Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001709.1 Hibiscus syriacus cultivar Beakdansim tig00003435_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1326839
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1037403 original size:19 final size:19
Alignment explanation
Indices: 1037379--1037418 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1037369 GGATTTAGGA
1037379 TATCTTATCAGAGAAAATG
1 TATCTTATCAGAGAAAATG
*
1037398 TATCTTATCATAGAAAATG
1 TATCTTATCAGAGAAAATG
1037417 TA
1 TA
1037419 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (19 bp):
TATCTTATCAGAGAAAATG
Found at i:1037870 original size:24 final size:24
Alignment explanation
Indices: 1037819--1037872 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1037809 GTATTCGAAA
*
1037819 TTTGATCTTGATCAATACCCGTAC
1 TTTGATCTTGATCAATACCCGGAC
* *
1037843 TTTGATCTTGATCAATACTCGGAT
1 TTTGATCTTGATCAATACCCGGAC
1037867 TTTGAT
1 TTTGAT
1037873 TATTTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGATCAATACCCGGAC
Found at i:1040166 original size:18 final size:18
Alignment explanation
Indices: 1040143--1040178 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1040133 AAGAAAAAGG
1040143 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
1040161 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
1040179 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:1040611 original size:25 final size:25
Alignment explanation
Indices: 1040573--1040622 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1040563 AAATCAATTA
*
1040573 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
1040598 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
1040623 GAAATTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:1041051 original size:24 final size:24
Alignment explanation
Indices: 1040999--1041051 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1040989 TTTCATATGT
* *
1040999 AATTGGAGTTTGAATTTAAATTTA
1 AATTTGAGTTTGAATTTAAATATA
*
1041023 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1041047 AATTT
1 AATTT
1041052 CGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1041999 original size:6 final size:6
Alignment explanation
Indices: 1041988--1042022 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1041978 AAGCAAAAGG
* *
1041988 AAATCA AAATCA AAATCG CAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
1042023 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:1042012 original size:18 final size:18
Alignment explanation
Indices: 1041989--1042029 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1041979 AGCAAAAGGA
*
1041989 AATCAAAATCAAAATCGC
1 AATCAAAATCAAAATCCC
1042007 AATCAAAATCAAAATCCC
1 AATCAAAATCAAAATCCC
1042025 AATCA
1 AATCA
1042030 CAACCGGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:1042284 original size:150 final size:150
Alignment explanation
Indices: 1042014--1042519 Score: 933
Period size: 150 Copynumber: 3.4 Consensus size: 150
1042004 CGCAATCAAA
*
1042014 ATCAAAATCCCAATCACAACCGGCTTTACCTTTTGGGACTTATTAACTTAGGT-ATTTTTAAATG
1 ATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATTTTTAAATG
1042078 CAAACGTTGTATTATGTGTATTTTATGTGTGAATGCATACATTTTCAGTTAGACATTCATTAGTA
66 CAAACGTTGTATTATGTGTATTTTATGTGTGAATGCATACATTTTCAGTTAGACATTCATTAGTA
1042143 ACTTGAGTTTGAACATTGCT
131 ACTTGAGTTTGAACATTGCT
1042163 ATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATTTTTAAATG
1 ATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATTTTTAAATG
1042228 CAAACGTTGTATTATGTGTATTTTATGTGTGAATGCATACATTTTCAGTTAGACATTCATTAGTA
66 CAAACGTTGTATTATGTGTATTTTATGTGTGAATGCATACATTTTCAGTTAGACATTCATTAGTA
*
1042293 ACTTGATTTTGAACATTGCT
131 ACTTGAGTTTGAACATTGCT
** *
1042313 ATCAAAATATCAATCACAACCGGCTTCACCTTTTAGGACTTATTAACTTAGGTGATTTTTAAATG
1 ATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATTTTTAAATG
* *
1042378 CAAACGTTGTATTATGTGTATTTTATTTATGAATGCATACATTTTCAGTTAGACATTCATTAGTA
66 CAAACGTTGTATTATGTGTATTTTATGTGTGAATGCATACATTTTCAGTTAGACATTCATTAGTA
1042443 ACTTGAGTTTGAACATTGCT
131 ACTTGAGTTTGAACATTGCT
*
1042463 ATCAAAATCCCAATCACAACTGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATT
1 ATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATT
1042520 GTTGAGTTAA
Statistics
Matches: 344, Mismatches: 12, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
149 52 0.15
150 292 0.85
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (150 bp):
ATCAAAATCCCAATCACAACCGGCTTCACCTTTTGGGACTTATTAACTTAGGTGATTTTTAAATG
CAAACGTTGTATTATGTGTATTTTATGTGTGAATGCATACATTTTCAGTTAGACATTCATTAGTA
ACTTGAGTTTGAACATTGCT
Found at i:1045401 original size:21 final size:21
Alignment explanation
Indices: 1045372--1045426 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
1045362 CATTGGGGGT
* *
1045372 ATCGATTCCCTCAATGAGGGA
1 ATCGGTTCCCTCAAAGAGGGA
*
1045393 ATCGGTTCCCATTCAAAGGGGGA
1 ATCGGTTCCC--TCAAAGAGGGA
1045416 ATCGGTTCCCT
1 ATCGGTTCCCT
1045427 TATGGGGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 10 0.34
23 19 0.66
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.25
Consensus pattern (21 bp):
ATCGGTTCCCTCAAAGAGGGA
Found at i:1050843 original size:20 final size:20
Alignment explanation
Indices: 1050814--1050864 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1050804 CCGTTAAACA
*
1050814 GGGGGGAATCGATACCCCCT
1 GGGGGGAATCGATACCCACT
* *
1050834 GGGGGAAATCTATACCCACT
1 GGGGGGAATCGATACCCACT
1050854 GGGGGGAATCG
1 GGGGGGAATCG
1050865 GTTCCTTCCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.37, T:0.16
Consensus pattern (20 bp):
GGGGGGAATCGATACCCACT
Found at i:1053273 original size:21 final size:21
Alignment explanation
Indices: 1053249--1053367 Score: 132
Period size: 21 Copynumber: 5.7 Consensus size: 21
1053239 GTGAAACGGG
* * * *
1053249 CTCTTGAACGGTGGGACGGAC
1 CTCTTGAACGATGAGAGGGGC
* *
1053270 CTCTTGAATGATGACAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* * *
1053291 CTCTTGAACGGTGGGAGGGGT
1 CTCTTGAACGATGAGAGGGGC
1053312 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1053333 CTCTTGAACGAT-AGGAGGCGC
1 CTCTTGAACGATGA-GAGGGGC
1053354 CTCTTGAACGATGA
1 CTCTTGAACGATGA
1053368 CATGTGAATC
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
20 1 0.01
21 79 0.98
22 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1053316 original size:42 final size:42
Alignment explanation
Indices: 1053249--1053369 Score: 170
Period size: 42 Copynumber: 2.9 Consensus size: 42
1053239 GTGAAACGGG
* * *
1053249 CTCTTGAACGGTGGGACGGACCTCTTGAATGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGC
* *
1053291 CTCTTGAACGGTGGGAGGGGTCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGC
* * *
1053333 CTCTTGAACGATAGGAGGCGCCTCTTGAACGATGACA
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACA
1053370 TGTGAATCGG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.22, C:0.21, G:0.36, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGC
Found at i:1053532 original size:4 final size:4
Alignment explanation
Indices: 1053511--1053556 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
1053501 GGGCCGCTGA
* * *
1053511 AAAT AAAT TAAT ACAT AAAT AAGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1053557 TGTCAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1055556 original size:20 final size:21
Alignment explanation
Indices: 1055527--1055565 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1055517 TCGCGTTGCG
*
1055527 ATTTTGGTGTTGC-AATTTTC
1 ATTTTCGTGTTGCGAATTTTC
1055547 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
1055566 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (21 bp):
ATTTTCGTGTTGCGAATTTTC
Found at i:1055938 original size:22 final size:22
Alignment explanation
Indices: 1055911--1055953 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1055901 GAGATAGACG
1055911 GATTTCGTCGGAGATGGGGACA
1 GATTTCGTCGGAGATGGGGACA
1055933 GATTTCGTCGGAGATGGGGAC
1 GATTTCGTCGGAGATGGGGAC
1055954 GGATGTTGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.21, C:0.14, G:0.42, T:0.23
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGACA
Found at i:1056138 original size:20 final size:20
Alignment explanation
Indices: 1056113--1056158 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1056103 TAAACGTTCT
*
1056113 TTGCGAATTTGACTTATGTG
1 TTGCGAAATTGACTTATGTG
*
1056133 TTGCGAAATTGACTTCTGTG
1 TTGCGAAATTGACTTATGTG
1056153 TTGCGA
1 TTGCGA
1056159 TTTACATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41
Consensus pattern (20 bp):
TTGCGAAATTGACTTATGTG
Found at i:1056818 original size:13 final size:15
Alignment explanation
Indices: 1056800--1056831 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1056790 AAACCTCATA
1056800 AAAACAT-AAAATT-
1 AAAACATGAAAATTC
1056813 AAAACATGAAAATTC
1 AAAACATGAAAATTC
1056828 AAAA
1 AAAA
1056832 GTGAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 6 0.35
15 4 0.24
ACGTcount: A:0.69, C:0.09, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAACATGAAAATTC
Found at i:1061277 original size:2 final size:2
Alignment explanation
Indices: 1061270--1061341 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
1061260 TGTAATTCAA
1061270 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1061312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1061342 TAATTAAATT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1061573 original size:2 final size:2
Alignment explanation
Indices: 1061566--1061644 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
1061556 ATTACGTCGT
1061566 TA TA TA TA TA TA 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 TA TA TA TA TA TA
1061608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1061645 TGTAAAGGGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1066166 original size:58 final size:58
Alignment explanation
Indices: 1066096--1066248 Score: 166
Period size: 58 Copynumber: 2.6 Consensus size: 58
1066086 TGTCTTAATG
* * * *
1066096 TATGACCCTCATTTTAAATTGGTCCTTAAGCTTTT-ACATGTTCCAATTTCATCCCTAAAC
1 TATGA-CCTCATTCTAAATTGGTCCTCAAACTTTTAACAT-TT-CAATTTCATCCCCAAAC
* * *
1066156 TATGA-CTCATTCTAAATTAGTCCTCAAATTTTTGAACATTTCAATTTTATCCCCAAAC
1 TATGACCTCATTCTAAATTGGTCCTCAAACTTTT-AACATTTCAATTTCATCCCCAAAC
* *
1066214 TATGACCTTCATTCTAAATTGGTCTTGAAACTTTT
1 TATGACC-TCATTCTAAATTGGTCCTCAAACTTTT
1066249 TGCACATCCA
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
58 43 0.55
59 3 0.04
60 32 0.41
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (58 bp):
TATGACCTCATTCTAAATTGGTCCTCAAACTTTTAACATTTCAATTTCATCCCCAAAC
Found at i:1074584 original size:21 final size:21
Alignment explanation
Indices: 1074538--1074634 Score: 92
Period size: 21 Copynumber: 4.6 Consensus size: 21
1074528 CGAGTGACGT
* *
1074538 TTATATATATTATTATTGTAT
1 TTATATATATTATTATTATAA
*
1074559 TTATAGATATTATTATTATAA
1 TTATATATATTATTATTATAA
* *
1074580 ATATA-ATAAATATTATTATAA
1 TTATATAT-ATTATTATTATAA
1074601 TTATATTATATTATATTATTATAA
1 TTATA-TATA-T-TATTATTATAA
1074625 TTA-AT-TATTA
1 TTATATATATTA
1074635 CAACCTTACA
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
19 2 0.03
20 3 0.05
21 40 0.62
22 2 0.03
23 3 0.05
24 14 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTATATATATTATTATTATAA
Found at i:1074616 original size:24 final size:23
Alignment explanation
Indices: 1074538--1074632 Score: 81
Period size: 24 Copynumber: 4.2 Consensus size: 23
1074528 CGAGTGACGT
*
1074538 TTATATATATTATTAT--TGTAT-
1 TTATAAATATTATTATAAT-TATA
* * *
1074559 TTATAGATATTATTATTATAAATA
1 TTATAAATATTATTATAAT-TATA
*
1074583 TAATAAATATTATTATAATTATA
1 TTATAAATATTATTATAATTATA
*
1074606 TTATATTATATTATTATAATTA-A
1 TTATA-AATATTATTATAATTATA
1074629 TTAT
1 TTAT
1074633 TACAACCTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
21 15 0.25
23 15 0.25
24 31 0.51
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTATAAATATTATTATAATTATA
Found at i:1074622 original size:13 final size:13
Alignment explanation
Indices: 1074589--1074634 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1074579 AATATAATAA
*
1074589 ATATTATTATAAT
1 ATATTATTATATT
1074602 -TA-TATTATATT
1 ATATTATTATATT
1074613 ATATTATTATAATT
1 ATATTATTAT-ATT
1074627 A-ATTATTA
1 ATATTATTA
1074635 CAACCTTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
11 8 0.28
12 4 0.14
13 13 0.45
14 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATATTATTATATT
Found at i:1074781 original size:17 final size:17
Alignment explanation
Indices: 1074759--1074796 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1074749 GCCCAGTAAG
1074759 CCCACGCTAGAAGCAAA
1 CCCACGCTAGAAGCAAA
1074776 CCCACGCTAGAAGCAAA
1 CCCACGCTAGAAGCAAA
1074793 CCCA
1 CCCA
1074797 AGTGCTGTTA
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:0.39, C:0.39, G:0.16, T:0.05
Consensus pattern (17 bp):
CCCACGCTAGAAGCAAA
Found at i:1075090 original size:19 final size:19
Alignment explanation
Indices: 1075066--1075108 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1075056 GCACAACTCA
1075066 CCACCATTAGGGTGAGTCG
1 CCACCATTAGGGTGAGTCG
*
1075085 CCACCATTATGGTGAGTCG
1 CCACCATTAGGGTGAGTCG
1075104 CCACC
1 CCACC
1075109 GTAGTTTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.21
Consensus pattern (19 bp):
CCACCATTAGGGTGAGTCG
Found at i:1075350 original size:2 final size:2
Alignment explanation
Indices: 1075302--1075330 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1075292 TAGGCCGGCC
1075302 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1075331 TTTTTTGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1076098 original size:14 final size:14
Alignment explanation
Indices: 1076079--1076109 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1076069 CGAACCTACG
1076079 AAGAGCAAACAACC
1 AAGAGCAAACAACC
*
1076093 AAGAGCAAGCAACC
1 AAGAGCAAACAACC
1076107 AAG
1 AAG
1076110 CAAAAGCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.26, G:0.19, T:0.00
Consensus pattern (14 bp):
AAGAGCAAACAACC
Found at i:1077073 original size:21 final size:21
Alignment explanation
Indices: 1077013--1077064 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1077003 AACCAACAAA
1077013 TTCGCAACGCAAAACTCCAGT
1 TTCGCAACGCAAAACTCCAGT
1077034 TTCGCAACGCAAAACTCCAGT
1 TTCGCAACGCAAAACTCCAGT
1077055 TTCGCAACGC
1 TTCGCAACGC
1077065 GATTATCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.35, G:0.15, T:0.19
Consensus pattern (21 bp):
TTCGCAACGCAAAACTCCAGT
Found at i:1077215 original size:19 final size:19
Alignment explanation
Indices: 1077188--1077226 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1077178 CAACTATTCG
*
1077188 CAACGCGATTCTCCAAATT
1 CAACACGATTCTCCAAATT
* *
1077207 CAACACGATTTTTCAAATT
1 CAACACGATTCTCCAAATT
1077226 C
1 C
1077227 GCAATGCGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (19 bp):
CAACACGATTCTCCAAATT
Found at i:1080330 original size:35 final size:34
Alignment explanation
Indices: 1080253--1080331 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 34
1080243 CAAAATAGCG
*
1080253 TCTTATAATTAAATGATTTTTTACTTTTAATAGTG
1 TCTTATAATTAAATGATTTTTTACTTTTAATAG-A
1080288 TCTTATAATTAAATGATTTTTTTTAACTTTTAATA-A
1 TCTTATAATTAAATGA--TTTTTT-ACTTTTAATAGA
1080324 TC-TATAAT
1 TCTTATAAT
1080332 CTCAATAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
35 22 0.55
36 2 0.05
37 6 0.15
38 10 0.25
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.54
Consensus pattern (34 bp):
TCTTATAATTAAATGATTTTTTACTTTTAATAGA
Found at i:1083947 original size:79 final size:80
Alignment explanation
Indices: 1083856--1084009 Score: 283
Period size: 80 Copynumber: 1.9 Consensus size: 80
1083846 TCATTTTGTC
1083856 TCCATAATATATTTAAATCAATAATTTT-ATTTTTTATTTTTTAAATTATATTAATTTTATCTTC
1 TCCATAATATATTTAAATCAATAATTTTGATTTTTTATTTTTTAAATTATATTAATTTTATCTTC
1083920 GAATTTATATCATCA
66 GAATTTATATCATCA
* *
1083935 TCCATAATATATTTAAATCAATAATTTTGCTTTTTTATTTTTTTAATTATATTAATTTTATCTTC
1 TCCATAATATATTTAAATCAATAATTTTGATTTTTTATTTTTTAAATTATATTAATTTTATCTTC
1084000 GAATTTATAT
66 GAATTTATAT
1084010 AATCGTGTCA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
79 28 0.39
80 44 0.61
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (80 bp):
TCCATAATATATTTAAATCAATAATTTTGATTTTTTATTTTTTAAATTATATTAATTTTATCTTC
GAATTTATATCATCA
Found at i:1084683 original size:23 final size:23
Alignment explanation
Indices: 1084636--1084684 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1084626 AATAACATAT
* **
1084636 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAACGCTTATATAATAAAA
*
1084659 TAGGTAACGCTTATGTAATAAAA
1 TAGGTAACGCTTATATAATAAAA
1084682 TAG
1 TAG
1084685 ATATTTAACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (23 bp):
TAGGTAACGCTTATATAATAAAA
Found at i:1084746 original size:87 final size:87
Alignment explanation
Indices: 1084600--1084759 Score: 293
Period size: 87 Copynumber: 1.8 Consensus size: 87
1084590 ATGTTATATC
*
1084600 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
1084665 ACGCTTATGTAATAAAATAGAT
66 ACGCTTATGTAATAAAATAGAT
*
1084687 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGTTTATATAATGTAATAGGTA
1 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
*
1084752 ACGTTTAT
66 ACGCTTAT
1084760 ATTGACCTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
ACGCTTATGTAATAAAATAGAT
Found at i:1085108 original size:199 final size:198
Alignment explanation
Indices: 1084756--1085478 Score: 992
Period size: 199 Copynumber: 3.6 Consensus size: 198
1084746 TAGGTAACGT
* *
1084756 TTATATTGACCTATTTTCTAACTAAACCGGTATATTTATACC-GGTAACATTGCAAATTTACCTA
1 TTATGTTGACCTATTTTCTAA-TAAACCGGTATATTTATACCGGGT-ACATTGTAAATTTACCTA
*
1084820 TTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT--TAAATGTATCGACACT
64 TTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACT
* * *
1084883 TTATGCGTGCACCTCATTGGGCATTCATTCTGGAAAAAAAGTATCGACACAAACTTAAAAAGTGT
128 TTATGCGTGCACCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAA-TTAAAAAGTGT
*
1084948 TGATACA
192 CGATACA
* * * *
1084955 TTATGTAGACCTATTTTCTCATAAAACCAGTATATTTCTACCGGGTACATTGTAAATTTACCTAT
1 TTATGTTGACCTATTTTCTAAT-AAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTAT
* * *
1085020 TACGTTGTAATTATTGGTTTCGAT-TTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
65 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
* *
1085084 ATGCGTGCACCTCGTTTAGCATTCATTCTGGACAAAATGTATCGACACAAATTTAAAAAGTGTCG
130 ATGCGTGCACCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAA-TTAAAAAGTGTCG
1085149 ATACA
194 ATACA
* * * *
1085154 TTATGTTGACCTATTCTCTCATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTAT
1 TTATGTTGACCTATTTTCTAAT-AAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTAT
* *
1085219 TACATTATAATTATCGGTTTCGATGTTATTGGGATTGATACTTTTAATAAATGTATCGACACTTT
65 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
* * * * *
1085284 ATGCGTGCA-CTCGTTTGGGTATTCATTCTAGACAATAAGTATCGACACAAATTCCACAAGTGTC
130 ATGCGTGCACCTCGTTT-GGCATTCATTCTGGACAAAAAGTATCGACACAAATT-AAAAAGTGTC
1085348 GATACA
193 GATACA
* * * * * *
1085354 TTATGTTGACATGTTTTCTAATTAACCGGTATA-TTATACAGGTTACATTGTTAATTTACCTATT
1 TTATGTTGACCTATTTTCTAATAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATT
* *
1085418 ACATTATAATTATTGGTTTCGATGTTTTTGGGGTCGATACTTTTAGA-AAATGTATCGACAC
66 ACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTA-ATAAATGTATCGACAC
1085479 ATATGTTTAT
Statistics
Matches: 469, Mismatches: 47, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
197 3 0.01
198 101 0.22
199 254 0.54
200 111 0.24
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (198 bp):
TTATGTTGACCTATTTTCTAATAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATT
ACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTA
TGCGTGCACCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAATTAAAAAGTGTCGAT
ACA
Found at i:1088226 original size:19 final size:19
Alignment explanation
Indices: 1088202--1088249 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1088192 TTATATTCAC
1088202 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1088221 ATACAAAATTATGAATCGT
1 ATACAAAATTATAAATCGT
1088240 ATACAAAATT
1 ATACAAAATT
1088250 TGTAAGGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1090074 original size:200 final size:200
Alignment explanation
Indices: 1089699--1090450 Score: 932
Period size: 200 Copynumber: 3.8 Consensus size: 200
1089689 TTAAAACAAA
* * * * *
1089699 TATCGATACAAATTT-AAAAGTGTCGCTACATTATATTA-ACCTATTTTCTAATTAAACTGGTAT
1 TATCGACACAAATTTAAAAAGTGTCGATACATTAT-GTAGACCTATTTTCTAATAAAACCGGTAT
* * * *
1089762 ATTTATACCGGTTATATTACAAAATTACCTATTACATAATAATTATGAGTTTCGATGTTTTTGGG
65 ATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGG
* * *
1089827 ATC-AAAAAATTTAATAAATGTATCGACACTTTATCCGTGCACTCGTTTGGGCATTCATTCTGGA
130 ATCGATACAATTT-ATAAATGTATCGACACTTTATGCGTGCACTCGTTTGGGCATTCATTCTGGA
1089891 CAAAAAG
194 CAAAAAG
** *
1089898 TATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCGCTCATAAAACCGGTATA
1 TATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATAAAACCGGTATA
* * * ** *
1089963 TTTATACCGCTTACATTGTAAAATTACCTATTACATTGTAATTATGGGTTTCGATGTTTTTGGAA
66 TTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGA
* * *
1090028 TCGATACAATTT-TAAATGTATCGACACTTTATGTGTGCACCTCGTTT-GGCTTTCATTCTGGAT
131 TCGATACAATTTATAAATGTATCGACACTTTATGCGTGCA-CTCGTTTGGGCATTCATTCTGGAC
1090091 AAAAAG
195 AAAAAG
* * * * * * * * *
1090097 TATCGATA-TAATTTAAAAAATATCGATACATCATGTTGACCTATTTTCTAAT-TAACCGATACA
1 TATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATAAAACCGGTATA
* * * *
1090160 TTTATACCGGTTATATTGTAAAGTTACATATTACATTATAATTATCAGTTTCGATGTTTTT-GGA
66 TTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGA
* *
1090224 TCAATACAATTT-TAAATGTATCGACACTTTATGCGTGGATCTCG-TTGGGCATTCATTCTGGAC
131 TCGATACAATTTATAAATGTATCGACACTTTATGCGTGCA-CTCGTTTGGGCATTCATTCTGGAC
1090287 AAAAAG
195 AAAAAG
* * *
1090293 TATCGACACAAATTTAGAGAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATA
1 TATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATAAAACCGGTATA
* * * * * *
1090358 TATCTATCGGTTACATTATAAATTTACGTATTACATTATAATTATCGGTTTCGATGTTTTTGGGA
66 TTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGA
* *
1090423 TTGATAC-TTTTAATAAATGTATCGACAC
131 TCGATACAATTT-ATAAATGTATCGACAC
1090451 ATTTGTTTAC
Statistics
Matches: 472, Mismatches: 71, Indels: 19
0.84 0.13 0.03
Matches are distributed among these distances:
195 2 0.00
196 69 0.15
197 98 0.21
198 100 0.21
199 76 0.16
200 120 0.25
201 7 0.01
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (200 bp):
TATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATAAAACCGGTATA
TTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGA
TCGATACAATTTATAAATGTATCGACACTTTATGCGTGCACTCGTTTGGGCATTCATTCTGGACA
AAAAG
Found at i:1091989 original size:24 final size:24
Alignment explanation
Indices: 1091970--1092025 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
1091960 CGAAATTTAT
1091970 ATTGAAATTCAAACTCAAATTGAA
1 ATTGAAATTCAAACTCAAATTGAA
* *
1091994 ATTTAAATTCAAACTCCAATT-AA
1 ATTGAAATTCAAACTCAAATTGAA
1092017 ATATGAAAT
1 AT-TGAAAT
1092026 GAACATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.32
Consensus pattern (24 bp):
ATTGAAATTCAAACTCAAATTGAA
Found at i:1091993 original size:18 final size:18
Alignment explanation
Indices: 1091970--1092006 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1091960 CGAAATTTAT
1091970 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1091988 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1092006 A
1 A
1092007 CTCCAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1096965 original size:23 final size:23
Alignment explanation
Indices: 1096901--1096954 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1096891 CGATTCCCAA
* * * *
1096901 AAAGAGGGAATCGGTTTCCATTC
1 AAAGGGGGAATCAGTTCCCCTTC
1096924 AAAGGGGGAATCAGTTCCCCTTC
1 AAAGGGGGAATCAGTTCCCCTTC
*
1096947 AAGGGGGG
1 AAAGGGGG
1096955 TATCGATTCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.20
Consensus pattern (23 bp):
AAAGGGGGAATCAGTTCCCCTTC
Found at i:1101028 original size:117 final size:117
Alignment explanation
Indices: 1100808--1101029 Score: 279
Period size: 117 Copynumber: 1.9 Consensus size: 117
1100798 CTTTCAAATC
* *
1100808 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* *
1100873 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * * * *
1100925 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACT-CTTTTCTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACAT
* * **
1100988 TTCATTTTGATTTTCCAAGTCTGTTTTAGTTT-TCAAAAGAAG
64 TTCATTTTGATTTTCAAAATCCATTTTAGTTTCT-AAAAGAAG
1101030 ATCATTTTTA
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
116 6 0.07
117 83 0.93
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.48
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:1103287 original size:15 final size:15
Alignment explanation
Indices: 1103246--1103295 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
1103236 AAAGAATCGA
*
1103246 TTGGTTGAGAAGGAGG
1 TTGGTTGAGAA-GAGC
1103262 TTGTCGTTGAGAAGAGC
1 TTG--GTTGAGAAGAGC
1103279 TTGGTTGAGAAGAGC
1 TTGGTTGAGAAGAGC
1103294 TT
1 TT
1103296 TGAGAAAGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 14 0.45
16 3 0.10
17 6 0.19
18 8 0.26
ACGTcount: A:0.24, C:0.06, G:0.40, T:0.30
Consensus pattern (15 bp):
TTGGTTGAGAAGAGC
Found at i:1103942 original size:199 final size:199
Alignment explanation
Indices: 1103602--1105682 Score: 3217
Period size: 199 Copynumber: 10.4 Consensus size: 199
1103592 AGTAATTTAA
* * * * * * * **
1103602 AAAAAGTATCGACACAAATTTTAAAAGTGTCAATACATAATGTAGACATATTTTCTCATAAAATT
1 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
*
1103667 GGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
* **
1103732 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGTGTGCAATTAGTTTGGCATTCATTCT
131 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTCT
*
1103797 AGAC
196 GGAC
* * * * * *
1103801 AAAAAGTATCGACACAAATTTTAAAAGTGTCGATAAATAATGTAGACCTATTCTCTCATAAAATC
1 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* *
1103866 GATATATTTATACCTGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
* *
1103931 TTAGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGACATTCATTCT
131 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTCT
*
1103996 GGAA
196 GGAC
* * *
1104000 AAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTATCTCATAAAATC
1 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * *
1104065 GGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTTGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
** *
1104130 TTGGGATAAATACAATTTTAAATGTATCGACACTTTATGCATGCACCTAGTTTGGCATTCATTCT
131 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTCT
1104195 GGAC
196 GGAC
* *
1104199 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACATATTCTCTTATAAAACC
1 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
*
1104264 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATATTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * *
1104329 TTGGGATAGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCTAGTTTGACATTCATTCT
131 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTCT
1104394 GGAC
196 GGAC
* * * *
1104398 AAAATGTATCGACATAAACTTAAAAAGTATCGATACATTATGTAGACTTATTCTCTAATAAAACC
1 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* *
1104463 GGTATATTTATATCGGTTACATTATAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
* *
1104528 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCATGCACCTAGTTTGACATTCATTCT
131 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTCT
1104593 GGAC
196 GGAC
1104597 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
1 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
*
1104662 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGATTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * ** *
1104727 TTGGGATCGATACAATTTTAAATGTATTGACACTTTATGTGTAAACCTAGTTTGGCATTTATTCT
131 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTCT
1104792 GGAC
196 GGAC
1104796 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
1 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * * *
1104861 GATATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTTTGGATTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
* *
1104926 TTGGGATCGATACAATTTTAAATGTATCGAGACTTTATGTGTGCACCTAGTTTGGCATTCATTCT
131 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTCT
1104991 GGAC
196 GGAC
*
1104995 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATC
1 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* *
1105060 GGTATATTTATACCGGTTACATTATAAATTTACATATTACATTATAATTATGGGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
* *
1105125 TAGGGATCGATACAATTTTAAATGTATCGACACTTTATGTGTGCACCTAGTTTGGCATTCATTCT
131 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTCT
1105190 GGAC
196 GGAC
* * **
1105194 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACTTATTTTCTCATAAAAAT
1 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * * * * *
1105259 GGTATATTTATACCGGTTATATTGCAAAATTATCTATTACATTATAATTATGGGTTCCGATATTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
* ** * *
1105324 TTGTGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTACACCTTGTTTGGGCATTCATT
131 TTGGGATCGATACAATTT-TAAATGTATCGACACTTTATGCGTGCACCTAGTTT-GGCATTCATT
1105389 CTGGAC
194 CTGGAC
* * * *
1105395 AAAAAGTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACTTATTCTCTCATAAAACC
1 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * * * *
1105460 GGTATATTTCTACCAGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCAATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
*
1105525 TTGGGATCGATACAATTTTAAATGTATCGACACTATATGCGTGCACCTAGTTTGGCATTCATTCT
131 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTCT
1105590 GGAC
196 GGAC
* * * * * * * * * * *
1105594 AAAAGGTATCAACACAAATTTCAAAAGTATCGATACATTATGTTGACCTGTTTTCTAATTAAACT
1 AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* *
1105659 GGTATATTTATACTGGTTATATTG
66 GGTATATTTATACCGGTTACATTG
1105683 CAAAATTAGG
Statistics
Matches: 1741, Mismatches: 139, Indels: 4
0.92 0.07 0.00
Matches are distributed among these distances:
199 1533 0.88
200 64 0.04
201 144 0.08
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (199 bp):
AAAATGTATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGCATTCATTCT
GGAC
Found at i:1107565 original size:14 final size:15
Alignment explanation
Indices: 1107543--1107571 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1107533 ATCATTTTTA
1107543 TTTCACCCTTCATCT
1 TTTCACCCTTCATCT
1107558 TTTC-CCCTTCATCT
1 TTTCACCCTTCATCT
1107572 AAGTTTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.10, C:0.41, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTCACCCTTCATCT
Found at i:1110378 original size:180 final size:179
Alignment explanation
Indices: 1110080--1110555 Score: 650
Period size: 180 Copynumber: 2.6 Consensus size: 179
1110070 TATGCGTACT
* * *
1110080 TATTAAAGTATCGACACTTTCGACATATCTAGTAGCGCTTTACCGGTCTTGTCATTTCGAGATCG
1 TATTAAAGTATCGACACTTTCAACATATCCAGTAGCGCTTTACCGGTTTTGTCATTTCGAGATCG
* * *
1110145 GTTTTGTCATATTTTTATCTGTTATATTGTTATTGATCGATATATTTTTATAAAGTATCGACACT
66 G--TTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACT
* * *
1110210 TTATAGGCGCTATTATTGTTTCTCTTTTAAATTTCCAAAGTGTCGATACTTA
129 TTATAGGCACTATTACTGCTTCTC-TTTAAATTTCCAAAGTGTCGATACTTA
* *
1110262 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCAGTAGCGCTTTACCGGTTTTGTCATTTCGAGATCG
*
1110327 GTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 GTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTT
*
1110392 ATAGGCACTATTACTGCTTCTCTTTAAATTTCCAAAGTGTCGATATTTA
131 ATAGGCACTATTACTGCTTCTCTTTAAATTTCCAAAGTGTCGATACTTA
** ** * **** * *
1110441 T-TTCAATCTAATTAATACTTTCAACATATCCAGTAATATTTTACCGGTTTTGTCATAAT-GAAA
1 TATT-AAAGT-ATCGACACTTTCAACATATCCAGTAGCGCTTTACCGGTTTTGTCAT-TTCGAGA
* *
1110504 TCGGTTTTCATATTTTTACCTGTTATATTGATATAGATCGATACATTTTTAT
63 TCGGTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTTAT
1110556 TTGTATCGAC
Statistics
Matches: 263, Mismatches: 28, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
178 2 0.01
179 30 0.11
180 169 0.64
181 1 0.00
182 61 0.23
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (179 bp):
TATTAAAGTATCGACACTTTCAACATATCCAGTAGCGCTTTACCGGTTTTGTCATTTCGAGATCG
GTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTT
ATAGGCACTATTACTGCTTCTCTTTAAATTTCCAAAGTGTCGATACTTA
Found at i:1119733 original size:2 final size:2
Alignment explanation
Indices: 1119726--1119757 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1119716 TGGCCCCACA
1119726 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1119758 TAAAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1125162 original size:15 final size:15
Alignment explanation
Indices: 1125142--1125174 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1125132 TAGTTTTAGT
1125142 TAAAAATTAAAACAC
1 TAAAAATTAAAACAC
1125157 TAAAAATTAAAACAC
1 TAAAAATTAAAACAC
1125172 TAA
1 TAA
1125175 GAATATTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAAAATTAAAACAC
Found at i:1125459 original size:2 final size:2
Alignment explanation
Indices: 1125452--1125483 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1125442 TGATGATTAC
1125452 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1125484 TAATTTTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1133262 original size:17 final size:19
Alignment explanation
Indices: 1133226--1133263 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1133216 TATAAACAAC
1133226 AACAACAAAATCAAGCAAAA
1 AACAACAAAA-CAAGCAAAA
1133246 AACAACAAAA-AAG-AAAA
1 AACAACAAAACAAGCAAAA
1133263 A
1 A
1133264 TAAAAGAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
20 10 0.56
ACGTcount: A:0.76, C:0.16, G:0.05, T:0.03
Consensus pattern (19 bp):
AACAACAAAACAAGCAAAA
Found at i:1134100 original size:24 final size:22
Alignment explanation
Indices: 1134051--1134105 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
1134041 GAGATAGTAA
*
1134051 GGTTGAG--TTAGGATTTTTAG
1 GGTTGAGTTTTAGGATATTTAG
1134071 GGTTGA-TTTTAGGAATATTTAG
1 GGTTGAGTTTTAGG-ATATTTAG
1134093 GGATTTGAGTTTT
1 GG--TTGAGTTTT
1134106 TTTTTGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 6 0.21
21 5 0.18
22 9 0.32
24 4 0.14
25 4 0.14
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (22 bp):
GGTTGAGTTTTAGGATATTTAG
Found at i:1134143 original size:18 final size:18
Alignment explanation
Indices: 1134123--1134156 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1134113 AATTTTAGAA
1134123 AAAAT-AGATTTTTTAAT
1 AAAATAAGATTTTTTAAT
*
1134140 AAAATAATATTTTTTAA
1 AAAATAAGATTTTTTAA
1134157 AATAATGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AAAATAAGATTTTTTAAT
Found at i:1136305 original size:4 final size:4
Alignment explanation
Indices: 1136296--1136322 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1136286 TTCAACTATG
1136296 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
1136323 ACATGTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:1140276 original size:2 final size:2
Alignment explanation
Indices: 1140269--1140297 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1140259 TAAATATGTG
1140269 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1140298 TTGTATTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1143450 original size:24 final size:25
Alignment explanation
Indices: 1143421--1143472 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
1143411 GTCAACGGTT
1143421 AACGGGTCGGGTC-AAACCGGGTCA
1 AACGGGTCGGGTCAAAACCGGGTCA
*
1143445 AACGGGTCGGGTCAAAACTGGGTCA
1 AACGGGTCGGGTCAAAACCGGGTCA
1143470 AAC
1 AAC
1143473 TGCCCCAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.29, C:0.23, G:0.35, T:0.13
Consensus pattern (25 bp):
AACGGGTCGGGTCAAAACCGGGTCA
Found at i:1143457 original size:14 final size:14
Alignment explanation
Indices: 1143421--1143460 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1143411 GTCAACGGTT
1143421 AACGGGTCGGGTCA
1 AACGGGTCGGGTCA
1143435 AAC----CGGGTCA
1 AACGGGTCGGGTCA
1143445 AACGGGTCGGGTCA
1 AACGGGTCGGGTCA
1143459 AA
1 AA
1143461 ACTGGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
10 10 0.45
14 12 0.55
ACGTcount: A:0.28, C:0.23, G:0.38, T:0.12
Consensus pattern (14 bp):
AACGGGTCGGGTCA
Found at i:1145403 original size:23 final size:23
Alignment explanation
Indices: 1145377--1145421 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1145367 CACCACAGCT
*
1145377 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1145400 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1145422 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1151557 original size:18 final size:18
Alignment explanation
Indices: 1151536--1151632 Score: 140
Period size: 18 Copynumber: 5.4 Consensus size: 18
1151526 TGTACTGAAT
*
1151536 GACCACTATGTCCTGAAG
1 GACCACTATGTCCCGAAG
* *
1151554 GACCACTATGTCCCAAAT
1 GACCACTATGTCCCGAAG
*
1151572 GACCATTATGTCCCGAAG
1 GACCACTATGTCCCGAAG
*
1151590 GACCACTATGTCCCAAAG
1 GACCACTATGTCCCGAAG
*
1151608 GACCACTATATCCCGAAG
1 GACCACTATGTCCCGAAG
1151626 GACCACT
1 GACCACT
1151633 GATAATCCCT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 69 1.00
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.20
Consensus pattern (18 bp):
GACCACTATGTCCCGAAG
Found at i:1151582 original size:36 final size:36
Alignment explanation
Indices: 1151533--1151632 Score: 164
Period size: 36 Copynumber: 2.8 Consensus size: 36
1151523 ATTTGTACTG
*
1151533 AATGACCACTATGTCCTGAAGGACCACTATGTCCCA
1 AATGACCACTATGTCCCGAAGGACCACTATGTCCCA
*
1151569 AATGACCATTATGTCCCGAAGGACCACTATGTCCCA
1 AATGACCACTATGTCCCGAAGGACCACTATGTCCCA
* *
1151605 AAGGACCACTATATCCCGAAGGACCACT
1 AATGACCACTATGTCCCGAAGGACCACT
1151633 GATAATCCCT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (36 bp):
AATGACCACTATGTCCCGAAGGACCACTATGTCCCA
Found at i:1152285 original size:19 final size:19
Alignment explanation
Indices: 1152261--1152308 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1152251 AGCAGGTGCG
1152261 TCGATGCACTCCTTATGCA
1 TCGATGCACTCCTTATGCA
*
1152280 TCGATGCACTTCTTATGCA
1 TCGATGCACTCCTTATGCA
1152299 TCGATGCACT
1 TCGATGCACT
1152309 AATTGCATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (19 bp):
TCGATGCACTCCTTATGCA
Found at i:1152908 original size:2 final size:2
Alignment explanation
Indices: 1152901--1152944 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1152891 CGTGTAACTA
1152901 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1152943 AT
1 AT
1152945 CCCTTCTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1155270 original size:23 final size:23
Alignment explanation
Indices: 1155244--1155310 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
1155234 CACCACAGCT
*
1155244 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1155267 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
1155290 CGTAGAAATGCACCGAAGTGC
1 CGTAGAAATGCACCGAAGTGC
1155311 GATATAAGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1155816 original size:2 final size:2
Alignment explanation
Indices: 1155811--1155843 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1155801 ACCTTATTCT
1155811 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1155844 CCGCAAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1162860 original size:2 final size:2
Alignment explanation
Indices: 1162853--1162930 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
1162843 CGTGTAACTA
1162853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1162895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1162931 CCCTTCTTTA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1163258 original size:52 final size:53
Alignment explanation
Indices: 1163127--1163277 Score: 250
Period size: 53 Copynumber: 2.9 Consensus size: 53
1163117 GGATCTCAAA
* * *
1163127 AAAAATAATTCATAAAATAAGGTGAAACGTTTTTAAAAATATCAAAATTTCTT
1 AAAAATAATTCATAAAATAAGGTGACACGTTTTTGAAAATATCAAAATCTCTT
*
1163180 AAAAATAATTCATAAAATAAGGTGACACATTTTTGAAAATATCAAAATCTCTT
1 AAAAATAATTCATAAAATAAGGTGACACGTTTTTGAAAATATCAAAATCTCTT
*
1163233 -AAAATAATTCATAAAATAAGGTGACACGTTTTTGAAAAAATCAAA
1 AAAAATAATTCATAAAATAAGGTGACACGTTTTTGAAAATATCAAA
1163278 GCCTCTGATA
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 43 0.47
53 49 0.53
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (53 bp):
AAAAATAATTCATAAAATAAGGTGACACGTTTTTGAAAATATCAAAATCTCTT
Found at i:1164676 original size:129 final size:129
Alignment explanation
Indices: 1164509--1164749 Score: 304
Period size: 129 Copynumber: 1.9 Consensus size: 129
1164499 ACGAGCTCGA
* * *
1164509 TTCGGGGCTTTCGGGTCAGAATTTGGCAAAACGGACTTCAAAATCAGATTCAAGGCATCAAAAAA
1 TTCGAGGCTTTCGGGTCAGAATTTGGAAAAACGGACTTCAAAATCAGATTCAAGACATCAAAAAA
* * **
1164574 CATAAAATTTAACTTTTCGAAAATTTTGACTTTTTGGTCAAAGTCAACGGGTTTGACTAACAAT
66 CATAAAATATAACTTTTCAAAAAAATTGACTTTTTGGTCAAAGTCAACGGGTTTGACTAACAAT
* * ** * * * **
1164638 TTCGAGGCTTTCGAGTTC-GAATTTGGAAAAATGGACTTCGGATTCGGATTCATGACATTGAAAA
1 TTCGAGGCTTTCG-GGTCAGAATTTGGAAAAACGGACTTCAAAATCAGATTCAAGACATCAAAAA
* *
1164702 ACATAAAATATGACTTTTCAAAAAAATTGACTTTTTGGTTAAAGTCAA
65 ACATAAAATATAACTTTTCAAAAAAATTGACTTTTTGGTCAAAGTCAA
1164750 TGTTCGGTCA
Statistics
Matches: 93, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
129 90 0.97
130 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.32
Consensus pattern (129 bp):
TTCGAGGCTTTCGGGTCAGAATTTGGAAAAACGGACTTCAAAATCAGATTCAAGACATCAAAAAA
CATAAAATATAACTTTTCAAAAAAATTGACTTTTTGGTCAAAGTCAACGGGTTTGACTAACAAT
Found at i:1164775 original size:14 final size:14
Alignment explanation
Indices: 1164756--1164784 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1164746 TCAATGTTCG
1164756 GTCAAAGGTCAACA
1 GTCAAAGGTCAACA
1164770 GTCAAAGGTCAACA
1 GTCAAAGGTCAACA
1164784 G
1 G
1164785 GTCGGGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (14 bp):
GTCAAAGGTCAACA
Found at i:1168164 original size:3 final size:3
Alignment explanation
Indices: 1168151--1168211 Score: 79
Period size: 3 Copynumber: 20.7 Consensus size: 3
1168141 ATTTAAAAAA
* * *
1168151 TAT TA- TAT TAT TAT TAT TGT TAT TAT TAT TAC TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1168198 TAT AAT TAT TAT TA
1 TAT TAT TAT TAT TA
1168212 ATATATTTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1169634 original size:30 final size:30
Alignment explanation
Indices: 1169573--1169636 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1169563 TGAATTCTTG
* **
1169573 TTTTGTTGTTTTATTCTTTTAAATTTATGT
1 TTTTGTTGTTTTAATCCCTTAAATTTATGT
* *
1169603 TTTTGTTGTTTTAATCCCTTAAGTTTTTGT
1 TTTTGTTGTTTTAATCCCTTAAATTTATGT
1169633 TTTT
1 TTTT
1169637 CTCTTGCAGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.14, C:0.06, G:0.11, T:0.69
Consensus pattern (30 bp):
TTTTGTTGTTTTAATCCCTTAAATTTATGT
Found at i:1175675 original size:60 final size:64
Alignment explanation
Indices: 1175595--1175764 Score: 213
Period size: 60 Copynumber: 2.7 Consensus size: 64
1175585 ATAATATTCG
*
1175595 AGATTGTATTTCAACTTCACAACGAATGATATCCAACTCAAAGCCAATTTGGTGAA-ACAA-T-
1 AGATTGGATTTCAACTTCACAACGAATGATATCCAACTCAAAGCCAATTTGGTGAAGACAACTC
* * *
1175656 A-CTTGGATTTCAACTTCACAATGAATGATATCCAACCCAAAGCCAATTTGGTGAAGTACAACTC
1 AGATTGGATTTCAACTTCACAACGAATGATATCCAACTCAAAGCCAATTTGGTGAAG-ACAACTC
* * * * *
1175720 GAGATTGTATTTCAACTTCACTACGAAGGATATCTAACTCGAAGC
1 -AGATTGGATTTCAACTTCACAACGAATGATATCCAACTCAAAGC
1175765 TCAACTTCAC
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
60 50 0.55
61 1 0.01
62 4 0.04
63 1 0.01
65 1 0.01
66 34 0.37
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (64 bp):
AGATTGGATTTCAACTTCACAACGAATGATATCCAACTCAAAGCCAATTTGGTGAAGACAACTC
Found at i:1176253 original size:40 final size:40
Alignment explanation
Indices: 1176198--1176304 Score: 178
Period size: 40 Copynumber: 2.7 Consensus size: 40
1176188 TGTCCTGTCG
* *
1176198 TCCTCATCACGTAGGAACCGTGTCATCCCTCTACTAGATC
1 TCCTCATCACGTAGGAACCGTATCATCCCTCGACTAGATC
1176238 TCCTCATCACGTAGGAACCGTATCATCCCTCGACTAGATC
1 TCCTCATCACGTAGGAACCGTATCATCCCTCGACTAGATC
* *
1176278 TCCTCATCACGTAGGAACTGTCTCATC
1 TCCTCATCACGTAGGAACCGTATCATC
1176305 ATCCTTAGAT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.23, C:0.35, G:0.15, T:0.27
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTATCATCCCTCGACTAGATC
Found at i:1176512 original size:3 final size:3
Alignment explanation
Indices: 1176499--1176577 Score: 142
Period size: 3 Copynumber: 26.7 Consensus size: 3
1176489 CCTTAAAAAA
*
1176499 TAT TA- TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1176546 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1176578 ACATATTTAC
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1177979 original size:30 final size:30
Alignment explanation
Indices: 1177918--1177979 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
1177908 TGAATTCTTG
* * **
1177918 TTTTGTTGTTTTATTCTTTTAAATTTCTGT
1 TTTTGATGTTTTAATCCCTTAAATTTCTGT
* *
1177948 TTTTGATGTTTTAATCCCTTAAGTTTTTGT
1 TTTTGATGTTTTAATCCCTTAAATTTCTGT
1177978 TT
1 TT
1177980 CTCTTGCATC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.08, G:0.11, T:0.66
Consensus pattern (30 bp):
TTTTGATGTTTTAATCCCTTAAATTTCTGT
Found at i:1183857 original size:18 final size:20
Alignment explanation
Indices: 1183817--1183859 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1183807 TGGTTTACGA
* *
1183817 AATATAAGATTACCAGTGGG
1 AATAAAAGATTACCAGTGAG
1183837 AATAAAAGATTACC-G-GAG
1 AATAAAAGATTACCAGTGAG
1183855 AATAA
1 AATAA
1183860 GATTACTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
20 13 0.62
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (20 bp):
AATAAAAGATTACCAGTGAG
Found at i:1184235 original size:36 final size:37
Alignment explanation
Indices: 1184195--1184267 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
1184185 ATAATATAGC
1184195 ATGTGTCACGTCACC-AAAAATGATATAATTAAAAAT
1 ATGTGTCACGTCACCAAAAAATGATATAATTAAAAAT
* *
1184231 ATGTGTCACGTTACCAAAAAATGATCTAATTAAAAAT
1 ATGTGTCACGTCACCAAAAAATGATATAATTAAAAAT
1184268 TGATAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 14 0.41
37 20 0.59
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.29
Consensus pattern (37 bp):
ATGTGTCACGTCACCAAAAAATGATATAATTAAAAAT
Found at i:1184716 original size:2 final size:2
Alignment explanation
Indices: 1184709--1184745 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1184699 ATATTAAAAT
1184709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1184746 AAAACTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1185095 original size:19 final size:19
Alignment explanation
Indices: 1185079--1185125 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
1185069 AGAAGGAACA
1185079 CAGGGGAGGGTTGGGAAAT
1 CAGGGGAGGGTTGGGAAAT
*
1185098 TAGGGGAGGGTTGGGAAAT
1 CAGGGGAGGGTTGGGAAAT
*
1185117 TAGGGGAGG
1 CAGGGGAGG
1185126 AAAAGTAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.26, C:0.02, G:0.55, T:0.17
Consensus pattern (19 bp):
CAGGGGAGGGTTGGGAAAT
Found at i:1191124 original size:61 final size:61
Alignment explanation
Indices: 1191029--1191161 Score: 266
Period size: 61 Copynumber: 2.2 Consensus size: 61
1191019 GAGATTGAGA
1191029 ATCATGTTCCATTCCCATGCATTGCATGTTAATCCCTTTGTGATTGGCCCCACAAGTGACC
1 ATCATGTTCCATTCCCATGCATTGCATGTTAATCCCTTTGTGATTGGCCCCACAAGTGACC
1191090 ATCATGTTCCATTCCCATGCATTGCATGTTAATCCCTTTGTGATTGGCCCCACAAGTGACC
1 ATCATGTTCCATTCCCATGCATTGCATGTTAATCCCTTTGTGATTGGCCCCACAAGTGACC
1191151 ATCATGTTCCA
1 ATCATGTTCCA
1191162 ATGCACGTTA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 72 1.00
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (61 bp):
ATCATGTTCCATTCCCATGCATTGCATGTTAATCCCTTTGTGATTGGCCCCACAAGTGACC
Found at i:1191245 original size:24 final size:23
Alignment explanation
Indices: 1191217--1191278 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
1191207 CATTTAATTC
* *
1191217 AAATATATTTTATAATTTTAAATA
1 AAATATATTATATAATATT-AATA
*
1191241 CAATATAATTATATAATATTAATA
1 AAATAT-ATTATATAATATTAATA
1191265 AAATATAATTATAT
1 AAATAT-ATTATAT
1191279 CTATAGAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 22 0.67
25 11 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATATATTATATAATATTAATA
Found at i:1192718 original size:16 final size:16
Alignment explanation
Indices: 1192697--1192729 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1192687 TCTAATGATC
1192697 CTAAAAAAGCGTAAAA
1 CTAAAAAAGCGTAAAA
1192713 CTAAAAAAGCGTAAAA
1 CTAAAAAAGCGTAAAA
1192729 C
1 C
1192730 AATTACAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.15, G:0.12, T:0.12
Consensus pattern (16 bp):
CTAAAAAAGCGTAAAA
Found at i:1193124 original size:2 final size:2
Alignment explanation
Indices: 1193117--1193149 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1193107 ATAGAATAAA
1193117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1193150 AAAGCTAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1198355 original size:35 final size:34
Alignment explanation
Indices: 1198257--1198572 Score: 226
Period size: 35 Copynumber: 8.9 Consensus size: 34
1198247 TTTTATTTAT
*
1198257 ATATATATTATATAG-TCTG-AAATCATTTTGAAA
1 ATATATATTATATAGTTTTGAAAAT-ATTTTGAAA
* * *** *
1198290 ATTATATAATATATGGTTTTTTTATTATTTTGAAA
1 A-TATATATTATATAGTTTTGAAAATATTTTGAAA
* *
1198325 ATATATAATATATAGTTTTTGAAAACATTTTTTGAAA
1 ATATATATTATATAG-TTTTG-AAA-ATATTTTGAAA
* * * * *
1198362 ATACATATTATATTGTTTTG-AATTTTTTTTAAA
1 ATATATATTATATAGTTTTGAAAATATTTTGAAA
* * *
1198395 TATATATAATATATAGCTTTTAAAAACATTCTTGAAAAA
1 -ATATATATTATATAG-TTTTGAAAATATT-TTG--AAA
* * **
1198434 CATATATATTATATAATTTTGAAAATTAGTTTCTAA
1 -ATATATATTATATAGTTTTGAAAA-TATTTTGAAA
*
1198470 ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
1 ATATATATTATATAGTTTTGAAAA-TA--TTTTGAAA
*
1198507 TATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
1 -ATATATATTATATAGTTTTGAAAA-TA-TTTTGAAA
1198544 A-ATATATTATATAGTTTTGAAAATTATTT
1 ATATATATTATATAGTTTTGAAAA-TATTT
1198573 ATACGTTATG
Statistics
Matches: 228, Mismatches: 39, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
33 10 0.04
34 42 0.18
35 71 0.31
36 15 0.07
37 35 0.15
38 37 0.16
39 18 0.08
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (34 bp):
ATATATATTATATAGTTTTGAAAATATTTTGAAA
Found at i:1198408 original size:34 final size:34
Alignment explanation
Indices: 1198282--1198415 Score: 126
Period size: 34 Copynumber: 3.8 Consensus size: 34
1198272 TCTGAAATCA
* ** *
1198282 TTTTGAAAATTATATAATATATGGTTTTTTTATTA
1 TTTTGAAAA-TATATAATATATAGTTTTTGAATTT
*
1198317 TTTTGAAAATATATAATATATAGTTTTTGAAAACATT
1 TTTTGAAAATATATAATATATAGTTTTTG--AA-TTT
* * *
1198354 TTTTGAAAATACATATTATATTG-TTTTGAATTT
1 TTTTGAAAATATATAATATATAGTTTTTGAATTT
* *
1198387 TTTTTAAATATATATAATATATAGCTTTT
1 TTTTGAAA-ATATATAATATATAGTTTTT
1198416 AAAAACATTC
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
33 9 0.11
34 32 0.40
35 13 0.16
36 6 0.07
37 21 0.26
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (34 bp):
TTTTGAAAATATATAATATATAGTTTTTGAATTT
Found at i:1198454 original size:73 final size:74
Alignment explanation
Indices: 1198323--1198566 Score: 219
Period size: 73 Copynumber: 3.4 Consensus size: 74
1198313 ATTATTTTGA
* *
1198323 AAATATATA-A-TATATAGTTTTTGAAAACATTTTTTGAAAATACATAT-TA-TAT-T-GTTTTG
1 AAATATATATAATATATAG-TTTTAAAAACA-GTTTTGAAAA-ACATATATATTATATAGTTTTG
*
1198382 -AATT-TTTTTT
63 AAATTAGTTTTT
*
1198392 AAATATATATAATATATAGCTTTTAAAAACA-TTCTTGAAAAACATATATATTATATAATTTTGA
1 AAATATATATAATATATAG-TTTTAAAAACAGTT-TTGAAAAACATATATATTATATAGTTTTG-
*
1198456 AAATTAGTTTCT
63 AAATTAGTTTTT
** * *
1198468 AAATATATAT--TATATAGTTTTGAAAATTAGTTTT-TAAAATATATATATTATATAGTTTTGAA
1 AAATATATATAATATATAGTTTT-AAAAACAGTTTTGAAAAACATATATATTATATAGTTTTG-A
1198530 AATTAGTTTTT
64 AATTAGTTTTT
* *
1198541 AAA-A-ATATATTATATAGTTTTGAAAA
1 AAATATATATAATATATAGTTTTAAAAA
1198567 TTATTTATAC
Statistics
Matches: 148, Mismatches: 13, Indels: 25
0.80 0.07 0.13
Matches are distributed among these distances:
69 17 0.11
70 10 0.07
71 24 0.16
72 5 0.03
73 58 0.39
74 14 0.09
75 6 0.04
76 14 0.09
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (74 bp):
AAATATATATAATATATAGTTTTAAAAACAGTTTTGAAAAACATATATATTATATAGTTTTGAAA
TTAGTTTTT
Found at i:1198561 original size:22 final size:21
Alignment explanation
Indices: 1198533--1198575 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1198523 TTTTGAAAAT
*
1198533 TAGTTTTTAAAAATATATTATA
1 TAGTTTTGAAAAATAT-TTATA
*
1198555 TAGTTTTGAAAATTATTTATA
1 TAGTTTTGAAAAATATTTATA
1198576 CGTTATGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
TAGTTTTGAAAAATATTTATA
Found at i:1198566 original size:21 final size:19
Alignment explanation
Indices: 1198537--1198575 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1198527 GAAAATTAGT
1198537 TTTTAAAAATATATTATATAG
1 TTTTAAAAAT-TATT-TATAG
*
1198558 TTTTGAAAATTATTTATA
1 TTTTAAAAATTATTTATA
1198576 CGTTATGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTTAAAAATTATTTATAG
Found at i:1198686 original size:4 final size:4
Alignment explanation
Indices: 1198641--1198695 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
1198631 AAATGTTTTA
* * * *
1198641 TATT AATT TATC TATT AATT TATT T-TT TTTT TCATT TA-T TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT T-ATT TATT TATT TATT
1198688 TATT TATT
1 TATT TATT
1198696 ATTGTTTGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
3 6 0.15
4 32 0.78
5 3 0.07
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:1198871 original size:16 final size:15
Alignment explanation
Indices: 1198850--1198880 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1198840 GGCCGGCCGG
1198850 CATCCCGGGACTGACC
1 CATCCCGGGA-TGACC
1198866 CATCCCGGGATGACC
1 CATCCCGGGATGACC
1198881 GGTCACACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.42, G:0.26, T:0.13
Consensus pattern (15 bp):
CATCCCGGGATGACC
Found at i:1199945 original size:22 final size:22
Alignment explanation
Indices: 1199920--1199962 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1199910 AACTTTAACC
*
1199920 TTTT-TTTTATCTATTTTTATTA
1 TTTTATTTTAT-TATTGTTATTA
1199942 TTTTATTTTATTATTGTTATT
1 TTTTATTTTATTATTGTTATT
1199963 TCTTTCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTATTTTATTATTGTTATTA
Found at i:1199948 original size:14 final size:15
Alignment explanation
Indices: 1199931--1199963 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
1199921 TTTTTTTATC
1199931 TATTTTTATTATT-T
1 TATTTTTATTATTGT
1199945 TA-TTTTATTATTGT
1 TATTTTTATTATTGT
1199959 TATTT
1 TATTT
1199964 CTTTCCCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.59
14 5 0.29
15 2 0.12
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TATTTTTATTATTGT
Found at i:1200166 original size:9 final size:10
Alignment explanation
Indices: 1200106--1200165 Score: 57
Period size: 10 Copynumber: 5.5 Consensus size: 10
1200096 ACTTTTTATC
1200106 TTTTTTATTCT
1 TTTTTTATT-T
1200117 TTTGTTTATTT
1 TTT-TTTATTT
**
1200128 TGACTTTAGTGTT
1 T-TTTTTA-T-TT
1200141 TTTTTTATTT
1 TTTTTTATTT
1200151 TTTTTTATTT
1 TTTTTTATTT
1200161 TTTTT
1 TTTTT
1200166 AATTCTTGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
10 17 0.41
11 10 0.24
12 11 0.27
13 3 0.07
ACGTcount: A:0.10, C:0.03, G:0.07, T:0.80
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:1201965 original size:20 final size:19
Alignment explanation
Indices: 1201930--1201975 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
1201920 ATTTAGACAT
1201930 TTTGCA-TTTCTTATTTTTC
1 TTTGCATTTTCTTA-TTTTC
*
1201949 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
1201968 TTTGCATT
1 TTTGCATT
1201976 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:1205517 original size:84 final size:83
Alignment explanation
Indices: 1205330--1206224 Score: 932
Period size: 84 Copynumber: 10.8 Consensus size: 83
1205320 TCATTTTTAA
* * * * **
1205330 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC--CGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACC-AAAGACCTTCGAGTTCGA
* ** * *
1205393 TTACATTCAGCTTCGAGGGC
65 CTACGCTCAGC-TCCAAGGC
1205413 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGA
1205478 CTACGCTCAGCTCCAAGGC
65 CTACGCTCAGCTCCAAGGC
* * * * * * *
1205497 ATATCATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGA
*
1205562 CTACGATCAGCTCCAAGGC
65 CTACGCTCAGCTCCAAGGC
* * **
1205581 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGAC
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGAC
* * *
1205643 TACACTCAGCTTCGAGGGC
66 TACGCTCAGC-TCCAAGGC
* * * * * * *
1205662 ACATCATTTACAGCGTAACTCAAGGCTAGAAGGGTTATCTGTGACCCAAAGACCTTCGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGA
*
1205727 CTACGCTCAGCTCTAAGGC
65 CTACGCTCAGCTCCAAGGC
* * ** *
1205746 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGAT
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGAC
* * *
1205808 TACACTCAGCTTCGAGGGC
66 TACGCTCAGC-TCCAAGGC
* * * *
1205827 ACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGGCCTTCGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGA
* * ** *
1205892 TTACACTCAGCTTTGAGGGC
65 CTACGCTCAGC-TCCAAGGC
* *
1205912 ACATCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGA
1205977 CTACGCTCAGCTCCAAGGC
65 CTACGCTCAGCTCCAAGGC
* ** * * * * * *
1205996 ATATCATTTGCAATACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAATTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGA
1206061 CTACGCTCAGCT-CAACGGC
65 CTACGCTCAGCTCCAA-GGC
* * * * **
1206080 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACC-AAAGACCTTCGAGTTCGA
*
1206145 CTCCGCTCAGCTCCAAGGC
65 CTACGCTCAGCTCCAAGGC
* * * *
1206164 ACATCATTTGCAGCATAGCTTAAGCCGAGAAGGGCTATCTG---CTAAAGACCTTCGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGA
1206225 TTATATTCAA
Statistics
Matches: 689, Mismatches: 107, Indels: 35
0.83 0.13 0.04
Matches are distributed among these distances:
80 70 0.10
81 84 0.12
83 49 0.07
84 333 0.48
85 153 0.22
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (83 bp):
ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGAC
TACGCTCAGCTCCAAGGC
Found at i:1205747 original size:165 final size:165
Alignment explanation
Indices: 1205330--1206224 Score: 998
Period size: 165 Copynumber: 5.4 Consensus size: 165
1205320 TCATTTTTAA
* * * ** *
1205330 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC--CGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
* ** * *
1205393 TTACATTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
66 CTACGCTCAGC-TCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---A
1205458 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
127 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * * * *
1205497 ATATCATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
* * * *
1205562 CTACGATCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAA
66 CTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAA
** * * *
1205626 AGACCCCCGAGTTCGACTACACTCAGCTTCGAGGGC
131 AGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGC
* * * * ** * *
1205662 ACATCATTTACAGCGTAACTCAAGGCTAGAAGGGTTATCTGTGACCCAAAGACCTTCGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
* *
1205727 CTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAA
66 CTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAA
** * * * *
1205791 AGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGC
131 AGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGC
* * *
1205827 ACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGGCCTTCGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
* * * * *
1205892 TTACACTCAGCTTTGAGGGCACATCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
66 CTACGCTCAGCTCT-AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---A
*
1205957 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
127 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* ** * * * *
1205996 ATATCATTTGCAATACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAATTCGA
1 ACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
* * * *
1206061 CTACGCTCAGCTC-AACGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGAC
66 CTACGCTCAGCTCTAA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC--TGAC
*
1206125 CAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGC
128 C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * * * *
1206164 ACATCATTTGCAGCATAGCTTAAGCCGAGAAGGGCTATCTG----CTAAAGACCTTCGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
1206225 TTATATTCAA
Statistics
Matches: 621, Mismatches: 95, Indels: 27
0.84 0.13 0.04
Matches are distributed among these distances:
164 45 0.07
165 220 0.35
166 42 0.07
167 47 0.08
168 150 0.24
169 89 0.14
170 28 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
ACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
CTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAA
AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
Found at i:1206894 original size:34 final size:34
Alignment explanation
Indices: 1206854--1207157 Score: 213
Period size: 35 Copynumber: 8.7 Consensus size: 34
1206844 TTTTATTTAT
* *
1206854 ATATATATTATATAG-TCTGAAATCATTTTGAAA
1 ATATATAATATATAGTTTTGAAATCATTTTGAAA
* ** *
1206887 ATTATATAATATATGGTTTTTTAATTATTTTGAAA
1 A-TATATAATATATAGTTTTGAAATCATTTTGAAA
*
1206922 ATATATAATATATAGTTTTGAAAACATTTTTTGAAA
1 ATATATAATATATAGTTTTGAAATCA--TTTTGAAA
* * * * **
1206958 ATACATATTATATTGTTTTG-AAT-TTTTTTTAA
1 ATATATAATATATAGTTTTGAAATCATTTTGAAA
* *
1206990 ATATATAATATATAGCTTTTAAAAACATTCTTGAAAA
1 ATATATAATATATAG-TTTTGAAATCATT-TTG-AAA
* * * **
1207027 ACATATATATATATA-TTTTGAAAATTAGTTTCTAA
1 ATATATA-ATATATAGTTTTG-AAATCATTTTGAAA
* * *
1207062 ATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
1 ATATATAATATATAGTTTTG-AAATCA-TTTTGAAA
* *
1207098 ATATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
1 ATATATA-A-TATATAGTTTTG-AAATCA-TTTTGAAA
*
1207136 A-ATATATTATATAGTTTTGAAA
1 ATATATAATATATAGTTTTGAAA
1207158 ATTATTTATA
Statistics
Matches: 216, Mismatches: 40, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
32 18 0.08
33 5 0.02
34 43 0.20
35 51 0.24
36 45 0.21
37 18 0.08
38 36 0.17
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.48
Consensus pattern (34 bp):
ATATATAATATATAGTTTTGAAATCATTTTGAAA
Found at i:1206954 original size:36 final size:35
Alignment explanation
Indices: 1206879--1207158 Score: 195
Period size: 36 Copynumber: 7.9 Consensus size: 35
1206869 TCTGAAATCA
* **
1206879 TTTTGAAAATTATATAATATATGGTTTT--TTAATT
1 TTTTGAAAA-TATATAATATATAGTTTTGAAAAATT
1206913 ATTTTGAAAATATATAATATATAGTTTTGAAAACATT
1 -TTTTGAAAATATATAATATATAGTTTTGAAAA-ATT
* * *
1206950 TTTTGAAAATACATATTATATTGTTTTG---AATT
1 TTTTGAAAATATATAATATATAGTTTTGAAAAATT
** *
1206982 TTTTTTAAATATATAATATATAGCTTTT-AAAAACAT
1 TTTTGAAAATATATAATATATAG-TTTTGAAAAA-TT
* *
1207018 TCTTGAAAAACATATATATATATA-TTTTG-AAAATT
1 TTTTG-AAAATATATA-ATATATAGTTTTGAAAAATT
* ** *
1207053 AGTTTCTAAATATATATTATATAGTTTTG-AAAATT
1 -TTTTGAAAATATATAATATATAGTTTTGAAAAATT
*
1207088 AGTTTTTAAAATATATATATTATATAGTTTTG-AAAATT
1 --TTTTGAAAATATATA-A-TATATAGTTTTGAAAAATT
* *
1207126 AGTTTTTAAAA-ATATATTATATAGTTTTGAAAA
1 --TTTTGAAAATATATAATATATAGTTTTGAAAA
1207159 TTATTTATAC
Statistics
Matches: 199, Mismatches: 29, Indels: 33
0.76 0.11 0.13
Matches are distributed among these distances:
32 21 0.11
33 5 0.03
34 23 0.12
35 43 0.22
36 55 0.28
37 16 0.08
38 36 0.18
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (35 bp):
TTTTGAAAATATATAATATATAGTTTTGAAAAATT
Found at i:1207081 original size:35 final size:35
Alignment explanation
Indices: 1206920--1207161 Score: 228
Period size: 35 Copynumber: 6.8 Consensus size: 35
1206910 ATTATTTTGA
* * *
1206920 AAATATATAATATATAGTTTTGAAAA-CATTTTTT
1 AAATATATATTATATAGTTTTGAAAATTAGTTTTT
* * *
1206954 GAAAATACATATTATATTGTTTTG--AATT-TTTTTT
1 --AAATATATATTATATAGTTTTGAAAATTAGTTTTT
* ** *
1206988 AAATATATAATATATAGCTTTT-AAAAACA-TTCTTGAA
1 AAATATATATTATATAG-TTTTGAAAATTAGTT-TT--T
* *
1207025 AAACATATATATATATA-TTTTGAAAATTAGTTTCT
1 AAATATATAT-TATATAGTTTTGAAAATTAGTTTTT
1207060 AAATATATATTATATAGTTTTGAAAATTAGTTTTT
1 AAATATATATTATATAGTTTTGAAAATTAGTTTTT
1207095 AAAATATATATATTATATAGTTTTGAAAATTAGTTTTT
1 --AA-ATATATATTATATAGTTTTGAAAATTAGTTTTT
*
1207133 AAAAATATATTATATAGTTTTGAAAATTA
1 AAATATATATTATATAGTTTTGAAAATTA
1207162 TTTATACGTT
Statistics
Matches: 172, Mismatches: 19, Indels: 31
0.77 0.09 0.14
Matches are distributed among these distances:
32 14 0.08
33 4 0.02
34 18 0.10
35 54 0.31
36 25 0.15
37 16 0.09
38 41 0.24
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (35 bp):
AAATATATATTATATAGTTTTGAAAATTAGTTTTT
Found at i:1207153 original size:22 final size:21
Alignment explanation
Indices: 1207125--1207167 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1207115 TTTTGAAAAT
*
1207125 TAGTTTTTAAAAATATATTATA
1 TAGTTTTGAAAAATAT-TTATA
*
1207147 TAGTTTTGAAAATTATTTATA
1 TAGTTTTGAAAAATATTTATA
1207168 CGTTATGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
TAGTTTTGAAAAATATTTATA
Found at i:1207158 original size:21 final size:19
Alignment explanation
Indices: 1207129--1207167 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1207119 GAAAATTAGT
1207129 TTTTAAAAATATATTATATAG
1 TTTTAAAAAT-TATT-TATAG
*
1207150 TTTTGAAAATTATTTATA
1 TTTTAAAAATTATTTATA
1207168 CGTTATGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTTAAAAATTATTTATAG
Found at i:1207298 original size:34 final size:35
Alignment explanation
Indices: 1207232--1207298 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
1207222 AAATGTTTTA
* * *
1207232 TATTAATTTATCTATTAATTTTTTTTTTTTTCATT
1 TATTAATTTATCTATTAATTATTGTTTGTTTCATT
* *
1207267 TATT-ATTTATTTATTTATTATTGTTTGTTTCA
1 TATTAATTTATCTATTAATTATTGTTTGTTTCA
1207299 GGTCCAAGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 23 0.85
35 4 0.15
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.70
Consensus pattern (35 bp):
TATTAATTTATCTATTAATTATTGTTTGTTTCATT
Found at i:1207461 original size:16 final size:15
Alignment explanation
Indices: 1207440--1207470 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1207430 GGCCGGCCGG
1207440 CATCCCGGGACTGACC
1 CATCCCGGGA-TGACC
1207456 CATCCCGGGATGACC
1 CATCCCGGGATGACC
1207471 GGTCACACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.42, G:0.26, T:0.13
Consensus pattern (15 bp):
CATCCCGGGATGACC
Found at i:1208532 original size:22 final size:22
Alignment explanation
Indices: 1208507--1208549 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1208497 AACTTTAACC
*
1208507 TTTT-TTTTATCTATTTTTATTA
1 TTTTATTTTAT-TATTGTTATTA
1208529 TTTTATTTTATTATTGTTATT
1 TTTTATTTTATTATTGTTATT
1208550 TCTTTCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTATTTTATTATTGTTATTA
Found at i:1208535 original size:14 final size:15
Alignment explanation
Indices: 1208518--1208550 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
1208508 TTTTTTTATC
1208518 TATTTTTATTATT-T
1 TATTTTTATTATTGT
1208532 TA-TTTTATTATTGT
1 TATTTTTATTATTGT
1208546 TATTT
1 TATTT
1208551 CTTTCCCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.59
14 5 0.29
15 2 0.12
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TATTTTTATTATTGT
Found at i:1208753 original size:9 final size:10
Alignment explanation
Indices: 1208693--1208752 Score: 57
Period size: 10 Copynumber: 5.5 Consensus size: 10
1208683 ACTTTTTATC
1208693 TTTTTTATTCT
1 TTTTTTATT-T
1208704 TTTGTTTATTT
1 TTT-TTTATTT
**
1208715 TGACTTTAGTGTT
1 T-TTTTTA-T-TT
1208728 TTTTTTATTT
1 TTTTTTATTT
1208738 TTTTTTATTT
1 TTTTTTATTT
1208748 TTTTT
1 TTTTT
1208753 AATTCTTGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
10 17 0.41
11 10 0.24
12 11 0.27
13 3 0.07
ACGTcount: A:0.10, C:0.03, G:0.07, T:0.80
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:1211721 original size:20 final size:20
Alignment explanation
Indices: 1211692--1211737 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1211682 GCACATTTTC
* *
1211692 TATTGATTTTGTTTGTAGTA
1 TATTGATTTTATTAGTAGTA
1211712 TGATTG-TTTTATTAGTAGTA
1 T-ATTGATTTTATTAGTAGTA
1211732 TATTGA
1 TATTGA
1211738 AGTCACTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.18
20 14 0.64
21 4 0.18
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.57
Consensus pattern (20 bp):
TATTGATTTTATTAGTAGTA
Found at i:1214056 original size:45 final size:47
Alignment explanation
Indices: 1213985--1214093 Score: 152
Period size: 45 Copynumber: 2.3 Consensus size: 47
1213975 CCGTGCTTTG
1213985 TTATTC-AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC-
1 TTATTCGAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA
* * *
1214030 TTGTTCGAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCA
1 TTATTCGAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA
1214076 TTTATTCGAAAAACGAAA
1 -TTATTCGAAAAA-GAAA
1214094 ATGAATGACT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
45 33 0.60
46 8 0.15
47 11 0.20
48 3 0.05
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (47 bp):
TTATTCGAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA
Found at i:1216100 original size:115 final size:115
Alignment explanation
Indices: 1215964--1216183 Score: 332
Period size: 115 Copynumber: 1.9 Consensus size: 115
1215954 TTATTTTAAG
* * * *
1215964 AAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAATAAAAGAGCTGTCTTAAGGTACCTAGA
1 AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
* * * *
1216029 AGCTCTTTTCTGATATTTTTGAATAAATAAATATCTTATTATATTAAAAT
66 AGCCCTTTTATGATATTTCTAAATAAATAAATATCTTATTATATTAAAAT
* * *
1216079 AAAATGTTTTTGATATTTATTTATTTTTTAATATCAAAGAAAAGAGTTGTCTTAAAGCACCTAGA
1 AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
*
1216144 AGCCCTTTTATGATATTTCTAAATAAGTAAATATCTTATT
66 AGCCCTTTTATGATATTTCTAAATAAATAAATATCTTATT
1216184 TATGTATATT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
115 93 1.00
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (115 bp):
AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
AGCCCTTTTATGATATTTCTAAATAAATAAATATCTTATTATATTAAAAT
Found at i:1218353 original size:30 final size:30
Alignment explanation
Indices: 1218295--1218353 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1218285 CATTCACATA
*
1218295 TTTACATTTGCATTTACATTTGCTTTTTTT
1 TTTACATTTGCATTTACATTTGCATTTTTT
* * *
1218325 TTTACGTTTGTATTTACATTTTCATTTTT
1 TTTACATTTGCATTTACATTTGCATTTTT
1218354 ACATAATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.64
Consensus pattern (30 bp):
TTTACATTTGCATTTACATTTGCATTTTTT
Found at i:1220799 original size:2 final size:2
Alignment explanation
Indices: 1220792--1220821 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1220782 TTATCCTTTA
1220792 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1220822 CCTTTGTTGT
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):
AT
Found at i:1225620 original size:54 final size:54
Alignment explanation
Indices: 1225538--1225703 Score: 253
Period size: 54 Copynumber: 3.1 Consensus size: 54
1225528 CAATGATTGA
1225538 GAACATCTGAGCAGAAA-TCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACT-ACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
1225592 GAACATCTGAGCAGAAACTACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACTACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
* * * * * **
1225646 GAACATCTGAGCAGAAGCCACATGAAAGGATGAATGCGCCGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACTACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
1225700 GAAC
1 GAAC
1225704 CTGCTATTCT
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
54 103 0.99
55 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (54 bp):
GAACATCTGAGCAGAAACTACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
Found at i:1226087 original size:22 final size:22
Alignment explanation
Indices: 1226061--1226139 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 22
1226051 ACATCTACAT
1226061 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
1226083 TCTTCAAAGATCATAGATTCCC
1 TCTTCAAAGATGATAGATTCTC
* * * *
1226105 TTTTTAAAAATGACAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
1226127 TTTTCAAATATGA
1 TCTTCAAAGATGA
1226140 AAGCTTTATC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1226745 original size:40 final size:40
Alignment explanation
Indices: 1226690--1226790 Score: 193
Period size: 40 Copynumber: 2.5 Consensus size: 40
1226680 TTTCCAGAGA
*
1226690 AAGTTCATAATGAGAAGAAGTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1226730 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1226770 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
1226791 TGTTCAACTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.19
Consensus pattern (40 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
Found at i:1226847 original size:113 final size:113
Alignment explanation
Indices: 1226730--1227362 Score: 598
Period size: 113 Copynumber: 5.3 Consensus size: 113
1226720 AAGGAAGAAG
1226730 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
1226795 CAA-CTTTTCGCTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGA
66 CAACCTTTT-GCTTGAATTCATCAATCGATGCATCAACATTTCCAGAGA
*
1226843 AAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
1226908 CAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTGCCAG-GTA
66 CAACCTTTTGCTTGAATTCATCAATCGATGCATCAACATTTCCAGAG-A
* * *
1226956 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * ** *
1227021 AAACCTTTTACTCG-ACTCTATCCCAGAAGGAGATAAATCAACATCAACATTTCCAGAGA
66 CAACCTTTTGCTTGAATTC-AT--C------A-ATCGAT--GCATCAACATTTCCAGAGA
*
1227080 AAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * *
1227144 CAACCTTTTGCTCG-ACTCTATCGTAGAAGGAGATAGATCTGCATCAA-TTTTTCAGAGA
66 CAACCTTTTGCTTGAATTC-ATC--------A-ATCGA--TGCATCAACATTTCCAGAGA
*
1227202 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * *
1227267 CAACC-TTTGTTTG-ATTCTATCACAGAATGAGATAGACCAGTATCAGCATTTCCATAAA
66 CAACCTTTTGCTTGAATTC-AT--C--AAT-CGAT-G--C---ATCAACATTTCCAGAGA
*
1227325 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1227363 GAATTTGTTC
Statistics
Matches: 453, Mismatches: 37, Indels: 50
0.84 0.07 0.09
Matches are distributed among these distances:
112 4 0.01
113 176 0.39
114 5 0.01
115 1 0.00
116 1 0.00
117 3 0.01
118 5 0.01
119 1 0.00
121 2 0.00
122 58 0.13
123 151 0.33
124 44 0.10
125 2 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (113 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTGCTTGAATTCATCAATCGATGCATCAACATTTCCAGAGA
Found at i:1226856 original size:153 final size:153
Alignment explanation
Indices: 1226578--1226903 Score: 607
Period size: 153 Copynumber: 2.1 Consensus size: 153
1226568 TGCCAGGTCG
*
1226578 AGTTCATAATGAGAAGAACTCATCTGAAGAATAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
1226643 AACTTTTCGCTTGAATTCATTATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGA
66 AACTTTTCGCTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAAA
*
1226708 AGTCATCTGAAGAAGGAAGAAGA
131 ACTCATCTGAAGAAGGAAGAAGA
*
1226731 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1226796 AACTTTTCGCTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAAA
66 AACTTTTCGCTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAAA
1226861 ACTCATCTGAAGAAGGAAGAAGA
131 ACTCATCTGAAGAAGGAAGAAGA
1226884 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
1226904 TGTTCAACCT
Statistics
Matches: 168, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
153 168 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (153 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTCGCTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAAA
ACTCATCTGAAGAAGGAAGAAGA
Found at i:1227159 original size:123 final size:124
Alignment explanation
Indices: 1226939--1227362 Score: 586
Period size: 123 Copynumber: 3.4 Consensus size: 124
1226929 CATTCGATGG
* * *
1226939 ATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCA
1 ATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * * * * *
1227003 TAATAAGAAGAACTTGTTAAACCTTTTACTCGACTCTATCCCAGAAGGAGATAAATCAAC
65 TAATGAGAAGAGCTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
1227063 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
** *
1227127 AATGAGAAGAGCTTGTTCAACCTTTTGCTCGACTCTATCGTAGAAGGAGATAGATCTGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
* *
1227186 ATCAA-TTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * * * *
1227250 AATGAGAAGAGCTTGTTCAACC-TTTGTTTGATTCTATCACAGAATGAGATAGACCAGT
66 AATGAGAAGAGCTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
* * * *
1227308 ATCAGCATTTCCATAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGA
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1227363 GAATTTGTTC
Statistics
Matches: 268, Mismatches: 29, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
122 70 0.26
123 154 0.57
124 43 0.16
125 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (124 bp):
ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
Found at i:1227889 original size:75 final size:76
Alignment explanation
Indices: 1227721--1227926 Score: 292
Period size: 76 Copynumber: 2.8 Consensus size: 76
1227711 CAAAGCTAAA
* * * **
1227721 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAATGGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
1227786 TTGGCCCCGAG
66 TTGGCCCCGAG
*
1227797 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
*
1227862 TT-GCTCCGAG
66 TTGGCCCCGAG
* * * *
1227872 AATTCCAGTATGCTCGGAGGGAACCGA-TCCCCCCA-AGGGGGTACCAATTCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCT
1227927 TGTACAACGG
Statistics
Matches: 118, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
73 17 0.14
74 8 0.07
75 32 0.27
76 61 0.52
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.20
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TTGGCCCCGAG
Found at i:1233735 original size:23 final size:20
Alignment explanation
Indices: 1233682--1233742 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 20
1233672 TTTTGGTGCA
1233682 GAGGGAATCGA-TCCCCCCT
1 GAGGGAATCGATTCCCCCCT
* *
1233701 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCC-CT
1233722 GAAGGGGAATCGATTCCCCCC
1 G-A-GGGAATCGATTCCCCCC
1233743 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.29
20 6 0.18
21 2 0.06
22 1 0.03
23 15 0.44
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.18
Consensus pattern (20 bp):
GAGGGAATCGATTCCCCCCT
Found at i:1235696 original size:17 final size:17
Alignment explanation
Indices: 1235674--1235721 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1235664 TTTCAACATT
1235674 TTTGATATTTTGGATTG
1 TTTGATATTTTGGATTG
1235691 TTTGAT-TTTGTGGATTG
1 TTTGATATTT-TGGATTG
*
1235708 -TTG-GATTTTGGATT
1 TTTGATATTTTGGATT
1235722 TATGAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (17 bp):
TTTGATATTTTGGATTG
Found at i:1236459 original size:77 final size:77
Alignment explanation
Indices: 1236306--1236514 Score: 291
Period size: 77 Copynumber: 2.7 Consensus size: 77
1236296 CAAAGCTAAA
* * * **
1236306 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1236371 TTTGGCCCCGAG
66 TTTGGCCCCGAG
*
1236383 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
*
1236448 TTTT-GCTCCGAG
65 TTTTGGCCCCGAG
* *
1236460 AATTCCA-ATATGCTCGGAGGGAACCGA-TCCCCCCA-AGGGGGTACCGATTCCCCCC
1 AATTCCAGA-ATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCC
1236515 CTTGTACAAC
Statistics
Matches: 120, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
74 18 0.15
75 7 0.06
76 2 0.02
77 56 0.47
78 37 0.31
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:1238963 original size:115 final size:115
Alignment explanation
Indices: 1238827--1239046 Score: 332
Period size: 115 Copynumber: 1.9 Consensus size: 115
1238817 TTATTTTAAG
* * * *
1238827 AAAATGTTTTGGTTATTTATTTATTTTTCAATATCAAATAAAAGAGCTGTCTTAAGGTACCTAGA
1 AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
* * * *
1238892 AGCTCTTTTCTGATATTTTTGAATAAATAAATATCTTATTATATTAAAAT
66 AGCCCTTTTATGATATTTCTAAATAAATAAATATCTTATTATATTAAAAT
* * *
1238942 AAAATGTTTTTGATATTTATTTATTTTTTAATATCAAAGAAAAGAGTTGTCTTAAAGCACCTAGA
1 AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
*
1239007 AGCCCTTTTATGATATTTCTAAATAAGTAAATATCTTATT
66 AGCCCTTTTATGATATTTCTAAATAAATAAATATCTTATT
1239047 TATGTATATT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
115 93 1.00
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (115 bp):
AAAATGTTTTGGATATTTATTTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGA
AGCCCTTTTATGATATTTCTAAATAAATAAATATCTTATTATATTAAAAT
Found at i:1244534 original size:24 final size:24
Alignment explanation
Indices: 1244481--1244534 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1244471 AATAACCCAT
*
1244481 AAATTATAATAAAAGACTAAAATG
1 AAATTTTAATAAAAGACTAAAATG
1244505 AAATTTTAATAAAAGACTAAAATG
1 AAATTTTAATAAAAGACTAAAATG
1244529 AAATTT
1 AAATTT
1244535 CACAGAGACG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (24 bp):
AAATTTTAATAAAAGACTAAAATG
Found at i:1245113 original size:2 final size:2
Alignment explanation
Indices: 1245106--1245150 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1245096 GTTTTGTACT
1245106 TA TA TA TA TA TA 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 TA TA TA TA TA TA
1245148 TA T
1 TA T
1245151 GTAATCTAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.