAATGTTTTAT
1378769 GTTTTTGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (18 bp):
AAAAAGTCAATGTTTTAT
Found at i:1378803 original size:13 final size:13
Alignment explanation
Indices: 1378785--1378816 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1378775 GGACGTCCTG
1378785 AGTCTGAATCCGA
1 AGTCTGAATCCGA
1378798 AGTCTGAATCCGA
1 AGTCTGAATCCGA
1378811 AGTCTG
1 AGTCTG
1378817 TTTCACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (13 bp):
AGTCTGAATCCGA
Found at i:1380646 original size:31 final size:32
Alignment explanation
Indices: 1380569--1380655 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 32
1380559 CCTAAGGAGA
* *
1380569 CCCTTGGGTAGACTCTTAAGCCCCGAGATGCT
1 CCCTTGGGTAGGCTCTTAAGCCCCGAGATACT
** * *
1380601 CCCTTAAGTAGGCTCTTAAG-CCCTAGGTACT
1 CCCTTGGGTAGGCTCTTAAGCCCCGAGATACT
*
1380632 TCCTTGGGTAGGCTC-TAAGGCCCC
1 CCCTTGGGTAGGCTCTTAA-GCCCC
1380656 AAGGTATCAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
30 3 0.07
31 21 0.48
32 20 0.45
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.26
Consensus pattern (32 bp):
CCCTTGGGTAGGCTCTTAAGCCCCGAGATACT
Found at i:1381101 original size:29 final size:26
Alignment explanation
Indices: 1381072--1381123 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1381062 CATCATCTGG
1381072 TGGTTTAGTACTACTAAGCTTCCCAA
1 TGGTTTAGTACTACTAAGCTTCCCAA
1381098 TGGTTTAGTACTACTAAGCTTCCCAA
1 TGGTTTAGTACTACTAAGCTTCCCAA
1381124 AGCTCACTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (26 bp):
TGGTTTAGTACTACTAAGCTTCCCAA
Found at i:1385013 original size:2 final size:2
Alignment explanation
Indices: 1385006--1385077 Score: 130
Period size: 2 Copynumber: 37.0 Consensus size: 2
1384996 TAGTGCCTCC
1385006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1385048 AT AT -T AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1385078 GACTGTTTTA
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 66 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1389697 original size:20 final size:20
Alignment explanation
Indices: 1389672--1389721 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1389662 ACCTGTACAT
1389672 TTGGTATCGATACCAGGATG
1 TTGGTATCGATACCAGGATG
*
1389692 TTGGTATCGATACCGGGATG
1 TTGGTATCGATACCAGGATG
1389712 TTGGTATCGA
1 TTGGTATCGA
1389722 GATCGAGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (20 bp):
TTGGTATCGATACCAGGATG
Found at i:1390505 original size:17 final size:17
Alignment explanation
Indices: 1390485--1390517 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1390475 TTATAAATAA
1390485 AATAATCATTTTATTTG
1 AATAATCATTTTATTTG
*
1390502 AATAATGATTTTATTT
1 AATAATCATTTTATTT
1390518 ATTTTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (17 bp):
AATAATCATTTTATTTG
Found at i:1395728 original size:43 final size:44
Alignment explanation
Indices: 1395638--1395754 Score: 155
Period size: 43 Copynumber: 2.7 Consensus size: 44
1395628 ATCAGCATCA
* * *
1395638 CTCGATTCCATCACATAAGGAGTTGGATCAGCATCACCACTTCG
1 CTCGATTCTATCACATAAGGAGTTGGATCAACAACACCACTTCG
* * * *
1395682 CTCGATTCTATCACA-AATGAGTTGGATCAACAACATCAGTTTG
1 CTCGATTCTATCACATAAGGAGTTGGATCAACAACACCACTTCG
*
1395725 CTCGATTCTTTCACATAAGGAGTTGGATCA
1 CTCGATTCTATCACATAAGGAGTTGGATCA
1395755 GCATTATCTC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 36 0.57
44 27 0.43
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (44 bp):
CTCGATTCTATCACATAAGGAGTTGGATCAACAACACCACTTCG
Found at i:1395967 original size:72 final size:71
Alignment explanation
Indices: 1395853--1396023 Score: 234
Period size: 72 Copynumber: 2.4 Consensus size: 71
1395843 TCATATGCGA
* * * * *
1395853 AAGAAATTCATAACGAGAAAACTTGTTGCTTGATTCCATCACAGAAAAAGTTGGATTAGCATTTC
1 AAGAAGTTCATAATGAGAAAACTTGTTGCTCGATTCCATCACAGAAAAAGTTGGATCAACATTTC
*
1395918 TCAAAG
66 CCAAAG
* * *
1395924 AAGAAGTTCATAATGAGAAGAATTTGTTTCTCGATTCCATCACAGAAGAAGTTGGATCAACATTT
1 AAGAAGTTCATAATGAGAA-AACTTGTTGCTCGATTCCATCACAGAAAAAGTTGGATCAACATTT
*
1395989 CCCGAAG
65 CCCAAAG
1395996 AAGAAGTTCATAATGAGAAAAACTTGTT
1 AAGAAGTTCATAATGAG-AAAACTTGTT
1396024 CAACCTTTCC
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
71 17 0.20
72 68 0.78
73 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (71 bp):
AAGAAGTTCATAATGAGAAAACTTGTTGCTCGATTCCATCACAGAAAAAGTTGGATCAACATTTC
CCAAAG
Found at i:1396202 original size:3 final size:3
Alignment explanation
Indices: 1396196--1396226 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1396186 TTCTTCGATG
1396196 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1396227 AGTAAACGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1397107 original size:6 final size:6
Alignment explanation
Indices: 1397096--1397181 Score: 63
Period size: 6 Copynumber: 14.8 Consensus size: 6
1397086 TCGTCCTGAC
* * * *
1397096 AATATT AATATT ATTATT -TTCTT TATTATT AATATT -A--TT AATATT
1 AATATT AATATT AATATT AATATT AAT-ATT AATATT AATATT AATATT
* * * *
1397141 ATTATT AATAAT ATTATT ATTATT AATATT AATATT AATAT
1 AATATT AATATT AATATT AATATT AATATT AATATT AATAT
1397182 ATGTTTTTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
3 2 0.03
4 1 0.02
5 5 0.08
6 52 0.81
7 4 0.06
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (6 bp):
AATATT
Found at i:1397133 original size:12 final size:12
Alignment explanation
Indices: 1397098--1397177 Score: 78
Period size: 12 Copynumber: 6.9 Consensus size: 12
1397088 GTCCTGACAA
1397098 TATTAATATTAT
1 TATTAATATTAT
1397110 TATT--T-TCT-T
1 TATTAATAT-TAT
* *
1397119 TATTATTAATAT
1 TATTAATATTAT
1397131 TATTAATATTAT
1 TATTAATATTAT
*
1397143 TATTAATAATAT
1 TATTAATATTAT
* *
1397155 TATTATTATTAA
1 TATTAATATTAT
1397167 TATTAATATTA
1 TATTAATATTA
1397178 ATATATGTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
9 6 0.11
10 2 0.04
11 2 0.04
12 45 0.82
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTAATATTAT
Found at i:1397140 original size:15 final size:15
Alignment explanation
Indices: 1397122--1397177 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
1397112 TTTTCTTTAT
1397122 TATTAATATTATTAA
1 TATTAATATTATTAA
* *
1397137 TATTATTATTAATAA
1 TATTAATATTATTAA
*
1397152 TATTATTATTATTAA
1 TATTAATATTATTAA
1397167 TATTAATATTA
1 TATTAATATTA
1397178 ATATATGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTAATATTATTAA
Found at i:1397164 original size:24 final size:24
Alignment explanation
Indices: 1397101--1397174 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
1397091 CTGACAATAT
* *
1397101 TAATATTATTATT-TTCTTTATTAT
1 TAATATTATTATTATT-ATTATTAA
*
1397125 TAATATTATTAATATTATTATTAA
1 TAATATTATTATTATTATTATTAA
*
1397149 TAATATTATTATTATTAATATTAA
1 TAATATTATTATTATTATTATTAA
1397173 TA
1 TA
1397175 TTAATATATG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (24 bp):
TAATATTATTATTATTATTATTAA
Found at i:1399437 original size:131 final size:131
Alignment explanation
Indices: 1399252--1399601 Score: 465
Period size: 131 Copynumber: 2.7 Consensus size: 131
1399242 GAAATATATT
1399252 TTCATTTC-AGTTGGAGTAATAAATAACTGCTTTAATGCATA--AGAGGTCATTTATTATCGATT
1 TTCATTTCGA-TTGGAGTAATAAATAACTGCTTTAA-G-ATATGAGAGGTCATTTATTATCGATT
* * * * *
1399314 GGAAATAATTAGATATTGTCGTTTTCTCTCGAATCAATATTGATTTTTAAGACGGAATAGTGATA
63 GGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTAAAGACGAAATAGTGATA
1399379 TCTC
128 TCTC
* * * *
1399383 TTCATTTCGATTGGGGCAATAAATTACTGCTTTAAGATATGAGAGATCATTTATTATCGATTGGA
1 TTCATTTCGATTGGAGTAATAAATAACTGCTTTAAGATATGAGAGGTCATTTATTATCGATTGGA
* **
1399448 AATCATTAGATATTATCGTTTTCACTCGAATTGATATTGAATTTAAAGACGAAATAGTGATATCT
66 AATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTAAAGACGAAATAGTGATATCT
1399513 C
131 C
* ** * *
1399514 TTTATTTCGATTGGAGTAATAAATGAA-TGCTTTAAGGCATGATAGGTCATTTATTCTCGATTGG
1 TTCATTTCGATTGGAGTAATAAAT-AACTGCTTTAAGATATGAGAGGTCATTTATTATCGATTGG
* *
1399578 AAATAATTATATATTATCATTTTC
65 AAATAATTAGATATTATCGTTTTC
1399602 GCTCTTATAA
Statistics
Matches: 191, Mismatches: 24, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
129 3 0.02
130 1 0.01
131 185 0.97
132 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (131 bp):
TTCATTTCGATTGGAGTAATAAATAACTGCTTTAAGATATGAGAGGTCATTTATTATCGATTGGA
AATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTAAAGACGAAATAGTGATATCT
C
Found at i:1402984 original size:3 final size:3
Alignment explanation
Indices: 1402972--1403024 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
1402962 CTACGAAAAC
*
1402972 ATT A-T ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT TTT ATT AATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
1403019 A-T ATT A
1 ATT ATT A
1403025 ATGATTTTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 6 0.14
3 35 0.80
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1404335 original size:19 final size:19
Alignment explanation
Indices: 1404294--1404335 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1404284 ATATTTTAAC
*
1404294 ATTTTTTCTCTTAATTTAT
1 ATTTTTTCTCTTAAGTTAT
*
1404313 ATTTTTTCCTCTTTAGTTA-
1 ATTTTTT-CTCTTAAGTTAT
1404332 ATTT
1 ATTT
1404336 AGTATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTTTCTCTTAAGTTAT
Found at i:1407341 original size:7 final size:7
Alignment explanation
Indices: 1407324--1407384 Score: 61
Period size: 7 Copynumber: 8.4 Consensus size: 7
1407314 AATAAGAAGC
1407324 AAAAAAGG
1 AAAAAA-G
1407332 AAAAAAG
1 AAAAAAG
*
1407339 AAAAGAAA
1 AAAA-AAG
*
1407347 AAAAAAC
1 AAAAAAG
1407354 AAAAAAGG
1 AAAAAA-G
1407362 AAAAAA-
1 AAAAAAG
*
1407368 ACAAAAG
1 AAAAAAG
1407375 AAAAAAG
1 AAAAAAG
1407382 AAA
1 AAA
1407385 GAGCAAAGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
6 5 0.11
7 22 0.49
8 18 0.40
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1407358 original size:16 final size:15
Alignment explanation
Indices: 1407332--1407380 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
1407322 GCAAAAAAGG
*
1407332 AAAAAAGAAAAGAAA
1 AAAAAACAAAAGAAA
1407347 AAAAAACAAAA-AAGGA
1 AAAAAACAAAAGAA--A
1407363 AAAAAACAAAAGAAA
1 AAAAAACAAAAGAAA
1407378 AAA
1 AAA
1407381 GAAAGAGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 2 0.07
15 14 0.47
16 12 0.40
17 2 0.07
ACGTcount: A:0.86, C:0.04, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAACAAAAGAAA
Found at i:1407359 original size:17 final size:16
Alignment explanation
Indices: 1407339--1407373 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1407329 AGGAAAAAAG
1407339 AAAAGAAAAAAAAACAA
1 AAAAG-AAAAAAAACAA
*
1407356 AAAAGGAAAAAAACAA
1 AAAAGAAAAAAAACAA
1407372 AA
1 AA
1407374 GAAAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.86, C:0.06, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAACAA
Found at i:1407359 original size:30 final size:31
Alignment explanation
Indices: 1407323--1407380 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1407313 CAATAAGAAG
*
1407323 CAAAAAAGG-AAAAAAGAAAAGAAAAAAAAA
1 CAAAAAAGGAAAAAAACAAAAGAAAAAAAAA
1407353 CAAAAAAGGAAAAAAACAAAAGAAAAAA
1 CAAAAAAGGAAAAAAACAAAAGAAAAAA
1407381 GAAAGAGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (31 bp):
CAAAAAAGGAAAAAAACAAAAGAAAAAAAAA
Found at i:1408042 original size:22 final size:22
Alignment explanation
Indices: 1408011--1408052 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1408001 CTACCCCATA
*
1408011 AAACCTTTGAACATCAAATGTC
1 AAACCATTGAACATCAAATGTC
*
1408033 AAACCATTGAGCATCAAATG
1 AAACCATTGAACATCAAATG
1408053 GACAAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (22 bp):
AAACCATTGAACATCAAATGTC
Found at i:1408927 original size:106 final size:106
Alignment explanation
Indices: 1408787--1409680 Score: 1438
Period size: 105 Copynumber: 8.5 Consensus size: 106
1408777 TTCAGTTTCA
* * *
1408787 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * *
1408852 CAACGAAGGGACGGCTTGTTGTCAACAAATAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
*
1408893 TTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
1408958 CGACGAAGGGACCGCTGGTTGTCAAC-AACAACATT-CCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTCCCAAT
* *
1408998 TTCAGAGCCAATTTCAACTTCAGAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
1409063 CGACGAATGGACTGCTGGTTGTCAAC-AACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
* **
1409103 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTTGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
1409168 CGACGAAGGGACCGCTGGTTGTCAAC-AATAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
1409208 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
1409273 CGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
*
1409314 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
1409379 CGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAAA
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
1409419 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
1409484 CAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
* * * *
1409525 TTCGGAGCCAATTTCAACTTCACAGCGAAGGATATCGGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
1409590 CAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
* * *
1409631 TTCTGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAAC
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAC
1409681 ACAACTTTCA
Statistics
Matches: 739, Mismatches: 45, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
104 2 0.00
105 389 0.53
106 348 0.47
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAAT
Done.