Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397264.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_130.0, 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: 8132550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 35170 characters in sequence are not A, C, G, or T
File 14 of 14
Found at i:7669234 original size:2 final size:2
Alignment explanation
Indices: 7669227--7669258 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
7669217 AATCATGTGA
*
7669227 AT AT AT AT AG 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
7669259 TTATCCAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7671673 original size:9 final size:9
Alignment explanation
Indices: 7671659--7671687 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
7671649 CTCTCTTTTG
7671659 AAAATTAAA
1 AAAATTAAA
7671668 AAAATT-AA
1 AAAATTAAA
7671676 AAAATTAAA
1 AAAATTAAA
7671685 AAA
1 AAA
7671688 TTGATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATTAAA
Found at i:7671677 original size:8 final size:8
Alignment explanation
Indices: 7671659--7671689 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
7671649 CTCTCTTTTG
7671659 AAAATTAAA
1 AAAATT-AA
7671668 AAAATTAA
1 AAAATTAA
7671676 AAAATTAA
1 AAAATTAA
7671684 AAAATT
1 AAAATT
7671690 GATATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAATTAA
Found at i:7672547 original size:4 final size:4
Alignment explanation
Indices: 7672540--7672564 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
7672530 TGCTAAGCAA
7672540 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
7672565 CAGAGGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:7673528 original size:21 final size:21
Alignment explanation
Indices: 7673496--7673547 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
7673486 TTCCAGCTGT
*
7673496 TTTGGC-TTTTTTGTAGCTAC
1 TTTGGCTTTTTTTGTAACTAC
*
7673516 TTTGGCTTTTTTTGTAATTAC
1 TTTGGCTTTTTTTGTAACTAC
*
7673537 TTTGACTTTTT
1 TTTGGCTTTTT
7673548 CAATTGTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.62
Consensus pattern (21 bp):
TTTGGCTTTTTTTGTAACTAC
Found at i:7678051 original size:2 final size:2
Alignment explanation
Indices: 7678044--7678070 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7678034 ATTATTGACT
7678044 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7678071 TCCCCGCCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7687576 original size:6 final size:6
Alignment explanation
Indices: 7687566--7687598 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
7687556 CCCCCCGTTT
*
7687566 CTCTCT CTCTCC CTCTCC CTCTCC CTCTCC CTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTC
7687599 CCTTTCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
CTCTCC
Found at i:7687663 original size:18 final size:19
Alignment explanation
Indices: 7687635--7687670 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
7687625 ACCTCAACAA
*
7687635 CTCCGTTCCGTTCGTCTCC
1 CTCCGTTCCGTTCCTCTCC
7687654 CTCC-TTCCGTTCCTCTC
1 CTCCGTTCCGTTCCTCTC
7687671 TTATCCTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.00, C:0.50, G:0.11, T:0.39
Consensus pattern (19 bp):
CTCCGTTCCGTTCCTCTCC
Found at i:7687888 original size:14 final size:14
Alignment explanation
Indices: 7687869--7687899 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
7687859 GGTGAAAAGA
*
7687869 GAGTGAGAGAGAGG
1 GAGTGAAAGAGAGG
7687883 GAGTGAAAGAGAGG
1 GAGTGAAAGAGAGG
7687897 GAG
1 GAG
7687900 AATATTTACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.55, T:0.06
Consensus pattern (14 bp):
GAGTGAAAGAGAGG
Found at i:7690699 original size:2 final size:2
Alignment explanation
Indices: 7690692--7690719 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7690682 TGAATGCAAG
7690692 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
7690720 GACTTGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7691553 original size:2 final size:2
Alignment explanation
Indices: 7691546--7691579 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
7691536 TGACATTTAC
* *
7691546 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7691580 TCAAGATCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:7705034 original size:17 final size:18
Alignment explanation
Indices: 7705003--7705036 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
7704993 AACTAGGAAC
*
7705003 TATACGAATACTTTCATA
1 TATACGAATAATTTCATA
7705021 TATAC-AATAATTTCAT
1 TATACGAATAATTTCAT
7705037 TGAATAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (18 bp):
TATACGAATAATTTCATA
Found at i:7706999 original size:2 final size:2
Alignment explanation
Indices: 7706992--7707025 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
7706982 TATACGATGC
7706992 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
7707026 GGGTAAGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7707336 original size:2 final size:2
Alignment explanation
Indices: 7707331--7707365 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7707321 TGAGAGAGTA
7707331 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
7707366 GGGAGAGAGA
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:7707373 original size:2 final size:2
Alignment explanation
Indices: 7707368--7707395 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7707358 TATATATAGG
7707368 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
7707396 CCATGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7711921 original size:16 final size:15
Alignment explanation
Indices: 7711877--7711921 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
7711867 TCACTCTTTT
*
7711877 TTTAATTATTTTTAA
1 TTTATTTATTTTTAA
*
7711892 TTTAATTTAATTTTATA
1 TTT-ATTTATTTTTA-A
7711909 TTTATTTATTTTT
1 TTTATTTATTTTT
7711922 TTGCTCGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 3 0.12
16 18 0.72
17 4 0.16
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTTATTTTTAA
Found at i:7724332 original size:27 final size:27
Alignment explanation
Indices: 7724294--7724351 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
7724284 GTAAATACGC
*
7724294 ATATGAAAATGTAAAACTATTTCACTT
1 ATATGAAAATGTAAAACCATTTCACTT
* *
7724321 ATATGAGAATGTAAAACCATTTCAGTT
1 ATATGAAAATGTAAAACCATTTCACTT
7724348 ATAT
1 ATAT
7724352 ATATAAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (27 bp):
ATATGAAAATGTAAAACCATTTCACTT
Found at i:7729480 original size:3 final size:3
Alignment explanation
Indices: 7729474--7729504 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
7729464 TCGAAATTAC
*
7729474 TGT TGT TGT TGT TGT TGT TGT TGT TGC TGT T
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT T
7729505 TTTTCCGCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.03, G:0.32, T:0.65
Consensus pattern (3 bp):
TGT
Found at i:7736530 original size:12 final size:12
Alignment explanation
Indices: 7736513--7736537 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7736503 ATTTTACTCG
7736513 TATTTTCTTTTA
1 TATTTTCTTTTA
7736525 TATTTTCTTTTA
1 TATTTTCTTTTA
7736537 T
1 T
7736538 GTAAGAAATT
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTCTTTTA
Found at i:7746452 original size:3 final size:3
Alignment explanation
Indices: 7746444--7746471 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
7746434 GAGAAACTGT
7746444 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
7746472 TGGAGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:7747241 original size:17 final size:18
Alignment explanation
Indices: 7747221--7747254 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
7747211 GTTCTTAGCC
7747221 TCCTGATGAT-CTTTTTT
1 TCCTGATGATCCTTTTTT
7747238 TCCTGATGATCCTTTTT
1 TCCTGATGATCCTTTTT
7747255 CCCTACTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.12, C:0.21, G:0.12, T:0.56
Consensus pattern (18 bp):
TCCTGATGATCCTTTTTT
Found at i:7751095 original size:45 final size:45
Alignment explanation
Indices: 7751023--7751110 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
7751013 ATATAATTAT
*
7751023 TATACAAATGTTTTCTACAACTCTGTCCAAAGATTGTGTAAACCG
1 TATACAAATATTTTCTACAACTCTGTCCAAAGATTGTGTAAACCG
* * *
7751068 TATACAAATATTTTTTAGAACTTTGTCCAAAGATTGTGTAAAC
1 TATACAAATATTTTCTACAACTCTGTCCAAAGATTGTGTAAAC
7751111 AGAATGATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (45 bp):
TATACAAATATTTTCTACAACTCTGTCCAAAGATTGTGTAAACCG
Found at i:7758511 original size:21 final size:21
Alignment explanation
Indices: 7758487--7758526 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
7758477 TTTAATTTCA
*
7758487 TTTATATTTATCTTTTTTATT
1 TTTATATTTATATTTTTTATT
* *
7758508 TTTATTTTTCTATTTTTTA
1 TTTATATTTATATTTTTTA
7758527 AATGACAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTATATTTATATTTTTTATT
Found at i:7758513 original size:19 final size:20
Alignment explanation
Indices: 7758486--7758524 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
7758476 ATTTAATTTC
7758486 ATTTATATTTATCT-TTTTT
1 ATTTATATTTATCTATTTTT
* *
7758505 ATTTTTATTTTTCTATTTTT
1 ATTTATATTTATCTATTTTT
7758525 TAAATGACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (20 bp):
ATTTATATTTATCTATTTTT
Found at i:7760808 original size:9 final size:9
Alignment explanation
Indices: 7760796--7760857 Score: 61
Period size: 9 Copynumber: 6.9 Consensus size: 9
7760786 GGAAGAAGAA
*
7760796 GACGACGAC
1 GACGACGAT
*
7760805 GACGACGAA
1 GACGACGAT
* *
7760814 GATGATGAT
1 GACGACGAT
**
7760823 GACGACGGG
1 GACGACGAT
*
7760832 GAAGACGAT
1 GACGACGAT
7760841 GACGACGAT
1 GACGACGAT
7760850 GACGACGA
1 GACGACGA
7760858 CGGAGGAGAA
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.37, T:0.08
Consensus pattern (9 bp):
GACGACGAT
Found at i:7760881 original size:30 final size:30
Alignment explanation
Indices: 7760814--7760881 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
7760804 CGACGACGAA
* * *
7760814 GATGATGATGACGACGGGGAAGACGATGAC
1 GATGATGACGACGACGGGGAAGAAGAGGAC
* *
7760844 GACGATGACGACGACGGAGG-AGAAGAGGAT
1 GATGATGACGACGACGG-GGAAGAAGAGGAC
7760874 GATGATGA
1 GATGATGA
7760882 GGAAGTGCAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.35, C:0.12, G:0.41, T:0.12
Consensus pattern (30 bp):
GATGATGACGACGACGGGGAAGAAGAGGAC
Found at i:7760985 original size:12 final size:12
Alignment explanation
Indices: 7760970--7761017 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
7760960 GGATGATGAA
*
7760970 GACGACGACGAC
1 GACGGCGACGAC
* * *
7760982 GACGGTGAAGGC
1 GACGGCGACGAC
7760994 GACGGCGACGAC
1 GACGGCGACGAC
7761006 GACGGCGACGAC
1 GACGGCGACGAC
7761018 AGTGATGACG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.27, C:0.29, G:0.42, T:0.02
Consensus pattern (12 bp):
GACGGCGACGAC
Found at i:7760990 original size:21 final size:21
Alignment explanation
Indices: 7760966--7761006 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
7760956 AAGAGGATGA
7760966 TGAAGACGACGACGACGACGG
1 TGAAGACGACGACGACGACGG
* *
7760987 TGAAGGCGACGGCGACGACG
1 TGAAGACGACGACGACGACG
7761007 ACGGCGACGA
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:0.29, C:0.24, G:0.41, T:0.05
Consensus pattern (21 bp):
TGAAGACGACGACGACGACGG
Found at i:7762092 original size:15 final size:15
Alignment explanation
Indices: 7762074--7762105 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7762064 GGACGCTGAG
7762074 GAAGAGGATGAAGAT
1 GAAGAGGATGAAGAT
*
7762089 GAAGATGATGAAGAT
1 GAAGAGGATGAAGAT
7762104 GA
1 GA
7762106 GGCTGGTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.38, T:0.16
Consensus pattern (15 bp):
GAAGAGGATGAAGAT
Found at i:7777083 original size:36 final size:36
Alignment explanation
Indices: 7777034--7777201 Score: 237
Period size: 36 Copynumber: 4.7 Consensus size: 36
7777024 GAAAACGTTG
*
7777034 TCCAATCTGGAAGAAGCGTGAGATTCAACATCGCTA
1 TCCAATCTGGAAGAAACGTGAGATTCAACATCGCTA
* ** * *
7777070 TGCAATCTGGAAGAAACAAGAGATTCAACTTCTCTA
1 TCCAATCTGGAAGAAACGTGAGATTCAACATCGCTA
7777106 TCCAATCTGGAAGAAACGTGAGATTCAACATCGCTA
1 TCCAATCTGGAAGAAACGTGAGATTCAACATCGCTA
* ** * *
7777142 TGCAATCTGGAAGAAACAAGAGATTCAACTTCTCTA
1 TCCAATCTGGAAGAAACGTGAGATTCAACATCGCTA
7777178 TCCAATCTGGAAGAAACGTGAGAT
1 TCCAATCTGGAAGAAACGTGAGAT
7777202 ATACTTCTCT
Statistics
Matches: 113, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 113 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (36 bp):
TCCAATCTGGAAGAAACGTGAGATTCAACATCGCTA
Found at i:7777151 original size:72 final size:72
Alignment explanation
Indices: 7777034--7777201 Score: 327
Period size: 72 Copynumber: 2.3 Consensus size: 72
7777024 GAAAACGTTG
*
7777034 TCCAATCTGGAAGAAGCGTGAGATTCAACATCGCTATGCAATCTGGAAGAAACAAGAGATTCAAC
1 TCCAATCTGGAAGAAACGTGAGATTCAACATCGCTATGCAATCTGGAAGAAACAAGAGATTCAAC
7777099 TTCTCTA
66 TTCTCTA
7777106 TCCAATCTGGAAGAAACGTGAGATTCAACATCGCTATGCAATCTGGAAGAAACAAGAGATTCAAC
1 TCCAATCTGGAAGAAACGTGAGATTCAACATCGCTATGCAATCTGGAAGAAACAAGAGATTCAAC
7777171 TTCTCTA
66 TTCTCTA
7777178 TCCAATCTGGAAGAAACGTGAGAT
1 TCCAATCTGGAAGAAACGTGAGAT
7777202 ATACTTCTCT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 95 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (72 bp):
TCCAATCTGGAAGAAACGTGAGATTCAACATCGCTATGCAATCTGGAAGAAACAAGAGATTCAAC
TTCTCTA
Found at i:7778042 original size:72 final size:72
Alignment explanation
Indices: 7777925--7778059 Score: 216
Period size: 72 Copynumber: 1.9 Consensus size: 72
7777915 GCAGCAGCCG
* * *
7777925 TTGCAACTGTTTCTGACAGCTGTTAAAATCCCCTGGAAGGACTCGAGTTTGATGTTTCTTCTATG
1 TTGCAACTGTCTCTGACAACTGTTAAAATCCCCTGGAAGGACTCGAGTCTGATGTTTCTTCTATG
7777990 GCAGTCT
66 GCAGTCT
* * *
7777997 TTGCAACTGTCTCTGACAACTTTTAGAATCCCTTGGAAGGACTCGAGTCTGATGTTTCTTCTA
1 TTGCAACTGTCTCTGACAACTGTTAAAATCCCCTGGAAGGACTCGAGTCTGATGTTTCTTCTA
7778060 CTGTTGAACT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (72 bp):
TTGCAACTGTCTCTGACAACTGTTAAAATCCCCTGGAAGGACTCGAGTCTGATGTTTCTTCTATG
GCAGTCT
Found at i:7782315 original size:78 final size:81
Alignment explanation
Indices: 7782182--7782343 Score: 276
Period size: 78 Copynumber: 2.0 Consensus size: 81
7782172 AGAAAAGCCA
7782182 CATCCCCCAAATTCAGTGAAACAGATTAAGCAATAAAATTTTCTCTCATAAAGCACAAAAAGAAG
1 CATCCCCCAAATTCAGTG-AACAGATTAAGCAATAAAATTTTCTCTCATAAAGCACAAAAAGAAG
*
7782247 TACATGGAAAACGATAG
65 TACATGAAAAACGATAG
*
7782264 CATCCCCCAAATTCAGTG-A-A-ATTAAGCAGTAAAATTTTCTCTCATAAAGCACAAAAAGAAGT
1 CATCCCCCAAATTCAGTGAACAGATTAAGCAATAAAATTTTCTCTCATAAAGCACAAAAAGAAGT
7782326 ACATGAAAAACGATAG
66 ACATGAAAAACGATAG
7782342 CA
1 CA
7782344 GTTCTTTAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
78 58 0.74
79 1 0.01
80 1 0.01
82 18 0.23
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (81 bp):
CATCCCCCAAATTCAGTGAACAGATTAAGCAATAAAATTTTCTCTCATAAAGCACAAAAAGAAGT
ACATGAAAAACGATAG
Found at i:7789804 original size:6 final size:6
Alignment explanation
Indices: 7789795--7789822 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
7789785 AGGCAGAGGC
7789795 TTGGGG TTGGGG TTGGGG TTGGGG TTGG
1 TTGGGG TTGGGG TTGGGG TTGGGG TTGG
7789823 TTTGCTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (6 bp):
TTGGGG
Found at i:7805380 original size:21 final size:21
Alignment explanation
Indices: 7805354--7805393 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
7805344 ATATTTTATC
7805354 TTCTTGACCTTGTAAGACCTT
1 TTCTTGACCTTGTAAGACCTT
7805375 TTCTTGACCTTGTAAGACC
1 TTCTTGACCTTGTAAGACC
7805394 CCGTTCAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (21 bp):
TTCTTGACCTTGTAAGACCTT
Found at i:7809216 original size:2 final size:2
Alignment explanation
Indices: 7809209--7809236 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7809199 CCTCGATCAA
7809209 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
7809237 TTTACTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7814058 original size:5 final size:5
Alignment explanation
Indices: 7814048--7814072 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
7814038 ATCTTCTTTT
7814048 CCATC CCATC CCATC CCATC CCATC
1 CCATC CCATC CCATC CCATC CCATC
7814073 GCACTCAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
CCATC
Found at i:7815625 original size:2 final size:2
Alignment explanation
Indices: 7815614--7815655 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
7815604 TTGGTCCATT
7815614 TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
7815655 T
1 T
7815656 GAAATCATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:7823489 original size:2 final size:2
Alignment explanation
Indices: 7823482--7823508 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7823472 GTTTCTTTCT
7823482 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7823509 TTAAAATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7834094 original size:2 final size:2
Alignment explanation
Indices: 7834089--7834116 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7834079 TTTTCTTTTT
7834089 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
7834117 ACAATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7834963 original size:2 final size:2
Alignment explanation
Indices: 7834958--7834993 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
7834948 GTGCATAAAC
*
7834958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7834994 TGACAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7848074 original size:2 final size:2
Alignment explanation
Indices: 7848067--7848091 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7848057 CTTGATATGC
7848067 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
7848092 CTCCTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:7884507 original size:90 final size:90
Alignment explanation
Indices: 7884351--7884528 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
7884341 TACTTTGTCT
* ** * * *
7884351 TTTAATGCGAGGGTGTTAAGGAAACCACAACTATCTGTTCTTTCTTCTCTGCCTATGGTGACCAC
1 TTTAATGCGAGGGTGTTAAGCAAACCACAACTATCTGCGCTCTCTTCTCTGCCTATGGCGAACAC
7884416 TTGTAAAGTCAACATGAAATAGTCC
66 TTGTAAAGTCAACATGAAATAGTCC
* *
7884441 TTTAATGCGAGGGTGTTAAGCAAACCACAACTATGTGCGCTCTCTTTTCTGCCTATGGCGAACAC
1 TTTAATGCGAGGGTGTTAAGCAAACCACAACTATCTGCGCTCTCTTCTCTGCCTATGGCGAACAC
7884506 TTGTAAAGTCAACATGAAATAGT
66 TTGTAAAGTCAACATGAAATAGT
7884529 TTGCGTGCCA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (90 bp):
TTTAATGCGAGGGTGTTAAGCAAACCACAACTATCTGCGCTCTCTTCTCTGCCTATGGCGAACAC
TTGTAAAGTCAACATGAAATAGTCC
Found at i:7899294 original size:2 final size:2
Alignment explanation
Indices: 7899289--7899314 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7899279 AGGGACATAA
7899289 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
7899315 TGATGGTGAT
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:7909746 original size:29 final size:29
Alignment explanation
Indices: 7909699--7909758 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
7909689 CATAAGCCAG
*
7909699 ATAAATTCATGCTAGTATGAATTGTCAAC
1 ATAAATTCATGCTAGTATGAATTGACAAC
7909728 ATAAATTCATGCTCA-TATGAATTGACAAC
1 ATAAATTCATGCT-AGTATGAATTGACAAC
7909757 AT
1 AT
7909759 CATCTTAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (29 bp):
ATAAATTCATGCTAGTATGAATTGACAAC
Found at i:7925946 original size:2 final size:2
Alignment explanation
Indices: 7925939--7925965 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7925929 CGTGTCCAAT
7925939 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7925966 GAGTAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7927417 original size:2 final size:2
Alignment explanation
Indices: 7927410--7927439 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7927400 NNNNNNNNNN
7927410 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
7927440 GCCACATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7937972 original size:2 final size:2
Alignment explanation
Indices: 7937965--7937990 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7937955 GGCATAAAGA
7937965 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
7937991 GTAAAATCAT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7945715 original size:6 final size:6
Alignment explanation
Indices: 7945704--7945729 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7945694 GCCGACGCGA
7945704 CTGCGG CTGCGG CTGCGG CTGCGG CT
1 CTGCGG CTGCGG CTGCGG CTGCGG CT
7945730 CAGAATAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.46, T:0.19
Consensus pattern (6 bp):
CTGCGG
Found at i:7960198 original size:7 final size:7
Alignment explanation
Indices: 7960186--7960224 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
7960176 TACAGCTAGT
7960186 AGAATAG
1 AGAATAG
7960193 AGAATAG
1 AGAATAG
7960200 AGAATAG
1 AGAATAG
7960207 AGAATAG
1 AGAATAG
7960214 AGAATAG
1 AGAATAG
7960221 AGAA
1 AGAA
7960225 GAAAGAGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (7 bp):
AGAATAG
Found at i:7964954 original size:4 final size:4
Alignment explanation
Indices: 7964945--7964979 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
7964935 GAAAAGGGGA
7964945 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
7964980 TGTTCATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:7968603 original size:18 final size:17
Alignment explanation
Indices: 7968576--7968609 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
7968566 TGTGATATAG
7968576 TATTTAAAAAATTTAAAT
1 TATTT-AAAAATTTAAAT
*
7968594 TATTTTAAAATTTAAA
1 TATTTAAAAATTTAAA
7968610 ATAAGTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTTAAAAATTTAAAT
Found at i:7970012 original size:2 final size:2
Alignment explanation
Indices: 7970005--7970031 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7969995 GCAAACATAC
7970005 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 A
7970032 GTACATATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7989298 original size:20 final size:20
Alignment explanation
Indices: 7989273--7989331 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 20
7989263 ATATATATAT
7989273 ATATAAGAAATGGACACTAA
1 ATATAAGAAATGGACACTAA
*
7989293 ATATAAGAAA--G-CAATGAA
1 ATATAAGAAATGGACACT-AA
7989311 AT-T-AGAAATGGACACTAA
1 ATATAAGAAATGGACACTAA
7989329 ATA
1 ATA
7989332 AGAGACAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
16 5 0.16
17 4 0.12
18 10 0.31
19 3 0.09
20 10 0.31
ACGTcount: A:0.56, C:0.08, G:0.15, T:0.20
Consensus pattern (20 bp):
ATATAAGAAATGGACACTAA
Found at i:8046124 original size:2 final size:2
Alignment explanation
Indices: 8046117--8046145 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8046107 TTTCAGTGGG
8046117 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
8046146 GAAAAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:8086347 original size:5 final size:5
Alignment explanation
Indices: 8086337--8086364 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
8086327 TCAATGTATC
8086337 GACAT GACAT GACAT GACAT GACAT GAC
1 GACAT GACAT GACAT GACAT GACAT GAC
8086365 GATGGCTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (5 bp):
GACAT
Found at i:8099687 original size:23 final size:23
Alignment explanation
Indices: 8099661--8099709 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
8099651 CAGTTTTCAC
*
8099661 AATTAATTCCTCTTCTTATTCTA
1 AATTAATTCCTCTTCTTATTCCA
* *
8099684 AATTAGTTCCTCTTCTTTTTCCA
1 AATTAATTCCTCTTCTTATTCCA
8099707 AAT
1 AAT
8099710 ACTGTCAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.02, T:0.51
Consensus pattern (23 bp):
AATTAATTCCTCTTCTTATTCCA
Found at i:8099904 original size:23 final size:23
Alignment explanation
Indices: 8099878--8099922 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
8099868 TTTCACAATC
*
8099878 AGTTCCCCTTCTTATTCTAAATT
1 AGTTCCCCTTCTCATTCTAAATT
* * *
8099901 AGTTTCTCTTCTCATTTTAAAT
1 AGTTCCCCTTCTCATTCTAAAT
8099923 ACTGTCGAAA
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:0.22, C:0.22, G:0.04, T:0.51
Consensus pattern (23 bp):
AGTTCCCCTTCTCATTCTAAATT
Found at i:8106031 original size:102 final size:102
Alignment explanation
Indices: 8105896--8106101 Score: 340
Period size: 102 Copynumber: 2.0 Consensus size: 102
8105886 GACTGCAATT
* * * * *
8105896 ATATTATATCATTGGTCGCAAGCTATATCGCTCAATCTTTGATCATAATTTATCATTAACGTTTT
1 ATATTATATCATTGGTCGCAAGCTATATCGCTCAAGCTTAGACCATAATTTATCAATAACATTTT
*
8105961 AGCCGCTAACTTTATCGCTCATGATTTGGCTGTAATG
66 AGCCGCTAACTTTATCACTCATGATTTGGCTGTAATG
*
8105998 ATATTATATTATTGGTCGCAAGCTATATCGCTCAAGCTTAGACCATAATTTATCAATAACATTTT
1 ATATTATATCATTGGTCGCAAGCTATATCGCTCAAGCTTAGACCATAATTTATCAATAACATTTT
*
8106063 AGCCGCTAGCTTTATCACTCATGATTTGGCTGTAATG
66 AGCCGCTAACTTTATCACTCATGATTTGGCTGTAATG
8106100 AT
1 AT
8106102 TGGCCGCAAG
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 96 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (102 bp):
ATATTATATCATTGGTCGCAAGCTATATCGCTCAAGCTTAGACCATAATTTATCAATAACATTTT
AGCCGCTAACTTTATCACTCATGATTTGGCTGTAATG
Found at i:8106201 original size:26 final size:27
Alignment explanation
Indices: 8106156--8106210 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
8106146 AAGGATGAAA
*
8106156 TAATCTCCTTCATATCAAGTT-AGAGT
1 TAATCTCCTTCATAACAAGTTGAGAGT
* *
8106182 TAATCTCCTTGATAAGAAGTTGAGAGT
1 TAATCTCCTTCATAACAAGTTGAGAGT
8106209 TA
1 TA
8106211 TCCTTTGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (27 bp):
TAATCTCCTTCATAACAAGTTGAGAGT
Found at i:8107002 original size:42 final size:42
Alignment explanation
Indices: 8106941--8107023 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
8106931 TCTCAAGAAC
* *
8106941 AACTTCAACAGCAAGAATAGCCTTAGTGTCAGGAACAACCTT
1 AACTTCAACAACAAGAATAGCCTCAGTGTCAGGAACAACCTT
*
8106983 AACTTCAACAACACA-AATAGTCTCAGTGTCAGGAACAACCT
1 AACTTCAACAACA-AGAATAGCCTCAGTGTCAGGAACAACCT
8107024 CATCTCGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 36 0.97
43 1 0.03
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.20
Consensus pattern (42 bp):
AACTTCAACAACAAGAATAGCCTCAGTGTCAGGAACAACCTT
Found at i:8107361 original size:12 final size:12
Alignment explanation
Indices: 8107335--8107390 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
8107325 TGATTATCCC
* *
8107335 TAAAAAAAAAAA
1 TAAAAAAATATA
*
8107347 TATAAAAATATA
1 TAAAAAAATATA
*
8107359 TATAAAAA-ATA
1 TAAAAAAATATA
8107370 -AAAAAAATATA
1 TAAAAAAATATA
8107381 TAAAAAAATA
1 TAAAAAAATA
8107391 AATGAACTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 6 0.16
11 6 0.16
12 26 0.68
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
TAAAAAAATATA
Found at i:8107367 original size:21 final size:21
Alignment explanation
Indices: 8107341--8107392 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
8107331 TCCCTAAAAA
*
8107341 AAAAAATATAAAAATATATAT
1 AAAAAATATAAAAAAATATAT
8107362 AAAAAATA-AAAAAAATATAT
1 AAAAAATATAAAAAAATATAT
8107382 AAAAAA-ATAAA
1 AAAAAATATAAA
8107393 TGAACTTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 20 0.69
21 8 0.28
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAAAATATAAAAAAATATAT
Found at i:8107373 original size:20 final size:21
Alignment explanation
Indices: 8107340--8107392 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
8107330 ATCCCTAAAA
*
8107340 AAAAAAAT-ATAAAAATATAT
1 AAAAAAATAAAAAAAATATAT
8107360 ATAAAAAATAAAAAAAATATAT
1 A-AAAAAATAAAAAAAATATAT
8107382 AAAAAAATAAA
1 AAAAAAATAAA
8107393 TGAACTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 1 0.03
21 17 0.57
22 12 0.40
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAAAAATAAAAAAAATATAT
Found at i:8109396 original size:15 final size:15
Alignment explanation
Indices: 8109376--8109404 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
8109366 GTCAATTAAG
8109376 AAAAATATATATATT
1 AAAAATATATATATT
8109391 AAAAATATATATAT
1 AAAAATATATATAT
8109405 ACATATACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAATATATATATT
Found at i:8109402 original size:17 final size:18
Alignment explanation
Indices: 8109370--8109405 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
8109360 ATATTTGTCA
8109370 ATTAAGAAAAATATATAT
1 ATTAAGAAAAATATATAT
*
8109388 ATTAA-AAATATATATAT
1 ATTAAGAAAAATATATAT
8109405 A
1 A
8109406 CATATACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
ATTAAGAAAAATATATAT
Found at i:8109826 original size:2 final size:2
Alignment explanation
Indices: 8109819--8109850 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8109809 TGTTTGAATG
*
8109819 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8109851 AAATCATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:8110257 original size:65 final size:67
Alignment explanation
Indices: 8110138--8110265 Score: 206
Period size: 65 Copynumber: 1.9 Consensus size: 67
8110128 TTATTATTTG
* * * *
8110138 TATCTTGAAAATCTTATTTATATAGAAAATTATTATTATGTAATCAATCAAATATTA-AAAAATA
1 TATCTTGAAAATCTTATATATATAGAAAAATATTATTACGAAATCAATCAAATATTACAAAAATA
8110202 TA
66 TA
8110204 TATCTTGAAAATCTTATATATAT-GAAAAATATTATTACGAAATCAATCAAATATTACAAAAA
1 TATCTTGAAAATCTTATATATATAGAAAAATATTATTACGAAATCAATCAAATATTACAAAAA
8110266 AAAATATTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
65 30 0.53
66 27 0.47
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.38
Consensus pattern (67 bp):
TATCTTGAAAATCTTATATATATAGAAAAATATTATTACGAAATCAATCAAATATTACAAAAATA
TA
Found at i:8115019 original size:15 final size:15
Alignment explanation
Indices: 8114999--8115062 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 15
8114989 GATATTATGT
8114999 TTAAATTTAAACAAA
1 TTAAATTTAAACAAA
*
8115014 TTAAATTTAAATATAA
1 TTAAATTTAAACA-AA
** *
8115030 TT-AATTT---TTAT
1 TTAAATTTAAACAAA
8115041 TTAAATTTAAACAAA
1 TTAAATTTAAACAAA
8115056 TTAAATT
1 TTAAATT
8115063 CAAATTTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
11 3 0.08
12 6 0.16
15 25 0.66
16 4 0.11
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATTTAAACAAA
Found at i:8115022 original size:21 final size:21
Alignment explanation
Indices: 8114998--8115070 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 21
8114988 GGATATTATG
8114998 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAACAAATTAAA
* ** * **
8115019 TTTAAATATAATTAATTTTTA
1 TTTAAATTTAAACAAATTAAA
8115040 TTTAAATTTAAACAAATTAAA
1 TTTAAATTTAAACAAATTAAA
*
8115061 TTCAAATTTA
1 TTTAAATTTA
8115071 TATCTTATCT
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAAATTTAAACAAATTAAA
Found at i:8120999 original size:16 final size:17
Alignment explanation
Indices: 8120970--8121001 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
8120960 GCAGATGCAT
8120970 ATATGGCTAATTAATAA
1 ATATGGCTAATTAATAA
8120987 ATATGGC-AATTAATA
1 ATATGGCTAATTAATA
8121002 CAAGGGATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (17 bp):
ATATGGCTAATTAATAA
Found at i:8124711 original size:83 final size:81
Alignment explanation
Indices: 8124575--8124727 Score: 189
Period size: 83 Copynumber: 1.9 Consensus size: 81
8124565 GAATATGACG
* * * ** *
8124575 TGTAATAAATTTTTTAACCATGGCGTATAACATATTTTTGTATATGATGTGTAACAATAATATTC
1 TGTAACAAATTTTTTAACCATGGCGTATAACATATTTTGGTACATGACATGTAACAACAATATT-
8124640 TTTTTTTCAACATGGCA
65 TTTTTTTCAACATGGCA
* * * * *
8124657 TGTAACAACATTTTTTAACCATGGTGTGTAATATATTTTGGTACATGGCATGTAACAACAGTATT
1 TGTAACAA-ATTTTTTAACCATGGCGTATAACATATTTTGGTACATGACATGTAACAACAATATT
8124722 TTTTTT
65 TTTTTT
8124728 AACATGATGT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
82 13 0.22
83 46 0.78
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (81 bp):
TGTAACAAATTTTTTAACCATGGCGTATAACATATTTTGGTACATGACATGTAACAACAATATTT
TTTTTTCAACATGGCA
Found at i:8124835 original size:45 final size:45
Alignment explanation
Indices: 8124736--8124867 Score: 165
Period size: 45 Copynumber: 2.9 Consensus size: 45
8124726 TTAACATGAT
* * * * *
8124736 GTGTAACAACCTAACCATGGCATGTCACACCTTTTTGTACATGGC
1 GTGTAACAATCTAACTATAGTATGTCACACGTTTTTGTACATGGC
8124781 GTGTAACAATCTAACTATAGTATGTCACACGTTTTTGTACATGGC
1 GTGTAACAATCTAACTATAGTATGTCACACGTTTTTGTACATGGC
* * * * * *
8124826 GTGTAACAATTTAACTATAATGTGTAACATGTTTCTGTACAT
1 GTGTAACAATCTAACTATAGTATGTCACACGTTTTTGTACAT
8124868 AATGTGTAAC
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (45 bp):
GTGTAACAATCTAACTATAGTATGTCACACGTTTTTGTACATGGC
Found at i:8126080 original size:15 final size:15
Alignment explanation
Indices: 8126056--8126088 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
8126046 TTTATTAGGC
*
8126056 ATTACGTGACTGAAT
1 ATTACATGACTGAAT
8126071 ATTACATGACTGAAT
1 ATTACATGACTGAAT
8126086 ATT
1 ATT
8126089 TGTTGAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (15 bp):
ATTACATGACTGAAT
Found at i:8127491 original size:340 final size:332
Alignment explanation
Indices: 8126573--8127934 Score: 1245
Period size: 340 Copynumber: 4.0 Consensus size: 332
8126563 AATACTTGAA
* **
8126573 AAAAATCCCTAAAAATCGGAATAAATAATTTAAAAAATTAAAAATATCTTAAAAGCATGAAAAAT
1 AAAAATTCCTAAAAATCGGAATAAATAA-TTAAAAAATTAAAAATCCCTTAAAAGCAT-AAAAAT
* * *
8126638 CTATAAAATT-CTTACAAAATTCTCTTACAAACCTTAAATATACTTAAAAGGACCTAGAAAATGC
64 CTATAAAATTCCTTA-AAAAATCTCTTAAAAACCTTAAATATACTTAAAAGGACAT-GAAAATGC
** * * * *
8126702 TTAAAAATCAGCAAAAAAAAAATCATAAAAATGCCTCAAAAGG-TATAAAAAATCTTT-AAAA-A
127 TTAAAAATCA--ATGAAAAAAACCTTAAAAATGCTTCAAAAGGCT-TCAAAAATCTTTAAAAATA
* * *
8126764 AATCAAACAA-CC-T--AAA----AAA-TCTAGAAAATTCTTGAAAACACCATACAAATCCTTTG
189 AAT-AAA-AACCCTTAAAAATTTTAAATTCTAAAAAATCCTTGAAAACACCATAAAAATCCTTTG
* * * * * *
8126820 AAATCCATGAAAAAAA-TTTAAAAATACTTAGAATGACCTTAAACATGCTTAAAAAGGGCCCAAA
252 AAATCCATGAAAAAAAGCTT-CAAA-ACTTAGAATAACCTTAAACATGATTAAAAAGAGCCTAAA
* * * ** *
8126884 AGTCCTTGAAAAAATATA
315 AATACTCGAAAAAAGCTT
* *
8126902 AAAAATAT-TTAAAAATGGGAATAAATAATT-AAAAATTAAAAA-CCTCTTGAAAA-CATTAAAA
1 AAAAAT-TCCTAAAAATCGGAATAAATAATTAAAAAATTAAAAATCC-CTT-AAAAGCA-TAAAA
* * * * * * * * *
8126963 GTCTTTAAAAATCCTTCATAAA-C-CCTAAAAACCTTAAATATATTTCAAAGGACATCAGAAATG
62 ATCTATAAAATTCCTTAAAAAATCTCTTAAAAACCTTAAATATACTTAAAAGGACATGA-AAATG
* * * * *
8127026 CTTAGAAATAAATGAAAAAATA--TTAAAAACGGTTC-AAAGGACTTCAAAAATCTTAAAAAAAT
126 CTTAAAAATCAATGAAAAAA-ACCTTAAAAATGCTTCAAAAGG-CTTCAAAAATCTT-TAAAAAT
* * * *
8127088 AAATTAAAAACCCTTAAAAATCCTTCAAATTGGTACAAAATCCTTGAAAACACCAAAAAAATCCT
188 AAA-TAAAAACCCTTAAAAAT--TTTAAATT-CTAAAAAATCCTTGAAAACACCATAAAAATCCT
* * *
8127153 TTGTAATCCGTGAAAAAAAGCTTACAAAACTTAGAATAACCTTAAACATGATTGAAAAGAGCCTA
249 TTGAAATCCATGAAAAAAAGCTT-CAAAACTTAGAATAACCTTAAACATGATTAAAAAGAGCCTA
* *
8127218 AAAGTACTCGAAAAAAGTTT
313 AAAATACTCGAAAAAAGCTT
**
8127238 AAAAATTCCTAAAAATTAGAATAAATAATTAAGAAAATTAAAAATCCCTTAAAAGCATAAAAATT
1 AAAAATTCCTAAAAATCGGAATAAATAATTAA-AAAATTAAAAATCCCTTAAAAGCATAAAAA-T
* * *
8127303 CTATCAAATTCCTTAAAAAATCTCTTAAAAATCTTAAATATACTTAAAAGGACAATGAAAATGTT
64 CTATAAAATTCCTTAAAAAATCTCTTAAAAACCTTAAATATACTTAAAAGGAC-ATGAAAATGCT
* * *
8127368 TACAAATCAATGGAACAAACCTTAAAAATGCTTCAAAAGGCTTCAAAAATCTTTAAAAATGAAAT
128 TAAAAATCAATGAAAAAAACCTTAAAAATGCTTCAAAAGGCTTCAAAAATCTTTAAAAAT-AAAT
*
8127433 AAAAACCCTTAAAAATTCTTAGAATTACTAAAAAATCCTTTG-AAACACCATAAAAATCCTTTAA
192 AAAAACCCTTAAAAATT-TTA-AATT-CTAAAAAATCC-TTGAAAACACCATAAAAATCCTTTGA
* * * * *
8127497 AATCCA--AAAAAAAACTTCAAAA-TGTACATAATTACCTTAAACATGCTTCAAAAGAGCCTAAA
253 AATCCATGAAAAAAAGCTTCAAAACT-T--AGAATAACCTTAAACATGATTAAAAAGAGCCTAAA
* * *
8127559 AATACTTGGAAAAACCTT
315 AATACTCGAAAAAAGCTT
* * * *
8127577 AAGAAATTCCTAAAAATCGGAGTAAATAATCCAGAAAATTAAAAATCCCTAAAAAGCATTAAAAA
1 AA-AAATTCCTAAAAATCGGAATAAATAAT-TAAAAAATTAAAAATCCCTTAAAAGCA-TAAAAA
* * * *
8127642 TCTATCAAATTCCTTAAAAAAGCTCTTAAAAACATTAAATATACTTAAAAGAACCATGAAAATGC
63 TCTATAAAATTCCTTAAAAAATCTCTTAAAAACCTTAAATATACTTAAAAGGA-CATGAAAATGC
* * ** * * *
8127707 TTAAAAATCAATGAAAAAAACCTTAAAATTGGTTTGAAATGCTTCAAAATTTTTTAAAAATGAAA
127 TTAAAAATCAATGAAAAAAACCTTAAAAATGCTTCAAAAGGCTTCAAAAATCTTTAAAAAT-AAA
** *
8127772 CGAAAACCCTTAAAAATATTTAAAATTCTTAAAAAATCCTTGAAAACACCATAAAAATCTTTTGA
191 TAAAAACCCTTAAAAAT-TTT-AAATTC-TAAAAAATCCTTGAAAACACCATAAAAATCCTTTGA
* * * * *
8127837 AATCCATGATAAAAGGCTTCAAAAGGCTTAGAA-AGATCTTAAACAT-ACTTAAAAAGAACATAA
253 AATCCATGAAAAAAAGCTTCAAAA--CTTAGAATA-ACCTTAAACATGA-TTAAAAAGAGCCTAA
8127900 AAATACCTC-AAAAAAGCTT
314 AAATA-CTCGAAAAAAGCTT
*
8127919 AAAAATACCTAAAAAT
1 AAAAATTCCTAAAAAT
8127935 AAAAAATTAA
Statistics
Matches: 847, Mismatches: 125, Indels: 110
0.78 0.12 0.10
Matches are distributed among these distances:
321 5 0.01
322 19 0.02
323 8 0.01
324 8 0.01
325 49 0.06
326 3 0.00
327 33 0.04
328 13 0.02
329 24 0.03
334 3 0.00
335 2 0.00
336 118 0.14
337 22 0.03
338 43 0.05
339 56 0.07
340 323 0.38
341 56 0.07
342 58 0.07
343 2 0.00
344 1 0.00
345 1 0.00
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.26
Consensus pattern (332 bp):
AAAAATTCCTAAAAATCGGAATAAATAATTAAAAAATTAAAAATCCCTTAAAAGCATAAAAATCT
ATAAAATTCCTTAAAAAATCTCTTAAAAACCTTAAATATACTTAAAAGGACATGAAAATGCTTAA
AAATCAATGAAAAAAACCTTAAAAATGCTTCAAAAGGCTTCAAAAATCTTTAAAAATAAATAAAA
ACCCTTAAAAATTTTAAATTCTAAAAAATCCTTGAAAACACCATAAAAATCCTTTGAAATCCATG
AAAAAAAGCTTCAAAACTTAGAATAACCTTAAACATGATTAAAAAGAGCCTAAAAATACTCGAAA
AAAGCTT
Found at i:8127509 original size:21 final size:21
Alignment explanation
Indices: 8127462--8127508 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
8127452 TAGAATTACT
8127462 AAAAAATCCTTTGAAACACCA
1 AAAAAATCCTTTGAAACACCA
*
8127483 TAAAAATCCTTT-AAA-ATCCA
1 AAAAAATCCTTTGAAACA-CCA
8127503 AAAAAA
1 AAAAAA
8127509 AACTTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 11 0.48
21 11 0.48
ACGTcount: A:0.57, C:0.19, G:0.02, T:0.21
Consensus pattern (21 bp):
AAAAAATCCTTTGAAACACCA
Found at i:8127912 original size:21 final size:21
Alignment explanation
Indices: 8127876--8127933 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
8127866 AGAAAGATCT
* *
8127876 TAAACATACTTAAAAAGAA-CA
1 TAAAAATACCTAAAAA-AAGCA
* *
8127897 TAAAAATACCTCAAAAAAGCT
1 TAAAAATACCTAAAAAAAGCA
8127918 TAAAAATACCTAAAAA
1 TAAAAATACCTAAAAA
8127934 TAAAAAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.62, C:0.16, G:0.03, T:0.19
Consensus pattern (21 bp):
TAAAAATACCTAAAAAAAGCA
Found at i:8128059 original size:13 final size:14
Alignment explanation
Indices: 8128037--8128069 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
8128027 CGGAGCTCGA
*
8128037 GGGTTAGGGG-TCG
1 GGGTTTGGGGATCG
8128050 GGGTTTGGGGATCG
1 GGGTTTGGGGATCG
8128064 GGGTTT
1 GGGTTT
8128070 TTTTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.06, C:0.06, G:0.58, T:0.30
Consensus pattern (14 bp):
GGGTTTGGGGATCG
Done.