Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006093.1 Hibiscus syriacus cultivar Beakdansim tig00014444_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: 3172561
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 13
Found at i:2448743 original size:2 final size:2
Alignment explanation
Indices: 2448732--2448792 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
2448722 TTATGCATGA
2448732 AT AT -T 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
2448773 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
2448793 TTATGTTTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2452628 original size:21 final size:21
Alignment explanation
Indices: 2452616--2452657 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2452606 TATTCAATAT
2452616 TTCAAAATATCTACAATTAAA
1 TTCAAAATATCTACAATTAAA
2452637 TTCAAAATATCTACAATTAAA
1 TTCAAAATATCTACAATTAAA
2452658 CCCCTAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.33
Consensus pattern (21 bp):
TTCAAAATATCTACAATTAAA
Found at i:2458307 original size:21 final size:21
Alignment explanation
Indices: 2458281--2458335 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
2458271 GGTTTTCTAT
2458281 GAACTTGAAGATGGAATCTTC
1 GAACTTGAAGATGGAATCTTC
*
2458302 GAACTTGAAGCTGGAATCTTC
1 GAACTTGAAGATGGAATCTTC
*
2458323 GAAGTTGAAGATG
1 GAACTTGAAGATG
2458336 AGCCTTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (21 bp):
GAACTTGAAGATGGAATCTTC
Found at i:2459025 original size:59 final size:59
Alignment explanation
Indices: 2458955--2459466 Score: 676
Period size: 59 Copynumber: 8.7 Consensus size: 59
2458945 TCCCATACAG
* * * * *
2458955 AAATTCATAAACTTAGCAT-AGATTTCTTATCATTTTAGCACAC-AAGGTGCCCAATACGG
1 AAATTCATACACTTAGTATGA-ATTTCTTAACATTTTAGCACACGAA-GTGCCCTATACGA
* * * * * *
2459014 AGAGTCATAAACTTAGTGTGAATTTCTTAACATTTTAGAACACGAAGTGCCCTATACAA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGA
* * * *
2459073 AAATTCATACACTTGGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCAATATGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGA
* * * *
2459132 AAATTCATACACTTCA-TATGAAATTCATAACATTTTAGCACACGAAGTGCCCAATACAA
1 AAATTCATACACTT-AGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGA
* *
2459191 AAATTCATACACTTAGTATAAATTTCTTAACATTTTAGCACACGAAGTGCCCTATAAGA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGA
* *
2459250 AAATTTATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTACCCTATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGA
* *
2459309 AAATTCATACACTTAGTATGAATTTCTTAACA-TTT--CACACTAAGTGCCCTATACAA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGA
* * * * *
2459365 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCATATGAAATGCTCTATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGA
*
2459424 AAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACAC
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
2459467 TTAGTGCCAT
Statistics
Matches: 397, Mismatches: 49, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
56 50 0.13
57 3 0.01
58 4 0.01
59 337 0.85
60 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGA
Found at i:2459989 original size:94 final size:95
Alignment explanation
Indices: 2459797--2460019 Score: 306
Period size: 94 Copynumber: 2.4 Consensus size: 95
2459787 TGGTTCTTCA
* * * *
2459797 GTATCGATACTCC-TACCATGGTATCGATACTACCCTACTTTGGTATTGATAGCCCCTTCCGGTA
1 GTATCGATAC-CCTTACCATGGTATCGATACTACCATACTATGGTACTGATAGCCCCTTCCAGTA
*
2459861 TCGATACCAAAATTAGATTCGATGTGGCCTG
65 TCGATACCAAAATTAGATTCGATGTGACCTG
* * *
2459892 GTATCGATACCCTTACCATGATATCGATACTACTATACTATGGTACTGATA-CCCCTTCTAGTAT
1 GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACTGATAGCCCCTTCCAGTAT
* * * *
2459956 CGATTCCAAAATTAGGTTCGATGTTACTTG
66 CGATACCAAAATTAGATTCGATGTGACCTG
*
2459986 GTATCGATACCTTTACCATGGTATCGATACTACC
1 GTATCGATACCCTTACCATGGTATCGATACTACC
2460020 TCATCGGTAT
Statistics
Matches: 112, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
94 69 0.62
95 43 0.38
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (95 bp):
GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACTGATAGCCCCTTCCAGTAT
CGATACCAAAATTAGATTCGATGTGACCTG
Found at i:2465953 original size:59 final size:59
Alignment explanation
Indices: 2465878--2466222 Score: 503
Period size: 59 Copynumber: 5.8 Consensus size: 59
2465868 TATATTTTCC
* *
2465878 ATACGAAAATCCATACACTTAGTATGAATTTCTTAACATTTTATCACACGAAGTGCCCT
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCT
* * * *
2465937 ATACGAAAATTTATACACTTAGTAAGAATTTCTTTACATTTTAGCACGCGAAGTGCCCT
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCT
*
2465996 ATAC-AGAAATTCATACACTTAGCATGAATTTCTTAACATTTTAGCACACGAAGTGCCCT
1 ATACGA-AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCT
* * * *
2466055 ATAAGGAAATTCATACACTTAGTATGATTTTTTTTAACATTTTAGCACACGAAGTGCCCT
1 ATACGAAAATTCATACACTTAGTATGA-ATTTCTTAACATTTTAGCACACGAAGTGCCCT
* * * *
2466115 ATACGGAAATTCATACACTTAGTATGAATTTCCTGACATTTAAGCACACGAAGTGCCCT
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCT
* * *
2466174 TTACGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACAC
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
2466223 TTAGTGTCAT
Statistics
Matches: 256, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
58 1 0.00
59 199 0.78
60 56 0.22
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.33
Consensus pattern (59 bp):
ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCT
Found at i:2466154 original size:119 final size:118
Alignment explanation
Indices: 2465878--2466222 Score: 503
Period size: 119 Copynumber: 2.9 Consensus size: 118
2465868 TATATTTTCC
* * * *
2465878 ATACGAAAATCCATACACTTAGTATGAATTTCTTAACATTTTATCACACGAAGTGCCCTATACGA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * * *
2465943 AAATTTATACACTTAGTAAGAATTTCTTT-ACATTTTAGCACGCGAAGTGCCCT
66 AAATTCATACACTTAGTATG-ATTTTTTTAACATTTTAGCACACGAAGTGCCCT
* * *
2465996 ATACAGAAATTCATACACTTAGCATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATAAGG
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
2466061 AAATTCATACACTTAGTATGATTTTTTTTAACATTTTAGCACACGAAGTGCCCT
66 AAATTCATACACTTAGTATGA-TTTTTTTAACATTTTAGCACACGAAGTGCCCT
* * * *
2466115 ATACGGAAATTCATACACTTAGTATGAATTTCCTGACATTTAAGCACACGAAGTGCCCTTTACGG
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * *
2466180 AAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACAC
66 AAATTCATACACTTAGTATGATTTTTTTAACATTTTAGCACAC
2466223 TTAGTGTCAT
Statistics
Matches: 204, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
117 1 0.00
118 101 0.50
119 102 0.50
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.33
Consensus pattern (118 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
AAATTCATACACTTAGTATGATTTTTTTAACATTTTAGCACACGAAGTGCCCT
Found at i:2466216 original size:178 final size:177
Alignment explanation
Indices: 2465884--2466222 Score: 534
Period size: 178 Copynumber: 1.9 Consensus size: 177
2465874 TTCCATACGA
* *
2465884 AAATCCATACACTTAGTATGAATTTCTTAACATTTTATCACACGAAGTGCCCTATACGAAAATTT
1 AAATCCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGAAAATTC
* * * *
2465949 ATACACTTAGTAAGAATTTCTTTACATTTTAGCACGCGAAGTGCCCTATACAGAAATTCATACAC
66 ATACACTTAGTAAGAATTTCCTGACATTTAAGCACACGAAGTGCCCTATACAGAAATTCATACAC
2466014 TTAGCATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATAAGG
131 TTAGCATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATAAGG
* * * *
2466061 AAATTCATACACTTAGTATGATTTTTTTTAACATTTTAGCACACGAAGTGCCCTATACGGAAATT
1 AAATCCATACACTTAGTATGA-ATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGAAAATT
* * *
2466126 CATACACTTAGTATGAATTTCCTGACATTTAAGCACACGAAGTGCCCTTTACGGAAATTCATACA
65 CATACACTTAGTAAGAATTTCCTGACATTTAAGCACACGAAGTGCCCTATACAGAAATTCATACA
* *
2466191 CTTAGTATGAATTTCTTATCATTTTAGCACAC
130 CTTAGCATGAATTTCTTAACATTTTAGCACAC
2466223 TTAGTGTCAT
Statistics
Matches: 146, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
177 20 0.14
178 126 0.86
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (177 bp):
AAATCCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGAAAATTC
ATACACTTAGTAAGAATTTCCTGACATTTAAGCACACGAAGTGCCCTATACAGAAATTCATACAC
TTAGCATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATAAGG
Found at i:2466577 original size:20 final size:21
Alignment explanation
Indices: 2466552--2466603 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 21
2466542 TGGTTCTTCA
2466552 GTATCGATACT-CCTACCATG
1 GTATCGATACTACCTACCATG
*
2466572 GTATCGATACTACCCTACTATG
1 GTATCGATACTA-CCTACCATG
2466594 GTATCGATAC
1 GTATCGATAC
2466604 CCCTTGTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 11 0.38
22 18 0.62
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (21 bp):
GTATCGATACTACCTACCATG
Found at i:2466690 original size:94 final size:95
Alignment explanation
Indices: 2466551--2466774 Score: 276
Period size: 95 Copynumber: 2.4 Consensus size: 95
2466541 ATGGTTCTTC
* * * *
2466551 AGTATCGATACTCC-TACCATGGTATCGATACTACCCTACTATGGTA-TCGATA-CCCCTTGTAG
1 AGTATCGACAC-CCTTACCATGGTATCGATACTACCATACAATGGTACT-GATACCCCCTTCTAG
*
2466613 TATCGATACCAAAATTA-GATTCAATGTGGCCT
64 TATCGATACCAAAATTAGGA-TCAATGTGACCT
* * *
2466645 AGTATCGACACCCTTTCCATGGTATCGATACTACTATACAATGGTACTGATACCCCCTTCTGGTA
1 AGTATCGACACCCTTACCATGGTATCGATACTACCATACAATGGTACTGATACCCCCTTCTAGTA
* * *
2466710 TCTATACCAAAATTAGGATCAATGTTACTT
66 TCGATACCAAAATTAGGATCAATGTGACCT
* *
2466740 GGTATCGATACCCTTACCATGGTATCGATACTACC
1 AGTATCGACACCCTTACCATGGTATCGATACTACC
2466775 TCGTCGATAC
Statistics
Matches: 111, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
93 2 0.02
94 42 0.38
95 65 0.59
96 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (95 bp):
AGTATCGACACCCTTACCATGGTATCGATACTACCATACAATGGTACTGATACCCCCTTCTAGTA
TCGATACCAAAATTAGGATCAATGTGACCT
Found at i:2468432 original size:115 final size:116
Alignment explanation
Indices: 2468208--2468437 Score: 311
Period size: 115 Copynumber: 2.0 Consensus size: 116
2468198 TATCGCAATC
* *
2468208 AGGTTTTGTGTTTTGTCTTAATGGAGGTGTTGTGAGTTGGAAAAGTTTAAAGCAAGACACAATAG
1 AGGTTTTGTGTTTTGTCTTAATAGAGGTGTTGTGAGCTGGAAAAGTTTAAAGCAAGACACAATAG
* **
2468273 TTGATTCTACAACAGATGCTGAATACATTGCAGCCGGTGAAGTAGCAAAAG
66 TTGATTCTACAACAGAGGCTGAATACATTGCAGCCAATGAAGTAGCAAAAG
* * * ** *
2468324 AGGTTTTGTTTTTTGTCTTAATAGAGGTGTTGTGAGCTGGAATAA-TTTCAAG-AAGGCTTAGTA
1 AGGTTTTGTGTTTTGTCTTAATAGAGGTGTTGTGAGCTGGAA-AAGTTTAAAGCAAGACACAATA
* * *
2468387 GTTGATTCTACAATAGAGGTTGAATACATTGCAGCCAATGAAGTAGTAAAA
65 GTTGATTCTACAACAGAGGCTGAATACATTGCAGCCAATGAAGTAGCAAAA
2468438 AGTTGTTTGG
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
115 52 0.53
116 45 0.45
117 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.33
Consensus pattern (116 bp):
AGGTTTTGTGTTTTGTCTTAATAGAGGTGTTGTGAGCTGGAAAAGTTTAAAGCAAGACACAATAG
TTGATTCTACAACAGAGGCTGAATACATTGCAGCCAATGAAGTAGCAAAAG
Found at i:2468439 original size:116 final size:116
Alignment explanation
Indices: 2468208--2468439 Score: 306
Period size: 116 Copynumber: 2.0 Consensus size: 116
2468198 TATCGCAATC
* *
2468208 AGGTTTTGTGTTTTGTCTTAATGGAGGTGTTGTGAGTTGGAAAAGTTTAAAGCAAGACACAATAG
1 AGGTTTTGTGTTTTGTCTTAATAGAGGTGTTGTGAGCTGGAAAAGTTTAAAGCAAGACACAATAG
* ** *
2468273 TTGATTCTACAACAGATGCTGAATACATTGCAGCCGGTGAAGTAGCAAAAG
66 TTGATTCTACAACAGAGGCTGAATACATTGCAGCCAATGAAGTAGAAAAAG
* * * ** *
2468324 AGGTTTTGTTTTTTGTCTTAATAGAGGTGTTGTGAGCTGGAATAA-TTTCAAG-AAGGCTTAGTA
1 AGGTTTTGTGTTTTGTCTTAATAGAGGTGTTGTGAGCTGGAA-AAGTTTAAAGCAAGACACAATA
* *
2468387 GTTGATTCTACAATAGAGGTTGAATACATTGCAGCCAATGAAGTAGTAAAAAG
65 GTTGATTCTACAACAGAGGCTGAATACATTGCAGCCAATGAAGTAG-AAAAAG
2468440 TTGTTTGGAT
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
115 48 0.48
116 50 0.50
117 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (116 bp):
AGGTTTTGTGTTTTGTCTTAATAGAGGTGTTGTGAGCTGGAAAAGTTTAAAGCAAGACACAATAG
TTGATTCTACAACAGAGGCTGAATACATTGCAGCCAATGAAGTAGAAAAAG
Found at i:2469434 original size:26 final size:25
Alignment explanation
Indices: 2469396--2469561 Score: 110
Period size: 26 Copynumber: 7.1 Consensus size: 25
2469386 TCATGCCTTA
*
2469396 ATGCATCATTTCATGCATTTTAGTT
1 ATGCATCCTTTCATGCATTTTAGTT
2469421 ATGGCATCCTTTCATGC--TTTA---
1 AT-GCATCCTTTCATGCATTTTAGTT
* *
2469442 ATGCAT-TTTTCATACATTTTAGTT
1 ATGCATCCTTTCATGCATTTTAGTT
* * * *
2469466 ATACCATCATTTCATGC--CTTA-AT
1 AT-GCATCCTTTCATGCATTTTAGTT
* *
2469489 -TGCATGCTTTCATGAATTTTAGTT
1 ATGCATCCTTTCATGCATTTTAGTT
*
2469513 ATTGCATCCTTTCATGC--CTTA---
1 A-TGCATCCTTTCATGCATTTTAGTT
2469534 ATGCATCCTTTCATGCATTTTAGTT
1 ATGCATCCTTTCATGCATTTTAGTT
2469559 ATG
1 ATG
2469562 AATTCGTTTT
Statistics
Matches: 105, Mismatches: 18, Indels: 36
0.66 0.11 0.23
Matches are distributed among these distances:
19 7 0.07
20 19 0.18
21 17 0.16
22 4 0.04
23 4 0.04
24 13 0.12
25 8 0.08
26 33 0.31
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.46
Consensus pattern (25 bp):
ATGCATCCTTTCATGCATTTTAGTT
Found at i:2469434 original size:46 final size:45
Alignment explanation
Indices: 2469359--2469561 Score: 262
Period size: 46 Copynumber: 4.4 Consensus size: 45
2469349 CTAGTAATTA
* * * *
2469359 TTCATGAATTTCAGTTATGACATCTTTTCATGCCTTAATGCATCAT
1 TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC-T
* *
2469405 TTCATGCATTTTAGTTATGGCATCCTTTCATGCTTTAATGCATTT
1 TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCT
* ** *
2469450 TTCATACATTTTAGTTATACCATCATTTCATGCCTTAATTGCATGCT
1 TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA-TGCAT-CT
* *
2469497 TTCATGAATTTTAGTTATTGCATCCTTTCATGCCTTAATGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCAT-CT
2469543 TTCATGCATTTTAGTTATG
1 TTCATGCATTTTAGTTATG
2469562 AATTCGTTTT
Statistics
Matches: 135, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
45 34 0.25
46 67 0.50
47 34 0.25
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.46
Consensus pattern (45 bp):
TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCT
Found at i:2477043 original size:24 final size:25
Alignment explanation
Indices: 2477016--2477065 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
2477006 GTTATCACCC
2477016 TCCA-TTTAAACTGAAACATCATCT
1 TCCATTTTAAACTGAAACATCATCT
2477040 TCCATTTTAAACTGAAACATCATCT
1 TCCATTTTAAACTGAAACATCATCT
2477065 T
1 T
2477066 TATTTTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (25 bp):
TCCATTTTAAACTGAAACATCATCT
Found at i:2477794 original size:20 final size:21
Alignment explanation
Indices: 2477746--2477810 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 21
2477736 AAAGAAAGTG
*
2477746 AAGCACTCAAAAGAAAGAAAA
1 AAGCACTAAAAAGAAAGAAAA
2477767 ATCCAGCACTAAAAAG-AAGAAAA
1 A---AGCACTAAAAAGAAAGAAAA
2477790 AAGCA-TAGAAAAGAAAGAAAA
1 AAGCACTA-AAAAGAAAGAAAA
2477811 GAAGTTGTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 2 0.05
20 9 0.24
21 8 0.21
23 8 0.21
24 11 0.29
ACGTcount: A:0.66, C:0.12, G:0.15, T:0.06
Consensus pattern (21 bp):
AAGCACTAAAAAGAAAGAAAA
Found at i:2480968 original size:15 final size:15
Alignment explanation
Indices: 2480956--2480985 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2480946 TTTTTTTTTG
2480956 TGATTTTTATTTTAT
1 TGATTTTTATTTTAT
*
2480971 TGATTTTCATTTTAT
1 TGATTTTTATTTTAT
2480986 AAAAGCATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (15 bp):
TGATTTTTATTTTAT
Found at i:2481568 original size:31 final size:30
Alignment explanation
Indices: 2481506--2481593 Score: 149
Period size: 31 Copynumber: 2.9 Consensus size: 30
2481496 GTTATGCTCA
2481506 AACTTGACCTATCTTTATTAAAAAATGACC
1 AACTTGACCTATCTTTATTAAAAAATGACC
2481536 AACTTGACCTATCTTTATTAAAAATATGACC
1 AACTTGACCTATCTTTATTAAAAA-ATGACC
*
2481567 AACTTGAACTATCTTTATTAACAAAAT
1 AACTTGACCTATCTTTATTAA-AAAAT
2481594 CATTTTTAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
30 24 0.44
31 28 0.51
32 3 0.05
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (30 bp):
AACTTGACCTATCTTTATTAAAAAATGACC
Found at i:2482428 original size:20 final size:19
Alignment explanation
Indices: 2482403--2482456 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2482393 GCGAAATAAA
2482403 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
2482423 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
2482443 AATCGCAACGCGAT
1 AATCGCAACGCGAT
2482457 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:2482531 original size:20 final size:19
Alignment explanation
Indices: 2482506--2482558 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
2482496 AATTTTCCAG
2482506 AATCGCAACGCAA-ATATGAA
1 AATCGCAACGCAACATAT--A
2482526 AATCGCAACGCGAACATATA
1 AATCGCAACGC-AACATATA
2482546 AATCGCAACGCAA
1 AATCGCAACGCAA
2482559 TTCTGACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.06
20 23 0.74
21 2 0.06
22 4 0.13
ACGTcount: A:0.47, C:0.25, G:0.15, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCAACATATA
Found at i:2482610 original size:81 final size:81
Alignment explanation
Indices: 2482525--2482803 Score: 282
Period size: 81 Copynumber: 3.5 Consensus size: 81
2482515 GCAAATATGA
* * * * * *
2482525 AAATCGCAACGCGAACATATAAATCGCAACGC-AATTCTG-ACTATCACAACTAGTATCCGTAAA
1 AAATCGCAACGCGAACATATAAATCGCAACGCGTA-TCTGTA-AATCGCAACGAGAATACGTAAA
2482588 ATCGCAACGCGTATCCGT
64 ATCGCAACGCGTATCCGT
* * *
2482606 AAATCGCAACGACAATACGTA-AAATCGCAACGTGTATCTGTAAATCGCAACGAGAATACG-AAA
1 AAATCGCAACG-CGA-ACATATAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAA
*
2482669 ATCGCAACGCGTATCTGT
64 ATCGCAACGCGTATCCGT
* * ** * * * * *
2482687 AAATCGCAACGAGAATACGTAAATCGTAATGCGTATCCGTAAATCGCAACGACAATGCGTAAAAT
1 AAATCGCAACGCGAACATATAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAAAT
*
2482752 CGCAACGCATATCCGT
66 CGCAACGCGTATCCGT
* *
2482768 AAATCGCAACGCGATCA-ATAATTCGCAACGCG-ATCT
1 AAATCGCAACGCGAACATATAAATCGCAACGCGTATCT
2482804 CCGGTATCGC
Statistics
Matches: 160, Mismatches: 32, Indels: 14
0.78 0.16 0.07
Matches are distributed among these distances:
79 4 0.03
80 45 0.28
81 75 0.47
82 30 0.19
83 6 0.04
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (81 bp):
AAATCGCAACGCGAACATATAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAAAT
CGCAACGCGTATCCGT
Found at i:2482611 original size:20 final size:20
Alignment explanation
Indices: 2482577--2482799 Score: 200
Period size: 20 Copynumber: 11.1 Consensus size: 20
2482567 ATCACAACTA
2482577 GTATCCGTAAAATCGCAACGC
1 GTATCCGT-AAATCGCAACGC
2482598 GTATCCGTAAATCGCAACGAC
1 GTATCCGTAAATCGCAACG-C
* * *
2482619 -AATACGTAAAATCGCAACGT
1 GTATCCGT-AAATCGCAACGC
* *
2482639 GTATCTGTAAATCGCAACGA
1 GTATCCGTAAATCGCAACGC
* * *
2482659 GAATACGAAAATCGCAACGC
1 GTATCCGTAAATCGCAACGC
* *
2482679 GTATCTGTAAATCGCAACGA
1 GTATCCGTAAATCGCAACGC
* * * *
2482699 GAATACGTAAATCGTAATGC
1 GTATCCGTAAATCGCAACGC
2482719 GTATCCGTAAATCGCAACGAC
1 GTATCCGTAAATCGCAACG-C
* *
2482740 -AATGCGTAAAATCGCAACGC
1 GTATCCGT-AAATCGCAACGC
*
2482760 ATATCCGTAAATCGCAACGC
1 GTATCCGTAAATCGCAACGC
** *
2482780 G-ATCAATAATTCGCAACGC
1 GTATCCGTAAATCGCAACGC
2482799 G
1 G
2482800 ATCTCCGGTA
Statistics
Matches: 161, Mismatches: 35, Indels: 14
0.77 0.17 0.07
Matches are distributed among these distances:
19 16 0.10
20 104 0.65
21 41 0.25
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
GTATCCGTAAATCGCAACGC
Found at i:2482683 original size:40 final size:41
Alignment explanation
Indices: 2482582--2482778 Score: 299
Period size: 40 Copynumber: 4.9 Consensus size: 41
2482572 AACTAGTATC
2482582 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
* * *
2482623 CGTAAAATCGCAACGTGTATCTGTAAATCGCAACGAGAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
* *
2482664 CG-AAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
* * *
2482704 CGT-AAATCGTAATGCGTATCCGTAAATCGCAACGACAATG
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
*
2482744 CGTAAAATCGCAACGCATATCCGTAAATCGCAACG
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACG
2482779 CGATCAATAA
Statistics
Matches: 142, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
40 74 0.52
41 68 0.48
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (41 bp):
CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
Found at i:2482879 original size:21 final size:21
Alignment explanation
Indices: 2482850--2482896 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2482840 ATTCTGACTA
2482850 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
2482871 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
2482892 TCGCA
1 TCGCA
2482897 ACGCGATTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:2482902 original size:21 final size:20
Alignment explanation
Indices: 2482886--2482937 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
2482876 TTGCGATTTT
*
2482886 CCTAATTCGCAACGCGATTA
1 CCTAAATCGCAACGCGATTA
* *
2482906 CGTAAATCGCAACGCGAATA
1 CCTAAATCGCAACGCGATTA
* *
2482926 CGTAAATTGCAA
1 CCTAAATCGCAA
2482938 TGTGAATCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (20 bp):
CCTAAATCGCAACGCGATTA
Found at i:2482917 original size:20 final size:20
Alignment explanation
Indices: 2482892--2482959 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
2482882 TTTTCCTAAT
*
2482892 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
2482912 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
* * *
2482932 TTGCAATGTGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
2482952 TCGCAACG
1 TCGCAACG
2482960 AGATTCTGAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.02
20 40 0.98
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:2483846 original size:24 final size:24
Alignment explanation
Indices: 2483819--2483872 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2483809 GTATTCGAAA
2483819 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2483843 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2483867 TTTGAT
1 TTTGAT
2483873 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2486340 original size:20 final size:20
Alignment explanation
Indices: 2486317--2486391 Score: 123
Period size: 20 Copynumber: 3.8 Consensus size: 20
2486307 CAATGCGAAT
*
2486317 ATGACTATCGCAACACGGAA
1 ATGACTATCGCAACGCGGAA
*
2486337 ATGACTATCGCAATGCGGAA
1 ATGACTATCGCAACGCGGAA
*
2486357 TTGACTATCGCAACGCGGAA
1 ATGACTATCGCAACGCGGAA
2486377 ATGACTATCGCAACG
1 ATGACTATCGCAACG
2486392 AGAGAATCGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.19
Consensus pattern (20 bp):
ATGACTATCGCAACGCGGAA
Found at i:2486362 original size:40 final size:40
Alignment explanation
Indices: 2486306--2486389 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 40
2486296 CGCGAAAATT
2486306 GCAATGCGAATATGACTATCGCAACACGGAAATGACTATC
1 GCAATGCGAATATGACTATCGCAACACGGAAATGACTATC
*
2486346 GCAATGCGGAAT-TGACTATCGCAACGCGGAAATGACTATC
1 GCAATGC-GAATATGACTATCGCAACACGGAAATGACTATC
2486386 GCAA
1 GCAA
2486390 CGAGAGAATC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
40 38 0.90
41 4 0.10
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.19
Consensus pattern (40 bp):
GCAATGCGAATATGACTATCGCAACACGGAAATGACTATC
Found at i:2486420 original size:19 final size:19
Alignment explanation
Indices: 2486396--2486623 Score: 170
Period size: 19 Copynumber: 12.8 Consensus size: 19
2486386 GCAACGAGAG
*
2486396 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
2486415 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2486434 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2486453 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2486472 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
2486486 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
* *
2486506 AATCGCAA--CG--TTGAC
1 AATCGCAATGCGAAATGAA
* * *
2486521 TATCGCAACGCGAAAATGAC
1 AATCGCAATGCG-AAATGAA
* *
2486541 TATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2486555 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
2486574 AATCACAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
2486588 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
* *
2486608 AATCGTAACGCGAAAT
1 AATCGCAATGCGAAAT
2486624 TAGTTTCGCG
Statistics
Matches: 169, Mismatches: 18, Indels: 44
0.73 0.08 0.19
Matches are distributed among these distances:
14 24 0.14
15 11 0.07
16 12 0.07
17 6 0.04
18 11 0.07
19 75 0.44
20 30 0.18
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2486500 original size:33 final size:34
Alignment explanation
Indices: 2486415--2486617 Score: 234
Period size: 33 Copynumber: 5.9 Consensus size: 34
2486405 ACGAAATGAA
*
2486415 AATCGCAATGCG-AAATGAAAATCGCAATGCGAAATG
1 AATCGCAATGCGAAAATGAAAATCGCAA--CG-AGTG
*
2486451 AAAATCACAATGCG-AAATGAAAATCGCAACGAGTG
1 --AATCGCAATGCGAAAATGAAAATCGCAACGAGTG
*
2486486 AATCGCAATGCGAAAATGAAAATCGCAACG-TTG
1 AATCGCAATGCGAAAATGAAAATCGCAACGAGTG
* ** *
2486519 ACTATCGCAACGCGAAAATGACTATCGCAACGAGAG
1 A--ATCGCAATGCGAAAATGAAAATCGCAACGAGTG
*
2486555 AATCGCAATGCG-AAATGAAAATCACAACGAGTG
1 AATCGCAATGCGAAAATGAAAATCGCAACGAGTG
*
2486588 AATCGCAATGCGAAAATGAAAATCGTAACG
1 AATCGCAATGCGAAAATGAAAATCGCAACG
2486618 CGAAATTAGT
Statistics
Matches: 144, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
33 43 0.30
34 42 0.29
35 29 0.20
36 4 0.03
38 26 0.18
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (34 bp):
AATCGCAATGCGAAAATGAAAATCGCAACGAGTG
Found at i:2486677 original size:34 final size:34
Alignment explanation
Indices: 2486634--2486727 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
2486624 TAGTTTCGCG
2486634 TTGCGATTTTCATTTTCGCATTGCGATTCACTCC
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCC
* *
2486668 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCC
* ** * *
2486701 TTGTGATAGTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTTTCGCATTGCGAT
2486728 AGTCTGTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 28 0.54
34 24 0.46
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTCACTCC
Found at i:2486848 original size:14 final size:14
Alignment explanation
Indices: 2486829--2486865 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2486819 CATCAATTAA
2486829 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2486843 ACAAATCATCTTTT
1 ACAAATCAACATTT
2486857 ACAAATCAA
1 ACAAATCAA
2486866 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2487540 original size:39 final size:39
Alignment explanation
Indices: 2487486--2487564 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 39
2487476 TGTCGTTGAT
2487486 TCTTCAAGTGAACTACGTGAAAAAG-CGTCGGCATAATTG
1 TCTTCAAGTGAACTACGTGAAAAAGTCG-CGGCATAATTG
*
2487525 TCTTCAAGTGAACTACGTGAAAACGTCGCGGCATAATTG
1 TCTTCAAGTGAACTACGTGAAAAAGTCGCGGCATAATTG
2487564 T
1 T
2487565 ATATCGCATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 36 0.95
40 2 0.05
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (39 bp):
TCTTCAAGTGAACTACGTGAAAAAGTCGCGGCATAATTG
Found at i:2488114 original size:42 final size:42
Alignment explanation
Indices: 2488049--2488159 Score: 136
Period size: 42 Copynumber: 2.6 Consensus size: 42
2488039 TCTAGAATGT
* * *
2488049 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGGA-CTCTTGAACGATGACAGAGGCCTCTTGAACGA
* *
2488091 TGGGAGAGGACTCTTGAAGGATGATAGAGGCCTCTTGAACGA
1 TGGGAGAGGACTCTTGAACGATGACAGAGGCCTCTTGAACGA
*
2488133 TAGGG-GAGGCCTCTTGAACGATGACAG
1 T-GGGAGAGGACTCTTGAACGATGACAG
2488160 GTGAGTCGGT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 53 0.90
43 6 0.10
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGACTCTTGAACGATGACAGAGGCCTCTTGAACGA
Found at i:2488153 original size:21 final size:20
Alignment explanation
Indices: 2488077--2488155 Score: 86
Period size: 21 Copynumber: 3.8 Consensus size: 20
2488067 CGATGACAGT
*
2488077 GGCCTCTTGAACGGTGGGAGA
1 GGCCTCTTGAACGATGGG-GA
* * **
2488098 GGACTCTTGAAGGATGATAGA
1 GGCCTCTTGAACGATG-GGGA
2488119 GGCCTCTTGAACGATAGGGGA
1 GGCCTCTTGAACGAT-GGGGA
2488140 GGCCTCTTGAACGATG
1 GGCCTCTTGAACGATG
2488156 ACAGGTGAGT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 45 0.96
22 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (20 bp):
GGCCTCTTGAACGATGGGGA
Found at i:2488680 original size:19 final size:19
Alignment explanation
Indices: 2488624--2488747 Score: 114
Period size: 20 Copynumber: 6.6 Consensus size: 19
2488614 GAAACTTAAA
*
2488624 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCG-AAATGACT
2488644 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCG-AAATGACT
*
2488664 ATCACAATGCGAAATGACT
1 ATCGCAATGCGAAATGACT
* *
2488683 ATCGCAATGAGAATTTGACT
1 ATCGCAATGCGAA-ATGACT
*
2488703 ATCGCAA--CGAGA-GA--
1 ATCGCAATGCGAAATGACT
**
2488717 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGACT
*
2488736 ATCGCAACGCGA
1 ATCGCAATGCGA
2488748 TTTTGGTTTC
Statistics
Matches: 88, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
14 7 0.08
16 6 0.07
17 2 0.02
18 2 0.02
19 30 0.34
20 41 0.47
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (19 bp):
ATCGCAATGCGAAATGACT
Found at i:2488714 original size:20 final size:20
Alignment explanation
Indices: 2488624--2488709 Score: 120
Period size: 20 Copynumber: 4.3 Consensus size: 20
2488614 GAAACTTAAA
*
2488624 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
2488644 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
2488664 ATCACAATGCG-AAATGACT
1 ATCGCAATGCGAAAATGACT
* **
2488683 ATCGCAATGAGAATTTGACT
1 ATCGCAATGCGAAAATGACT
2488703 ATCGCAA
1 ATCGCAA
2488710 CGAGAGAATC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.29
20 42 0.71
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:2488766 original size:19 final size:19
Alignment explanation
Indices: 2488744--2488820 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
2488734 AAATCGCAAC
2488744 GCGATTTTGGTTTCGCGTT
1 GCGATTTTGGTTTCGCGTT
2488763 GCGATTTT-G--T--CGTT
1 GCGATTTTGGTTTCGCGTT
*
2488777 GCAATTTTGGTTTCGCGTT
1 GCGATTTTGGTTTCGCGTT
** *
2488796 GCGATTTTCATTTCTCGTT
1 GCGATTTTGGTTTCGCGTT
2488815 GCGATT
1 GCGATT
2488821 CTCTCGTTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
14 11 0.23
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 33 0.69
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (19 bp):
GCGATTTTGGTTTCGCGTT
Found at i:2488815 original size:52 final size:50
Alignment explanation
Indices: 2488744--2488874 Score: 127
Period size: 52 Copynumber: 2.5 Consensus size: 50
2488734 AAATCGCAAC
** * * **
2488744 GCGATTTTGGTTTCGCGTTGCGATTTTGTCGTTGCAATTTTGGTTTCGCGTT
1 GCGATTTTCATTTCACGTTGCGATTTTCTCGTTGCAA--TTCATTTCGCGTT
* * *
2488796 GCGATTTTCATTTCTCGTTGCGATTCTCTCGTTGCGATTCATTTCGCGTT
1 GCGATTTTCATTTCACGTTGCGATTTTCTCGTTGCAATTCATTTCGCGTT
**
2488846 GCGATAGTCATTTTTCACGTTGCGATTTT
1 GCGATTTTCA--TTTCACGTTGCGATTTT
2488875 AAGTTTCGTG
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
50 19 0.29
52 46 0.71
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (50 bp):
GCGATTTTCATTTCACGTTGCGATTTTCTCGTTGCAATTCATTTCGCGTT
Found at i:2488858 original size:19 final size:17
Alignment explanation
Indices: 2488787--2488850 Score: 71
Period size: 14 Copynumber: 3.8 Consensus size: 17
2488777 GCAATTTTGG
2488787 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGA--TTCA
*
2488806 TTTCTCGTTGCGATTC-
1 TTTCGCGTTGCGATTCA
*
2488822 --TCTCGTTGCGATTCA
1 TTTCGCGTTGCGATTCA
2488837 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
2488851 AGTCATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 14 0.35
17 14 0.35
19 12 0.30
ACGTcount: A:0.09, C:0.23, G:0.22, T:0.45
Consensus pattern (17 bp):
TTTCGCGTTGCGATTCA
Found at i:2489081 original size:93 final size:93
Alignment explanation
Indices: 2488938--2489302 Score: 515
Period size: 94 Copynumber: 4.1 Consensus size: 93
2488928 ATGGATTGCA
* *
2488938 TTACTTTAACCAAAAGAC-AAAC-AAGACAAATACTAACTTCAGAGTATTAAAGAATACACAG-T
1 TTACTTTAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
2489000 TAGCAGAATTGGTAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2489028 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTT-AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
2489093 TTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
2489122 TTACTTTCAACCAAAAGACAAAACAAAGATAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTT-AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
2489187 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
2489216 TTACTTT------AA-TC---A-AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTT
1 TTACTTTAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
* ** *
2489270 TAGCAGTATTGGCAGCAACTAAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2489298 TTACT
1 TTACT
2489303 AAGCAATCTA
Statistics
Matches: 260, Mismatches: 11, Indels: 16
0.91 0.04 0.06
Matches are distributed among these distances:
82 70 0.27
83 1 0.00
86 1 0.00
87 2 0.01
90 7 0.03
91 11 0.04
92 4 0.02
93 37 0.14
94 127 0.49
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
TTACTTTAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2489283 original size:82 final size:82
Alignment explanation
Indices: 2489146--2489302 Score: 269
Period size: 82 Copynumber: 1.9 Consensus size: 82
2489136 AAGACAAAAC
* * *
2489146 AAAGATAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCAAA
2489211 TAAATTTACTTTAATCA
66 TAAATTTACTTTAATCA
* *
2489228 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACTAAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCAAA
2489293 TAAATTTACT
66 TAAATTTACT
2489303 AAGCAATCTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (82 bp):
AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCAAA
TAAATTTACTTTAATCA
Found at i:2491011 original size:20 final size:20
Alignment explanation
Indices: 2490988--2491043 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
2490978 TGAAATGAAA
2490988 ATCGCAATGAGAGAATGACT
1 ATCGCAATGAGAGAATGACT
*
2491008 ATCGCAATGCG-GAAATGACT
1 ATCGCAATGAGAG-AATGACT
*
2491028 ATCGCAACGAGAGAAT
1 ATCGCAATGAGAGAAT
2491044 CGCAACGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
ATCGCAATGAGAGAATGACT
Found at i:2491023 original size:40 final size:37
Alignment explanation
Indices: 2490979--2491135 Score: 149
Period size: 33 Copynumber: 4.5 Consensus size: 37
2490969 TCTTTTGGTT
*
2490979 GAAATGAAAATCGCAATGAGAGAATGACTATCGCAATGC
1 GAAATGAAAATCGCAATGAGAGAATGA--ATCGCAACGC
** *
2491018 GGAAATGACTATCGCAA--CGAG-A-GAATCGCAACGC
1 -GAAATGAAAATCGCAATGAGAGAATGAATCGCAACGC
2491052 GAAATGAAAATCGCAAT--GAG-A-GAATCGCAACGC
1 GAAATGAAAATCGCAATGAGAGAATGAATCGCAACGC
* *
2491085 GAAATGAAAATCGCAA--CGAG-A-GAATCACAACGC
1 GAAATGAAAATCGCAATGAGAGAATGAATCGCAACGC
2491118 GAAATGAAAATCGCAATG
1 GAAATGAAAATCGCAATG
2491136 CGATTTTGGT
Statistics
Matches: 106, Mismatches: 7, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
33 77 0.73
34 9 0.08
36 2 0.02
37 1 0.01
38 3 0.03
40 14 0.13
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (37 bp):
GAAATGAAAATCGCAATGAGAGAATGAATCGCAACGC
Found at i:2491047 original size:14 final size:14
Alignment explanation
Indices: 2491028--2491116 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
2491018 GGAAATGACT
2491028 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
2491042 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
*
2491061 ATCGCAATGAGAGA
1 ATCGCAACGAGAGA
*
2491075 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
2491094 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
2491108 ATCACAACG
1 ATCGCAACG
2491117 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 28 0.48
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.34
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:2491058 original size:33 final size:33
Alignment explanation
Indices: 2491008--2491133 Score: 198
Period size: 33 Copynumber: 3.8 Consensus size: 33
2490998 GAGAATGACT
* **
2491008 ATCGCAATGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAACGC-GAAATGAAAATCGCAACGAGAGA
*
2491042 ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
2491075 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
2491108 ATCACAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
2491134 TGCGATTTTG
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
33 77 0.90
34 9 0.10
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:2491065 original size:19 final size:19
Alignment explanation
Indices: 2491041--2491138 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2491031 GCAACGAGAG
2491041 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
2491060 AATCGCAA--TG--A-GAG
1 AATCGCAACGCGAAATGAA
2491074 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2491093 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
2491107 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2491126 AATCGCAATGCGA
1 AATCGCAACGCGA
2491139 TTTTGGTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 19 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 31 0.52
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2491098 original size:66 final size:70
Alignment explanation
Indices: 2490979--2491135 Score: 223
Period size: 66 Copynumber: 2.3 Consensus size: 70
2490969 TCTTTTGGTT
* **
2490979 GAAATGAAAATCGCAATGAGAGAATGACTATCGCAATGCGGAAATGACTATCGCAACGAGAGAAT
1 GAAATGAAAATCGCAAT--GAGAATGAC-ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAAT
*
2491044 CGCAACGC
63 CACAACGC
2491052 GAAATGAAAATCGCAATGAG-A-GA-ATCGCAACGC-GAAATGAAAATCGCAACGAGAGAATCAC
1 GAAATGAAAATCGCAATGAGAATGACATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCAC
2491113 AACGC
66 AACGC
2491118 GAAATGAAAATCGCAATG
1 GAAATGAAAATCGCAATG
2491136 CGATTTTGGT
Statistics
Matches: 80, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
66 48 0.60
67 9 0.11
69 2 0.03
70 1 0.01
71 3 0.04
73 17 0.21
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (70 bp):
GAAATGAAAATCGCAATGAGAATGACATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCAC
AACGC
Found at i:2491184 original size:21 final size:21
Alignment explanation
Indices: 2491165--2491236 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
2491155 CGATTCTCTC
*
2491165 GTTGCGATTTTCATTTCTCTT
1 GTTGCGATTTTCATTTCTCAT
** *
2491186 GTTGCGATAGTCATTT-TCGT
1 GTTGCGATTTTCATTTCTCAT
*
2491206 GTTGCGATTTTCATTTTTCAT
1 GTTGCGATTTTCATTTCTCAT
2491227 GTTGCGATTT
1 GTTGCGATTT
2491237 GAAGTTTAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
20 17 0.39
21 27 0.61
ACGTcount: A:0.12, C:0.15, G:0.19, T:0.53
Consensus pattern (21 bp):
GTTGCGATTTTCATTTCTCAT
Found at i:2491823 original size:20 final size:20
Alignment explanation
Indices: 2491798--2491990 Score: 201
Period size: 20 Copynumber: 9.6 Consensus size: 20
2491788 CTTTAAAAAT
*
2491798 CGCGTTGCGATTTACGGAAA
1 CGCGTTGCGATTTACGGATA
*
2491818 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2491838 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
** * *
2491859 CGTATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
2491879 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
2491899 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
2491919 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2491939 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2491959 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
2491980 CTCGTTGCGAT
1 CGCGTTGCGAT
2491991 AGTCAGAATC
Statistics
Matches: 139, Mismatches: 28, Indels: 12
0.78 0.16 0.07
Matches are distributed among these distances:
20 107 0.77
21 32 0.23
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2491884 original size:40 final size:41
Alignment explanation
Indices: 2491800--2491990 Score: 305
Period size: 40 Copynumber: 4.7 Consensus size: 41
2491790 TTAAAAATCG
* *
2491800 CGTTGCGATTTACGGAAACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
**
2491841 CGTTGCGATTTACGGATACGTATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
2491881 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
2491921 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
2491962 CGTTGCGATTTACGGATACTCGTTGCGAT
1 CGTTGCGATTTACGGATACGCGTTGCGAT
2491991 AGTCAGAATC
Statistics
Matches: 139, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 75 0.54
41 64 0.46
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:2492022 original size:20 final size:20
Alignment explanation
Indices: 2491999--2492051 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2491989 ATAGTCAGAA
*
2491999 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
2492019 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
2492039 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2492052 CTGGAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:2492024 original size:121 final size:121
Alignment explanation
Indices: 2491797--2492051 Score: 356
Period size: 121 Copynumber: 2.1 Consensus size: 121
2491787 GCTTTAAAAA
2491797 TCGCGTTGCGATTTACGGAAACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGT
1 TCGCGTTGCGATTTACGGAAACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGT
* * * *
2491862 ATTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTAT
66 ATTGCGATTCACGTAATCGCGTTGCGATTTACAGATACGCGTTGCGATTTACATAT
* *
2491918 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC-T
1 TCGCGTTGCGATTTACGGAAACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGT
* * * *
2491982 CGTTGCGATAGTCA-G-AATCGCGTTGCGATTTATATG-TTCGCGTTGCGATTTTCATAT
66 -ATTGCGAT--TCACGTAATCGCGTTGCGATTTACA-GATACGCGTTGCGATTTACATAT
2492039 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2492052 CTGGAAAATT
Statistics
Matches: 119, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
120 1 0.01
121 114 0.96
122 2 0.02
123 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (121 bp):
TCGCGTTGCGATTTACGGAAACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGT
ATTGCGATTCACGTAATCGCGTTGCGATTTACAGATACGCGTTGCGATTTACATAT
Found at i:2492150 original size:20 final size:19
Alignment explanation
Indices: 2492101--2492154 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2492091 ATTCTTCATA
*
2492101 ATCGCGTTGCGATTCTGAG
1 ATCGAGTTGCGATTCTGAG
* *
2492120 AACTGATTTGCGATTCTGGAG
1 ATC-GAGTTGCGATTCT-GAG
2492141 ATCGAGTTGCGATT
1 ATCGAGTTGCGATT
2492155 TTTATTTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.07
20 21 0.75
21 5 0.18
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (19 bp):
ATCGAGTTGCGATTCTGAG
Found at i:2497355 original size:26 final size:26
Alignment explanation
Indices: 2497325--2497488 Score: 121
Period size: 26 Copynumber: 7.0 Consensus size: 26
2497315 ATGTCTTAAT
*
2497325 GCATCCTTTAATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
2497351 GCATCCTTTAATGC--TTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
2497371 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
** *
2497397 GCATTATTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
2497417 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
* * *
2497443 GCATACTTCCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
2497463 GCATCGTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
2497489 AATTCATTTT
Statistics
Matches: 106, Mismatches: 14, Indels: 36
0.68 0.09 0.23
Matches are distributed among these distances:
20 36 0.34
21 6 0.06
22 10 0.09
24 10 0.09
25 6 0.06
26 38 0.36
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.45
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTTAGTTATG
Found at i:2497370 original size:46 final size:46
Alignment explanation
Indices: 2497286--2497488 Score: 289
Period size: 46 Copynumber: 4.4 Consensus size: 46
2497276 CTAGTAATTA
* * * * *
2497286 TTCATGAATTTCAGTTGTGGCATCCTTTTATGTCTTAATGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCT
* * *
2497332 TTAATGCATTTTAGTTATGGCATCCTTTAATGCTTTAATGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCT
**
2497378 TTCATGCATTTTAGTTATGGCATTATTTCATGCCTTAATGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCT
* * *
2497424 TTCATGCATTTTAGTTATGGCATACTTCCATGCCTTAATGCATCGT
1 TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCT
2497470 TTCATGCATTTTAGTTATG
1 TTCATGCATTTTAGTTATG
2497489 AATTCATTTT
Statistics
Matches: 141, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 141 1.00
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.45
Consensus pattern (46 bp):
TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCT
Found at i:2497426 original size:20 final size:20
Alignment explanation
Indices: 2497305--2497476 Score: 76
Period size: 20 Copynumber: 7.7 Consensus size: 20
2497295 TTCAGTTGTG
*
2497305 GCATCCTTTTATG-TCTTAAT
1 GCATCCTTTCATGCT-TTAAT
*
2497325 GCATCCTTTAATGCATTTTAGTTAT
1 GCATCCTTTCATGC--TTTA---AT
*
2497350 GGCATCCTTTAATGCTTTAAT
1 -GCATCCTTTCATGCTTTAAT
2497371 GCATCCTTTCATGCATTTTAGTTAT
1 GCATCCTTTCATGC--TTTA---AT
** *
2497396 GGCATTATTTCATGCCTTAAT
1 -GCATCCTTTCATGCTTTAAT
2497417 GCATCCTTTCATGCATTTTAGTTAT
1 GCATCCTTTCATGC--TTTA---AT
* * *
2497442 GGCATACTTCCATGCCTTAAT
1 -GCATCCTTTCATGCTTTAAT
*
2497463 GCATCGTTTCATGC
1 GCATCCTTTCATGC
2497477 ATTTTAGTTA
Statistics
Matches: 119, Mismatches: 14, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
20 48 0.40
21 6 0.05
22 10 0.08
23 1 0.01
24 10 0.08
25 6 0.05
26 38 0.32
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (20 bp):
GCATCCTTTCATGCTTTAAT
Found at i:2500471 original size:22 final size:23
Alignment explanation
Indices: 2500441--2500485 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2500431 TTGTTGGGAG
* *
2500441 CATATGGGTATCGGTAC-ACCTT
1 CATAGGGGTATCGATACTACCTT
2500463 CATAGGGGTATCGATACTACCTT
1 CATAGGGGTATCGATACTACCTT
2500486 TAAAAATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (23 bp):
CATAGGGGTATCGATACTACCTT
Found at i:2507520 original size:20 final size:19
Alignment explanation
Indices: 2507481--2507527 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
2507471 CAGTCAAGAG
*
2507481 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
2507500 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATT-AAAAT
2507520 CATGTATT
1 CATGTATT
2507528 CTCAAATGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:2510094 original size:18 final size:18
Alignment explanation
Indices: 2510071--2510113 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
2510061 AATGGTGTTC
2510071 TTGAAAGCAAAATGAATA
1 TTGAAAGCAAAATGAATA
2510089 TTGAAAGCAAAATGAATA
1 TTGAAAGCAAAATGAATA
2510107 TTGAAAG
1 TTGAAAG
2510114 GATTTTGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.53, C:0.05, G:0.19, T:0.23
Consensus pattern (18 bp):
TTGAAAGCAAAATGAATA
Found at i:2519618 original size:45 final size:45
Alignment explanation
Indices: 2519554--2519768 Score: 245
Period size: 45 Copynumber: 4.7 Consensus size: 45
2519544 TTAAAAAGAA
*
2519554 AAATGCATATGGGTACATTATCAACAGAACAA-TATGCTAAAGTTG
1 AAATGCATATGGGTACATTATCAACAGAA-AAGTATACTAAAGTTG
* *
2519599 AAATGTATATGGGTACATTATCAACATAAAAGTATA-TATATTGAGTTG
1 AAATGCATATGGGTACATTATCAACAGAAAAGTATACTA-A---AGTTG
* **
2519647 AAATGCATATGGGTACATTATCAATAGAAAAGTATACTACGGTTG
1 AAATGCATATGGGTACATTATCAACAGAAAAGTATACTAAAGTTG
* * * * * *
2519692 AAATGTATATGGCTGCATTTTCAACATAAAAGTATACTATAGTTG
1 AAATGCATATGGGTACATTATCAACAGAAAAGTATACTAAAGTTG
* *
2519737 AAATGCATACGGGTGCATTATCAACAGAAAAG
1 AAATGCATATGGGTACATTATCAACAGAAAAG
2519769 ATGTTAGAAT
Statistics
Matches: 143, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
44 4 0.03
45 99 0.69
48 38 0.27
49 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (45 bp):
AAATGCATATGGGTACATTATCAACAGAAAAGTATACTAAAGTTG
Found at i:2519716 original size:93 final size:90
Alignment explanation
Indices: 2519554--2519768 Score: 297
Period size: 93 Copynumber: 2.4 Consensus size: 90
2519544 TTAAAAAGAA
* *
2519554 AAATGCATATGGGTACATTATCAACAGAACAA-TATGCTAAAGTTGAAATGTATATGGGTACATT
1 AAATGCATATGGGTACATTATCAACAGAA-AAGTATACTAAAGTTGAAATGTATATGGCTACATT
2519618 ATCAACATAAAAGTATATATATTGAGTTG
65 ATCAACATAAAAGTATA-ATA-T-AGTTG
* ** * *
2519647 AAATGCATATGGGTACATTATCAATAGAAAAGTATACTACGGTTGAAATGTATATGGCTGCATTT
1 AAATGCATATGGGTACATTATCAACAGAAAAGTATACTAAAGTTGAAATGTATATGGCTACATTA
*
2519712 TCAACATAAAAGTATACTATAGTTG
66 TCAACATAAAAGTATAATATAGTTG
* *
2519737 AAATGCATACGGGTGCATTATCAACAGAAAAG
1 AAATGCATATGGGTACATTATCAACAGAAAAG
2519769 ATGTTAGAAT
Statistics
Matches: 110, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
90 34 0.31
91 1 0.01
92 4 0.04
93 71 0.65
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (90 bp):
AAATGCATATGGGTACATTATCAACAGAAAAGTATACTAAAGTTGAAATGTATATGGCTACATTA
TCAACATAAAAGTATAATATAGTTG
Found at i:2519855 original size:13 final size:14
Alignment explanation
Indices: 2519832--2519862 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
2519822 AAATGAAAAG
2519832 AATGAATCATGATA
1 AATGAATCATGATA
2519846 AATG-ATCATGATA
1 AATGAATCATGATA
2519859 AATG
1 AATG
2519863 GGGAATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.29
Consensus pattern (14 bp):
AATGAATCATGATA
Found at i:2525415 original size:48 final size:48
Alignment explanation
Indices: 2525322--2525516 Score: 293
Period size: 48 Copynumber: 4.1 Consensus size: 48
2525312 CATACTTTGT
* *
2525322 GTATGATGGTTATCGATCGA-TTTGTTTAATGCATAAGTTACATTTTC
1 GTATGATGGTTATCGATCGATTTTGTTTAACGCATAAGTTGCATTTTC
* *
2525369 ATATGATGGTTATCGATCGATTTTGTTTAACGCATAAGTTGTATTTTC
1 GTATGATGGTTATCGATCGATTTTGTTTAACGCATAAGTTGCATTTTC
* *
2525417 GTGTGATGGTTATCGATCGATTTAGTTTAACGCATAAGTTGCATTTTC
1 GTATGATGGTTATCGATCGATTTTGTTTAACGCATAAGTTGCATTTTC
* ** *
2525465 GTATGATGGTTATCGATCGATTTTGTTTAATGCATGTGTTTCATTTTC
1 GTATGATGGTTATCGATCGATTTTGTTTAACGCATAAGTTGCATTTTC
2525513 GTAT
1 GTAT
2525517 CAGTACATAC
Statistics
Matches: 133, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
47 19 0.14
48 114 0.86
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.46
Consensus pattern (48 bp):
GTATGATGGTTATCGATCGATTTTGTTTAACGCATAAGTTGCATTTTC
Found at i:2525595 original size:53 final size:53
Alignment explanation
Indices: 2525527--2525642 Score: 146
Period size: 53 Copynumber: 2.2 Consensus size: 53
2525517 CAGTACATAC
* *
2525527 TTTCAGCACTATGTGTGAACCCAAT-GTATTCATAATGAGTTTATGAATGACCA
1 TTTCGGCACTATGTGTGAACCC-ATGGAATTCATAATGAGTTTATGAATGACCA
* * * *
2525580 TCTT-GGCACTATGTGTGCATCCATGGAATTCATAATGAGTTTGTGAATTACCA
1 T-TTCGGCACTATGTGTGAACCCATGGAATTCATAATGAGTTTATGAATGACCA
2525633 TTTCGGCACT
1 TTTCGGCACT
2525643 TAGGTGAAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
52 4 0.07
53 48 0.89
54 2 0.04
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (53 bp):
TTTCGGCACTATGTGTGAACCCATGGAATTCATAATGAGTTTATGAATGACCA
Found at i:2539442 original size:11 final size:11
Alignment explanation
Indices: 2539426--2539454 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2539416 TGCCTTGTAC
2539426 TTTGTGAGCTG
1 TTTGTGAGCTG
2539437 TTTGTGAGCTG
1 TTTGTGAGCTG
2539448 TTTGTGA
1 TTTGTGA
2539455 CTTCCAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.07, G:0.34, T:0.48
Consensus pattern (11 bp):
TTTGTGAGCTG
Found at i:2539693 original size:283 final size:283
Alignment explanation
Indices: 2539186--2539747 Score: 1106
Period size: 283 Copynumber: 2.0 Consensus size: 283
2539176 GGGCGTGCAT
2539186 GTGTCTCCTTCCAAGCTAGCTTGAGTGTTGAGCTAGCTAGCAAGAATGGGGCTGTTTATGAATGA
1 GTGTCTCCTTCCAAGCTAGCTTGAGTGTTGAGCTAGCTAGCAAGAATGGGGCTGTTTATGAATGA
*
2539251 TCTTCCTAGCCGAGTCCTTTTTAGCTCCATAACAGCATGTTCAGCTACATTCAGCTACCTTTGTC
66 TCTTCCTAGCCGAGTCCTTTTGAGCTCCATAACAGCATGTTCAGCTACATTCAGCTACCTTTGTC
2539316 ATCACTTTTAGCAACTCAGCTTCAAATAGTCCAACTAGCTAAGTTTAGCTAGCCTGAAGCTTCTC
131 ATCACTTTTAGCAACTCAGCTTCAAATAGTCCAACTAGCTAAGTTTAGCTAGCCTGAAGCTTCTC
2539381 CAGCTGAATCGAGCTTCCCTTAGCATTCCATGAGCTGCCTTGTACTTTGTGAGCTGTTTGTGAGC
196 CAGCTGAATCGAGCTTCCCTTAGCATTCCATGAGCTGCCTTGTACTTTGTGAGCTGTTTGTGAGC
2539446 TGTTTGTGACTTCCAAATCGTTC
261 TGTTTGTGACTTCCAAATCGTTC
*
2539469 GTGTCTCCTTCCAAGCTAGCTTGAGTGTTGAGCTAGTTAGCAAGAATGGGGCTGTTTATGAATGA
1 GTGTCTCCTTCCAAGCTAGCTTGAGTGTTGAGCTAGCTAGCAAGAATGGGGCTGTTTATGAATGA
2539534 TCTTCCTAGCCGAGTCCTTTTGAGCTCCATAACAGCATGTTCAGCTACATTCAGCTACCTTTGTC
66 TCTTCCTAGCCGAGTCCTTTTGAGCTCCATAACAGCATGTTCAGCTACATTCAGCTACCTTTGTC
2539599 ATCACTTTTAGCAACTCAGCTTCAAATAGTCCAACTAGCTAAGTTTAGCTAGCCTGAAGCTTCTC
131 ATCACTTTTAGCAACTCAGCTTCAAATAGTCCAACTAGCTAAGTTTAGCTAGCCTGAAGCTTCTC
2539664 CAGCTGAATCGAGCTTCCCTTAGCATTCCATGAGCTGCCTTGTACTTTGTGAGCTGTTTGTGAGC
196 CAGCTGAATCGAGCTTCCCTTAGCATTCCATGAGCTGCCTTGTACTTTGTGAGCTGTTTGTGAGC
2539729 TGTTTGTGACTTCCAAATC
261 TGTTTGTGACTTCCAAATC
2539748 ATTCATCAAG
Statistics
Matches: 277, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
283 277 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (283 bp):
GTGTCTCCTTCCAAGCTAGCTTGAGTGTTGAGCTAGCTAGCAAGAATGGGGCTGTTTATGAATGA
TCTTCCTAGCCGAGTCCTTTTGAGCTCCATAACAGCATGTTCAGCTACATTCAGCTACCTTTGTC
ATCACTTTTAGCAACTCAGCTTCAAATAGTCCAACTAGCTAAGTTTAGCTAGCCTGAAGCTTCTC
CAGCTGAATCGAGCTTCCCTTAGCATTCCATGAGCTGCCTTGTACTTTGTGAGCTGTTTGTGAGC
TGTTTGTGACTTCCAAATCGTTC
Found at i:2539725 original size:11 final size:11
Alignment explanation
Indices: 2539709--2539737 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2539699 TGCCTTGTAC
2539709 TTTGTGAGCTG
1 TTTGTGAGCTG
2539720 TTTGTGAGCTG
1 TTTGTGAGCTG
2539731 TTTGTGA
1 TTTGTGA
2539738 CTTCCAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.07, G:0.34, T:0.48
Consensus pattern (11 bp):
TTTGTGAGCTG
Found at i:2541262 original size:13 final size:13
Alignment explanation
Indices: 2541240--2541269 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2541230 ACTAAACACC
2541240 TTTC-ACATACCT
1 TTTCAACATACCT
2541252 TTTCAACATACCT
1 TTTCAACATACCT
2541265 TTTCA
1 TTTCA
2541270 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:2545277 original size:11 final size:11
Alignment explanation
Indices: 2545261--2545289 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2545251 TGCCTTGTAC
2545261 TTTGTGAGCTG
1 TTTGTGAGCTG
2545272 TTTGTGAGCTG
1 TTTGTGAGCTG
2545283 TTTGTGA
1 TTTGTGA
2545290 CTTCCAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.07, G:0.34, T:0.48
Consensus pattern (11 bp):
TTTGTGAGCTG
Found at i:2562535 original size:17 final size:18
Alignment explanation
Indices: 2562503--2562536 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2562493 GTTTGTTGCG
2562503 TAGGCTATAGAAAATGGT
1 TAGGCTATAGAAAATGGT
*
2562521 TAGGGTATA-AAAATGG
1 TAGGCTATAGAAAATGG
2562537 ATATGGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.03, G:0.29, T:0.26
Consensus pattern (18 bp):
TAGGCTATAGAAAATGGT
Found at i:2562544 original size:17 final size:18
Alignment explanation
Indices: 2562503--2562544 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
2562493 GTTTGTTGCG
* *
2562503 TAGGCTATAGAAAATGGT
1 TAGGGTATAGAAAATGGA
2562521 TAGGGTATA-AAAATGGA
1 TAGGGTATAGAAAATGGA
*
2562538 TATGGTA
1 TAGGGTA
2562545 AAGGTATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.40, C:0.02, G:0.29, T:0.29
Consensus pattern (18 bp):
TAGGGTATAGAAAATGGA
Found at i:2573251 original size:26 final size:28
Alignment explanation
Indices: 2573222--2573273 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
2573212 AGAAAAAGTG
2573222 CAAGCAC-TCAAAAGAAGAAA-AAAATT
1 CAAGCACTTCAAAAGAAGAAAGAAAATT
*
2573248 CAAGCACTTGAAAAGAAGAAAGAAAA
1 CAAGCACTTCAAAAGAAGAAAGAAAA
2573274 GAAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
27 12 0.52
28 4 0.17
ACGTcount: A:0.62, C:0.13, G:0.15, T:0.10
Consensus pattern (28 bp):
CAAGCACTTCAAAAGAAGAAAGAAAATT
Found at i:2573281 original size:10 final size:9
Alignment explanation
Indices: 2573263--2573293 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
2573253 ACTTGAAAAG
2573263 AAGAAAGAA
1 AAGAAAGAA
2573272 AAGAAAAGAA
1 AAG-AAAGAA
2573282 AAGAAAGAA
1 AAGAAAGAA
2573291 AAG
1 AAG
2573294 TTGAAGCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AAGAAAGAA
Found at i:2601998 original size:34 final size:34
Alignment explanation
Indices: 2601944--2602028 Score: 102
Period size: 34 Copynumber: 2.4 Consensus size: 34
2601934 TTTCCTTGGC
2601944 TTTCTTTCTTTTTGAATTTTTCTTT-TTCTTTTCT
1 TTTCTTTCTTTTTGAATTTTT-TTTCTTCTTTTCT
*
2601978 TTTC-TTCTTTTCTGATTTTTTTTTCTTCTTTTGTCTT
1 TTTCTTTCTTTT-TGAATTTTTTTTCTTC-TTT-TC-T
2602015 TTTCTTTCTTTTTG
1 TTTCTTTCTTTTTG
2602029 CACTCCAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
33 10 0.23
34 15 0.34
35 3 0.07
36 2 0.05
37 7 0.16
38 7 0.16
ACGTcount: A:0.04, C:0.15, G:0.05, T:0.76
Consensus pattern (34 bp):
TTTCTTTCTTTTTGAATTTTTTTTCTTCTTTTCT
Found at i:2602017 original size:21 final size:19
Alignment explanation
Indices: 2601963--2602021 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
2601953 TTTTGAATTT
2601963 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTTCTTTTCTTTTC
* *
2601982 TTCTTTTCTGATTTTTTTTTC
1 TTCTTTT-T-CTTTTCTTTTC
2602003 TTCTTTTGTCTTTTTCTTT
1 TTCTTTT-TC-TTTTCTTT
2602022 CTTTTTGCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 7 0.22
20 1 0.03
21 24 0.75
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (19 bp):
TTCTTTTTCTTTTCTTTTC
Found at i:2612723 original size:24 final size:24
Alignment explanation
Indices: 2612696--2612745 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
2612686 ATAGGCGTGA
*
2612696 CTCTTTCTGATCCACAAGACATGT
1 CTCTTTCTGATCCACAAAACATGT
* *
2612720 CTCTTTGTGATTCACAAAACATGT
1 CTCTTTCTGATCCACAAAACATGT
2612744 CT
1 CT
2612746 GTTGATGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (24 bp):
CTCTTTCTGATCCACAAAACATGT
Found at i:2615608 original size:19 final size:19
Alignment explanation
Indices: 2615584--2615628 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
2615574 CGGCCAAGAG
2615584 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
2615603 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
2615622 CATGTAT
1 CATGTAT
2615629 TTTTATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.42
Consensus pattern (19 bp):
CATGTATCTTCATTAAAAT
Found at i:2626106 original size:69 final size:69
Alignment explanation
Indices: 2625995--2626133 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
2625985 TCTGGGTCTT
2625995 TGTTCTTTAACATTGGTTCTTCTTTGAGTCTTCTTTGAGATAATACTTTTCATATTCATCTCCAT
1 TGTTCTTTAACATTGGTTCTTCTTTGAGTCTTCTTTGAGATAATACTTTTCATATTCATCTCCAT
2626060 CACC
66 CACC
2626064 TGTTCTTTAACATTGGTTCTTCTTTGAGTCTTCTTTGAGATAATACTTTTCATATTCATCTCCAT
1 TGTTCTTTAACATTGGTTCTTCTTTGAGTCTTCTTTGAGATAATACTTTTCATATTCATCTCCAT
2626129 CACC
66 CACC
2626133 T
1 T
2626134 TCATTCTACT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.48
Consensus pattern (69 bp):
TGTTCTTTAACATTGGTTCTTCTTTGAGTCTTCTTTGAGATAATACTTTTCATATTCATCTCCAT
CACC
Found at i:2632291 original size:27 final size:28
Alignment explanation
Indices: 2632261--2632325 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
2632251 TTTCTTTTCT
* *
2632261 TTTCTTTTCTTCTTTTTGAATGC-TGAA
1 TTTCTTTTCTTCTTTTGGAATGCTTCAA
*
2632288 TTTC-TTTCTTTCTTTTGGAGTGCTTCAA
1 TTTCTTTTC-TTCTTTTGGAATGCTTCAA
2632316 TTTCTTTTCT
1 TTTCTTTTCT
2632326 GATTTTCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 4 0.12
27 16 0.50
28 8 0.25
29 4 0.12
ACGTcount: A:0.11, C:0.17, G:0.11, T:0.62
Consensus pattern (28 bp):
TTTCTTTTCTTCTTTTGGAATGCTTCAA
Found at i:2642897 original size:27 final size:27
Alignment explanation
Indices: 2642852--2642908 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2642842 TTTCTTTTAT
* *
2642852 TTTCTTCTTTTTGAATGC-TGAATTTC
1 TTTCTTCTTTTGGAATGCTTCAATTTC
*
2642878 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTTGGAATGCTTCAATTTC
2642906 TTT
1 TTT
2642909 TCTGATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 12 0.46
28 10 0.38
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.60
Consensus pattern (27 bp):
TTTCTTCTTTTGGAATGCTTCAATTTC
Found at i:2653923 original size:24 final size:21
Alignment explanation
Indices: 2653888--2653930 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2653878 GGCTCATTCT
*
2653888 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
2653911 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
2653931 ATCTTGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:2663257 original size:11 final size:12
Alignment explanation
Indices: 2663215--2663260 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
2663205 ATTATTTAAA
2663215 CGGGTATTGGGT
1 CGGGTATTGGGT
2663227 CGGGTATTGGGT
1 CGGGTATTGGGT
2663239 CGGGTATTGGGT
1 CGGGTATTGGGT
2663251 C-GGTATTGGG
1 CGGGTATTGGG
2663261 CTGGGAATCG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 9 0.26
12 25 0.74
ACGTcount: A:0.09, C:0.09, G:0.50, T:0.33
Consensus pattern (12 bp):
CGGGTATTGGGT
Found at i:2663418 original size:13 final size:13
Alignment explanation
Indices: 2663379--2663420 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
2663369 TTTATCGGAT
2663379 CGGGT-ATCGGGG
1 CGGGTAATCGGGG
*
2663391 CAGGTAATCGGGG
1 CGGGTAATCGGGG
2663404 CGGGTAATCGGGG
1 CGGGTAATCGGGG
2663417 CGGG
1 CGGG
2663421 GATTACCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 4 0.15
13 23 0.85
ACGTcount: A:0.14, C:0.17, G:0.55, T:0.14
Consensus pattern (13 bp):
CGGGTAATCGGGG
Found at i:2663442 original size:6 final size:6
Alignment explanation
Indices: 2663431--2663459 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2663421 GATTACCAAA
2663431 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
1 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
2663460 TTAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.17, T:0.17
Consensus pattern (6 bp):
CCCGTC
Found at i:2664854 original size:24 final size:21
Alignment explanation
Indices: 2664819--2664861 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2664809 GGCTCATTCT
*
2664819 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
2664842 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
2664862 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:2668278 original size:2 final size:2
Alignment explanation
Indices: 2668271--2668305 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2668261 TGGTAGCGGA
2668271 AT 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 AT A
2668306 AGATGGTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2677261 original size:27 final size:26
Alignment explanation
Indices: 2677233--2677289 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
2677223 CAACTTTTCT
*
2677233 TTCTTTTTTTTCTTCTTTTTGAGTGC
1 TTCTTTTATTTCTTCTTTTTGAGTGC
* *
2677259 -T-TTTAATTTCTTCTTTTTGTGTGC
1 TTCTTTTATTTCTTCTTTTTGAGTGC
2677283 TTCTTTT
1 TTCTTTT
2677290 CTGATTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 20 0.80
25 2 0.08
26 3 0.12
ACGTcount: A:0.05, C:0.14, G:0.11, T:0.70
Consensus pattern (26 bp):
TTCTTTTATTTCTTCTTTTTGAGTGC
Found at i:2691075 original size:8 final size:8
Alignment explanation
Indices: 2691004--2691065 Score: 61
Period size: 8 Copynumber: 6.9 Consensus size: 8
2690994 TTTTTTTCCA
2691004 AAAAAAAC
1 AAAAAAAC
2691012 AAAAAAAC
1 AAAAAAAC
2691020 AAAACAAAAGGC
1 -AAA-AAAA--C
2691032 AAAAAAAC
1 AAAAAAAC
2691040 AAAAAAAAACC
1 --AAAAAAA-C
2691051 AAAAAAAC
1 AAAAAAAC
2691059 AAAAAAA
1 AAAAAAA
2691066 AAACCAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
8 17 0.36
9 10 0.21
10 15 0.32
11 4 0.09
12 1 0.02
ACGTcount: A:0.84, C:0.13, G:0.03, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:2691075 original size:11 final size:11
Alignment explanation
Indices: 2691032--2691075 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
2691022 AACAAAAGGC
2691032 AAAAAAA-CAA
1 AAAAAAACCAA
2691042 AAAAAAACC--
1 AAAAAAACCAA
*
2691051 AAAAAAACAAA
1 AAAAAAACCAA
2691062 AAAAAAACCAA
1 AAAAAAACCAA
2691073 AAA
1 AAA
2691076 GCCAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 8 0.28
10 7 0.24
11 14 0.48
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACCAA
Found at i:2691082 original size:20 final size:20
Alignment explanation
Indices: 2691003--2691075 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
2690993 ATTTTTTTCC
2691003 AAAAAAAA-CAAAAAAACAA
1 AAAAAAAACCAAAAAAACAA
* **
2691022 AACAAAAGGCAAAAAAAC-A
1 AAAAAAAACCAAAAAAACAA
2691041 AAAAAAAACCAAAAAAACAA
1 AAAAAAAACCAAAAAAACAA
2691061 AAAAAAAACCAAAAA
1 AAAAAAAACCAAAAA
2691076 GCCAAAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
19 22 0.47
20 25 0.53
ACGTcount: A:0.84, C:0.14, G:0.03, T:0.00
Consensus pattern (20 bp):
AAAAAAAACCAAAAAAACAA
Found at i:2696551 original size:13 final size:13
Alignment explanation
Indices: 2696526--2696569 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
2696516 GTTGTAGGAG
2696526 TCTTTTC-TTTTC
1 TCTTTTCTTTTTC
*
2696538 TCTTTTGTTTTTC
1 TCTTTTCTTTTTC
2696551 T-TCTTTCTTTTTC
1 TCT-TTTCTTTTTC
2696564 TCTTTT
1 TCTTTT
2696570 TGTTGCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 7 0.26
13 19 0.70
14 1 0.04
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.77
Consensus pattern (13 bp):
TCTTTTCTTTTTC
Found at i:2698321 original size:23 final size:23
Alignment explanation
Indices: 2698276--2698321 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2698266 TTATACCTAT
*
2698276 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
2698299 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
2698322 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:2699502 original size:24 final size:24
Alignment explanation
Indices: 2699471--2699518 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
2699461 TAGTGGGTTG
2699471 AAGACATTA-T-ATATTCATTTCTT
1 AAGACATTATTAATA-TCATTTCTT
2699494 AAGACCATTATTAATATCATTTCTT
1 AAGA-CATTATTAATATCATTTCTT
2699519 TCTTATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.18
24 5 0.23
25 10 0.45
26 3 0.14
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (24 bp):
AAGACATTATTAATATCATTTCTT
Found at i:2699765 original size:13 final size:12
Alignment explanation
Indices: 2699747--2699816 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 12
2699737 GTGCAAAAAG
2699747 AAAGAAAAGACAA
1 AAAGAAAAGA-AA
* *
2699760 AAAGAAGAGAGAG
1 AAAGAAAAGA-AA
**
2699773 AAA-ATCAGAAA
1 AAAGAAAAGAAA
2699784 AGAAGAAAAGAAGA
1 A-AAGAAAAGAA-A
2699798 AAAGAAAAGAAA
1 AAAGAAAAGAAA
2699810 AAGAGAA
1 AA-AGAA
2699817 GTTCAAAAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
11 2 0.04
12 9 0.20
13 32 0.71
14 2 0.04
ACGTcount: A:0.73, C:0.03, G:0.23, T:0.01
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:2699785 original size:30 final size:29
Alignment explanation
Indices: 2699749--2699805 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
2699739 GCAAAAAGAA
*
2699749 AGAAAAGACA-AAAAGAAGAGAGAGAAAATC
1 AGAAAAGA-AGAAAAGAAGA-AAAGAAAATC
2699779 AGAAAAGAAGAAAAGAAGAAAAGAAAA
1 AGAAAAGAAGAAAAGAAGAAAAGAAAA
2699806 GAAAAAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.72, C:0.04, G:0.23, T:0.02
Consensus pattern (29 bp):
AGAAAAGAAGAAAAGAAGAAAAGAAAATC
Found at i:2699790 original size:8 final size:8
Alignment explanation
Indices: 2699742--2699803 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
2699732 TTGGAGTGCA
2699742 AAAAGAAAG
1 AAAAG-AAG
2699751 AAAAGACA-
1 AAAAGA-AG
2699759 AAAAGAAG
1 AAAAGAAG
*
2699767 -AGAG-AG
1 AAAAGAAG
**
2699773 AAAATCAG
1 AAAAGAAG
2699781 AAAAGAAG
1 AAAAGAAG
2699789 AAAAGAAG
1 AAAAGAAG
2699797 AAAAGAA
1 AAAAGAA
2699804 AAGAAAAAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
6 2 0.05
7 6 0.14
8 30 0.68
9 6 0.14
ACGTcount: A:0.73, C:0.03, G:0.23, T:0.02
Consensus pattern (8 bp):
AAAAGAAG
Found at i:2699813 original size:16 final size:16
Alignment explanation
Indices: 2699741--2699813 Score: 53
Period size: 16 Copynumber: 4.4 Consensus size: 16
2699731 ATTGGAGTGC
2699741 AAAAAG-AAAGAAAAG
1 AAAAAGAAAAGAAAAG
* *
2699756 ACAAAA-AGAAGAGAGAG
1 A-AAAAGAAAAGA-AAAG
2699773 AAAATCAGAAAAGAAGAA-
1 AAAA--AGAAAAGAA-AAG
*
2699791 AAGAAGAAAAGAAAAG
1 AAAAAGAAAAGAAAAG
2699807 AAAAAGA
1 AAAAAGA
2699814 GAAGTTCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
15 3 0.07
16 26 0.59
17 4 0.09
18 5 0.11
19 6 0.14
ACGTcount: A:0.74, C:0.03, G:0.22, T:0.01
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAG
Found at i:2702150 original size:23 final size:23
Alignment explanation
Indices: 2702105--2702150 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2702095 TTATACCTAT
*
2702105 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
2702128 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
2702151 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:2705968 original size:35 final size:37
Alignment explanation
Indices: 2705917--2705996 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
2705907 TTTGAGAATT
* *
2705917 TGGTTATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
2705952 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
2705989 TGGTGATG
1 TGGTGATG
2705997 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:2707118 original size:154 final size:154
Alignment explanation
Indices: 2706838--2707149 Score: 606
Period size: 154 Copynumber: 2.0 Consensus size: 154
2706828 AGACCATATT
*
2706838 TGTAGTGCTCTTTGTGGTGAAGATGATGGTGCAACTCTCCAGCTGAAATGAAGTCTCTAGCTAGC
1 TGTAGTGCTCTGTGTGGTGAAGATGATGGTGCAACTCTCCAGCTGAAATGAAGTCTCTAGCTAGC
2706903 TCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCGGGGGTCAGCTAACAACTTTTCACCGTTTGTTA
66 TCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCGGGGGTCAGCTAACAACTTTTCACCGTTTGTTA
2706968 TTCATGATCTCCCGAGTCATCCTA
131 TTCATGATCTCCCGAGTCATCCTA
2706992 TGTAGTGCTCTGTGTGGTGAAGATGATGGTGCAACTCTCCAGCTGAAATGAAGTCTCTAGCTAGC
1 TGTAGTGCTCTGTGTGGTGAAGATGATGGTGCAACTCTCCAGCTGAAATGAAGTCTCTAGCTAGC
*
2707057 TCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCGGGGGTCAGCTAACAACTTTTCACCGTTTGTTC
66 TCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCGGGGGTCAGCTAACAACTTTTCACCGTTTGTTA
2707122 TTCATGATCTCCCGAGTCATCCTA
131 TTCATGATCTCCCGAGTCATCCTA
2707146 TGTA
1 TGTA
2707150 AGATTTCCTA
Statistics
Matches: 156, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 156 1.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.30
Consensus pattern (154 bp):
TGTAGTGCTCTGTGTGGTGAAGATGATGGTGCAACTCTCCAGCTGAAATGAAGTCTCTAGCTAGC
TCAAAAGTCCAGCTCAAGTGAGCTATGAGCTCGGGGGTCAGCTAACAACTTTTCACCGTTTGTTA
TTCATGATCTCCCGAGTCATCCTA
Found at i:2707625 original size:13 final size:13
Alignment explanation
Indices: 2707603--2707632 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2707593 ACTAAACACC
2707603 TTTC-ACATACCT
1 TTTCAACATACCT
2707615 TTTCAACATACCT
1 TTTCAACATACCT
2707628 TTTCA
1 TTTCA
2707633 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:2710683 original size:28 final size:28
Alignment explanation
Indices: 2710643--2710696 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
2710633 TGAATTAACT
2710643 AAACAAATGATGAACAT-TCTGTTATGCA
1 AAACAAATGATGAACATGT-TGTTATGCA
2710671 AAACAAATGATGAACATGTTGTTATG
1 AAACAAATGATGAACATGTTGTTATG
2710697 TGAATGTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.30
Consensus pattern (28 bp):
AAACAAATGATGAACATGTTGTTATGCA
Found at i:2710759 original size:81 final size:80
Alignment explanation
Indices: 2710603--2710777 Score: 251
Period size: 81 Copynumber: 2.2 Consensus size: 80
2710593 GATAATGAAA
* * * * * *
2710603 AACATGCTGTAAAGTGAATATGGGTGCACGTGAATTAACTAAACAAATGATGAACATTCTGTTAT
1 AACATGCTGTTATGTGAATATGAGTGCACGTGAATTAACAAAACAAATGATAAACATGCTGTTAT
2710668 GCAAAACAAATGATG
66 GCAAAACAAATGATG
* * * *
2710683 AACATGTTGTTATGTGAATGTGAGTGCACGTGAATTTAACAAAATAAATGATAAATATGCTGTTA
1 AACATGCTGTTATGTGAATATGAGTGCACGTGAA-TTAACAAAACAAATGATAAACATGCTGTTA
2710748 TGCAAAACAAATGATG
65 TGCAAAACAAATGATG
2710764 AACATGCTGTTATG
1 AACATGCTGTTATG
2710778 AACCCCACGA
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
80 29 0.35
81 54 0.65
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (80 bp):
AACATGCTGTTATGTGAATATGAGTGCACGTGAATTAACAAAACAAATGATAAACATGCTGTTAT
GCAAAACAAATGATG
Found at i:2710762 original size:28 final size:28
Alignment explanation
Indices: 2710722--2710777 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2710712 GTGAATTTAA
* *
2710722 CAAAATAAATGATAAATATGCTGTTATG
1 CAAAACAAATGATAAACATGCTGTTATG
*
2710750 CAAAACAAATGATGAACATGCTGTTATG
1 CAAAACAAATGATAAACATGCTGTTATG
2710778 AACCCCACGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (28 bp):
CAAAACAAATGATAAACATGCTGTTATG
Found at i:2711950 original size:24 final size:24
Alignment explanation
Indices: 2711907--2711960 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
2711897 TTTTCTTTTC
* *
2711907 TTTTTTTAATTTTTGAAATTTGTTT
1 TTTTTTTAATTTTCGAAA-TTCTTT
*
2711932 TTTTTTTAA-TTTCGGAATTCTTT
1 TTTTTTTAATTTTCGAAATTCTTT
2711955 TTTTTT
1 TTTTTT
2711961 CAAGATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 6 0.23
25 9 0.35
ACGTcount: A:0.17, C:0.04, G:0.07, T:0.72
Consensus pattern (24 bp):
TTTTTTTAATTTTCGAAATTCTTT
Found at i:2711957 original size:25 final size:26
Alignment explanation
Indices: 2711899--2711960 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
2711889 CACTTTTCTT
* *
2711899 TTCTTTTCTTTTTTTAATTTTTGAAA
1 TTCTTTTTTTTTTTTAATTTTCGAAA
* *
2711925 TT-TGTTTTTTTTTTAA-TTTCGGAA
1 TTCTTTTTTTTTTTTAATTTTCGAAA
2711949 TTCTTTTTTTTT
1 TTCTTTTTTTTT
2711961 CAAGATAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 8 0.27
25 20 0.67
26 2 0.07
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (26 bp):
TTCTTTTTTTTTTTTAATTTTCGAAA
Found at i:2714687 original size:3 final size:3
Alignment explanation
Indices: 2714679--2714703 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2714669 GAATAGGGTT
2714679 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
2714704 AACCACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:2716235 original size:15 final size:15
Alignment explanation
Indices: 2716200--2716228 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2716190 GTGCTTCAAC
2716200 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
2716214 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
2716229 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:2719540 original size:30 final size:30
Alignment explanation
Indices: 2719488--2719549 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
2719478 TGACAGCTTG
*
2719488 GTGGAGCACTTGGAATACATATACAACTTA
1 GTGGAGCACTTGGAAGACATATACAACTTA
* * * *
2719518 GTGGAGCATTTGGAAGATATATAGAGCTTA
1 GTGGAGCACTTGGAAGACATATACAACTTA
2719548 GT
1 GT
2719550 TGATGTGATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (30 bp):
GTGGAGCACTTGGAAGACATATACAACTTA
Found at i:2721406 original size:2 final size:2
Alignment explanation
Indices: 2721399--2721439 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2721389 AGTTATTTTC
2721399 AT AT AT AT 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 AT AT AT AT A
2721440 GTTATTATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2726852 original size:12 final size:12
Alignment explanation
Indices: 2726815--2726852 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2726805 TTGGTGCTGG
2726815 AAACAAGATAAA
1 AAACAAGATAAA
* *
2726827 AAATAAGAT-TA
1 AAACAAGATAAA
2726838 AAACAAGATAAA
1 AAACAAGATAAA
2726850 AAA
1 AAA
2726853 ATATAGAGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:2729516 original size:21 final size:21
Alignment explanation
Indices: 2729491--2729543 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2729481 TTTGAAGGAT
2729491 TACCTTGGTAAGAGAATGAAG
1 TACCTTGGTAAGAGAATGAAG
* *
2729512 TACCTTGGTAAGAGGATGGAG
1 TACCTTGGTAAGAGAATGAAG
2729533 TACCTTGGTAA
1 TACCTTGGTAA
2729544 TGTTCTCGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.26
Consensus pattern (21 bp):
TACCTTGGTAAGAGAATGAAG
Found at i:2731203 original size:18 final size:18
Alignment explanation
Indices: 2731182--2731216 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2731172 TTTTTGAAAT
2731182 TTTGGCTTTTTTTGTTTC
1 TTTGGCTTTTTTTGTTTC
**
2731200 TTTGTTTTTTTTTGTTT
1 TTTGGCTTTTTTTGTTT
2731217 TTTTTTTTGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.14, T:0.80
Consensus pattern (18 bp):
TTTGGCTTTTTTTGTTTC
Found at i:2743314 original size:9 final size:9
Alignment explanation
Indices: 2743302--2743330 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
2743292 CATCCATCTC
2743302 TTCCATCAA
1 TTCCATCAA
2743311 TTCCATCAA
1 TTCCATCAA
2743320 TTCCATCAA
1 TTCCATCAA
2743329 TT
1 TT
2743331 ACACAACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (9 bp):
TTCCATCAA
Found at i:2743751 original size:2 final size:2
Alignment explanation
Indices: 2743746--2743775 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2743736 AATTTTCAGA
2743746 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
2743776 TACTTTCAAG
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:2745168 original size:61 final size:61
Alignment explanation
Indices: 2745057--2745175 Score: 141
Period size: 61 Copynumber: 2.0 Consensus size: 61
2745047 ACGCATTGCA
* * * * *
2745057 AACAGCCTGTTGGAGCATTATAAGGACATATACCATTCAGTAGAGCATGAAAAACGTTAAT
1 AACAACCTGTTGAAACATTATAAAGACATATACCATTCAGTACAGCATGAAAAACGTTAAT
** * *
2745118 AACAACCTGTTGAAACATTATAAAGACATAT-CCACTTCTTTACAGTATGAAACACGTT
1 AACAACCTGTTGAAACATTATAAAGACATATACCA-TTCAGTACAGCATGAAAAACGTT
2745176 GGGAGACATA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
60 3 0.06
61 45 0.94
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (61 bp):
AACAACCTGTTGAAACATTATAAAGACATATACCATTCAGTACAGCATGAAAAACGTTAAT
Found at i:2747957 original size:18 final size:18
Alignment explanation
Indices: 2747934--2747979 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2747924 GCATGTATTC
*
2747934 ATTCTTGTATATTAGAAT
1 ATTCTTGCATATTAGAAT
2747952 ATTCTTGCATATTAGAAT
1 ATTCTTGCATATTAGAAT
*
2747970 AGTCTTGCAT
1 ATTCTTGCAT
2747980 TACTTATCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (18 bp):
ATTCTTGCATATTAGAAT
Found at i:2754291 original size:2 final size:2
Alignment explanation
Indices: 2754280--2754342 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
2754270 TAACTATAGG
2754280 TA TA -A 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
2754321 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
2754343 ATAAACTATC
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.