Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_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: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 29
Found at i:6245588 original size:33 final size:33
Alignment explanation
Indices: 6245546--6245621 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
6245536 ATGACTATCA
6245546 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
*
6245579 CAATGCGAAATGAAAATCGCAACGATAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
*
6245612 CAACGCGAAA
1 CAATGCGAAA
6245622 CACAAATCGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCG
Found at i:6245629 original size:33 final size:33
Alignment explanation
Indices: 6245550--6245632 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
6245540 CTATCACAAT
* *
6245550 GCGAAATGAAAATCGCAACGACAAAATCGCAAT
1 GCGAAATCAAAATCGCAACGACAAAATCGCAAC
* *
6245583 GCGAAATGAAAATCGCAACGATAAAATCGCAAC
1 GCGAAATCAAAATCGCAACGACAAAATCGCAAC
6245616 GCGAAA-CACAAATCGCA
1 GCGAAATCA-AAATCGCA
6245633 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 1 0.02
33 45 0.98
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
GCGAAATCAAAATCGCAACGACAAAATCGCAAC
Found at i:6245650 original size:19 final size:19
Alignment explanation
Indices: 6245628--6245724 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
6245618 GAAACACAAA
6245628 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
6245647 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
6245663 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
6245680 TCGTATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
6245696 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6245713 TCGCATTGCGAT
1 TCGCATTGCGAT
6245725 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 23 0.37
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:6245669 original size:14 final size:14
Alignment explanation
Indices: 6245650--6245708 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
6245640 TTTCATTTCG
6245650 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
6245664 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
6245681 CGTATTGCGATTTTGT
1 CG--TTGCGATTTTGT
6245697 CGTTGCGATTTT
1 CGTTGCGATTTT
6245709 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:6245675 original size:33 final size:33
Alignment explanation
Indices: 6245633--6245724 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
6245623 ACAAATCGCA
*
6245633 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
6245666 TTGCGATTTTCATTTCGTATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
6245699 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
6245725 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:6245743 original size:20 final size:19
Alignment explanation
Indices: 6245709--6245763 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
6245699 TTGCGATTTT
*
6245709 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
6245728 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
6245748 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
6245764 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:6246327 original size:18 final size:18
Alignment explanation
Indices: 6246304--6246351 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
6246294 CGGGTCGATC
6246304 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
6246322 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
6246340 AGGTGATGGCTC
1 AGGTGATGGCTC
6246352 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:6247719 original size:20 final size:20
Alignment explanation
Indices: 6247671--6247729 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
6247661 AATAGTTTCT
* *
6247671 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
6247691 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
6247711 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
6247730 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:6248011 original size:22 final size:22
Alignment explanation
Indices: 6247984--6248026 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
6247974 ATGGAGATAG
6247984 ACGGATTTCGCCGGAGATGGGA
1 ACGGATTTCGCCGGAGATGGGA
*
6248006 ACGGATTTCGTCGGAGATGGG
1 ACGGATTTCGCCGGAGATGGG
6248027 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.16, G:0.42, T:0.21
Consensus pattern (22 bp):
ACGGATTTCGCCGGAGATGGGA
Found at i:6248274 original size:20 final size:20
Alignment explanation
Indices: 6248223--6248285 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
6248213 TATCTCATTT
*
6248223 CGAAAGTCAGTATTGAGTTG
1 CGAAAGTCAGTATCGAGTTG
* *
6248243 CGAAATTAAGTATCGAGTTG
1 CGAAAGTCAGTATCGAGTTG
*
6248263 CGAAAGTCAGTATCGCGTTG
1 CGAAAGTCAGTATCGAGTTG
6248283 CGA
1 CGA
6248286 TTTTGTATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (20 bp):
CGAAAGTCAGTATCGAGTTG
Found at i:6248320 original size:21 final size:21
Alignment explanation
Indices: 6248296--6248368 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
6248286 TTTTGTATTA
*
6248296 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
6248317 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
6248338 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
6248358 TCGCATTGCGA
1 TCGCATTGCGA
6248369 ATTGGGAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:6254633 original size:21 final size:21
Alignment explanation
Indices: 6254591--6254633 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
6254581 TTTCTGGGTT
* * *
6254591 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
6254612 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
6254633 A
1 A
6254634 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:6254694 original size:67 final size:68
Alignment explanation
Indices: 6254613--6254764 Score: 261
Period size: 67 Copynumber: 2.2 Consensus size: 68
6254603 ACCCATTCAA
* *
6254613 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATAAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
6254678 -GG
66 GGG
*
6254680 GGGGAACCGATACCCCCTCAACGAATATAAAATTCCAGAATGCTAGGGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATAAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
6254745 GGG
66 GGG
*
6254748 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
6254765 ATGAGAAAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
67 62 0.77
68 18 0.22
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATAAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:6254751 original size:21 final size:21
Alignment explanation
Indices: 6254725--6254765 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6254715 CAGAATGCTA
*
6254725 GGGGGGAATCGATACCCCCAG
1 GGGGGGAACCGATACCCCCAG
*
6254746 GGGGGGAACCGATTCCCCCA
1 GGGGGGAACCGATACCCCCA
6254766 TGAGAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.32, G:0.37, T:0.10
Consensus pattern (21 bp):
GGGGGGAACCGATACCCCCAG
Found at i:6255403 original size:149 final size:149
Alignment explanation
Indices: 6255218--6255513 Score: 583
Period size: 149 Copynumber: 2.0 Consensus size: 149
6255208 GGTCTACGCA
6255218 GTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATC
1 GTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATC
6255283 CCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATGGCAC
66 CCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATGGCAC
6255348 TACGGTGCAATTCTACGTG
131 TACGGTGCAATTCTACGTG
6255367 GTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATC
1 GTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATC
6255432 CCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATGGCAC
66 CCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATGGCAC
*
6255497 TACGGTGTAATTCTACG
131 TACGGTGCAATTCTACG
6255514 GGGCACTTCG
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 146 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38
Consensus pattern (149 bp):
GTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATC
CCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATGGCAC
TACGGTGCAATTCTACGTG
Found at i:6255536 original size:23 final size:23
Alignment explanation
Indices: 6255492--6255536 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
6255482 ATTATTATAT
* *
6255492 GGCACTACGGTGTAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
6255515 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
6255537 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:6261634 original size:21 final size:21
Alignment explanation
Indices: 6261592--6261634 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
6261582 TTTCTGGGTT
* * *
6261592 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
6261613 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
6261634 A
1 A
6261635 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:6261695 original size:67 final size:68
Alignment explanation
Indices: 6261614--6261765 Score: 270
Period size: 67 Copynumber: 2.2 Consensus size: 68
6261604 ACCCATTCAA
*
6261614 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
6261679 -GG
66 GGG
*
6261681 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGGGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
6261746 GGG
66 GGG
*
6261749 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
6261766 ATGAGAAAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
67 63 0.78
68 18 0.22
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:6261752 original size:21 final size:21
Alignment explanation
Indices: 6261726--6261766 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6261716 CAGAATGCTA
*
6261726 GGGGGGAATCGATACCCCCAG
1 GGGGGGAACCGATACCCCCAG
*
6261747 GGGGGGAACCGATTCCCCCA
1 GGGGGGAACCGATACCCCCA
6261767 TGAGAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.32, G:0.37, T:0.10
Consensus pattern (21 bp):
GGGGGGAACCGATACCCCCAG
Found at i:6262407 original size:149 final size:149
Alignment explanation
Indices: 6262211--6262514 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
6262201 GGGTAGAGGG
*
6262211 TCTATGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
6262276 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
*
6262341 TATGGCACTACGGTGCAAT
131 TATAGCACTACGGTGCAAT
6262360 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
6262425 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
6262490 TATAGCACTACGGTGCAAT
131 TATAGCACTACGGTGCAAT
6262509 TCTACG
1 TCTACG
6262515 GGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
TATAGCACTACGGTGCAAT
Found at i:6262537 original size:23 final size:23
Alignment explanation
Indices: 6262494--6262537 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6262484 TTATTATATA
*
6262494 GCACTACGGTGCAATTCTACGGG
1 GCACTACGGTGCAATTATACGGG
* *
6262517 GCACTTCGGTGCATTTATACG
1 GCACTACGGTGCAATTATACG
6262538 AGTTGTGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GCACTACGGTGCAATTATACGGG
Found at i:6268278 original size:14 final size:14
Alignment explanation
Indices: 6268259--6268286 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6268249 TTTGCGGTCC
6268259 ATCTTGGGAGTTGA
1 ATCTTGGGAGTTGA
6268273 ATCTTGGGAGTTGA
1 ATCTTGGGAGTTGA
6268287 TGATAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.36, T:0.36
Consensus pattern (14 bp):
ATCTTGGGAGTTGA
Found at i:6276244 original size:18 final size:20
Alignment explanation
Indices: 6276228--6276284 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
6276218 ATCATATTCC
*
6276228 CTGGTAATCTTATATTCTCA
1 CTGGTAATCTTATATTCACA
*
6276248 CTGATAATCTTATATTCACA
1 CTGGTAATCTTATATTCACA
* *
6276268 CTAGTAATCTTACATTC
1 CTGGTAATCTTATATTC
6276285 CGTGAACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTATATTCACA
Found at i:6277996 original size:21 final size:21
Alignment explanation
Indices: 6277949--6277996 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
6277939 TTGTGTACAT
*
6277949 CTTAAATTTTAAAATTTCAAA
1 CTTAAATATTAAAATTTCAAA
* *
6277970 CATAAATATTAAAATTTTAAA
1 CTTAAATATTAAAATTTCAAA
*
6277991 TTTAAA
1 CTTAAA
6277997 AATGTAAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (21 bp):
CTTAAATATTAAAATTTCAAA
Found at i:6279156 original size:11 final size:11
Alignment explanation
Indices: 6279140--6279172 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
6279130 TTACCATGGA
6279140 ATAATATTTTC
1 ATAATATTTTC
6279151 ATAATATTTTC
1 ATAATATTTTC
6279162 ATAATATTTTC
1 ATAATATTTTC
6279173 CACTCGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (11 bp):
ATAATATTTTC
Found at i:6279700 original size:16 final size:15
Alignment explanation
Indices: 6279681--6279721 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
6279671 TATAAGGTGA
6279681 AAAATAATATTATTAT
1 AAAATAATATTATT-T
6279697 AAAAT-ATAATTATTT
1 AAAATAAT-ATTATTT
6279712 AAAATAATAT
1 AAAATAATAT
6279722 ATAAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATAATATTATTT
Found at i:6279725 original size:27 final size:26
Alignment explanation
Indices: 6279694--6279749 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
6279684 ATAATATTAT
6279694 TATAAAATATAA-TTATTTAAAATAATA
1 TATAAAATATAAGTTA-TTAAAA-AATA
*
6279721 TAT-AAATTTAAGTTATTAAAAAATA
1 TATAAAATATAAGTTATTAAAAAATA
6279746 TATA
1 TATA
6279750 TTATATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 7 0.27
26 13 0.50
27 6 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
TATAAAATATAAGTTATTAAAAAATA
Found at i:6281520 original size:31 final size:33
Alignment explanation
Indices: 6281485--6281561 Score: 79
Period size: 33 Copynumber: 2.3 Consensus size: 33
6281475 AGTTTAAAAT
*
6281485 ATAAAATCTA-ATAATCTATATATATA-AAT-AA
1 ATAAAAT-TATATAATATATATATATATAATAAA
*
6281516 ATAAATAATTATATTATATATATATATATAATAAA
1 AT-AA-AATTATATAATATATATATATATAATAAA
*
6281551 ATAAAAATATA
1 ATAAAATTATA
6281562 AACTAACTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
31 2 0.05
32 4 0.11
33 23 0.61
34 5 0.13
35 4 0.11
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (33 bp):
ATAAAATTATATAATATATATATATATAATAAA
Found at i:6285351 original size:2 final size:2
Alignment explanation
Indices: 6285344--6285369 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6285334 TAGACATTAA
6285344 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
6285370 TGTTCAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6288952 original size:23 final size:23
Alignment explanation
Indices: 6288926--6288980 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
6288916 ATATATATTA
*
6288926 ATATT-TTAAGAATTTTTATTTTT
1 ATATTATTAA-AATTATTATTTTT
6288949 ATATTATTAAAATTATTA--TTT
1 ATATTATTAAAATTATTATTTTT
6288970 A-ATTATTAAAA
1 ATATTATTAAAA
6288981 AATAAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 10 0.33
21 4 0.13
23 12 0.40
24 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATTATTAAAATTATTATTTTT
Found at i:6288974 original size:20 final size:20
Alignment explanation
Indices: 6288941--6288980 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6288931 TTAAGAATTT
6288941 TTATTTTTATATTATTAAAA
1 TTATTTTTATATTATTAAAA
6288961 TTATTATTTA-ATTATTAAAA
1 TTATT-TTTATATTATTAAAA
6288981 AATAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTTTTATATTATTAAAA
Found at i:6288999 original size:14 final size:15
Alignment explanation
Indices: 6288970--6289005 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
6288960 ATTATTATTT
6288970 AATTATTAAAAAATA
1 AATTATTAAAAAATA
*
6288985 AATTATT-ATAAATA
1 AATTATTAAAAAATA
6288999 AATTATT
1 AATTATT
6289006 TTAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTATTAAAAAATA
Found at i:6291581 original size:82 final size:80
Alignment explanation
Indices: 6291478--6291684 Score: 267
Period size: 81 Copynumber: 2.6 Consensus size: 80
6291468 ATAGTGGCAA
* * *
6291478 CTTTTATAAAATGCTGTAATAGGGTTCACCTATAGTGGCATTTTTTCAATAAA-CACGACAATAA
1 CTTTTATAAAACGCCGTAATAGGGTTCACCTATAGTGG-ATTTTTTCAATAAAGC-CG-CAACAA
*
6291542 ATTAGTACTTTAGCGGTG
63 ATTAGTACTTTAGCGGCG
* *
6291560 CTTTTATAAAACGCCGCAATAGGGTTCACCTATAGTGGTTTTTTTCAATAAATGCCGCAACAAAT
1 CTTTTATAAAACGCCGTAATAGGGTTCACCTATAGTGGATTTTTTCAATAAA-GCCGCAACAAAT
6291625 TAGTACTTTAGCGGCG
65 TAGTACTTTAGCGGCG
* * * *
6291641 TTTTTAT-AATCACCGTAATAGGATTCACCTATAGT-GATTTTTTC
1 CTTTTATAAAACGCCGTAATAGGGTTCACCTATAGTGGATTTTTTC
6291685 TCACGACGCC
Statistics
Matches: 111, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
79 8 0.07
80 24 0.22
81 41 0.37
82 37 0.33
83 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (80 bp):
CTTTTATAAAACGCCGTAATAGGGTTCACCTATAGTGGATTTTTTCAATAAAGCCGCAACAAATT
AGTACTTTAGCGGCG
Found at i:6298733 original size:162 final size:161
Alignment explanation
Indices: 6298446--6298769 Score: 614
Period size: 162 Copynumber: 2.0 Consensus size: 161
6298436 TTAAACCGTG
6298446 GGCAAGTTAGCCCTAGCCAGTTCGAGCATGGTCGGTACGTCACTTGGAGGATGATGGAAATAGAG
1 GGCAAGTTAGCCCTAGCCAGTTCGAGCATGGTCGGTACGTCACTTGGAGGATGATGGAAATAGAG
6298511 GAAACCAGAGATCTCAGTTCGAGCTAAAGCATCGGATGTGGTATTCGCTTCTCTTTGGATACAGC
66 GAAACCAGAGATCTCAGTTCGAGCTAAAGCATCGGATGTGGTATTCGCTTCTCTTTGGATACAGC
6298576 TGACTTGAACTCTCCACTGTTGG-TTCAGGA
131 TGACTTGAACTCTCCACTGTTGGTTTCAGGA
*
6298606 GGCAAGTTTAGCCCTATCCAGTTTCGAGCATGGTCGGTACGTCACTTGGAGGATGATGGAAATAG
1 GGCAAG-TTAGCCCTAGCCAG-TTCGAGCATGGTCGGTACGTCACTTGGAGGATGATGGAAATAG
6298671 AGGAAACCAGAGATCTCAGTTCGAGCTAAAGCATCGGATGTGGTATTCGCTTCTCTTTGGATACA
64 AGGAAACCAGAGATCTCAGTTCGAGCTAAAGCATCGGATGTGGTATTCGCTTCTCTTTGGATACA
6298736 GCTGACTTGAACTCTCCACTGTTGGTTTCAGGA
129 GCTGACTTGAACTCTCCACTGTTGGTTTCAGGA
6298769 G
1 G
6298770 ATTCCGAATT
Statistics
Matches: 160, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
160 6 0.04
161 13 0.08
162 133 0.83
163 8 0.05
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (161 bp):
GGCAAGTTAGCCCTAGCCAGTTCGAGCATGGTCGGTACGTCACTTGGAGGATGATGGAAATAGAG
GAAACCAGAGATCTCAGTTCGAGCTAAAGCATCGGATGTGGTATTCGCTTCTCTTTGGATACAGC
TGACTTGAACTCTCCACTGTTGGTTTCAGGA
Found at i:6300002 original size:17 final size:18
Alignment explanation
Indices: 6299980--6300016 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
6299970 ACAAGAGGAT
6299980 CACGGTCT-GGATCCACG
1 CACGGTCTGGGATCCACG
6299997 CACGGTCTGGGATCCACG
1 CACGGTCTGGGATCCACG
6300015 CA
1 CA
6300017 TCCTTCCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.19, C:0.35, G:0.30, T:0.16
Consensus pattern (18 bp):
CACGGTCTGGGATCCACG
Found at i:6306430 original size:4 final size:4
Alignment explanation
Indices: 6306421--6306459 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
6306411 CATGATACAG
* *
6306421 ATAC ATAC ATGC ATAC AAAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
6306460 GCAAAGAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:6306442 original size:12 final size:12
Alignment explanation
Indices: 6306421--6306464 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
6306411 CATGATACAG
* *
6306421 ATACATACATGC
1 ATACAAACATAC
6306433 ATACAAACATAC
1 ATACAAACATAC
*
6306445 ATACATACATAC
1 ATACAAACATAC
6306457 ATAGCAAA
1 ATA-CAAA
6306465 GAAATGAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 24 0.89
13 3 0.11
ACGTcount: A:0.52, C:0.23, G:0.05, T:0.20
Consensus pattern (12 bp):
ATACAAACATAC
Found at i:6317135 original size:27 final size:27
Alignment explanation
Indices: 6317092--6317159 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
6317082 ATATTGTCCA
*
6317092 TACATTTAAAATATAATCCTCT-TCTTT
1 TACATTTAAAATTTAAT-CTCTATCTTT
* *
6317119 TACTTTTAAAATTTAATCTTTATCTTT
1 TACATTTAAAATTTAATCTCTATCTTT
*
6317146 TAGATTTAAAATTT
1 TACATTTAAAATTT
6317160 TAAATTCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 3 0.09
27 32 0.91
ACGTcount: A:0.34, C:0.12, G:0.01, T:0.53
Consensus pattern (27 bp):
TACATTTAAAATTTAATCTCTATCTTT
Found at i:6318091 original size:8 final size:8
Alignment explanation
Indices: 6318072--6318197 Score: 90
Period size: 8 Copynumber: 15.8 Consensus size: 8
6318062 TTCCCCGATC
*
6318072 CTCAATCT
1 CTCAAACT
*
6318080 CTTAAACT
1 CTCAAACT
* *
6318088 CTTAAATT
1 CTCAAACT
6318096 CTCAAACT
1 CTCAAACT
**
6318104 CTTTAACT
1 CTCAAACT
* * *
6318112 ATGAAATT
1 CTCAAACT
*
6318120 ATCAAACT
1 CTCAAACT
6318128 CTCAAACT
1 CTCAAACT
*
6318136 TTCAAACT
1 CTCAAACT
*
6318144 CTCAAATT
1 CTCAAACT
6318152 CTCAAACT
1 CTCAAACT
**
6318160 CTTTAACT
1 CTCAAACT
* *
6318168 CTGAAATT
1 CTCAAACT
*
6318176 ATCAAACT
1 CTCAAACT
*
6318184 CTCAAATT
1 CTCAAACT
6318192 CTCAAA
1 CTCAAA
6318198 ATGACTCTTA
Statistics
Matches: 90, Mismatches: 28, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
8 90 1.00
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (8 bp):
CTCAAACT
Found at i:6318105 original size:24 final size:24
Alignment explanation
Indices: 6318072--6318197 Score: 101
Period size: 24 Copynumber: 5.2 Consensus size: 24
6318062 TTCCCCGATC
* *
6318072 CTCAATCTCTTAAACTCTTAAATT
1 CTCAAACTCTCAAACTCTTAAATT
** * *
6318096 CTCAAACTCTTTAACTATGAAATT
1 CTCAAACTCTCAAACTCTTAAATT
* *
6318120 ATCAAACTCTCAAACT-TTCAAACT
1 CTCAAACTCTCAAACTCTT-AAATT
* * *
6318144 CTCAAATTCTCAAACTCTTTAACT
1 CTCAAACTCTCAAACTCTTAAATT
* * * *
6318168 CTGAAATTATCAAACTCTCAAATT
1 CTCAAACTCTCAAACTCTTAAATT
6318192 CTCAAA
1 CTCAAA
6318198 ATGACTCTTA
Statistics
Matches: 82, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.96
25 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (24 bp):
CTCAAACTCTCAAACTCTTAAATT
Found at i:6318144 original size:56 final size:56
Alignment explanation
Indices: 6318083--6318197 Score: 196
Period size: 56 Copynumber: 2.1 Consensus size: 56
6318073 TCAATCTCTT
*
6318083 AAACTCTTAAATTCTCAAACTCTTTAACTATGAAATTATCAAACTCTCAAACTT-TC
1 AAACTCTCAAATTCTCAAACTCTTTAACTATGAAATTATCAAACTCTCAAA-TTCTC
*
6318139 AAACTCTCAAATTCTCAAACTCTTTAACTCTGAAATTATCAAACTCTCAAATTCTC
1 AAACTCTCAAATTCTCAAACTCTTTAACTATGAAATTATCAAACTCTCAAATTCTC
6318195 AAA
1 AAA
6318198 ATGACTCTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
55 2 0.04
56 54 0.96
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (56 bp):
AAACTCTCAAATTCTCAAACTCTTTAACTATGAAATTATCAAACTCTCAAATTCTC
Found at i:6322545 original size:2 final size:2
Alignment explanation
Indices: 6322538--6322563 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6322528 CACATATTTC
6322538 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
6322564 GCCATTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6323927 original size:3 final size:3
Alignment explanation
Indices: 6323921--6323945 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6323911 CTATTATTGT
6323921 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
6323946 CATTACTATT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:6324601 original size:20 final size:20
Alignment explanation
Indices: 6324576--6324615 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
6324566 CGAAAACCAA
6324576 GCGTGCAGGAGAGTGACTTT
1 GCGTGCAGGAGAGTGACTTT
*
6324596 GCGTGCCGGAGAGTGACTTT
1 GCGTGCAGGAGAGTGACTTT
6324616 CTTTAAGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.40, T:0.25
Consensus pattern (20 bp):
GCGTGCAGGAGAGTGACTTT
Found at i:6330374 original size:39 final size:39
Alignment explanation
Indices: 6330331--6330425 Score: 190
Period size: 39 Copynumber: 2.4 Consensus size: 39
6330321 ATCCGAGTAA
6330331 CATCAGTAACTTAGTATTAAACTTGCCTATGTCAACAAC
1 CATCAGTAACTTAGTATTAAACTTGCCTATGTCAACAAC
6330370 CATCAGTAACTTAGTATTAAACTTGCCTATGTCAACAAC
1 CATCAGTAACTTAGTATTAAACTTGCCTATGTCAACAAC
6330409 CATCAGTAACTTAGTAT
1 CATCAGTAACTTAGTAT
6330426 CCAAAGGCGC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.32
Consensus pattern (39 bp):
CATCAGTAACTTAGTATTAAACTTGCCTATGTCAACAAC
Found at i:6335668 original size:20 final size:21
Alignment explanation
Indices: 6335643--6335735 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
6335633 TTTTCCCAAT
*
6335643 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
6335663 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
6335684 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
6335704 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
6335725 TCGCAATGCGA
1 TCGCAATGCGA
6335736 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:6335749 original size:20 final size:20
Alignment explanation
Indices: 6335724--6335838 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
6335714 AATTGGGAAA
*
6335724 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
6335744 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* * *
6335765 ATCTCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
6335785 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
6335805 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
6335825 TTCGCAACGCGATA
1 ATCGCAACGCGATA
6335839 ATACATAATC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:6335750 original size:41 final size:41
Alignment explanation
Indices: 6335643--6335735 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
6335633 TTTTCCCAAT
6335643 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
6335684 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
6335725 TCGCAATGCGA
1 TCGCAATGCGA
6335736 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:6336054 original size:22 final size:22
Alignment explanation
Indices: 6336026--6336069 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
6336016 CACTCTCTCA
6336026 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
6336048 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
6336070 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:6336385 original size:20 final size:20
Alignment explanation
Indices: 6336332--6336389 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
6336322 CGATTCTCTC
**
6336332 GTTGCGATAGTCAAATTCGT
1 GTTGCGATAGTCATTTTCGT
6336352 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
6336372 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
6336390 AGAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.45
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:6337725 original size:18 final size:18
Alignment explanation
Indices: 6337704--6337748 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
6337694 TCCACTTCGG
* *
6337704 GAGCCATCACCTCGCTCA
1 GAGCCATCACCTCACCCA
*
6337722 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
6337740 GAGCCATCA
1 GAGCCATCA
6337749 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:6338284 original size:19 final size:20
Alignment explanation
Indices: 6338230--6338296 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
6338220 TAGTTTACTT
* *
6338230 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
6338250 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
6338270 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
6338289 TCGCAACG
1 TCGCAACG
6338297 ACAAAATCTC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:6338304 original size:14 final size:14
Alignment explanation
Indices: 6338285--6338342 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
6338275 ATGCGAAATG
6338285 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
6338299 AAAATCTCAATGCGAA
1 AAAATCGCAA--CGAC
6338315 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
6338331 AAAATCACAACG
1 AAAATCGCAACG
6338343 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.54
16 8 0.23
18 8 0.23
ACGTcount: A:0.50, C:0.24, G:0.14, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:6338327 original size:32 final size:33
Alignment explanation
Indices: 6338273--6338359 Score: 149
Period size: 32 Copynumber: 2.7 Consensus size: 33
6338263 ATGGCTATCG
*
6338273 CAATGCGAAATGAAAATCGCAACGACAAAATCT
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
6338306 CAATGCGAAATG-AAATCGCAACGACAAAATCA
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
6338338 CAACGCGAAATGAAAATCGCAA
1 CAATGCGAAATGAAAATCGCAA
6338360 TGCGATTTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 30 0.59
33 21 0.41
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.13
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCA
Found at i:6338397 original size:14 final size:14
Alignment explanation
Indices: 6338378--6338433 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
6338368 GTGTTTCGCA
6338378 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
6338392 TTGCGATTTGATTTCGCG
1 TTGCGATTT--TGT--CG
6338410 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
6338424 TTGCGATTTT
1 TTGCGATTTT
6338434 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 21 0.58
16 4 0.11
18 11 0.31
ACGTcount: A:0.09, C:0.14, G:0.27, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:6338414 original size:32 final size:32
Alignment explanation
Indices: 6338360--6338449 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
6338350 AAAATCGCAA
*
6338360 TGCGATTTGTGTTTCGCATTGCGATTTTGTCGT
1 TGCGATTTG-ATTTCGCATTGCGATTTTGTCGT
*
6338393 TGCGATTTGATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTGATTTCGCATTGCGATTTTGTCGT
*
6338425 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGA-TTTGATTTCGCATTGCGAT
6338450 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 26 0.50
33 26 0.50
ACGTcount: A:0.11, C:0.17, G:0.26, T:0.47
Consensus pattern (32 bp):
TGCGATTTGATTTCGCATTGCGATTTTGTCGT
Found at i:6340353 original size:14 final size:14
Alignment explanation
Indices: 6340334--6340369 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
6340324 ATTGTTTAAT
6340334 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
6340348 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
6340362 TGATTTGT
1 TGATTTGT
6340370 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:6340508 original size:19 final size:19
Alignment explanation
Indices: 6340486--6340553 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
6340476 ATCGCAACGA
6340486 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
6340505 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
6340524 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
6340538 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
6340554 TTTCATTTCG
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:6340596 original size:20 final size:20
Alignment explanation
Indices: 6340571--6340628 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
6340561 TCGCATTGCG
*
6340571 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
6340591 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
6340611 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
6340629 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:6341736 original size:24 final size:24
Alignment explanation
Indices: 6341685--6341738 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
6341675 GTATTCGAAA
* * *
6341685 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACAGAC
*
6341709 TTTGATATTGGTCAATACACAGAT
1 TTTGATATTGGTCAATACACAGAC
6341733 TTTGAT
1 TTTGAT
6341739 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACAGAC
Found at i:6341930 original size:12 final size:12
Alignment explanation
Indices: 6341913--6341937 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6341903 ATATAATCCT
6341913 GAAGAAGAAAAA
1 GAAGAAGAAAAA
6341925 GAAGAAGAAAAA
1 GAAGAAGAAAAA
6341937 G
1 G
6341938 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:6344252 original size:19 final size:19
Alignment explanation
Indices: 6344230--6344288 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
6344220 GGAAATTACT
6344230 ATCGCAATACGAAATGAAA
1 ATCGCAATACGAAATGAAA
*
6344249 ATCGC-A-ACG--AT-AGA
1 ATCGCAATACGAAATGAAA
* *
6344263 ATCGCAATGCAAAATGAAA
1 ATCGCAATACGAAATGAAA
6344282 ATCGCAA
1 ATCGCAA
6344289 CGATAGAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 7 0.23
15 3 0.10
16 1 0.03
17 3 0.10
18 3 0.10
19 14 0.45
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (19 bp):
ATCGCAATACGAAATGAAA
Found at i:6344278 original size:33 final size:33
Alignment explanation
Indices: 6344230--6344422 Score: 257
Period size: 33 Copynumber: 5.8 Consensus size: 33
6344220 GGAAATTACT
*
6344230 ATCGCAATACGAAATGAAAATCGCAACGATAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
*
6344263 ATCGCAATGCAAAATGAAAATCGCAACGATAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
** *
6344296 ATCGCAATGTAAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
*
6344328 TTTCGCAATGCGAAATGAAAATCGCAAC-ACTA-A
1 -ATCGCAATGCGAAATGAAAATCGCAACGA-TAGA
* **
6344361 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGATAGA
6344395 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
6344423 CGAATTTAAT
Statistics
Matches: 145, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
32 1 0.01
33 142 0.98
34 2 0.01
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGATAGA
Found at i:6344319 original size:19 final size:18
Alignment explanation
Indices: 6344262--6344321 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
6344252 GCAACGATAG
6344262 AATCGCAATGCAAAATGAA
1 AATCGCAATG-AAAATGAA
* *
6344281 AATCGCAACG---AT-AG
1 AATCGCAATGAAAATGAA
6344295 AATCGCAATGTAAAATGAA
1 AATCGCAATG-AAAATGAA
6344314 AATCGCAA
1 AATCGCAA
6344322 CGCTAATTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
14 10 0.31
15 2 0.06
18 2 0.06
19 18 0.56
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (18 bp):
AATCGCAATGAAAATGAA
Found at i:6344387 original size:99 final size:99
Alignment explanation
Indices: 6344231--6344429 Score: 294
Period size: 99 Copynumber: 2.0 Consensus size: 99
6344221 GAAATTACTA
*
6344231 TCGCAATACGAAATGAAAATCGCAACGATAGAATCGCAATGCAAAATGAAAATCGCAACGATAGA
1 TCGCAATACGAAATGAAAATCGCAACGATAGAATCGCAATGCAAAATGAAAATCGCAACGAGAGA
* *
6344296 ATCGCAATGTAAAATGAAAATCGCAACGCTAATT
66 ATCGCAATGCAAAATGAAAATCGCAACGCGAATT
* * * *
6344330 TCGCAATGCGAAATGAAAATCGCAAC-ACTA-ATTTCGCAATGCGAAATGAAAATCGCAACGAGG
1 TCGCAATACGAAATGAAAATCGCAACGA-TAGA-ATCGCAATGCAAAATGAAAATCGCAACGAGA
*
6344393 GAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
64 GAATCGCAATGCAAAATGAAAATCGCAACGCGAATT
6344429 T
1 T
6344430 AATTTTGCAT
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
98 2 0.02
99 88 0.98
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (99 bp):
TCGCAATACGAAATGAAAATCGCAACGATAGAATCGCAATGCAAAATGAAAATCGCAACGAGAGA
ATCGCAATGCAAAATGAAAATCGCAACGCGAATT
Found at i:6344473 original size:19 final size:19
Alignment explanation
Indices: 6344451--6344511 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
6344441 GCGTTTCTCT
6344451 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
6344470 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
6344484 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
6344503 CATTGCGAT
1 CGTTGCGAT
6344512 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:6344482 original size:33 final size:33
Alignment explanation
Indices: 6344422--6344511 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
6344412 AAATCGCAAC
* * * *
6344422 GCGAATTTAATTTTGCATTGCGTTTCTCTCGTT
1 GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
*
6344455 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
6344488 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCATTGCGAT
6344512 AGTACTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (33 bp):
GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
Found at i:6344636 original size:14 final size:14
Alignment explanation
Indices: 6344617--6344653 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
6344607 CATCAATTAA
6344617 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
6344631 ACAAATCACCTTTT
1 ACAAATCAACTTTT
6344645 ACAAATCAA
1 ACAAATCAA
6344654 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:6346077 original size:21 final size:21
Alignment explanation
Indices: 6346011--6346077 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
6346001 GTGAATCGGG
*
6346011 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
6346031 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
6346053 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
6346074 CTCT
1 CTCT
6346078 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:6346096 original size:42 final size:41
Alignment explanation
Indices: 6346011--6346133 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
6346001 GTGAATCGGG
* * * *
6346011 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
6346053 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
6346095 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
6346134 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:6346527 original size:91 final size:90
Alignment explanation
Indices: 6346349--6346535 Score: 295
Period size: 91 Copynumber: 2.0 Consensus size: 90
6346339 ATATTTCAAA
*
6346349 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
*
6346414 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGAAGCAACCGAATAAATTT
6346442 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
6346506 CAGTATTGGAAGCAACCGAATAAATTT
64 CAGAATTGGAAGCAACCGAATAAATTT
6346533 ACT
1 ACT
6346536 AAGCAATCTA
Statistics
Matches: 89, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.46
93 21 0.24
95 27 0.30
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGAAGCAACCGAATAAATTT
Found at i:6346738 original size:63 final size:63
Alignment explanation
Indices: 6346679--6346820 Score: 160
Period size: 63 Copynumber: 2.3 Consensus size: 63
6346669 CTTAGAGCGG
* * *
6346679 CAACCTCAC-CACGTAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTC-CTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* * * *** *
6346742 CGATCTCCTCACGCAAGGCATTGACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* *
6346805 CGATCTCCTCACGCAA
1 CAACCTCCTCACGCAA
6346821 GGCATTGACC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
62 1 0.01
63 69 0.99
ACGTcount: A:0.27, C:0.37, G:0.17, T:0.19
Consensus pattern (63 bp):
CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
Found at i:6346821 original size:63 final size:63
Alignment explanation
Indices: 6346702--6346832 Score: 262
Period size: 63 Copynumber: 2.1 Consensus size: 63
6346692 TAAAGTAGAC
6346702 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
6346765 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
6346828 ACCTC
1 ACCTC
6346833 AGCACGTAAC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:6348333 original size:19 final size:19
Alignment explanation
Indices: 6348282--6348393 Score: 126
Period size: 19 Copynumber: 6.1 Consensus size: 19
6348272 TCTTTTGGTT
*
6348282 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
6348301 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
6348321 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
6348338 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
6348354 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
6348373 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
6348392 GA
1 GA
6348394 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 47 0.59
20 17 0.22
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:6348349 original size:33 final size:33
Alignment explanation
Indices: 6348307--6348371 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
6348297 ACGAGATAAT
**
6348307 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
6348340 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGAAAATCGCAACG
6348372 CGAAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:6348411 original size:19 final size:19
Alignment explanation
Indices: 6348389--6348433 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
6348379 AAAATCGCAA
*
6348389 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
6348408 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
6348427 TGCGATT
1 TGCGATT
6348434 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:6349009 original size:20 final size:20
Alignment explanation
Indices: 6348984--6349036 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
6348974 GCGCTATGTA
6348984 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
6349004 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
6349024 TATCTCGTTGCGA
1 AATCGCGTTGCGA
6349037 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:6349189 original size:21 final size:21
Alignment explanation
Indices: 6349149--6349189 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6349139 ACTGTAGACC
**
6349149 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
6349170 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
6349190 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:6349474 original size:37 final size:37
Alignment explanation
Indices: 6349373--6349474 Score: 152
Period size: 37 Copynumber: 2.8 Consensus size: 37
6349363 AGATAACACC
* *
6349373 TTTAGCATACGTTTGATTCACAGCATGTAAGATTTCA
1 TTTAACATACGTTTGATTCACAGAATGTAAGATTTCA
*
6349410 TTTAACATACGTTTGGTTCACCA-AATGTAAGATTTCA
1 TTTAACATACGTTTGATTCA-CAGAATGTAAGATTTCA
*
6349447 TTTAACATACGTTTGATTCACGGAATGT
1 TTTAACATACGTTTGATTCACAGAATGT
6349475 TGTTTGGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
36 1 0.02
37 55 0.95
38 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (37 bp):
TTTAACATACGTTTGATTCACAGAATGTAAGATTTCA
Found at i:6351871 original size:29 final size:29
Alignment explanation
Indices: 6351778--6351873 Score: 74
Period size: 29 Copynumber: 3.3 Consensus size: 29
6351768 CTATAACCTT
6351778 TATT-TAAATTAGTCCTTAAACTTTTGAA
1 TATTCTAAATTAGTCCTTAAACTTTTGAA
* * * **
6351806 TATTCCAATTTCA-TCAC-GAAAC-TACGAA
1 TATTCTAAATT-AGTC-CTTAAACTTTTGAA
6351834 TCTCATTCTAAATTAGTCCTTAAACTTTTGAA
1 --T-ATTCTAAATTAGTCCTTAAACTTTTGAA
6351866 TATTCTAA
1 TATTCTAA
6351874 TTTCATCCCT
Statistics
Matches: 49, Mismatches: 10, Indels: 17
0.64 0.13 0.22
Matches are distributed among these distances:
28 8 0.16
29 17 0.35
30 6 0.12
31 14 0.29
32 4 0.08
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (29 bp):
TATTCTAAATTAGTCCTTAAACTTTTGAA
Found at i:6351886 original size:29 final size:29
Alignment explanation
Indices: 6351794--6351887 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
6351784 AATTAGTCCT
* *
6351794 TAAACTTTTGAATATTCCAATTTCATCAC
1 TAAACTTTTGAATATTCTAATTTCATCCC
* ** * *
6351823 GAAAC-TACGAATCTCATTCTAAATT-AGTCCT
1 TAAACTTTTGAA--T-ATTCTAATTTCA-TCCC
6351854 TAAACTTTTGAATATTCTAATTTCATCCC
1 TAAACTTTTGAATATTCTAATTTCATCCC
6351883 TAAAC
1 TAAAC
6351888 CATGACCATC
Statistics
Matches: 47, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
28 4 0.09
29 21 0.45
30 4 0.09
31 14 0.30
32 4 0.09
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.38
Consensus pattern (29 bp):
TAAACTTTTGAATATTCTAATTTCATCCC
Found at i:6351906 original size:60 final size:59
Alignment explanation
Indices: 6351778--6351942 Score: 190
Period size: 60 Copynumber: 2.8 Consensus size: 59
6351768 CTATAACCTT
* * *
6351778 TATT-TAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCACGAAACTACGAATC
1 TATTATAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCGAAACCACGAATC
* * *
6351836 TCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAACCATGACCATC
1 T-ATTATAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCGAAACCACGA--ATC
** ** *
6351898 T-TTATAAATCGGTCCCCAAACTTTTGAATATCCTAATTTCATCCC
1 TATTATAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCC
6351943 CGAATTAATC
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
58 1 0.01
59 3 0.03
60 84 0.91
62 4 0.04
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (59 bp):
TATTATAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCGAAACCACGAATC
Found at i:6352160 original size:29 final size:28
Alignment explanation
Indices: 6352069--6352175 Score: 89
Period size: 26 Copynumber: 3.8 Consensus size: 28
6352059 ATATACGTAT
*
6352069 AGTTTGGGATGAAATTGGAATGTTCAAA
1 AGTTTGGGATGAAATTGAAATGTTCAAA
* *
6352097 AGTTTGGG-TGCCAATTTAGAATG--CAACTA
1 AGTTTGGGATG-AAATTGA-AATGTTCAA--A
6352126 TAGTTTAGGGATGAAATTGAAATGTTCAAA
1 -AGTTT-GGGATGAAATTGAAATGTTCAAA
*
6352156 AGTTT--GATGAAATTAAAATG
1 AGTTTGGGATGAAATTGAAATG
6352176 ATAGCCATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
26 14 0.22
27 5 0.08
28 12 0.19
29 10 0.16
30 10 0.16
31 8 0.12
32 5 0.08
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (28 bp):
AGTTTGGGATGAAATTGAAATGTTCAAA
Found at i:6362330 original size:4 final size:4
Alignment explanation
Indices: 6362321--6362367 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
6362311 TCTGCAATTG
6362321 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
6362368 GCATGGATGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:6362478 original size:6 final size:6
Alignment explanation
Indices: 6362462--6362505 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
6362452 TTTTACCTAG
* * *
6362462 GGTGCCT GGTGCT GGTGCT GGTGCG GGTGCG GGTGCC GGTGCT G
1 GGTG-CT GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT G
6362506 CTTGAGCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
6 30 0.88
7 4 0.12
ACGTcount: A:0.00, C:0.20, G:0.55, T:0.25
Consensus pattern (6 bp):
GGTGCT
Found at i:6363223 original size:76 final size:76
Alignment explanation
Indices: 6363097--6363237 Score: 255
Period size: 76 Copynumber: 1.9 Consensus size: 76
6363087 ACAGACCACG
*
6363097 GACAGCTGGTTGTGTTGGGTTGGGATTAGGGCTGAACAACGAAAGTGAGAAAATCGAAAAATATG
1 GACAGCTGGTTGTGTTGGGTTGGGATTAGGGCTGAACAACGAAAGTGAGAAAATCAAAAAATATG
6363162 CATTGATCACA
66 CATTGATCACA
* *
6363173 GACAGTTGGTTGTGTTGGGTTGGGATTAGGGCTGATCAACGAAAGTGAGAAAATCAAAAAATATG
1 GACAGCTGGTTGTGTTGGGTTGGGATTAGGGCTGAACAACGAAAGTGAGAAAATCAAAAAATATG
6363238 TTTCACATAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.34, C:0.10, G:0.31, T:0.25
Consensus pattern (76 bp):
GACAGCTGGTTGTGTTGGGTTGGGATTAGGGCTGAACAACGAAAGTGAGAAAATCAAAAAATATG
CATTGATCACA
Found at i:6364038 original size:40 final size:40
Alignment explanation
Indices: 6363994--6364073 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
6363984 TCAAAGGACT
6363994 TAATAAAATAATATCATATAGTCAAAGGACCATTTATGTA
1 TAATAAAATAATATCATATAGTCAAAGGACCATTTATGTA
* * * *
6364034 TAATAAAATAGTATCCTATAGTCCAATGACCATTTATGTA
1 TAATAAAATAATATCATATAGTCAAAGGACCATTTATGTA
6364074 CTTTACCTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (40 bp):
TAATAAAATAATATCATATAGTCAAAGGACCATTTATGTA
Found at i:6365178 original size:24 final size:23
Alignment explanation
Indices: 6365146--6365193 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
6365136 ATCAATACTC
6365146 TTTCAAGAGTATCGATACTTTAGG
1 TTTCAAGAGTATCGATA-TTTAGG
6365170 TTTCAAGAGTATCGATATTTAGG
1 TTTCAAGAGTATCGATATTTAGG
6365193 T
1 T
6365194 CATAGTTTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (23 bp):
TTTCAAGAGTATCGATATTTAGG
Found at i:6378556 original size:13 final size:13
Alignment explanation
Indices: 6378538--6378570 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
6378528 ACATGGCGCA
6378538 GCGACGAAGACGG
1 GCGACGAAGACGG
6378551 GCGACGAAGACGG
1 GCGACGAAGACGG
6378564 GCGACGA
1 GCGACGA
6378571 TGGACCGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.24, G:0.45, T:0.00
Consensus pattern (13 bp):
GCGACGAAGACGG
Found at i:6379016 original size:21 final size:21
Alignment explanation
Indices: 6378965--6379017 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
6378955 ATTATGACTA
6378965 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
6378986 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
6379007 TCGCAATGCGA
1 TCGCAATGCGA
6379018 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:6379032 original size:20 final size:21
Alignment explanation
Indices: 6379007--6379058 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
6378997 TTTTCCCAAT
*
6379007 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
6379027 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
6379048 TCGCAATGCGA
1 TCGCAATGCGA
6379059 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:6379072 original size:20 final size:20
Alignment explanation
Indices: 6379048--6379221 Score: 208
Period size: 20 Copynumber: 8.7 Consensus size: 20
6379038 ATTTGGAAAA
* *
6379048 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
* *
6379068 TCGCAACGCGATAAT-ACAAAAT
1 TCGCAACGCGATACTGAC---TT
6379090 T-GCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
6379109 TCGCAACGTGATACTGACTT
1 TCGCAACGCGATACTGACTT
**
6379129 TCGCAACGCGATTTTGACTT
1 TCGCAACGCGATACTGACTT
*
6379149 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
6379169 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
6379189 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
6379209 TCGCAACGAGATA
1 TCGCAACGCGATA
6379222 ATACAGAATC
Statistics
Matches: 136, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
19 4 0.03
20 117 0.86
21 12 0.09
22 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:6379792 original size:20 final size:20
Alignment explanation
Indices: 6379767--6379842 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
6379757 CAACGGGGAA
*
6379767 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
6379787 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
6379807 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
6379827 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
6379843 CGTAATGTGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:6379905 original size:19 final size:19
Alignment explanation
Indices: 6379883--6379925 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
6379873 TTTCTCGTTT
6379883 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
*
6379902 CGATTTTCATTTTGCATTG
1 CGATTTTCATTTCGCATTG
6379921 CGATT
1 CGATT
6379926 CTCTCGTTGC
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:0.16, C:0.19, G:0.16, T:0.49
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTG
Found at i:6381507 original size:40 final size:42
Alignment explanation
Indices: 6381463--6381552 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
6381453 ACCTCTTCAC
*
6381463 GATGACAGTGGCCTATTGAACG-GTGG-GGGGACTCTTGAGG
1 GATGACAGAGGCCTATTGAACGAGTGGAGGGGACTCTTGAGG
* * *
6381503 GATGATAGAGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGAGGCCTATTGAACGAGTGGAGGGGACTCTTGAGG
6381545 GATGACAG
1 GATGACAG
6381553 GTGAGTCGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 19 0.44
41 3 0.07
42 21 0.49
ACGTcount: A:0.23, C:0.14, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGAGGCCTATTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:6381912 original size:20 final size:20
Alignment explanation
Indices: 6381887--6381939 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
6381877 GAAGAATAGT
*
6381887 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
6381907 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* *
6381927 TGACTATCGCAAC
1 TTACTTTCGCAAC
6381940 GCGGAAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:6381967 original size:19 final size:19
Alignment explanation
Indices: 6381893--6381998 Score: 104
Period size: 20 Copynumber: 5.4 Consensus size: 19
6381883 TAGTTTACTT
* * *
6381893 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAA-TGACTA
6381913 TCGCAACGCGAAAATGACTA
1 TCGCAACGCG-AAATGACTA
*
6381933 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
**
6381953 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
* **
6381972 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
6381991 TCGCAACG
1 TCGCAACG
6381999 ACAAAATCGC
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
19 32 0.43
20 39 0.52
21 4 0.05
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.16
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:6382010 original size:33 final size:33
Alignment explanation
Indices: 6381968--6382031 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
6381958 ACGCGAAATG
6381968 AAAATCGCAATGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAATGCGAAATGAAAATCGCAACGAC
6382001 AAAATCGCAATGCGAAATGAAAATCGCAACG
1 AAAATCGCAATGCGAAATGAAAATCGCAACG
6382032 CGAAACACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.48, C:0.20, G:0.19, T:0.12
Consensus pattern (33 bp):
AAAATCGCAATGCGAAATGAAAATCGCAACGAC
Found at i:6382047 original size:19 final size:19
Alignment explanation
Indices: 6381913--6382036 Score: 123
Period size: 19 Copynumber: 6.7 Consensus size: 19
6381903 AAACTTACTT
**
6381913 TCGCAACGCGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
6381933 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
6381953 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
6381972 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
6381991 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
6382005 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
6382024 TCGCAACGCGAAA
1 TCGCAACGCGAAA
6382037 CACAAATCGC
Statistics
Matches: 90, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 47 0.52
20 26 0.29
21 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:6382053 original size:19 final size:19
Alignment explanation
Indices: 6381952--6382053 Score: 99
Period size: 19 Copynumber: 5.6 Consensus size: 19
6381942 GGAAATGGCT
* *
6381952 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
*
6381971 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
6381990 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATCAAA
*
6382004 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
*
6382023 ATCGCAACGCGAAA-CACAA
1 ATCGCAATGCGAAATCA-AA
*
6382042 ATCGCATTGCGA
1 ATCGCAATGCGA
6382054 TTTTCATTTC
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 53 0.76
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATCAAA
Found at i:6382090 original size:33 final size:33
Alignment explanation
Indices: 6382046--6382139 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
6382036 ACACAAATCG
* *
6382046 CATTGCGATTTTCATTTCACGTTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
*
6382079 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
*
6382112 CATTACGATTTTCATTTCGCATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGAT
6382140 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.47
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:6382139 original size:19 final size:19
Alignment explanation
Indices: 6382043--6382139 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
6382033 GAAACACAAA
6382043 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
6382062 TCACGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
6382078 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
6382095 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
6382111 T--CATTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
6382128 TCGCATTGCGAT
1 TCGCATTGCGAT
6382140 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 13 0.22
15 6 0.10
16 5 0.08
17 6 0.10
18 6 0.10
19 23 0.39
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:6382158 original size:20 final size:19
Alignment explanation
Indices: 6382124--6382178 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
6382114 TTACGATTTT
*
6382124 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
6382143 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
6382163 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
6382179 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:6382735 original size:18 final size:18
Alignment explanation
Indices: 6382712--6382759 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
6382702 CGGGTCGATC
6382712 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
6382730 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
6382748 AGATGATGGCTC
1 AGGTGATGGCTC
6382760 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:6384085 original size:20 final size:20
Alignment explanation
Indices: 6384052--6384109 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
6384042 AATAGTTTTT
** *
6384052 GAAAATGAAAATCGCAATAC
1 GAAAATGACTATCGCAACAC
*
6384072 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACAC
**
6384092 GAATTTGACTATCGCAAC
1 GAAAATGACTATCGCAAC
6384110 GAGAGAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:6384392 original size:22 final size:22
Alignment explanation
Indices: 6384367--6384410 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6384357 GATGGAGATA
*
6384367 GACGGATTTCGCCATAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
6384389 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
6384411 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.16, G:0.39, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:6384625 original size:20 final size:20
Alignment explanation
Indices: 6384597--6384710 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
6384587 GATTATGTAT
*
6384597 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6384617 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
6384637 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
6384657 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
6384678 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6384698 TATCGCATTGCGA
1 TATCGCGTTGCGA
6384711 TTTTCCCAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 64 0.78
21 13 0.16
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:6384714 original size:41 final size:41
Alignment explanation
Indices: 6384577--6384712 Score: 177
Period size: 41 Copynumber: 3.3 Consensus size: 41
6384567 CGCTTTGAAA
*
6384577 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * *
6384618 ATCGCGTTGCGA--AAGTAAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * *
6384658 ATCGCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
6384699 ATCGCATTGCGATT
1 ATCGCATTGCGATT
6384713 TTCCCAATTC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
39 3 0.04
40 33 0.40
41 44 0.54
42 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:6384730 original size:41 final size:41
Alignment explanation
Indices: 6384577--6384732 Score: 129
Period size: 41 Copynumber: 3.8 Consensus size: 41
6384567 CGCTTTGAAA
* ** * * *
6384577 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* *** *
6384618 ATCGCGTTGCGAAAGT--AAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAA-TATCGCGTTGCGATAGTCAGT
* ** * *
6384658 ATCGCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
6384699 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
6384733 TTACTTATTC
Statistics
Matches: 94, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
39 1 0.01
40 33 0.35
41 57 0.61
42 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
Found at i:6384793 original size:21 final size:22
Alignment explanation
Indices: 6384741--6384793 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
6384731 ATTTACTTAT
6384741 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
6384762 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
6384783 TCGCATTGCGA
1 TCGCATTGCGA
6384794 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:6385024 original size:20 final size:22
Alignment explanation
Indices: 6384984--6385026 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
6384974 TGGGGAAATA
6384984 TTAATGTTATATTTAAATATTT
1 TTAATGTTATATTTAAATATTT
6385006 TTAATG-TATATTT-AATATTT
1 TTAATGTTATATTTAAATATTT
6385026 T
1 T
6385027 AATTTTCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.38
21 7 0.33
22 6 0.29
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TTAATGTTATATTTAAATATTT
Found at i:6387004 original size:106 final size:106
Alignment explanation
Indices: 6386872--6387084 Score: 426
Period size: 106 Copynumber: 2.0 Consensus size: 106
6386862 GCGAGCTTGT
6386872 GGAAGAAATTGGGGGGTTTACACAGCTTTGCACAGAATTATTTTACTACTTTATTCCAATCGCAA
1 GGAAGAAATTGGGGGGTTTACACAGCTTTGCACAGAATTATTTTACTACTTTATTCCAATCGCAA
6386937 GGGGTGGAGGAGGATGACCATATTTTTGCGGGTATCGATAG
66 GGGGTGGAGGAGGATGACCATATTTTTGCGGGTATCGATAG
6386978 GGAAGAAATTGGGGGGTTTACACAGCTTTGCACAGAATTATTTTACTACTTTATTCCAATCGCAA
1 GGAAGAAATTGGGGGGTTTACACAGCTTTGCACAGAATTATTTTACTACTTTATTCCAATCGCAA
6387043 GGGGTGGAGGAGGATGACCATATTTTTGCGGGTATCGATAG
66 GGGGTGGAGGAGGATGACCATATTTTTGCGGGTATCGATAG
6387084 G
1 G
6387085 TGCATTACGA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 107 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (106 bp):
GGAAGAAATTGGGGGGTTTACACAGCTTTGCACAGAATTATTTTACTACTTTATTCCAATCGCAA
GGGGTGGAGGAGGATGACCATATTTTTGCGGGTATCGATAG
Found at i:6388724 original size:17 final size:17
Alignment explanation
Indices: 6388702--6388741 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
6388692 TAATGTGAAT
6388702 ATTTTTATTATTATTTC
1 ATTTTTATTATTATTTC
*
6388719 ATTTTTATTTTTATTTC
1 ATTTTTATTATTATTTC
6388736 ATTTTT
1 ATTTTT
6388742 TCTCTTCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTTATTATTATTTC
Found at i:6391332 original size:60 final size:58
Alignment explanation
Indices: 6391237--6391395 Score: 176
Period size: 60 Copynumber: 2.7 Consensus size: 58
6391227 GAATTGGGGA
** * * *
6391237 ATGAAATTGGAATATTCAAAAGTTTGGGGACTAATTTAATAAGAGGGTTGTAGTTTAGGG
1 ATGAAATTGGAATATTCAAAAGTTTAAGGATTAATTTAATAAGA--GTTATAGTGTAGGG
* * * *
6391297 ATGAAATTAGAATGTTCAAAAGTTTAAGAATTAATTTAGAATAAGAGTTATAGTGTGGGG
1 ATGAAATTGGAATATTCAAAAGTTTAAGGATTAATTT--AATAAGAGTTATAGTGTAGGG
*
6391357 ATGAAATTGGAATATT-AAAAGATTTAAGGATCAATTTAA
1 ATGAAATTGGAATATTCAAAAG-TTTAAGGATTAATTTAA
6391396 AATGATGATT
Statistics
Matches: 83, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 5 0.06
60 69 0.83
62 7 0.08
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (58 bp):
ATGAAATTGGAATATTCAAAAGTTTAAGGATTAATTTAATAAGAGTTATAGTGTAGGG
Found at i:6391408 original size:60 final size:60
Alignment explanation
Indices: 6391231--6391410 Score: 170
Period size: 60 Copynumber: 3.0 Consensus size: 60
6391221 TTGGATGAAT
** * * * *
6391231 TGGGGAATGAAATTGGAATATTCAAAAGTTTGGGGA-CTAATTTAATAA-GAGGGTTGTAGTT
1 TGGGG-ATGAAATTGGAATATTCAAAAGTTTAAGGATC-AATTTAA-AATGAAGATTATAGTG
* * * * * *
6391292 TAGGGATGAAATTAGAATGTTCAAAAGTTTAAGAATTAATTTAGAAT-AAGAGTTATAGTG
1 TGGGGATGAAATTGGAATATTCAAAAGTTTAAGGATCAATTTAAAATGAAGA-TTATAGTG
*
6391352 TGGGGATGAAATTGGAATATT-AAAAGATTTAAGGATCAATTTAAAATGATGATTATAGT
1 TGGGGATGAAATTGGAATATTCAAAAG-TTTAAGGATCAATTTAAAATGAAGATTATAGT
6391411 TTGAGGACAT
Statistics
Matches: 95, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
59 9 0.09
60 79 0.83
61 7 0.07
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.33
Consensus pattern (60 bp):
TGGGGATGAAATTGGAATATTCAAAAGTTTAAGGATCAATTTAAAATGAAGATTATAGTG
Found at i:6392722 original size:16 final size:16
Alignment explanation
Indices: 6392701--6392732 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6392691 ATTCCAAGCT
6392701 TACATCTCCCACCAAA
1 TACATCTCCCACCAAA
6392717 TACATCTCCCACCAAA
1 TACATCTCCCACCAAA
6392733 ATCTGGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.19
Consensus pattern (16 bp):
TACATCTCCCACCAAA
Found at i:6393087 original size:10 final size:10
Alignment explanation
Indices: 6393074--6393135 Score: 70
Period size: 10 Copynumber: 5.8 Consensus size: 10
6393064 TATGTACATG
6393074 TACATATATA
1 TACATATATA
*
6393084 TACATACATA
1 TACATATATA
*
6393094 TACATACATA
1 TACATATATA
6393104 TACATATACATA
1 TACATAT--ATA
6393116 TACATATACATA
1 TACATAT--ATA
6393128 TACATATA
1 TACATATA
6393136 CATTAGAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
10 26 0.54
12 22 0.46
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (10 bp):
TACATATATA
Found at i:6393087 original size:16 final size:16
Alignment explanation
Indices: 6393056--6393129 Score: 80
Period size: 16 Copynumber: 4.6 Consensus size: 16
6393046 CCTTATATAT
* *
6393056 TATACATGTATGTACA
1 TATACATATATATACA
*
6393072 TGTACATATATATAC-
1 TATACATATATATACA
*
6393087 -ATACATATACATACA
1 TATACATATATATACA
6393102 TATACATATACATATACA
1 TATACATAT--ATATACA
6393120 TATACATATA
1 TATACATATA
6393130 CATATACATT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
14 12 0.25
16 21 0.44
18 15 0.31
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (16 bp):
TATACATATATATACA
Found at i:6393096 original size:6 final size:6
Alignment explanation
Indices: 6393068--6393138 Score: 92
Period size: 6 Copynumber: 11.8 Consensus size: 6
6393058 TACATGTATG
* *
6393068 TACATG TACATA TATATACA TACATA TAC--A TACATA TACATA TACATA
1 TACATA TACATA TACAT--A TACATA TACATA TACATA TACATA TACATA
6393116 TACATA TACATA TACATA TACAT
1 TACATA TACATA TACATA TACAT
6393139 TAGAAGAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
4 4 0.07
6 49 0.84
8 5 0.09
ACGTcount: A:0.48, C:0.17, G:0.01, T:0.34
Consensus pattern (6 bp):
TACATA
Found at i:6396007 original size:22 final size:22
Alignment explanation
Indices: 6395981--6396033 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
6395971 TTTATATACT
6395981 CTCAATCATTTGACAATGAACG
1 CTCAATCATTTGACAATGAACG
*
6396003 TTCAATCATTTGACAATGAACG
1 CTCAATCATTTGACAATGAACG
6396025 CTCAATCAT
1 CTCAATCAT
6396034 CCTGCTACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (22 bp):
CTCAATCATTTGACAATGAACG
Done.