Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 92 of 198
Found at i:29366036 original size:27 final size:28
Alignment explanation
Indices: 29365984--29366083 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 28
29365974 CTTTCATCAT
* ** *
29365984 TTGCCACAAAGGCTTTCCTTCCCATAGA
1 TTGCCACAAAGGCTTTCCATATCATATA
*
29366012 TCGCCACAAAGGC-TTCCATATCATATA
1 TTGCCACAAAGGCTTTCCATATCATATA
* * * *
29366039 TTGCCATAAAGGCTTTTCGTTTCATATA
1 TTGCCACAAAGGCTTTCCATATCATATA
29366067 TTGCCACAAAGGCTTTC
1 TTGCCACAAAGGCTTTC
29366084 ATTTTTTGGC
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
27 21 0.36
28 38 0.64
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (28 bp):
TTGCCACAAAGGCTTTCCATATCATATA
Found at i:29371343 original size:17 final size:17
Alignment explanation
Indices: 29371321--29371353 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29371311 TTGATTACCC
29371321 AATTAAATTAATTCAAT
1 AATTAAATTAATTCAAT
*
29371338 AATTAATTTAATTCAA
1 AATTAAATTAATTCAA
29371354 GCGACAACCA
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:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTAAATTAATTCAAT
Found at i:29377538 original size:21 final size:20
Alignment explanation
Indices: 29377514--29377559 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 20
29377504 GATTTTGGGC
29377514 TAAATTGAATGAGTTATATAT
1 TAAATTG-ATGAGTTATATAT
29377535 TAAA-T--TGAGTTATATAT
1 TAAATTGATGAGTTATATAT
29377552 TAAATTGA
1 TAAATTGA
29377560 GTTAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
17 16 0.73
18 1 0.05
20 1 0.05
21 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (20 bp):
TAAATTGATGAGTTATATAT
Found at i:29377545 original size:17 final size:17
Alignment explanation
Indices: 29377523--29377563 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
29377513 CTAAATTGAA
29377523 TGAGTTATATATTAAAT
1 TGAGTTATATATTAAAT
29377540 TGAGTTATATATTAAAT
1 TGAGTTATATATTAAAT
29377557 TGAGTTA
1 TGAGTTA
29377564 AATTTATCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (17 bp):
TGAGTTATATATTAAAT
Found at i:29377971 original size:25 final size:25
Alignment explanation
Indices: 29377941--29378034 Score: 91
Period size: 25 Copynumber: 3.8 Consensus size: 25
29377931 GGTTCGACCC
**
29377941 ACAGCTCGTGTGAGCATACCGATTT
1 ACAGCTCGTAAGAGCATACCGATTT
* ** *
29377966 ACAGCTCATAAGAGCATATTGATCT
1 ACAGCTCGTAAGAGCATACCGATTT
* * *
29377991 ACAACTCGTAAGAGCATATCGATTC
1 ACAGCTCGTAAGAGCATACCGATTT
29378016 ACAGCTCGTATA-AGCATAC
1 ACAGCTCGTA-AGAGCATAC
29378035 ATGTAAAGGA
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
25 54 0.98
26 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (25 bp):
ACAGCTCGTAAGAGCATACCGATTT
Found at i:29378493 original size:17 final size:16
Alignment explanation
Indices: 29378467--29378499 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
29378457 TGTTTTATAG
29378467 TCAATTGGAAGCTCGT
1 TCAATTGGAAGCTCGT
29378483 TCAAGTTGGAAGCTCGT
1 TCAA-TTGGAAGCTCGT
29378500 CGGAGCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (16 bp):
TCAATTGGAAGCTCGT
Found at i:29382994 original size:9 final size:9
Alignment explanation
Indices: 29382978--29383019 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
29382968 GAGTTAAACA
29382978 AATCGAGTT
1 AATCGAGTT
*
29382987 ATTCGAGTT
1 AATCGAGTT
29382996 AATCGAGTT
1 AATCGAGTT
29383005 AATCGAGTT
1 AATCGAGTT
*
29383014 ATTCGA
1 AATCGA
29383020 ATCAACTCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (9 bp):
AATCGAGTT
Found at i:29386552 original size:21 final size:20
Alignment explanation
Indices: 29386527--29386576 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
29386517 GTATCGATCC
29386527 GGTATCGATACATTTTTAT-TT
1 GGTATCGATA-A-TTTTATCTT
*
29386548 GGTATTGATAATTTTATCTT
1 GGTATCGATAATTTTATCTT
29386568 GGTATCGAT
1 GGTATCGAT
29386577 TTTATAGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 6 0.23
20 11 0.42
21 9 0.35
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (20 bp):
GGTATCGATAATTTTATCTT
Found at i:29396227 original size:27 final size:27
Alignment explanation
Indices: 29396190--29396244 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
29396180 AATGTTCCAA
29396190 AAATATTCTATGGCAACTTAATCTTTC
1 AAATATTCTATGGCAACTTAATCTTTC
29396217 AAATATTCTATGGCAACTTAATCTTTC
1 AAATATTCTATGGCAACTTAATCTTTC
29396244 A
1 A
29396245 TGAACTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (27 bp):
AAATATTCTATGGCAACTTAATCTTTC
Found at i:29403176 original size:443 final size:443
Alignment explanation
Indices: 29402350--29403230 Score: 1627
Period size: 443 Copynumber: 2.0 Consensus size: 443
29402340 TTCTAGCTCT
29402350 AATGGTGCAGGAATTGCAATTGTTGGCTGACTTTCCTCCTTCTCAGTAGGTTCATCTTTAACCAC
1 AATGGTGCAGGAATTGCAATTGTTGGCTGACTTTCCTCCTTCTCAGTAGGTTCATCTTTAACCAC
*
29402415 AACTTCCTTGGGTTCCAAATTCTTACCACTTCGTAAACCAACTACCTTGCAATGTTCCTTACACA
66 AACTTCCTTGGGTTCCAAATTCTTACCACTTCGTAAACCAACTACCTTGCAATGTTCCTTACAAA
*
29402480 AATGCCTTGGATTTTCCCTATCGTTTGGCAAGGCTACTTGCGATCGATTACGAAGCTCCGTAGCT
131 AATGCCTTGGATTTTCCCTATCGTTTGGCAAGGCTACTTGCGATCGATTACAAAGCTCCGTAGCT
29402545 AACTAATCTATTTGGTTCTCCAAAATTTTCAGTTTTGCTGATTGGCTTTGGATTAAGGTGTCATT
196 AACTAATCTATTTGGTTCTCCAAAATTTTCAGTTTTGCTGATTGGCTTTGGATTAAGGTGTCATT
*
29402610 CTTCACCATGTACACCTTCAAAAAATTCTCCAAACTGTTAGATGGTTCAGCTTATGGTGGTTTTA
261 CTTCACCATGTACACCTTCAAAAAATTCTCCAAACTGTTAGATGGTTCAGCTTATGGTCGTTTTA
29402675 AAACTTGTTGATTAAACTCTTGGGGTTAACTTGGTCTATGTTGCATGTAGGCGTTGTTGGGTCCA
326 AAACTTGTTGATTAAACTCTTGGGGTTAACTTGGTCTATGTTGCATGTAGGCGTTGTTGGGTCCA
29402740 TTTCCTTTATTACTCTAAGAAAAGTTGGGATGATTACGCCATGAAGGAATTTC
391 TTTCCTTTATTACTCTAAGAAAAGTTGGGATGATTACGCCATGAAGGAATTTC
*
29402793 AATGGTGCAGGAATTTCAATTGTTGGCTGACTTTCCTCCTTCTCAGTAGGTTCATCTTTAACCAC
1 AATGGTGCAGGAATTGCAATTGTTGGCTGACTTTCCTCCTTCTCAGTAGGTTCATCTTTAACCAC
* *
29402858 AGCTTCCTTGGGTTCCAAATTCTTACCACTTCGTAAAGCAACTACCTTGCAATGTTCCTTACAAA
66 AACTTCCTTGGGTTCCAAATTCTTACCACTTCGTAAACCAACTACCTTGCAATGTTCCTTACAAA
**
29402923 AATGCCTTGGATTTTCTGTATCGTTTGGCAAGGCTACTTGCGATCGATTACAAAGCTCCGTAGCT
131 AATGCCTTGGATTTTCCCTATCGTTTGGCAAGGCTACTTGCGATCGATTACAAAGCTCCGTAGCT
29402988 AACTAATCTATTTGGTTCTCCAAAATTTTCAGTTTTGCTGATTGGCTTTGGATTAAGGTGTCATT
196 AACTAATCTATTTGGTTCTCCAAAATTTTCAGTTTTGCTGATTGGCTTTGGATTAAGGTGTCATT
* *
29403053 CTTCACCATGTACACCTTCAACAAATTCTCCAAACTGTTAGATGGTTCAGGTTATGGTCGTTTTA
261 CTTCACCATGTACACCTTCAAAAAATTCTCCAAACTGTTAGATGGTTCAGCTTATGGTCGTTTTA
* * * *
29403118 AATCTTGTTGATTAAACTCTTGGGGTTGACTTGGTCTATGTTGCGTGTAGGTGTTGTTGGGTCCA
326 AAACTTGTTGATTAAACTCTTGGGGTTAACTTGGTCTATGTTGCATGTAGGCGTTGTTGGGTCCA
*
29403183 TTTCCTTTATTACTTTAAGAAAAGTTGGGATGATTACGCCATGAAGGA
391 TTTCCTTTATTACTCTAAGAAAAGTTGGGATGATTACGCCATGAAGGA
29403231 TTATAAAAGT
Statistics
Matches: 423, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
443 423 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (443 bp):
AATGGTGCAGGAATTGCAATTGTTGGCTGACTTTCCTCCTTCTCAGTAGGTTCATCTTTAACCAC
AACTTCCTTGGGTTCCAAATTCTTACCACTTCGTAAACCAACTACCTTGCAATGTTCCTTACAAA
AATGCCTTGGATTTTCCCTATCGTTTGGCAAGGCTACTTGCGATCGATTACAAAGCTCCGTAGCT
AACTAATCTATTTGGTTCTCCAAAATTTTCAGTTTTGCTGATTGGCTTTGGATTAAGGTGTCATT
CTTCACCATGTACACCTTCAAAAAATTCTCCAAACTGTTAGATGGTTCAGCTTATGGTCGTTTTA
AAACTTGTTGATTAAACTCTTGGGGTTAACTTGGTCTATGTTGCATGTAGGCGTTGTTGGGTCCA
TTTCCTTTATTACTCTAAGAAAAGTTGGGATGATTACGCCATGAAGGAATTTC
Found at i:29407099 original size:13 final size:13
Alignment explanation
Indices: 29407081--29407108 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29407071 AGTGTGTTGA
29407081 ATAATTAAAACGT
1 ATAATTAAAACGT
29407094 ATAATTAAAACGT
1 ATAATTAAAACGT
29407107 AT
1 AT
29407109 GAAATGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (13 bp):
ATAATTAAAACGT
Found at i:29412380 original size:21 final size:21
Alignment explanation
Indices: 29412356--29412395 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29412346 TCATAAAAAC
*
29412356 TTAACAAAACCTTAAAAAATT
1 TTAACAAAACATTAAAAAATT
*
29412377 TTAACAAAACATTTAAAAA
1 TTAACAAAACATTAAAAAA
29412396 GAGTTTAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (21 bp):
TTAACAAAACATTAAAAAATT
Found at i:29414153 original size:12 final size:13
Alignment explanation
Indices: 29414132--29414160 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
29414122 CCAAAACAGG
29414132 TTTTTAGCGGCGC
1 TTTTTAGCGGCGC
29414145 TTTTT-GCGGCGC
1 TTTTTAGCGGCGC
29414157 TTTT
1 TTTT
29414161 AAAAGCGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.03, C:0.21, G:0.28, T:0.48
Consensus pattern (13 bp):
TTTTTAGCGGCGC
Found at i:29414280 original size:43 final size:43
Alignment explanation
Indices: 29414231--29414493 Score: 334
Period size: 43 Copynumber: 6.1 Consensus size: 43
29414221 AATAAATGCT
* * *
29414231 GCTAAAGACCAAGACCTTTACCGGTGATTTTTCCACAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCC
* * * * *
29414274 GTTAAAGACCATGACCTTCAGCGGCGCTTTTCCCACAAGCGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCC
* *
29414317 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCATAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCC
*
29414360 GCTAAAGACCAAGACCTTTAGCGGCGC-TTTTCCTAAAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTTCC-ACAAACGCC
* *
29414403 ACGAAAGACCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCC
* * **
29414446 GCTATAGA--ATAGACCTTTAGCGACGCTTTTGACACAAACGCC
1 GCTAAAGACCA-AGACCTTTAGCGGCGCTTTTTCCACAAACGCC
29414488 GCTAAA
1 GCTAAA
29414494 AATATATCTT
Statistics
Matches: 192, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.01
42 39 0.20
43 146 0.76
44 6 0.03
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (43 bp):
GCTAAAGACCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCC
Found at i:29419022 original size:21 final size:21
Alignment explanation
Indices: 29418959--29419008 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
29418949 ATAATTTGGT
29418959 CCTATCCAAAATAGATAGTTA
1 CCTATCCAAAATAGATAGTTA
29418980 CCTATCCAAAATAGATAGTTA
1 CCTATCCAAAATAGATAGTTA
29419001 CCTATCCA
1 CCTATCCA
29419009 CATCAATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (21 bp):
CCTATCCAAAATAGATAGTTA
Found at i:29419539 original size:16 final size:17
Alignment explanation
Indices: 29419503--29419544 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
29419493 CACTATAATC
29419503 ATTATTTTAATATATTAA
1 ATTA-TTTAATATATTAA
29419521 ATTATTTAATATA-TAA
1 ATTATTTAATATATTAA
29419537 ATTATTTA
1 ATTATTTA
29419545 TAAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTTAATATATTAA
Found at i:29419562 original size:27 final size:28
Alignment explanation
Indices: 29419518--29419591 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 28
29419508 TTTAATATAT
*
29419518 TAAATTATTTAATATATAA-ATTATTTA
1 TAAATAATTTAATATATAACATTATTTA
29419545 TAAATAATTTAA-ACTATAATCATTATTTTAA
1 TAAATAATTTAATA-TATAA-CATTA-TTT-A
*
29419576 TATATCAATTTAATAT
1 TAAAT-AATTTAATAT
29419592 TATCTCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 1 0.03
27 16 0.42
29 4 0.11
30 3 0.08
31 5 0.13
32 8 0.21
33 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (28 bp):
TAAATAATTTAATATATAACATTATTTA
Found at i:29419667 original size:7 final size:7
Alignment explanation
Indices: 29419651--29419854 Score: 81
Period size: 7 Copynumber: 29.0 Consensus size: 7
29419641 ACTAATTAAT
29419651 CTAAACC
1 CTAAACC
*
29419658 CTAAATC
1 CTAAACC
29419665 CTAAACCC
1 CTAAA-CC
*
29419673 CT-AACT
1 CTAAACC
*
29419679 CTTAACC
1 CTAAACC
*
29419686 CTCAACC
1 CTAAACC
* *
29419693 CTTTACCC
1 C-TAAACC
*
29419701 CTAACCC
1 CTAAACC
29419708 CTAAACC
1 CTAAACC
*
29419715 TTAAACC
1 CTAAACC
*
29419722 C-CAACC
1 CTAAACC
* *
29419728 CTTAA-T
1 CTAAACC
29419734 CTATAACC
1 CTA-AACC
*
29419742 TTAAACC
1 CTAAACC
* *
29419749 ATAAGCC
1 CTAAACC
* *
29419756 ATAACCC
1 CTAAACC
*
29419763 CTAAATC
1 CTAAACC
29419770 CTAAACC
1 CTAAACC
*
29419777 TTAAACC
1 CTAAACC
* *
29419784 ATAAACT
1 CTAAACC
*
29419791 GTAAACC
1 CTAAACC
* *
29419798 ATAACCC
1 CTAAACC
29419805 CTAAACC
1 CTAAACC
*
29419812 CATAATCC
1 C-TAAACC
*
29419820 ATAAACC
1 CTAAACC
* *
29419827 TTAAACT
1 CTAAACC
*
29419834 CTACACC
1 CTAAACC
* *
29419841 ATATACC
1 CTAAACC
29419848 CTAAACC
1 CTAAACC
29419855 AAAAACCTTA
Statistics
Matches: 145, Mismatches: 45, Indels: 14
0.71 0.22 0.07
Matches are distributed among these distances:
6 10 0.07
7 120 0.83
8 15 0.10
ACGTcount: A:0.39, C:0.38, G:0.01, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:29419767 original size:21 final size:21
Alignment explanation
Indices: 29419738--29419867 Score: 93
Period size: 21 Copynumber: 6.1 Consensus size: 21
29419728 CTTAATCTAT
* *
29419738 AACCTTAAACCATAAGCCATA
1 AACCCTAAACCATAAACCATA
* *
29419759 ACCCCTAAATCC-TAAACCTTA
1 AACCCTAAA-CCATAAACCATA
* **
29419780 AACCATAAACTGTAAACCATA
1 AACCCTAAACCATAAACCATA
* *
29419801 ACCCCTAAACCCATAATCCATA
1 AACCCTAAA-CCATAAACCATA
* *
29419823 AACCTTAAACTC-TACACCATA
1 AACCCTAAAC-CATAAACCATA
* * *
29419844 TACCCTAAACCAAAAACCTTA
1 AACCCTAAACCATAAACCATA
29419865 AAC
1 AAC
29419868 TATAGAGATA
Statistics
Matches: 81, Mismatches: 23, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
20 2 0.02
21 60 0.74
22 19 0.23
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.20
Consensus pattern (21 bp):
AACCCTAAACCATAAACCATA
Found at i:29420232 original size:41 final size:41
Alignment explanation
Indices: 29420187--29420374 Score: 331
Period size: 41 Copynumber: 4.6 Consensus size: 41
29420177 GGCGTTTTTA
29420187 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTC
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTC
*
29420228 CAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGCTTCTC
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTC
*
29420269 TAAAAACGCCGCTAAAGCCCCTGAGCATTAGCGGCGCTTCTC
1 CAAAAACGCCGCTAAAG-CCCTGAGCATTAGCGGCGCTTCTC
*
29420311 CAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCTC
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTC
*
29420352 CAAAAACGCCGCTAAAGGCCTGA
1 CAAAAACGCCGCTAAAGCCCTGA
29420375 AAGGTCAAAA
Statistics
Matches: 141, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
41 102 0.72
42 39 0.28
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.17
Consensus pattern (41 bp):
CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTC
Found at i:29420313 original size:83 final size:82
Alignment explanation
Indices: 29420187--29420374 Score: 333
Period size: 83 Copynumber: 2.3 Consensus size: 82
29420177 GGCGTTTTTA
29420187 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCCAAAAACGCCGCTAAA-GCCTTGA
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCC-TGA
29420251 GCATTAGCGGCGCTTCTC
65 GCATTAGCGGCGCTTCTC
*
29420269 TAAAAACGCCGCTAAAGCCCCTGAGCATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCTGA
1 CAAAAACGCCGCTAAAG-CCCTGAGCATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCTGA
29420334 GCATTAGCGGCGCTTCTC
65 GCATTAGCGGCGCTTCTC
*
29420352 CAAAAACGCCGCTAAAGGCCTGA
1 CAAAAACGCCGCTAAAGCCCTGA
29420375 AAGGTCAAAA
Statistics
Matches: 101, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
82 21 0.21
83 77 0.76
84 3 0.03
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.17
Consensus pattern (82 bp):
CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGGCCTGAG
CATTAGCGGCGCTTCTC
Found at i:29420471 original size:40 final size:40
Alignment explanation
Indices: 29420424--29420558 Score: 180
Period size: 40 Copynumber: 3.4 Consensus size: 40
29420414 GCGTTTTCCT
29420424 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGTGTTTTATA
1 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGTGTTTTATA
29420464 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGTGTTTTATA
1 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGTGTTTTATA
* * * * * * *
29420504 TAAAGCACAGCTAATTCTCAATTTTTAGCGGCGTTTTTTA
1 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGTGTTTTATA
* *
29420544 TGCAAGCGCCACTAA
1 T-AAAGCGCCGCTAA
29420559 AAATGCCGTT
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 74 0.89
41 9 0.11
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (40 bp):
TAAAGCGCCGCTAATGCTCGATCTTTAGCGGTGTTTTATA
Found at i:29422462 original size:15 final size:15
Alignment explanation
Indices: 29422444--29422493 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 15
29422434 TGCAATTTGG
29422444 TTTTTTT-ATTTTTA
1 TTTTTTTAATTTTTA
29422458 TTTTTATTAATCTTTTA
1 TTTTT-TTAAT-TTTTA
*
29422475 TTTTTTGTGA-TTTTA
1 TTTTTT-TAATTTTTA
29422490 TTTT
1 TTTT
29422494 CAGGTGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 5 0.16
15 11 0.35
16 3 0.10
17 12 0.39
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (15 bp):
TTTTTTTAATTTTTA
Found at i:29431158 original size:20 final size:20
Alignment explanation
Indices: 29431135--29431199 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
29431125 ATTTAACAAC
29431135 AAAACTTAATATTCTATCAT
1 AAAACTTAATATTCTATCAT
* **
29431155 AAAACTTCAGAAAAACT-TC--
1 AAAACTT-A-ATATTCTATCAT
29431174 -AAACTTAATATTCTATCAT
1 AAAACTTAATATTCTATCAT
29431193 AAAACTT
1 AAAACTT
29431200 CAGAAAAACT
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
18 6 0.18
20 13 0.39
21 3 0.09
22 4 0.12
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAACTTAATATTCTATCAT
Found at i:29431187 original size:38 final size:38
Alignment explanation
Indices: 29431136--29431216 Score: 162
Period size: 38 Copynumber: 2.1 Consensus size: 38
29431126 TTTAACAACA
29431136 AAACTTAATATTCTATCATAAAACTTCAGAAAAACTTC
1 AAACTTAATATTCTATCATAAAACTTCAGAAAAACTTC
29431174 AAACTTAATATTCTATCATAAAACTTCAGAAAAACTTC
1 AAACTTAATATTCTATCATAAAACTTCAGAAAAACTTC
29431212 AAACT
1 AAACT
29431217 CATCAATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (38 bp):
AAACTTAATATTCTATCATAAAACTTCAGAAAAACTTC
Found at i:29441461 original size:17 final size:17
Alignment explanation
Indices: 29441439--29441476 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
29441429 AATTCCAAAT
29441439 GTGGTAAAAGGCATAGA
1 GTGGTAAAAGGCATAGA
29441456 GTGGTAAAAGGCATAGA
1 GTGGTAAAAGGCATAGA
29441473 GTGG
1 GTGG
29441477 AGAGTTACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.39, T:0.18
Consensus pattern (17 bp):
GTGGTAAAAGGCATAGA
Found at i:29442573 original size:6 final size:6
Alignment explanation
Indices: 29442545--29442614 Score: 63
Period size: 6 Copynumber: 11.3 Consensus size: 6
29442535 AAAAAAGAAT
* **
29442545 GAAAAA GAACAA -AAAAA GAAAAA CGAAAAA GAAAAA GAAATT GAAAGAA
1 GAAAAA GAAAAA GAAAAA GAAAAA -GAAAAA GAAAAA GAAAAA GAAA-AA
29442594 -AAAAA GAAAGAAA GAAAAA GA
1 GAAAAA G-AA-AAA GAAAAA GA
29442615 GAGCGAGCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
5 6 0.12
6 32 0.62
7 10 0.19
8 4 0.08
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:29442590 original size:18 final size:18
Alignment explanation
Indices: 29442569--29442662 Score: 63
Period size: 18 Copynumber: 5.4 Consensus size: 18
29442559 AAAGAAAAAC
29442569 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATT
29442587 GAAAGAA-AAAAAGAAA--
1 GAAA-AAGAAAAAGAAATT
* **
29442603 G--AAAGAAAAAGAGAGC
1 GAAAAAGAAAAAGAAATT
** * **
29442619 GAGCAAGAAAATGACTTT
1 GAAAAAGAAAAAGAAATT
*
29442637 GAAAAAGAAAAAGAAAAT
1 GAAAAAGAAAAAGAAATT
29442655 GAAAAAGA
1 GAAAAAGA
29442663 GGAAAACGAT
Statistics
Matches: 57, Mismatches: 13, Indels: 12
0.70 0.16 0.15
Matches are distributed among these distances:
13 2 0.04
14 9 0.16
16 2 0.04
18 42 0.74
19 2 0.04
ACGTcount: A:0.68, C:0.03, G:0.21, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATT
Found at i:29442591 original size:16 final size:14
Alignment explanation
Indices: 29442536--29442614 Score: 56
Period size: 13 Copynumber: 5.5 Consensus size: 14
29442526 TGAACAAGTA
*
29442536 AAAAAGAATGAAA-
1 AAAAAGAAAGAAAG
* * *
29442549 AAGAACAAAAAAAG
1 AAAAAGAAAGAAAG
29442563 AAAAACG-AA-AAAG
1 AAAAA-GAAAGAAAG
29442576 AAAAAGAAATTGAAAG
1 AAAAAGAAA--GAAAG
29442592 AAAAAAAGAAAGAAAG
1 --AAAAAGAAAGAAAG
29442608 AAAAAGA
1 AAAAAGA
29442615 GAGCGAGCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
12 1 0.02
13 20 0.38
14 13 0.25
16 9 0.17
18 9 0.17
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.04
Consensus pattern (14 bp):
AAAAAGAAAGAAAG
Found at i:29450873 original size:21 final size:21
Alignment explanation
Indices: 29450829--29450881 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
29450819 AATTTAACAA
*
29450829 AAAAATTAATAATATTAATGAT
1 AAAAATTAA-AATATAAATGAT
29450851 AAAAATTAAAATATAAAAT-AT
1 AAAAATTAAAATAT-AAATGAT
29450872 AAAAATTAAA
1 AAAAATTAAA
29450882 TTTCGATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAAATTAAAATATAAATGAT
Found at i:29451361 original size:8 final size:8
Alignment explanation
Indices: 29451350--29451377 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
29451340 ATATAAATAT
29451350 AAATTTTA
1 AAATTTTA
29451358 AAATTTTA
1 AAATTTTA
29451366 AAATTTTA
1 AAATTTTA
29451374 AAAT
1 AAAT
29451378 AATATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATTTTA
Found at i:29451384 original size:29 final size:29
Alignment explanation
Indices: 29451343--29451402 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
29451333 TATATAAATA
29451343 TAAATATAAATTTTAAAATT-TTAAAATTT
1 TAAATATAAA-TTTAAAATTATTAAAATTT
* *
29451372 TAAA-ATAATATTTAAATTTATTTAAATTT
1 TAAATATAA-ATTTAAAATTATTAAAATTT
29451401 TA
1 TA
29451403 GAAAATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TAAATATAAATTTAAAATTATTAAAATTT
Found at i:29455825 original size:30 final size:30
Alignment explanation
Indices: 29455790--29455851 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
29455780 CTACTCAGTT
29455790 TTTTGTGAATGTGTTACGAGGTTAGTCGAG
1 TTTTGTGAATGTGTTACGAGGTTAGTCGAG
29455820 TTTTGTGAATGTGTTACGAGGTTAGTCGAG
1 TTTTGTGAATGTGTTACGAGGTTAGTCGAG
29455850 TT
1 TT
29455852 GTTTTCCCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.06, G:0.32, T:0.42
Consensus pattern (30 bp):
TTTTGTGAATGTGTTACGAGGTTAGTCGAG
Found at i:29455979 original size:33 final size:33
Alignment explanation
Indices: 29455942--29456008 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
29455932 TTACTAATTA
29455942 AAACAAGAAACTAAAATAGAAAATTAAAAACAT
1 AAACAAGAAACTAAAATAGAAAATTAAAAACAT
29455975 AAACAAGAAACTAAAATAGAAAATTAAAAACAT
1 AAACAAGAAACTAAAATAGAAAATTAAAAACAT
29456008 A
1 A
29456009 CTTTTGACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.70, C:0.09, G:0.06, T:0.15
Consensus pattern (33 bp):
AAACAAGAAACTAAAATAGAAAATTAAAAACAT
Found at i:29472417 original size:50 final size:49
Alignment explanation
Indices: 29472355--29472454 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 49
29472345 CGAGTCGATA
* * *
29472355 AGACACTAGGTGTCAATTTACTACTTCGGATTAATTCGATGAGGCATTGG
1 AGACACTAGGTGTCAATTTACTACTTCGAATT-ATCCGATGAGGCACTGG
* *
29472405 AGACACTGGGTGTCAATTTATTACTTCGAATTATCCGATGAGGCACTGG
1 AGACACTAGGTGTCAATTTACTACTTCGAATTATCCGATGAGGCACTGG
29472454 A
1 A
29472455 TGCCAAACTG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 16 0.36
50 29 0.64
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (49 bp):
AGACACTAGGTGTCAATTTACTACTTCGAATTATCCGATGAGGCACTGG
Found at i:29472589 original size:19 final size:19
Alignment explanation
Indices: 29472565--29472604 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29472555 TGATATTATA
29472565 TGTGAAATGAAA-ATGGGAT
1 TGTGAAATGAAATAT-GGAT
*
29472584 TGTGAATTGAAATATGGAT
1 TGTGAAATGAAATATGGAT
29472603 TG
1 TG
29472605 AGGCACATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.33
Consensus pattern (19 bp):
TGTGAAATGAAATATGGAT
Found at i:29476106 original size:17 final size:17
Alignment explanation
Indices: 29476084--29476125 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
29476074 AATAATTATT
29476084 TAATTTAATATTTA-TAA
1 TAATTTAAT-TTTATTAA
29476101 TAATTT-ATTTTATTAA
1 TAATTTAATTTTATTAA
29476117 TAACTTTAA
1 TAA-TTTAA
29476126 AAATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.18
16 8 0.36
17 9 0.41
18 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TAATTTAATTTTATTAA
Found at i:29482990 original size:10 final size:11
Alignment explanation
Indices: 29482964--29482988 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29482954 AAAAAAAACC
29482964 AAAATTTAAAA
1 AAAATTTAAAA
29482975 AAAATTTAAAA
1 AAAATTTAAAA
29482986 AAA
1 AAA
29482989 TTATGTCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATTTAAAA
Found at i:29495173 original size:97 final size:95
Alignment explanation
Indices: 29495015--29495219 Score: 216
Period size: 97 Copynumber: 2.1 Consensus size: 95
29495005 TCTTATATAG
* * * * * * *
29495015 TTCCCCATGTTTAACGTCCTGGCGGACTTCCCCATTTTTATTATCCTAACATATTACCATTCATT
1 TTCCCCATGTTTAACGTCATGGCCGACTTACCCATCTTTATTATCCCAACAGAGTACCATTCATT
* **
29495080 TTCATATTTGA-ACTATGGTCTTACACATCATAA
66 GTCATAGCTGAGA-TATGGTCTTA-A-A-CATAA
* * * * *
29495113 TTCCCCATGTTTAATGTCATGGCCGAC-TACCCGTCTTTATTGTCCCAGCAGAGTACCATTCGTT
1 TTCCCCATGTTTAACGTCATGGCCGACTTACCCATCTTTATTATCCCAACAGAGTACCATTCATT
*
29495177 GTCATAGCTGAGATATGGTCTTAAACATTA
66 GTCATAGCTGAGATATGGTCTTAAACATAA
29495207 TTCCCCATGTTTA
1 TTCCCCATGTTTA
29495220 GTATCCTAAT
Statistics
Matches: 90, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
94 17 0.19
95 1 0.01
96 1 0.01
97 46 0.51
98 25 0.28
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (95 bp):
TTCCCCATGTTTAACGTCATGGCCGACTTACCCATCTTTATTATCCCAACAGAGTACCATTCATT
GTCATAGCTGAGATATGGTCTTAAACATAA
Found at i:29497047 original size:43 final size:43
Alignment explanation
Indices: 29496773--29497039 Score: 290
Period size: 43 Copynumber: 6.2 Consensus size: 43
29496763 TAAAAATAAG
** * **
29496773 CGCCGCTAAAGGTCGTGACCTTTAG-GGTTCTTT-TCCAACAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCTCCAA-AAA
*
29496815 CGCCGCTAAAGAACATGACCTTTAGCGACGCTTTC-CCAAAAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCTCC-AAAAA
* * * * *
29496858 TGTCGCTAAAGAACATAACCTTTAGCGGCGTTTTTTCCAAAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCTCCAAAAA
* ** * * * *
29496901 TGCTACTAAAGAACATGACCTTTAACGGTGCTTTCCCCAAAAT
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCTCCAAAAA
* * *
29496944 CGCCGCTAAAGAACAAT-ACCTTTAGCAGTGCTTTCCCCAAAAA
1 CGCCGCTAAAGAAC-ATGACCTTTAGCGGCGCTTTCTCCAAAAA
29496987 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCTCCAAAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCTCCAAAAA
29497030 CGCCGCTAAA
1 CGCCGCTAAA
29497040 AGTCATGAAA
Statistics
Matches: 188, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
42 24 0.13
43 158 0.84
44 6 0.03
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCTCCAAAAA
Found at i:29497047 original size:129 final size:128
Alignment explanation
Indices: 29496773--29497047 Score: 324
Period size: 129 Copynumber: 2.1 Consensus size: 128
29496763 TAAAAATAAG
* * * * *
29496773 CGCCGCTAAAGGTCGTGACCTTTAGGGTTCTTTTCCAACAAACGCCGCTAAAGAACATGACCTTT
1 CGCCGCTAAAAGTCATGACCTTTACGGTGCTTTCCCAACAAACGCCGCTAAAGAACATGACCTTT
* * * *
29496838 AGCGACGCTTTCCCAAAAAATGTCGCTAAAGAACATAACCTTTAGCGGCGTTTTTTCCAAAAA
66 AGCGACGCTTTCCCAAAAAACGCCGCTAAAGAACATAACCTTTAGCGGCGCTTTCTCCAAAAA
* ** * *
29496901 TGCTACT-AAAGAACATGACCTTTAACGGTGCTTTCCCCAA-AATCGCCGCTAAAGAACAAT-AC
1 CGCCGCTAAAAG-TCATGACCTTT-ACGGTGCTTT-CCCAACAAACGCCGCTAAAGAAC-ATGAC
* * *
29496963 CTTTAGC-AGTGCTTTCCCCAAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCTCCAA
62 CTTTAGCGA-CGCTTTCCCAAAAAACGCCGCTAAAGAACATAACCTTTAGCGGCGCTTTCTCCAA
29497027 AAA
126 AAA
29497030 CGCCGCTAAAAGTCATGA
1 CGCCGCTAAAAGTCATGA
29497048 AAAATAAAAA
Statistics
Matches: 120, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
127 3 0.03
128 14 0.12
129 93 0.77
130 10 0.08
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (128 bp):
CGCCGCTAAAAGTCATGACCTTTACGGTGCTTTCCCAACAAACGCCGCTAAAGAACATGACCTTT
AGCGACGCTTTCCCAAAAAACGCCGCTAAAGAACATAACCTTTAGCGGCGCTTTCTCCAAAAA
Found at i:29497912 original size:23 final size:23
Alignment explanation
Indices: 29497886--29498297 Score: 321
Period size: 23 Copynumber: 18.0 Consensus size: 23
29497876 AATGGAAAGT
*
29497886 AGCACTTTAACACTTCAATTTAC
1 AGCACTTAAACACTTCAATTTAC
* *
29497909 AGCATTTAAACACTTCAATTTGC
1 AGCACTTAAACACTTCAATTTAC
* *
29497932 AGCACTTTAACA-TATCAATTAAC
1 AGCACTTAAACACT-TCAATTTAC
* * * *
29497955 AACATTTATACACATCAA-TTAC
1 AGCACTTAAACACTTCAATTTAC
*
29497977 AGCGAC-TAAACACTTCAATTTGC
1 AGC-ACTTAAACACTTCAATTTAC
29498000 AGCACTTAAACACTTCAATTTGA-
1 AGCACTTAAACACTTCAATTT-AC
29498023 AGCACTTAAACACTTCAATTTAC
1 AGCACTTAAACACTTCAATTTAC
* * *
29498046 AGCATTTAAACACTTAAATTTGC
1 AGCACTTAAACACTTCAATTTAC
*
29498069 AGCACTTAAACA-TATCAATTAAC
1 AGCACTTAAACACT-TCAATTTAC
* * * *
29498092 AACATTTATACACATCAA-TTAC
1 AGCACTTAAACACTTCAATTTAC
* *
29498114 AGCGA-TAAAACA-TCTCAATTTCC
1 AGC-ACTTAAACACT-TCAATTTAC
*
29498137 AGCAAC-TAAACACTTCAATTTGC
1 AGC-ACTTAAACACTTCAATTTAC
* *
29498160 AGCACTTAAGCACTTCAATTTGC
1 AGCACTTAAACACTTCAATTTAC
* *
29498183 AGCACTTTAACA-TATCAATTAAC
1 AGCACTTAAACACT-TCAATTTAC
* * * *
29498206 AACATTTATACACCTCAA-TTAC
1 AGCACTTAAACACTTCAATTTAC
* *
29498228 AGCGA-TAAAACA-TCTCAATTTCC
1 AGC-ACTTAAACACT-TCAATTTAC
* *
29498251 AGCAAC-TAAATACTTCAATTTGC
1 AGC-ACTTAAACACTTCAATTTAC
*
29498274 AGTACTTAAACACTTCAATTTAC
1 AGCACTTAAACACTTCAATTTAC
29498297 A
1 A
29498298 AATCCACCAT
Statistics
Matches: 304, Mismatches: 62, Indels: 46
0.74 0.15 0.11
Matches are distributed among these distances:
22 53 0.17
23 249 0.82
24 2 0.01
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.30
Consensus pattern (23 bp):
AGCACTTAAACACTTCAATTTAC
Found at i:29498086 original size:114 final size:112
Alignment explanation
Indices: 29497886--29498294 Score: 359
Period size: 114 Copynumber: 3.6 Consensus size: 112
29497876 AATGGAAAGT
* *
29497886 AGCACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTT-AACA-TATCA
1 AGCACTTAAACACTTCAATTTA-AGCACTTAAACACTTCAATTTGCAGCA-TTTAAACACT-TCA
** * * * * * * *
29497949 ATTAACAACATTTATACACATCAATTACAGCGA-CTAAACACTTCAATTTGC
63 ATTTGCAGCACTTAAACATATCAATTACAAC-ATCTAAACACATCAA-TTAC
* *
29498000 AGCACTTAAACACTTCAATTTGAAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAAT
1 AGCACTTAAACACTTCAATTT-AAGCACTTAAACACTTCAATTTGCAGCATTTAAACACTTCAAT
* *
29498065 TTGCAGCACTTAAACATATCAATTAACAACATTTATACACATCAATTAC
65 TTGCAGCACTTAAACATATCAATT-ACAACATCTAAACACATCAATTAC
* * * *
29498114 AGCGA-TAAAACA-TCTCAATTTCCAGCAAC-TAAACACTTCAATTTGCAGCACTTAAGCACTTC
1 AGC-ACTTAAACACT-TCAATTT-AAGC-ACTTAAACACTTCAATTTGCAGCATTTAAACACTTC
* * * *
29498176 AATTTGCAGCACTTTAACATATCAATTAACAACATTTATACACCTCAATTAC
62 AATTTGCAGCACTTAAACATATCAATT-ACAACATCTAAACACATCAATTAC
* * * * *
29498228 AGCGA-TAAAACA-TCTCAATTTCCAGCAAC-TAAATACTTCAATTTGCAGTACTTAAACACTTC
1 AGC-ACTTAAACACT-TCAATTT-AAGC-ACTTAAACACTTCAATTTGCAGCATTTAAACACTTC
29498290 AATTT
62 AATTT
29498295 ACAAATCCAC
Statistics
Matches: 260, Mismatches: 27, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
113 4 0.02
114 237 0.91
115 19 0.07
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (112 bp):
AGCACTTAAACACTTCAATTTAAGCACTTAAACACTTCAATTTGCAGCATTTAAACACTTCAATT
TGCAGCACTTAAACATATCAATTACAACATCTAAACACATCAATTAC
Found at i:29498132 original size:137 final size:137
Alignment explanation
Indices: 29497886--29498192 Score: 494
Period size: 137 Copynumber: 2.2 Consensus size: 137
29497876 AATGGAAAGT
* * *
29497886 AGCACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACATATCAAT
1 AGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAACATATCAAT
*
29497951 TAACAACATTTATACACATCAATTACAGCGACTAAACACTTCAATTTGCAGC-ACTTAAACACTT
66 TAACAACATTTATACACATCAATTACAGCGACTAAACACTTCAATTTCCAGCAAC-TAAACACTT
29498015 CAATTTGA
130 CAATTTGA
29498023 AGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAACATATCAAT
1 AGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAACATATCAAT
29498088 TAACAACATTTATACACATCAATTACAGCGA-TAAA-ACATCTCAATTTCCAGCAACTAAACACT
66 TAACAACATTTATACACATCAATTACAGCGACTAAACAC-T-TCAATTTCCAGCAACTAAACACT
*
29498151 TCAATTTGC
129 TCAATTTGA
* *
29498160 AGCACTTAAGCACTTCAATTTGCAGCACTTTAA
1 AGCACTTAAACACTTCAATTTACAGCA-TTTAA
29498193 CATATCAATT
Statistics
Matches: 159, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
135 2 0.01
136 5 0.03
137 145 0.91
138 7 0.04
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.30
Consensus pattern (137 bp):
AGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAACATATCAAT
TAACAACATTTATACACATCAATTACAGCGACTAAACACTTCAATTTCCAGCAACTAAACACTTC
AATTTGA
Found at i:29498224 original size:137 final size:135
Alignment explanation
Indices: 29497886--29498294 Score: 474
Period size: 137 Copynumber: 3.0 Consensus size: 135
29497876 AATGGAAAGT
29497886 AGCACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACATATCAAT
1 AGCAC-TTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCA-TTTAACATATCAAT
*
29497951 TAACAACATTTATACACATCAATTACAGCGACTAAACACTTCAATTTGCAGCACTTAAACACTTC
64 TAACAACATTTATACACATCAATTACAGCGACTAAACACTTCAATTTCCAGCACTTAAACACTTC
29498016 AATTTGA
129 AATTTGA
* *
29498023 AGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAACATATCAAT
1 AGCACTT-AACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCA-TTTAACATATCAAT
29498088 TAACAACATTTATACACATCAATTACAGCGA-TAAA-ACATCTCAATTTCCAGCAAC-TAAACAC
64 TAACAACATTTATACACATCAATTACAGCGACTAAACAC-T-TCAATTTCCAGC-ACTTAAACAC
*
29498150 TTCAATTTGC
126 TTCAATTTGA
* ** * **
29498160 AGCACTTAAGCACTTCAATTTGCAGCACTTT-AACA-TATCAATTAACAACATTTATACACCTCA
1 AGCACTTAA-CACTTCAATTTACAGCA-TTTAAACACT-TCAATTTGCAGCATTTA-ACATATCA
* * * * * * * *
29498223 ATT-ACAGCGA-TAAAACATC-TCAATTTCCAGCAACTAAATACTTCAATTTGCAGTACTTAAAC
62 ATTAACAAC-ATTTATACA-CATCAA-TTACAGCGACTAAACACTTCAATTTCCAGCACTTAAAC
29498285 ACTTCAATTT
124 ACTTCAATTT
29498295 ACAAATCCAC
Statistics
Matches: 239, Mismatches: 19, Indels: 28
0.84 0.07 0.10
Matches are distributed among these distances:
135 2 0.01
136 28 0.12
137 197 0.82
138 10 0.04
139 2 0.01
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (135 bp):
AGCACTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCATTTAACATATCAATTA
ACAACATTTATACACATCAATTACAGCGACTAAACACTTCAATTTCCAGCACTTAAACACTTCAA
TTTGA
Found at i:29501651 original size:41 final size:41
Alignment explanation
Indices: 29501605--29501934 Score: 419
Period size: 41 Copynumber: 8.0 Consensus size: 41
29501595 TTCAAAAATA
* **
29501605 GAGCATTAGCGGCGCTTCTTTAAAAACGTTGCTAAAGCCCC
1 GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCC
* * * * * *
29501646 GAGCATTAGCAGCGCTTCTTTAAAAGCGCTGGTAAATCCCC
1 GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCC
* *
29501687 GAGCATTAGCAGCGCTTCTTCAAAAACGCTGCTAAAGCCCC
1 GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCC
* *
29501728 GTGCATTAGCGACGCTTCTTCAAAAACGCCGCTAAAGCCCC
1 GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCC
*
29501769 AAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCC
1 GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCC
* * * *
29501810 GAGCATTAGTGGCGCTTTTTAAAAAACGCCGCTAAAGCCTC
1 GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCC
* * * * * *
29501851 GAGCATTAGCGGTGCTTTTTAAAAAACGCCGTTAAAACCCT
1 GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCC
*
29501892 GAGCATTAGCGGCGCTT-TTCCAAAAACGCCGCTAATGCCCC
1 GAGCATTAGCGGCGCTTCTT-CAAAAACGCCGCTAAAGCCCC
29501933 GA
1 GA
29501935 AAACTCAAAA
Statistics
Matches: 255, Mismatches: 33, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 2 0.01
41 253 0.99
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (41 bp):
GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCC
Found at i:29502060 original size:40 final size:40
Alignment explanation
Indices: 29502011--29502119 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 40
29502001 GCTCATTTTC
29502011 AGTGGCGTTTTTTAAAAAGCGCCACTAATACTCGATCT-TT
1 AGTGGCGTTTTTTAAAAAGCGCCACTAATACTCGAT-TGTT
* ** * *
29502051 AGTGGCGTTTTTTTAAAAGCGCCGTTAATGCTTGATTGTT
1 AGTGGCGTTTTTTAAAAAGCGCCACTAATACTCGATTGTT
* **
29502091 AGCGGCGTTTTTTATCCAAGCGCCACTAA
1 AGTGGCGTTTTTTA-AAAAGCGCCACTAA
29502120 AAATGCCGCT
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
39 1 0.02
40 45 0.80
41 10 0.18
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (40 bp):
AGTGGCGTTTTTTAAAAAGCGCCACTAATACTCGATTGTT
Found at i:29511097 original size:2 final size:2
Alignment explanation
Indices: 29511090--29511119 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29511080 TACCAATAAG
29511090 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29511120 CTCTATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29511760 original size:41 final size:42
Alignment explanation
Indices: 29511692--29511878 Score: 231
Period size: 41 Copynumber: 4.6 Consensus size: 42
29511682 ACCTGCACTT
* * * * *
29511692 AGCCTACTAGACATAAA-GTTTGATATGTTTCACCGGCAACA
1 AGCCTGCTAGACGTAAATGTCTGGTATGTTTCACCGGCATCA
* *
29511733 AGTCTGCTAGACGTAAAT-TCTGGTATGTTTCATCGGCATCA
1 AGCCTGCTAGACGTAAATGTCTGGTATGTTTCACCGGCATCA
* *
29511774 AGCCTTCTAGACGT-AATGTATGGTATGTTTCACCGGCATCA
1 AGCCTGCTAGACGTAAATGTCTGGTATGTTTCACCGGCATCA
* **
29511815 AGCTTGCTAGACGT-AATGTCTGGTATGTTTCACTTGCATCA
1 AGCCTGCTAGACGTAAATGTCTGGTATGTTTCACCGGCATCA
29511856 AGCCTGCTAGACGT-AATGTCTGG
1 AGCCTGCTAGACGTAAATGTCTGG
29511879 ATTACTTCAT
Statistics
Matches: 127, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
40 3 0.02
41 124 0.98
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (42 bp):
AGCCTGCTAGACGTAAATGTCTGGTATGTTTCACCGGCATCA
Found at i:29516187 original size:41 final size:41
Alignment explanation
Indices: 29516162--29516359 Score: 335
Period size: 41 Copynumber: 4.8 Consensus size: 41
29516152 AGTTTGATAC
*
29516162 GTTTCACCGGCATCAAGTCTGCTAGACGTAAAT-TCTGGTAT
1 GTTTCACCGGCATCAAGCCTGCTAGACGT-AATGTCTGGTAT
29516203 GTTTCACCGGCATCAAGCCTGCTAGACGTAATGTCTGGTAT
1 GTTTCACCGGCATCAAGCCTGCTAGACGTAATGTCTGGTAT
* *
29516244 GTTTCACCGACATCAAGCCTGGTAGACGTAATGTCTGGTAT
1 GTTTCACCGGCATCAAGCCTGCTAGACGTAATGTCTGGTAT
*
29516285 GTTTCACCGGCATCAAGCATGCTAGACGTAATGTCTGGTAT
1 GTTTCACCGGCATCAAGCCTGCTAGACGTAATGTCTGGTAT
*
29516326 GTTTCACCAGCATCAAGCCTGCTAGACGTAATGT
1 GTTTCACCGGCATCAAGCCTGCTAGACGTAATGT
29516360 ATGGATTACT
Statistics
Matches: 148, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 3 0.02
41 145 0.98
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.29
Consensus pattern (41 bp):
GTTTCACCGGCATCAAGCCTGCTAGACGTAATGTCTGGTAT
Found at i:29517012 original size:2 final size:2
Alignment explanation
Indices: 29517007--29517044 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
29516997 CTTCGAATCT
* *
29517007 TA TA TA TA TA CA TA TA TA TA TA TA TA TA -A TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29517045 GTTTGATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:29525734 original size:3 final size:3
Alignment explanation
Indices: 29525726--29525761 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
29525716 TATTAAAGAG
*
29525726 TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
29525762 ATAAGAGAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:29528138 original size:33 final size:33
Alignment explanation
Indices: 29528101--29528167 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
29528091 GTTTCTTTAT
29528101 TTCTTTACCAATGGTGGACGGAAAGGAACAAGA
1 TTCTTTACCAATGGTGGACGGAAAGGAACAAGA
*
29528134 TTCTTTACCAATGGTGGATGGAAAGGAACAAGA
1 TTCTTTACCAATGGTGGACGGAAAGGAACAAGA
29528167 T
1 T
29528168 GAAGTGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (33 bp):
TTCTTTACCAATGGTGGACGGAAAGGAACAAGA
Found at i:29528600 original size:41 final size:39
Alignment explanation
Indices: 29528555--29528722 Score: 139
Period size: 40 Copynumber: 4.2 Consensus size: 39
29528545 GGCGGTATTT
* *
29528555 TTAGCGGCG-TTTGGACAAAAAACGCCGCTAAAAATTGAGCA
1 TTAGCGGCGCTTT-GA-AAAAAACGCAGCT-AAAATAGAGCA
* *
29528596 TTAGCGGCGCTTTTAGAAAAACGCAGCTAAAATAGAGCA
1 TTAGCGGCGCTTTGAAAAAAACGCAGCTAAAATAGAGCA
* * *
29528635 TTCGCGGCGCTTTTTGAAAAATAC-CA-CTAAAAATAGAACA
1 TTAGCGGCGC--TTTGAAAAAAACGCAGCT-AAAATAGAGCA
* *
29528675 TTAGCAGCGCTTTTTGAAAAACAC-C-GCTAAAAATAGAGCA
1 TTAGCGGCGC--TTTGAAAAAAACGCAGCT-AAAATAGAGCA
29528715 TTAGCGGC
1 TTAGCGGC
29528723 ATTTTCCAAG
Statistics
Matches: 108, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
39 21 0.19
40 65 0.60
41 19 0.18
42 3 0.03
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (39 bp):
TTAGCGGCGCTTTGAAAAAAACGCAGCTAAAATAGAGCA
Found at i:29528642 original size:39 final size:40
Alignment explanation
Indices: 29528572--29528722 Score: 191
Period size: 40 Copynumber: 3.8 Consensus size: 40
29528562 CGTTTGGACA
* * *
29528572 AAAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTTAG
1 AAAAACGCAGCTAAAAATAGAGCATTAGCGGCGCTTTTTG
*
29528612 AAAAACGCAGCT-AAAATAGAGCATTCGCGGCGCTTTTTG
1 AAAAACGCAGCTAAAAATAGAGCATTAGCGGCGCTTTTTG
* *
29528651 AAAAATAC-CA-CTAAAAATAGAACATTAGCAGCGCTTTTTG
1 -AAAA-ACGCAGCTAAAAATAGAGCATTAGCGGCGCTTTTTG
* *
29528691 AAAAACACCGCTAAAAATAGAGCATTAGCGGC
1 AAAAACGCAGCTAAAAATAGAGCATTAGCGGC
29528723 ATTTTCCAAG
Statistics
Matches: 96, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
38 2 0.02
39 31 0.32
40 61 0.64
41 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (40 bp):
AAAAACGCAGCTAAAAATAGAGCATTAGCGGCGCTTTTTG
Found at i:29529168 original size:14 final size:14
Alignment explanation
Indices: 29529149--29529346 Score: 134
Period size: 14 Copynumber: 13.9 Consensus size: 14
29529139 TATCACTACA
*
29529149 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
29529163 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* *
29529177 GTTTAGAGTTTAAG
1 GTTTAGGGTTTATG
**
29529191 GTTTA-GGTGTTACC
1 GTTTAGGGT-TTATG
* *
29529205 ATTTGAAGGTTTATG
1 GTTT-AGGGTTTATG
*
29529220 GATTATGGGTTTATG
1 GTTTA-GGGTTTATG
* *
29529235 GGTTATGGTTTATG
1 GTTTAGGGTTTATG
* *
29529249 GTTTATGGTTTAAAG
1 GTTTAGGGTTT-ATG
* *
29529264 G-TTGGGGTTTAAG
1 GTTTAGGGTTTATG
*
29529277 GTTTAGAGG-TTATTT
1 GTTTAG-GGTTTA-TG
*
29529292 GTTAAGGGTTTATG
1 GTTTAGGGTTTATG
*
29529306 GTTTTAGGGTTTTAGG
1 G-TTTAGGG-TTTATG
29529322 GTTTA-GGTTTATG
1 GTTTAGGGTTTATG
29529335 GTTTAGGGTTTA
1 GTTTAGGGTTTA
29529347 GATTAACTAG
Statistics
Matches: 144, Mismatches: 28, Indels: 24
0.73 0.14 0.12
Matches are distributed among these distances:
13 16 0.11
14 78 0.54
15 41 0.28
16 9 0.06
ACGTcount: A:0.19, C:0.01, G:0.33, T:0.47
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:29529227 original size:7 final size:7
Alignment explanation
Indices: 29529212--29529346 Score: 78
Period size: 7 Copynumber: 18.9 Consensus size: 7
29529202 ACCATTTGAA
29529212 GGTTTAT
1 GGTTTAT
*
29529219 GGATTAT
1 GGTTTAT
29529226 GGGTTTAT
1 -GGTTTAT
*
29529234 GGGTTAT
1 GGTTTAT
29529241 GGTTTAT
1 GGTTTAT
29529248 GGTTTAT
1 GGTTTAT
*
29529255 GGTTTAAA
1 GGTTT-AT
**
29529263 GG-TTGG
1 GGTTTAT
*
29529269 GGTTTAA
1 GGTTTAT
29529276 GGTTTA-
1 GGTTTAT
*
29529282 GAGGTTATT
1 G-GTTTA-T
* * *
29529291 TGTTAAG
1 GGTTTAT
29529298 GGTTTAT
1 GGTTTAT
*
29529305 GGTTTTAG
1 GG-TTTAT
*
29529313 GGTTTTAG
1 GG-TTTAT
29529321 GGTTTA-
1 GGTTTAT
29529327 GGTTTAT
1 GGTTTAT
*
29529334 GGTTTAG
1 GGTTTAT
29529341 GGTTTA
1 GGTTTA
29529347 GATTAACTAG
Statistics
Matches: 101, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
6 9 0.09
7 66 0.65
8 26 0.26
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (7 bp):
GGTTTAT
Found at i:29529241 original size:22 final size:21
Alignment explanation
Indices: 29529215--29529256 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
29529205 ATTTGAAGGT
29529215 TTATGGATTATGGGTTTATGGG
1 TTATGGATTAT-GGTTTATGGG
*
29529237 TTATGGTTTATGGTTTATGG
1 TTATGGATTATGGTTTATGG
29529257 TTTAAAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (21 bp):
TTATGGATTATGGTTTATGGG
Found at i:29529347 original size:7 final size:7
Alignment explanation
Indices: 29529149--29529347 Score: 75
Period size: 7 Copynumber: 27.9 Consensus size: 7
29529139 TATCACTACA
29529149 GTTTAGG
1 GTTTAGG
**
29529156 GTTTTTG
1 GTTTAGG
29529163 GTTTAGG
1 GTTTAGG
* *
29529170 GTATATG
1 GTTTAGG
*
29529177 GTTTAGA
1 GTTTAGG
*
29529184 GTTTAAG
1 GTTTAGG
29529191 GTTTA-G
1 GTTTAGG
**
29529197 GTGTTACC
1 GT-TTAGG
* *
29529205 ATTTGAAG
1 GTTT-AGG
*
29529213 GTTTATG
1 GTTTAGG
*
29529220 GATTATGG
1 GTTTA-GG
29529228 GTTTATGG
1 GTTTA-GG
*
29529236 G-TTATG
1 GTTTAGG
*
29529242 GTTTATG
1 GTTTAGG
*
29529249 GTTTATG
1 GTTTAGG
*
29529256 GTTTAAAG
1 GTTT-AGG
*
29529264 G-TTGGG
1 GTTTAGG
*
29529270 GTTTAAG
1 GTTTAGG
29529277 GTTTAGAG
1 GTTTAG-G
**
29529285 G-TTATTT
1 GTTTA-GG
*
29529292 GTTAAGG
1 GTTTAGG
29529299 GTTTATGG
1 GTTTA-GG
*
29529307 TTTTAGG
1 GTTTAGG
29529314 GTTTTAGG
1 G-TTTAGG
29529322 GTTTA-G
1 GTTTAGG
*
29529328 GTTTATG
1 GTTTAGG
29529335 GTTTAGG
1 GTTTAGG
29529342 GTTTAG
1 GTTTAG
29529348 ATTAACTAGT
Statistics
Matches: 143, Mismatches: 36, Indels: 26
0.70 0.18 0.13
Matches are distributed among these distances:
6 13 0.09
7 96 0.67
8 34 0.24
ACGTcount: A:0.19, C:0.01, G:0.33, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:29529414 original size:14 final size:14
Alignment explanation
Indices: 29529392--29529431 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
29529382 TTAATTATCA
29529392 TTATAGTTTAGGGT
1 TTATAGTTTAGGGT
*
29529406 TTATGGTTTAGGGT
1 TTATAGTTTAGGGT
*
29529420 TTAAAGTTTAGG
1 TTATAGTTTAGG
29529432 AGTTACTATC
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:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (14 bp):
TTATAGTTTAGGGT
Found at i:29529471 original size:22 final size:20
Alignment explanation
Indices: 29529446--29529500 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 20
29529436 ACTATCTTAA
29529446 GGTTTATGGGTTATGAATTAT
1 GGTTTA-GGGTTATGAATTAT
*
29529467 GGGTTTAGGGATTATGATTTAT
1 -GGTTTAGGG-TTATGAATTAT
29529489 GGTTTAAGGGTT
1 GGTTT-AGGGTT
29529501 GGGATTTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (20 bp):
GGTTTAGGGTTATGAATTAT
Found at i:29534441 original size:43 final size:43
Alignment explanation
Indices: 29534393--29534541 Score: 147
Period size: 43 Copynumber: 3.5 Consensus size: 43
29534383 TCTTTGGCGG
* * * **
29534393 ATGTTCTTTAGCGGCATTTGTTGGTAAAGCGTCGCTAAAGGTC
1 ATGTTCTTTAGCGGCGTTTGTGGGTAAAGCATCGCTAAAACTC
* * * *
29534436 ATGTTCTTTAACAGCGTTTGTGGGTAAAGTATCGCTAAAACTT
1 ATGTTCTTTAGCGGCGTTTGTGGGTAAAGCATCGCTAAAACTC
* * * * *
29534479 ATGTTCTATAGCGGCGTTTGTGGGAAAAGCACCACTAAAAGTC
1 ATGTTCTTTAGCGGCGTTTGTGGGTAAAGCATCGCTAAAACTC
* *
29534522 ATGATC-ATAGCGGCGTTTGT
1 ATGTTCTTTAGCGGCGTTTGT
29534542 AGGAGAAGCG
Statistics
Matches: 87, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
42 14 0.16
43 73 0.84
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
ATGTTCTTTAGCGGCGTTTGTGGGTAAAGCATCGCTAAAACTC
Found at i:29534556 original size:42 final size:42
Alignment explanation
Indices: 29534486--29534581 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
29534476 CTTATGTTCT
*
29534486 ATAGCGGCGTTTGTGGGAAAAGCACCACTAAAAGTCATGATC
1 ATAGCGGCGTTTGTAGGAAAAGCACCACTAAAAGTCATGATC
* *
29534528 ATAGCGGCGTTTGTAGGAGAAGCGCCACTAAAAGTCATGATC
1 ATAGCGGCGTTTGTAGGAAAAGCACCACTAAAAGTCATGATC
29534570 ATAGCGGCGTTT
1 ATAGCGGCGTTT
29534582 ATTTCTAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (42 bp):
ATAGCGGCGTTTGTAGGAAAAGCACCACTAAAAGTCATGATC
Found at i:29536285 original size:21 final size:22
Alignment explanation
Indices: 29536225--29536287 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 22
29536215 TTTAGAGCTT
*
29536225 TAATATTTATTTAT-AATTAAT
1 TAATATTTATTTATAAATTAAC
* *
29536246 TATTATCTATGTTAAATAAATT-AC
1 TAATATTTAT-TT--ATAAATTAAC
29536270 TAATATTTATTTATAAAT
1 TAATATTTATTTATAAAT
29536288 GCTCCAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
21 14 0.42
22 2 0.06
23 2 0.06
24 11 0.33
25 4 0.12
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (22 bp):
TAATATTTATTTATAAATTAAC
Found at i:29539429 original size:13 final size:13
Alignment explanation
Indices: 29539413--29539488 Score: 64
Period size: 13 Copynumber: 5.7 Consensus size: 13
29539403 ATTTTGGTAA
29539413 ATATTTTTTTTGT
1 ATATTTTTTTTGT
*
29539426 ATATTATTTTTTTT
1 ATATT-TTTTTTGT
* * *
29539440 GTATTATTTTGGT
1 ATATTTTTTTTGT
29539453 AAATATTTTTTTTGT
1 --ATATTTTTTTTGT
* *
29539468 ATATTATTTTGGT
1 ATATTTTTTTTGT
29539481 AT-TTTTTT
1 ATATTTTTT
29539489 ATTTTTTATT
Statistics
Matches: 49, Mismatches: 11, Indels: 7
0.73 0.16 0.10
Matches are distributed among these distances:
12 5 0.10
13 23 0.47
14 11 0.22
15 10 0.20
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (13 bp):
ATATTTTTTTTGT
Found at i:29539433 original size:16 final size:16
Alignment explanation
Indices: 29539414--29539477 Score: 68
Period size: 16 Copynumber: 4.4 Consensus size: 16
29539404 TTTTGGTAAA
29539414 TATTTTTTTTGTATAT
1 TATTTTTTTTGTATAT
29539430 TATTTTTTTTG--TAT
1 TATTTTTTTTGTATAT
* *
29539444 TA---TTTTGGTA-AA
1 TATTTTTTTTGTATAT
29539456 TATTTTTTTTGTATAT
1 TATTTTTTTTGTATAT
29539472 TATTTT
1 TATTTT
29539478 GGTATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
11 5 0.13
12 3 0.08
14 5 0.13
15 7 0.18
16 18 0.47
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (16 bp):
TATTTTTTTTGTATAT
Found at i:29539449 original size:26 final size:26
Alignment explanation
Indices: 29539420--29539478 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
29539410 TAAATATTTT
*
29539420 TTTTGTATATTATTTTTTTTG-TATTA
1 TTTTGTA-AATATTTTTTTTGATATTA
29539446 TTTTGGTAAATATTTTTTTTGTATATTA
1 TTTT-GTAAATATTTTTTTTG-ATATTA
29539474 TTTTG
1 TTTTG
29539479 GTATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 16 0.55
27 4 0.14
28 9 0.31
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.69
Consensus pattern (26 bp):
TTTTGTAAATATTTTTTTTGATATTA
Found at i:29539449 original size:42 final size:42
Alignment explanation
Indices: 29539390--29539477 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
29539380 CCGTCTTTGT
29539390 TTTTTTTTGTATTATTTTGGTAAATATTTTTTTTGTATATTA
1 TTTTTTTTGTATTATTTTGGTAAATATTTTTTTTGTATATTA
29539432 TTTTTTTTGTATTATTTTGGTAAATATTTTTTTTGTATATTA
1 TTTTTTTTGTATTATTTTGGTAAATATTTTTTTTGTATATTA
29539474 TTTT
1 TTTT
29539478 GGTATTTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.70
Consensus pattern (42 bp):
TTTTTTTTGTATTATTTTGGTAAATATTTTTTTTGTATATTA
Found at i:29539479 original size:28 final size:26
Alignment explanation
Indices: 29539430--29539481 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
29539420 TTTTGTATAT
29539430 TATTTTTTTTGTATTATTTTGGTAAA
1 TATTTTTTTTGTATTATTTTGGTAAA
29539456 TATTTTTTTTGTATATTATTTTGGTA
1 TATTTTTTTTG--TATTATTTTGGTA
29539482 TTTTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 11 0.46
28 13 0.54
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (26 bp):
TATTTTTTTTGTATTATTTTGGTAAA
Found at i:29539498 original size:26 final size:25
Alignment explanation
Indices: 29539413--29539498 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 25
29539403 ATTTTGGTAA
* *
29539413 ATATTTTTTTTGTATATTATTTTTTTT
1 ATATTATTTTGGTAT-TT-TTTTTTTT
* *
29539440 GTATTATTTTGGTAAATATTTTTTTTGT
1 ATATTATTTTGGT--AT-TTTTTTTTTT
29539468 ATATTATTTTGGTATTTTTTTATTTT
1 ATATTATTTTGGTATTTTTTT-TTTT
*
29539494 TTATT
1 ATATT
29539499 GGTAATATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
25 6 0.12
26 9 0.18
27 10 0.20
28 19 0.39
29 5 0.10
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (25 bp):
ATATTATTTTGGTATTTTTTTTTTT
Found at i:29544737 original size:20 final size:20
Alignment explanation
Indices: 29544695--29544742 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29544685 ATAAGGTATC
* *
29544695 GATACTTTGTGAAAGTTATT
1 GATACTTTGTGAAAGATAAT
*
29544715 GATACTTTGTTAAAGATAAT
1 GATACTTTGTGAAAGATAAT
*
29544735 GATGCTTT
1 GATACTTT
29544743 TGATTTTTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (20 bp):
GATACTTTGTGAAAGATAAT
Found at i:29551096 original size:21 final size:21
Alignment explanation
Indices: 29551070--29551112 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
29551060 GGCCCAAACA
*
29551070 CTAAACCCAATTAGCCTTAGC
1 CTAAACCCAATTAGCCTAAGC
29551091 CTAAACCCAATTAGCCTAAGC
1 CTAAACCCAATTAGCCTAAGC
29551112 C
1 C
29551113 CAATAACCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.35, G:0.09, T:0.21
Consensus pattern (21 bp):
CTAAACCCAATTAGCCTAAGC
Found at i:29551106 original size:15 final size:15
Alignment explanation
Indices: 29551086--29551116 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29551076 CCAATTAGCC
29551086 TTAGCCTAAACCCAA
1 TTAGCCTAAACCCAA
*
29551101 TTAGCCTAAGCCCAA
1 TTAGCCTAAACCCAA
29551116 T
1 T
29551117 AACCCTAGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.23
Consensus pattern (15 bp):
TTAGCCTAAACCCAA
Found at i:29552118 original size:3 final size:3
Alignment explanation
Indices: 29552112--29552184 Score: 55
Period size: 3 Copynumber: 25.3 Consensus size: 3
29552102 TAATTTTTTT
* * * * *
29552112 TTA TTA TTA TTG CTA TTA TTA TT- TT- TTA TCA CTA TT- TT- TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
29552156 TTA TTA TTA TTA TTA TTA TAA TTGA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA T
29552185 AAGTCTATTC
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
2 8 0.15
3 44 0.80
4 3 0.05
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:29557291 original size:25 final size:26
Alignment explanation
Indices: 29557249--29557297 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
29557239 TAAATTCCAA
29557249 AAAAAAATCAAGAACAAAA-AAAAGG
1 AAAAAAATCAAGAACAAAATAAAAGG
*
29557274 AAAAAAATCAA-AGTCAAAATAAAA
1 AAAAAAATCAAGA-ACAAAATAAAA
29557298 AATATGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 16 0.76
26 4 0.19
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (26 bp):
AAAAAAATCAAGAACAAAATAAAAGG
Found at i:29558105 original size:13 final size:13
Alignment explanation
Indices: 29558087--29558116 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29558077 GAAAAGTGAA
*
29558087 AAAATGAAAATGG
1 AAAATGAAAAAGG
29558100 AAAATGAAAAAGG
1 AAAATGAAAAAGG
29558113 AAAA
1 AAAA
29558117 AGTAAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (13 bp):
AAAATGAAAAAGG
Found at i:29559439 original size:44 final size:44
Alignment explanation
Indices: 29559385--29559506 Score: 122
Period size: 43 Copynumber: 2.8 Consensus size: 44
29559375 TCCCTCGGTT
*
29559385 GCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTCCCTAAGCA
1 GCAGTAGAGCAGGTTAAAGATAGCAGATCTTGCCTCCCTAAGCA
* * * * * ** **
29559429 GTAGTAGAGCAGATCAAAGATA-CTAG-CCTTACCTCCCTCGGTT
1 GCAGTAGAGCAGGTTAAAGATAGC-AGATCTTGCCTCCCTAAGCA
*
29559472 GCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCT
1 GCAGTAGAGCAGGTTAAAGATAGCAGATCTTGCCT
29559507 TCCTGTGCTG
Statistics
Matches: 59, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
43 32 0.54
44 27 0.46
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (44 bp):
GCAGTAGAGCAGGTTAAAGATAGCAGATCTTGCCTCCCTAAGCA
Found at i:29559574 original size:88 final size:88
Alignment explanation
Indices: 29559366--29560153 Score: 1163
Period size: 88 Copynumber: 9.0 Consensus size: 88
29559356 TCGAAAACAA
* *
29559366 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTCCCTAAGCA--
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCT--GCACT
* * * *
29559429 G-TAG-TAGAGCAGATCAAAGATACT
64 GACAGCGA-AGCAGATCGAAGATACC
* * **
29559453 AGCCTTACCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGTGCTGA
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACTGA
29559518 CAGCGAAGCAGATCGAAGATACC
66 CAGCGAAGCAGATCGAAGATACC
* *
29559541 AGCCTTACCTCCCTCGGTTGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACTGA
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACTGA
29559606 CAGCGAAGCAGATCGAAGATACC
66 CAGCGAAGCAGATCGAAGATACC
* * *
29559629 AGCCTTGCCTCCCTGGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTTCGCTGA
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACTGA
29559694 CAGCGAAGCAGATCGAAGATACC
66 CAGCGAAGCAGATCGAAGATACC
* * *
29559717 AGCCTTGCCTCCCTGGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCGCTAA
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACTGA
29559782 CAGCGAAGCAGATCGAAGATACC
66 CAGCGAAGCAGATCGAAGATACC
* *
29559805 AACCTTGCCTCCCTAGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACTGA
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACTGA
*
29559870 CAGTGAAGCAGATCGAAGATACC
66 CAGCGAAGCAGATCGAAGATACC
* * *
29559893 AGCCTTGCCTCCCTCGGTTGCAGCGGAGTAGATTGAAGATAGCAGATCTTGCCTTCCTGCACTGA
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACTGA
29559958 CAGCGAAGCAGATCGAAGATACC
66 CAGCGAAGCAGATCGAAGATACC
* *
29559981 AGCCTTGCCTCCCT-GAGTTGCAGTGGAGCAGGTTGAAGATTGCAGATCTTGCCTTCCTGTACTG
1 AGCCTTGCCTCCCTCG-GTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACTG
* * * *
29560045 ACAGTGAAGTAGATCGAAGACACT
65 ACAGCGAAGCAGATCGAAGATACC
* * * * * * *
29560069 AGCCTTGCCCCCCTGGGTTGCAGTGGAGCAGGTTGAATATAACAAATCTTGCCTTCTTGTACTGA
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACTGA
*
29560134 CAGCGAAGCAAATCGAAGAT
66 CAGCGAAGCAGATCGAAGAT
29560154 TACAAGTCAT
Statistics
Matches: 646, Mismatches: 49, Indels: 11
0.92 0.07 0.02
Matches are distributed among these distances:
85 1 0.00
87 58 0.09
88 585 0.91
89 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (88 bp):
AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACTGA
CAGCGAAGCAGATCGAAGATACC
Found at i:29560544 original size:21 final size:21
Alignment explanation
Indices: 29560518--29560560 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
29560508 GGCCCAAACA
*
29560518 CTAAACCCAATTAGCCTTAGC
1 CTAAACCCAATTAGCCTAAGC
29560539 CTAAACCCAATTAGCCTAAGC
1 CTAAACCCAATTAGCCTAAGC
29560560 C
1 C
29560561 CAATAACCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.35, G:0.09, T:0.21
Consensus pattern (21 bp):
CTAAACCCAATTAGCCTAAGC
Found at i:29560554 original size:15 final size:15
Alignment explanation
Indices: 29560534--29560564 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29560524 CCAATTAGCC
29560534 TTAGCCTAAACCCAA
1 TTAGCCTAAACCCAA
*
29560549 TTAGCCTAAGCCCAA
1 TTAGCCTAAACCCAA
29560564 T
1 T
29560565 AACCCTAGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.23
Consensus pattern (15 bp):
TTAGCCTAAACCCAA
Found at i:29561542 original size:3 final size:3
Alignment explanation
Indices: 29561534--29561610 Score: 57
Period size: 3 Copynumber: 25.3 Consensus size: 3
29561524 AATTTTAATT
* * * * * *
29561534 TTA TTA TTA TTG CTA TTG TTA TTA TT- TTA TCA CTA TTTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* *
29561579 CTA TTA TTA TTA TTA TTG TTA TTA TTGA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA T
29561611 AAGTCTATTC
Statistics
Matches: 55, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
2 2 0.04
3 48 0.87
4 5 0.09
ACGTcount: A:0.26, C:0.05, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:29561557 original size:18 final size:18
Alignment explanation
Indices: 29561534--29561610 Score: 72
Period size: 18 Copynumber: 4.4 Consensus size: 18
29561524 AATTTTAATT
*
29561534 TTATTATTATTGCTATTG
1 TTATTATTATTGCTATTA
*
29561552 TTATTA-T-TT--TATCA
1 TTATTATTATTGCTATTA
*
29561566 CTATTTATTATTGCTATTA
1 TTA-TTATTATTGCTATTA
*
29561585 TTATTATTATTGTTATTA
1 TTATTATTATTGCTATTA
29561603 TTGATTAT
1 TT-ATTAT
29561611 AAGTCTATTC
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
14 5 0.11
15 3 0.06
16 3 0.06
17 3 0.06
18 22 0.47
19 11 0.23
ACGTcount: A:0.26, C:0.05, G:0.06, T:0.62
Consensus pattern (18 bp):
TTATTATTATTGCTATTA
Found at i:29562595 original size:19 final size:19
Alignment explanation
Indices: 29562556--29562605 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
29562546 AATCTGAGAC
29562556 AATTTTGAAACAAAATAGAA
1 AATTTTGAAA-AAAATAGAA
*
29562576 AATTTTGAAAAAATTAGAA
1 AATTTTGAAAAAAATAGAA
29562595 AATTTTGAAAA
1 AATTTTGAAAA
29562606 CAGGGATCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.30
Consensus pattern (19 bp):
AATTTTGAAAAAAATAGAA
Found at i:29568263 original size:207 final size:207
Alignment explanation
Indices: 29567908--29568284 Score: 558
Period size: 207 Copynumber: 1.8 Consensus size: 207
29567898 ATCAGAGCTA
* * * ** *
29567908 TTCTAGGTACAATTTTTATTACAAATTTGACTTCTTTAATTGGTGACAACCCAAGTAATTCTTTA
1 TTCTAGGTACAAGTTTGATTACAAATTTGACTTCTCTAATCAGTGACAACCCAAGTAATTCTTAA
* * **
29567973 GGAAACCCATCAACAAATTCTTTAACTATCGGTACTTGATCAATTTTCGATTCTAACACTCGTGA
66 AGAAACACATCAACAAATTCTTTAACTATCGACACTTGATCAATTTTCGATTCTAACACTCGTGA
** * *
29568038 ATTAAGAATGTATGCAAGATACTCCCCACAACCTTTTCTAATAAATTTTTGAGCTAACAATGTTG
131 AGCAAGAATGCATGCAAGATACTCACCACAACCTTTTCTAATAAATTTTTGAGCTAACAATGTTG
29568103 AAATCGAAACTG
196 AAATCGAAACTG
* **
29568115 TTCTAGGTACAAGTTTGATTACAAATTTGACTTCTCTAATCAGTGGCAACCTGAGTAATTCTTAA
1 TTCTAGGTACAAGTTTGATTACAAATTTGACTTCTCTAATCAGTGACAACCCAAGTAATTCTTAA
*
29568180 AGAAACACATCAGCAAATTCTTTAACTATCGACACTTGATCAATTTTCGATTCTAACAC-CTGTG
66 AGAAACACATCAACAAATTCTTTAACTATCGACACTTGATCAATTTTCGATTCTAACACTC-GTG
* *
29568244 AAGCAAGAATGCATGCAAGATACTCATCACAACTTTTTCTA
130 AAGCAAGAATGCATGCAAGATACTCACCACAACCTTTTCTA
29568285 GTCAATTTCT
Statistics
Matches: 149, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
206 1 0.01
207 148 0.99
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (207 bp):
TTCTAGGTACAAGTTTGATTACAAATTTGACTTCTCTAATCAGTGACAACCCAAGTAATTCTTAA
AGAAACACATCAACAAATTCTTTAACTATCGACACTTGATCAATTTTCGATTCTAACACTCGTGA
AGCAAGAATGCATGCAAGATACTCACCACAACCTTTTCTAATAAATTTTTGAGCTAACAATGTTG
AAATCGAAACTG
Found at i:29575986 original size:46 final size:46
Alignment explanation
Indices: 29575919--29576010 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
29575909 CTTTTGCGAG
29575919 AAGGAGAACTGGATAATTTGCTTAAATGCATTGAAAGTAGTGTTTC
1 AAGGAGAACTGGATAATTTGCTTAAATGCATTGAAAGTAGTGTTTC
29575965 AAGGAGAACTGGATAATTTGCTTAAATGCATTGAAAGTAGTGTTTC
1 AAGGAGAACTGGATAATTTGCTTAAATGCATTGAAAGTAGTGTTTC
29576011 TGTGCATTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.33
Consensus pattern (46 bp):
AAGGAGAACTGGATAATTTGCTTAAATGCATTGAAAGTAGTGTTTC
Found at i:29577359 original size:23 final size:23
Alignment explanation
Indices: 29577315--29577359 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
29577305 ATTATATAGT
**
29577315 ATTATATATTATGATTTTATTAA
1 ATTATATATTATGATTAAATTAA
* *
29577338 ATTATATATTTTTATTAAATTA
1 ATTATATATTATGATTAAATTA
29577360 TAGGATCTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTATATATTATGATTAAATTAA
Found at i:29577555 original size:59 final size:59
Alignment explanation
Indices: 29577492--29577675 Score: 155
Period size: 59 Copynumber: 3.1 Consensus size: 59
29577482 GATAGTATCA
*
29577492 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTATGAATTTTATTAAAT
1 TATATTATGATTTAAGTAAATTCATATAAGAATATTGATTATTATGAATTTTATTAAAT
* * * * * * * *
29577551 TATATATTTTACTTAAAATATATTTA-ATAATAAT-TATG-TTAAATTAT--ATTTTA-TAGTAT
1 TATAT-TATGA-TTTAAGTAAATTCATATAAGAATAT-TGATT--ATTATGAATTTTATTA-AAT
* *
29577610 CATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTAAGTAAATTCATATAAGAATATTGATTATTATGAATTTTATTAAAT
29577671 TATAT
1 TATAT
29577676 ATTTTAATTA
Statistics
Matches: 92, Mismatches: 19, Indels: 28
0.66 0.14 0.20
Matches are distributed among these distances:
58 2 0.02
59 34 0.37
60 24 0.26
61 30 0.33
62 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (59 bp):
TATATTATGATTTAAGTAAATTCATATAAGAATATTGATTATTATGAATTTTATTAAAT
Found at i:29577572 original size:18 final size:17
Alignment explanation
Indices: 29577539--29577573 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29577529 ATTATTATGA
*
29577539 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29577556 ATTTTACTTAAAATATAT
1 ATTTTA-TTAAAATATAT
29577574 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29577601 original size:120 final size:120
Alignment explanation
Indices: 29577444--29577713 Score: 461
Period size: 120 Copynumber: 2.2 Consensus size: 120
29577434 TATATTTAGA
*
29577444 AAAATTATATTTAATAATAATTAT-TTCAAATTATATTTGATAGTATCATATATTATGATTTTAG
1 AAAA-TATATTTAATAATAATTATGTT-AAATTATATTTGATAGTATCATATATTATGATTTGAG
* *
29577508 TAAATTCATATAAGAATATTGATTATTATGAATTTTATTAAATTATATATTTTACTT
64 TAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATT
*
29577565 AAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTA
1 AAAATATATTTAATAATAATTATGTTAAATTATATTTGATAGTATCATATATTATGATTTGAGTA
29577630 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATT
66 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATT
* *
29577685 ATAATATATTTAATAATAATTGTGTTAAA
1 AAAATATATTTAATAATAATTATGTTAAA
29577714 ATATGATTAA
Statistics
Matches: 142, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
120 136 0.96
121 6 0.04
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
AAAATATATTTAATAATAATTATGTTAAATTATATTTGATAGTATCATATATTATGATTTGAGTA
AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATT
Found at i:29577676 original size:61 final size:60
Alignment explanation
Indices: 29577491--29577678 Score: 174
Period size: 61 Copynumber: 3.1 Consensus size: 60
29577481 TGATAGTATC
*
29577491 ATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTATGAATTTTATTAAATT
1 ATATATTATGA-TTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * *
29577552 ATATATT-TTACTTA--AAATAT-ATTTAATAATAATT-ATGT-TAAATTATATTTTA-TAGTAT
1 ATATATTATGATTTAGTAAAT-TCATATAAGAAT-ATTGAT-TATTAA-GA-ATTTTATTA-AAT
*
29577610 C
60 T
29577611 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTT-AGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
29577672 ATATATT
1 ATATATT
29577679 TTAATTATAA
Statistics
Matches: 96, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
57 16 0.17
58 8 0.08
59 18 0.19
60 6 0.06
61 23 0.24
62 8 0.08
63 17 0.18
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (60 bp):
ATATATTATGATTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
Found at i:29577698 original size:15 final size:15
Alignment explanation
Indices: 29577663--29577704 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29577653 TTAAGAATTT
*
29577663 TATTAAATTAT-ATA
1 TATTTAATTATAATA
29577677 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
29577691 TATTTAATAATAAT
1 TATTTAATTATAAT
29577705 TGTGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:29577948 original size:16 final size:16
Alignment explanation
Indices: 29577927--29577991 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
29577917 TTGATTTGCT
29577927 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
29577943 ATTACGCTTCTATTCC
1 ATTACGCCTCTATTCC
* *
29577959 ATTACACCTCTTTTCC
1 ATTACGCCTCTATTCC
29577975 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
29577991 A
1 A
29577992 ATACAGCGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.20, C:0.35, G:0.05, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:29578888 original size:24 final size:24
Alignment explanation
Indices: 29578861--29578912 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
29578851 AGAAAATTTC
29578861 ATATTAACTAAAAT-TAAAA-AACAA
1 ATATTAA-TAAAATATAAAATAA-AA
*
29578885 ATATTAATACAATATAAAATAAAA
1 ATATTAATAAAATATAAAATAAAA
29578909 ATAT
1 ATAT
29578913 ATGTATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 5 0.20
24 18 0.72
25 2 0.08
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (24 bp):
ATATTAATAAAATATAAAATAAAA
Found at i:29579548 original size:40 final size:40
Alignment explanation
Indices: 29579464--29579556 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
29579454 GTTTGGATAA
* *
29579464 AAAACGCCGGTAAAAATCGAGCATTAGCGGCGCTTGAGAG
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGATTGAGAG
* * * *
29579504 AAAACACCGCTAAAAATTGAGCATTAGCGGCGATTCTA-AT
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGATT-GAGAG
29579544 AAAACGCCGCTAA
1 AAAACGCCGCTAA
29579557 TAATATTCAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 44 0.98
41 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.17
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCGAGCATTAGCGGCGATTGAGAG
Found at i:29579856 original size:45 final size:46
Alignment explanation
Indices: 29579781--29579874 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 46
29579771 GTGAAACGCT
* * * *
29579781 GCAAAAAATTAAATCCAAACGCATCGTTTTGATTTGAGATGTAGTG
1 GCAAAAAAATAAATCAAAACCCATCATTTTGATTTGAGATGTAGTG
29579827 GCAAAAAAAT-AATCAAAACCCATCATTTTGATTTGAGATGTAGTG
1 GCAAAAAAATAAATCAAAACCCATCATTTTGATTTGAGATGTAGTG
29579872 GCA
1 GCA
29579875 TTAGCGGAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 35 0.80
46 9 0.20
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (46 bp):
GCAAAAAAATAAATCAAAACCCATCATTTTGATTTGAGATGTAGTG
Found at i:29580434 original size:21 final size:21
Alignment explanation
Indices: 29580423--29580477 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
29580413 TTGTGTTTGT
29580423 GGTTTACGGGTTTATGATTTAG
1 GGTTTA-GGGTTTATGATTTAG
* *
29580445 GGTTTAGGGTTTAAG-GTTAG
1 GGTTTAGGGTTTATGATTTAG
*
29580465 TGTTTAGGGTTTA
1 GGTTTAGGGTTTA
29580478 ATTTAAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 16 0.53
21 8 0.27
22 6 0.20
ACGTcount: A:0.18, C:0.02, G:0.35, T:0.45
Consensus pattern (21 bp):
GGTTTAGGGTTTATGATTTAG
Found at i:29580450 original size:7 final size:7
Alignment explanation
Indices: 29580423--29580477 Score: 58
Period size: 7 Copynumber: 7.9 Consensus size: 7
29580413 TTGTGTTTGT
29580423 GGTTTACG
1 GGTTTA-G
*
29580431 GGTTTAT
1 GGTTTAG
*
29580438 GATTTAG
1 GGTTTAG
29580445 GGTTTAG
1 GGTTTAG
*
29580452 GGTTTAA
1 GGTTTAG
29580459 GG-TTAG
1 GGTTTAG
*
29580465 TGTTTAG
1 GGTTTAG
29580472 GGTTTA
1 GGTTTA
29580478 ATTTAAGTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
6 4 0.11
7 28 0.74
8 6 0.16
ACGTcount: A:0.18, C:0.02, G:0.35, T:0.45
Consensus pattern (7 bp):
GGTTTAG
Found at i:29581808 original size:21 final size:21
Alignment explanation
Indices: 29581783--29581826 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
29581773 TGACCGTCAC
29581783 CGTCGCCTGCTTCATCACCAT
1 CGTCGCCTGCTTCATCACCAT
29581804 CGTCGCCTGCTTCATCACCAT
1 CGTCGCCTGCTTCATCACCAT
29581825 CG
1 CG
29581827 CTGTCTCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.43, G:0.16, T:0.27
Consensus pattern (21 bp):
CGTCGCCTGCTTCATCACCAT
Found at i:29582093 original size:14 final size:14
Alignment explanation
Indices: 29582074--29582100 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29582064 GAATATTTCA
29582074 GATTTTGTTATTCG
1 GATTTTGTTATTCG
29582088 GATTTTGTTATTC
1 GATTTTGTTATTC
29582101 AGGTTTCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.19, T:0.59
Consensus pattern (14 bp):
GATTTTGTTATTCG
Found at i:29583263 original size:69 final size:69
Alignment explanation
Indices: 29583178--29583319 Score: 223
Period size: 69 Copynumber: 2.1 Consensus size: 69
29583168 AAATTTTATT
* *
29583178 AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGTTATTCTT-TAAATATTAAAACCTATA
1 AATAATAAATTTTATAATTTTAAAAATAATTGAAAATGTTATT-TTCTAAAGATTAAAACCTATA
29583242 ATTTC
65 ATTTC
* *
29583247 AATAATAAATTTTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAACACCTATAT
1 AATAATAAATTTTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAAAACCTATAA
*
29583312 TTTT
66 TTTC
29583316 AATA
1 AATA
29583320 TATCACCCCA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
68 2 0.03
69 65 0.97
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (69 bp):
AATAATAAATTTTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAAAACCTATAA
TTTC
Found at i:29583640 original size:21 final size:21
Alignment explanation
Indices: 29583614--29583654 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29583604 AACTTAAAGC
*
29583614 AGAGGCGGCAGCGAGGGAAGT
1 AGAGGCGGCAGCGAGAGAAGT
*
29583635 AGAGGCTGCAGCGAGAGAAG
1 AGAGGCGGCAGCGAGAGAAG
29583655 CAGATGTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.15, G:0.49, T:0.05
Consensus pattern (21 bp):
AGAGGCGGCAGCGAGAGAAGT
Found at i:29583726 original size:87 final size:87
Alignment explanation
Indices: 29583573--29583745 Score: 265
Period size: 87 Copynumber: 2.0 Consensus size: 87
29583563 CACAGTTGAG
* ** *
29583573 GTTCAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGGGAAGTAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGAAAAGCAGA
* *
29583638 GGCTGCAGCGAGAGAAGCAGAT
66 GGCTGCAACAAGAGAAGCAGAT
* *
29583660 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGGCATCGAGAAAAGCAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGAAAAGCAGA
*
29583725 GGCTGCAACAAGGGAAGCAGA
66 GGCTGCAACAAGAGAAGCAGA
29583746 GCAGAGCAGA
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.40, C:0.18, G:0.29, T:0.13
Consensus pattern (87 bp):
GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGAAAAGCAGA
GGCTGCAACAAGAGAAGCAGAT
Found at i:29584119 original size:43 final size:43
Alignment explanation
Indices: 29584070--29584449 Score: 454
Period size: 43 Copynumber: 8.8 Consensus size: 43
29584060 TTTTTAAACC
* * * * *
29584070 AAGCGCCGCTAAAAGTTATGGCCTACAGTGACGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAA
** *
29584113 AAGCGCCGCTAAAGGTCATGGCCTATAGTAGCGTTTGTGGGAG
1 AAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAA
** * *
29584156 AAGTACCGCTAAAGGTCATGGCCTATAGTGGCGTTTGTGGGAG
1 AAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAA
* * *
29584199 AAGCGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTGTGGGAA
1 AAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAA
* * * *
29584242 AAGTGCTGCTAAAGGTTATGGCCTATAGCGGCGTTTATGGGAA
1 AAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAA
* * * * *
29584285 AAGCGCCGCTAAAGATCATGGTCTATAGCTGCGTTTGCGGGAG
1 AAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAA
* * ** ** *
29584328 AAGCGTCGCTAAAGATCATGTTCTATAGCAACGTTTGTGGGAG
1 AAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAA
*
29584371 AAGCGCCACTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAA
* *
29584414 AAGCGCCGCTAAAGATCATGGTCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTT
29584450 ATTTCTAAAA
Statistics
Matches: 289, Mismatches: 48, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 289 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAA
Found at i:29587694 original size:16 final size:17
Alignment explanation
Indices: 29587668--29587700 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29587658 TATTTTTCTA
29587668 TTTCACTTTTTCATTTT
1 TTTCACTTTTTCATTTT
*
29587685 TTTC-CTTTTTCCTTTT
1 TTTCACTTTTTCATTTT
29587701 CTTTTATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCACTTTTTCATTTT
Found at i:29590378 original size:33 final size:33
Alignment explanation
Indices: 29590341--29590544 Score: 138
Period size: 33 Copynumber: 5.6 Consensus size: 33
29590331 TCCCCCAAGG
29590341 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
29590374 GGTTGCTAAGTGTTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
* *
29590416 GGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
** * *
29590449 GGTTGCTAAGTGCTGACCCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGA-TTCC-CCG-A--TT-CAT-TG---GT
* *
29590492 GGTTGCTAAGTGCTAATTCCCTGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
29590525 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
29590545 ATCGTATTTT
Statistics
Matches: 133, Mismatches: 19, Indels: 38
0.70 0.10 0.20
Matches are distributed among these distances:
33 56 0.42
34 5 0.04
35 4 0.03
36 4 0.03
37 6 0.05
38 6 0.05
39 3 0.02
40 4 0.03
41 5 0.04
42 24 0.18
43 16 0.12
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:29590502 original size:76 final size:75
Alignment explanation
Indices: 29590337--29590579 Score: 360
Period size: 76 Copynumber: 3.2 Consensus size: 75
29590327 TGATTCCCCC
*
29590337 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
29590402 TTAAATGTGA
66 TTAAATGTGA
* * * **
29590412 AGGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGACCCCCACCGTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGA-TTCCACCGTAT
*
29590477 CTTAAATGTGA
65 TTTAAATGTGA
* * *
29590488 AAGGGGTTGCTAAGTGCTAATTCCCTGATTCATTGGTGGTTGCTAAGTGCTGATTCCATCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA-T
*
29590553 TTTGAATGTGA
65 TTTAAATGTGA
*
29590564 AAGGGATTGCTAAGTG
1 AAGGGGTTGCTAAGTG
29590580 TTGGATCCAC
Statistics
Matches: 148, Mismatches: 18, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
75 56 0.38
76 92 0.62
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
TTAAATGTGA
Found at i:29592732 original size:43 final size:43
Alignment explanation
Indices: 29592683--29592781 Score: 135
Period size: 43 Copynumber: 2.3 Consensus size: 43
29592673 GGTTTGATTT
* * *
29592683 CGTGTAAGACCATGTCTTGGACATTGGCATCGATATGAGATTA
1 CGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGAGATAA
* * *
29592726 TGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATGTGATAA
1 CGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGAGATAA
*
29592769 CATGTAAGACCAT
1 CGTGTAAGACCAT
29592782 ATATGGGATA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACAGTGGCATCGATATGAGATAA
Found at i:29592789 original size:43 final size:42
Alignment explanation
Indices: 29592685--29592808 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 42
29592675 TTTGATTTCG
* * * **
29592685 TGTAAGACCATGTCTTGGACATTGGCATCGATATGAGATTATG
1 TGTAAGACCATGTCTGGGACA-TGGCATCGATATGTGATAACA
*
29592728 TGTAAGACCCTGTCTGGGACAGTGGCATCGATATGTGATAACA
1 TGTAAGACCATGTCTGGGACA-TGGCATCGATATGTGATAACA
* * * *
29592771 TGTAAGACCATATATGGGATATGGCATTG-TATGTGATA
1 TGTAAGACCATGTCTGGGACATGGCATCGATATGTGATA
29592809 TATGTGTTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
41 9 0.13
42 7 0.10
43 53 0.77
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATGGCATCGATATGTGATAACA
Found at i:29597701 original size:29 final size:28
Alignment explanation
Indices: 29597668--29597722 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
29597658 TTATAGATTG
*
29597668 ATGGGTTTTTTTATTATGTTAACTTTTTT
1 ATGGGTTTTTTTATGATGTTAA-TTTTTT
*
29597697 ATGGGTTTTTTTGTGATGTTAATTTT
1 ATGGGTTTTTTTATGATGTTAATTTT
29597723 CTGGATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.16, C:0.02, G:0.18, T:0.64
Consensus pattern (28 bp):
ATGGGTTTTTTTATGATGTTAATTTTTT
Found at i:29607079 original size:17 final size:17
Alignment explanation
Indices: 29607057--29607097 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
29607047 TGTCTCAGCC
29607057 GTGTGTCACACACGACT
1 GTGTGTCACACACGACT
* **
29607074 GTGTGTGACACACGGTT
1 GTGTGTCACACACGACT
29607091 GTGTGTC
1 GTGTGTC
29607098 CCCTGTATCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.17, C:0.22, G:0.32, T:0.29
Consensus pattern (17 bp):
GTGTGTCACACACGACT
Found at i:29609598 original size:3 final size:3
Alignment explanation
Indices: 29609590--29609628 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
29609580 CTCAACATTT
29609590 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
29609629 GGACTAAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:29621115 original size:8 final size:8
Alignment explanation
Indices: 29621102--29621150 Score: 64
Period size: 8 Copynumber: 5.9 Consensus size: 8
29621092 AATTTATTAA
29621102 AAATTTAT
1 AAATTTAT
29621110 AAATTTAT
1 AAATTTAT
29621118 AAATTTAT
1 AAATTTAT
29621126 AAATTATAATT
1 AAATT-T-A-T
29621137 AAATTTAT
1 AAATTTAT
29621145 -AATTTA
1 AAATTTA
29621151 ATTGACAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
7 6 0.16
8 22 0.58
9 2 0.05
10 2 0.05
11 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
AAATTTAT
Found at i:29621116 original size:19 final size:18
Alignment explanation
Indices: 29621092--29621150 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
29621082 ACTCTAAAAT
29621092 AATTTATTAAAAATTTATA
1 AATTTA-TAAAAATTTATA
29621111 AATTTAT--AAATTTATA
1 AATTTATAAAAATTTATA
29621127 AA-TTATAATTAAATTTAT-
1 AATTTATAA--AAATTTATA
29621145 AATTTA
1 AATTTA
29621151 ATTGACAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
15 4 0.11
16 11 0.31
18 3 0.09
19 17 0.49
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTTATAAAAATTTATA
Found at i:29621181 original size:6 final size:6
Alignment explanation
Indices: 29621170--29621225 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
29621160 CCCTAACAAA
* ***
29621170 AACCCT AACCCT AAACCTT AAACCCT AACAAA AACCCT AACCCT AACCCT
1 AACCCT AACCCT -AACCCT -AACCCT AACCCT AACCCT AACCCT AACCCT
29621220 AACCCT
1 AACCCT
29621226 TAACTTAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
6 30 0.73
7 11 0.27
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (6 bp):
AACCCT
Found at i:29621244 original size:21 final size:21
Alignment explanation
Indices: 29621218--29621263 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
29621208 AACCCTAACC
29621218 CTAACCCTTAACTTAAAAAAT
1 CTAACCCTTAACTTAAAAAAT
*
29621239 CTAACCCTTAACTTAAAAACT
1 CTAACCCTTAACTTAAAAAAT
29621260 CTAA
1 CTAA
29621264 ACTAATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (21 bp):
CTAACCCTTAACTTAAAAAAT
Found at i:29621313 original size:21 final size:22
Alignment explanation
Indices: 29621274--29621314 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
29621264 ACTAATTTAT
**
29621274 TAAAAACCTTAAACTCTAACCC
1 TAAAAACCCAAAACTCTAACCC
29621296 TAAAAACCCAAAAC-CTAAC
1 TAAAAACCCAAAACTCTAAC
29621315 GGTGGAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (22 bp):
TAAAAACCCAAAACTCTAACCC
Found at i:29629227 original size:101 final size:104
Alignment explanation
Indices: 29629033--29629276 Score: 291
Period size: 101 Copynumber: 2.4 Consensus size: 104
29629023 ATTTGGGTAA
* *
29629033 AGAGATCCCATGTAAGACCATGTCTGAGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCCC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CCTTGAGATCA-GAGAGGTCCC
* * * * **
29629098 AGGTAAGATCATGTTTGAGACATGGCGTTGGCACGGAGACG
64 AGGTAAGACCATGTTAGAGACATAGCGTTGACACCAAGACG
* *
29629139 AGAGGTCCTATGTAAGACCAATGTCTGGGACATGGCGTTGGCA-C-TGAG-TC-GAGAGGTCCCA
1 AGAGGTCCCATGTAAGACC-ATGTCTGGGACATGGCATTGGCACCTTGAGATCAGAGAGGTCCCA
* *
29629200 TGTAAGACCATGTCTAG-GACATAGCGTTGACACCAAGATG
65 GGTAAGACCATGT-TAGAGACATAGCGTTGACACCAAGACG
**
29629240 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCAT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAT
29629277 GGACACCGAT
Statistics
Matches: 120, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
100 17 0.14
101 56 0.47
102 2 0.02
103 2 0.02
104 4 0.03
105 1 0.01
106 17 0.14
107 21 0.17
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (104 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCTTGAGATCAGAGAGGTCCCAG
GTAAGACCATGTTAGAGACATAGCGTTGACACCAAGACG
Found at i:29629243 original size:50 final size:50
Alignment explanation
Indices: 29629033--29629324 Score: 271
Period size: 50 Copynumber: 5.7 Consensus size: 50
29629023 ATTTGGGTAA
* * * *
29629033 AGAGATCCCATGTAAGACCATGTCTGAGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGACA-CC--GAG---ATG
* * * * * * *
29629089 AGAGGTCCCAGGTAAGATCATGTTTGAGACATGGCGTTGGCACGGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGACACCGAGATG
* * *
29629139 AGAGGTCCTATGTAAGACCAATGTCTGGGACATGGCGTTGGCACTGAG-TCG
1 AGAGGTCCCATGTAAGACC-ATGTCTGGGACATGGCGTTGACACCGAGAT-G
* * *
29629190 AGAGGTCCCATGTAAGACCATGTCTAGGACATAGCGTTGACACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGACACCGAGATG
** * * *
29629240 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGACACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGACACCGAGATG
** * *
29629290 AGAACTCCCATGTAAGACCATATCTGGGATATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
29629325 ACTGGTAGTT
Statistics
Matches: 199, Mismatches: 34, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
50 113 0.57
51 45 0.23
53 3 0.02
55 1 0.01
56 37 0.19
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGACACCGAGATG
Found at i:29629325 original size:50 final size:50
Alignment explanation
Indices: 29629148--29629373 Score: 167
Period size: 50 Copynumber: 4.5 Consensus size: 50
29629138 GAGAGGTCCT
* ** **
29629148 ATGTAAGACCAATGTCTGGGACATGGCGTTGG-CACTGAG-TCGAGAGGTCCC
1 ATGTAAGACC-ATGTCTGGGACATGGC-ATGGACACCAAGAT-GAGAACTCCC
* * * * **
29629199 ATGTAAGACCATGTCTAGGACATAGCGTTGACACCAAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATGGACACCAAGATGAGAACTCCC
** * *
29629249 CCGTAAGACCATGTCTGGGACATGGCATGGACACCGATATGAGAACTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATGGACACCAAGATGAGAACTCCC
* * ***
29629299 ATGTAAGACCATATCTGGGATATGGCACTGGTAGTTC---ATGA-AACATCCC
1 ATGTAAGACCATGTCTGGGACATGGCA-TGG-ACACCAAGATGAGAAC-TCCC
*
29629348 ATGTAAGACCATGTCTAGGACATGGC
1 ATGTAAGACCATGTCTGGGACATGGC
29629374 TTTGGCATGT
Statistics
Matches: 144, Mismatches: 26, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
48 3 0.02
49 33 0.23
50 92 0.64
51 14 0.10
52 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.22
Consensus pattern (50 bp):
ATGTAAGACCATGTCTGGGACATGGCATGGACACCAAGATGAGAACTCCC
Found at i:29636780 original size:50 final size:50
Alignment explanation
Indices: 29636645--29636939 Score: 283
Period size: 50 Copynumber: 5.8 Consensus size: 50
29636635 ATTTGGGTAA
* * *
29636645 AGAGATCCCCTGTAAGACCATGTCTGAGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
29636701 AGAGGT-TCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
29636750 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
29636800 AGAGGTCCCCCGTAAGATCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * * * *
29636850 AGAACTCCCAT-TAAGATCATATTTGGGATATGGAATTGGTA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** *
29636898 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
29636940 TGTTATTGTC
Statistics
Matches: 203, Mismatches: 33, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
47 1 0.00
48 12 0.06
49 56 0.28
50 93 0.46
52 3 0.01
54 2 0.01
55 31 0.15
56 5 0.02
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Done.