Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008199.1 Hibiscus syriacus cultivar Beakdansim tig00110819_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: 2638622
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:592495 original size:2 final size:2
Alignment explanation
Indices: 592490--592526 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
592480 AAAAAAATTA
592490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
592527 GACATTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:597103 original size:26 final size:26
Alignment explanation
Indices: 597072--597126 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
597062 AGTTTATTAA
597072 CTTAGAATGATTTAACTGAATACAAT
1 CTTAGAATGATTTAACTGAATACAAT
597098 CTTAGAATGATTTAACTGAATACAAT
1 CTTAGAATGATTTAACTGAATACAAT
597124 CTT
1 CTT
597127 GCTTGAACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (26 bp):
CTTAGAATGATTTAACTGAATACAAT
Found at i:608249 original size:89 final size:91
Alignment explanation
Indices: 608080--608256 Score: 220
Period size: 89 Copynumber: 2.0 Consensus size: 91
608070 AATTTGTGAT
* ** * *
608080 GGGTTTTAACCTAAAAATGTTATTTTGTCTATTCTAAAAAGTTATACATTTAGTAATAATTGTTG
1 GGGTTTTAACCT-AAAATGTTATCTTGTCTACCCTAAAAAGTTATAAATTGAGTAATAATTGTTG
*
608145 TTAGAATCGATAATGTTACATTACATC
65 TTAGAATCGAGAATGTTACATTACATC
*
608172 GGGTTTTAACCT-AAATGTTATCTTGTCTACCCT-AAAGGTTATATAATTGA-TAATAATT-TTG
1 GGGTTTTAACCTAAAATGTTATCTTGTCTACCCTAAAAAGTTATA-AATTGAGTAATAATTGTT-
608233 GTT-GCAATCGAGAATGTTACATTA
64 GTTAG-AATCGAGAATGTTACATTA
608257 GTTTCATGAC
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
88 3 0.04
89 38 0.51
90 22 0.29
92 12 0.16
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (91 bp):
GGGTTTTAACCTAAAATGTTATCTTGTCTACCCTAAAAAGTTATAAATTGAGTAATAATTGTTGT
TAGAATCGAGAATGTTACATTACATC
Found at i:609654 original size:2 final size:2
Alignment explanation
Indices: 609649--609673 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
609639 ACACACACAC
609649 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 A
609674 AAAGATATAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:610885 original size:19 final size:19
Alignment explanation
Indices: 610863--610955 Score: 62
Period size: 20 Copynumber: 4.7 Consensus size: 19
610853 GAATCGCAAC
610863 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
610882 GCGATTTTCA-TTTTGCGTT
1 GCGATTTT-AGTTTCGCGTT
* * **
610901 GCGATAGTCAAATTCGCGTT
1 GCGAT-TTTAGTTTCGCGTT
* * * *
610921 GCGATAGTCATTTTCGTGTT
1 GCGAT-TTTAGTTTCGCGTT
610941 GCGATTTTAAGTTTC
1 GCGATTTT-AGTTTC
610956 AGAAACTATT
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
19 23 0.39
20 36 0.61
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:610921 original size:20 final size:20
Alignment explanation
Indices: 610873--610945 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
610863 GCGATTTTAG
**
610873 TTTCGCGTTGCGATTTTC-A
1 TTTCGCGTTGCGATAGTCAA
*
610892 TTTTGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAA
* *
610912 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAA
*
610932 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
610946 TTTAAGTTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 15 0.33
20 30 0.67
ACGTcount: A:0.15, C:0.18, G:0.25, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAA
Found at i:612578 original size:21 final size:21
Alignment explanation
Indices: 612535--612579 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
612525 TGGTACATGG
* *
612535 CGTGATGAGGTATCTACTTTA
1 CGTGATGAGGTATCCACTCTA
* *
612556 CGTGGTGAGGTATCCGCTCTA
1 CGTGATGAGGTATCCACTCTA
612577 CGT
1 CGT
612580 AAGATGGTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (21 bp):
CGTGATGAGGTATCCACTCTA
Found at i:612883 original size:20 final size:20
Alignment explanation
Indices: 612860--612908 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
612850 GAAACTTAAA
*
612860 ATCGCAACGTGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
612880 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
612900 ATCGCAACG
1 ATCGCAACG
612909 GGATAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:612977 original size:19 final size:19
Alignment explanation
Indices: 612955--612997 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
612945 AAATCGCAAC
*
612955 GCGA-ATTTAGTTTCGCGTT
1 GCGATATTTA-TTTCGCATT
*
612974 GCGATTTTTATTTCGCATT
1 GCGATATTTATTTCGCATT
612993 GCGAT
1 GCGAT
612998 TGTCCAGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.44
Consensus pattern (19 bp):
GCGATATTTATTTCGCATT
Found at i:612998 original size:19 final size:20
Alignment explanation
Indices: 612960--612998 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
612950 GCAACGCGAA
*
612960 TTTAGTTTCGCGTTGCGATT
1 TTTAGTTTCGCATTGCGATT
612980 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
612999 GTCCAGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:613029 original size:20 final size:20
Alignment explanation
Indices: 613004--613051 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
612994 CGATTGTCCA
613004 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
**
613024 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
613044 GTTGCGAT
1 GTTGCGAT
613052 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:613061 original size:20 final size:20
Alignment explanation
Indices: 613019--613081 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
613009 GATAGTCAAA
** * *
613019 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTAAGT
613039 TTCGCGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTAAGT
*
613059 TTCGTGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTAAGT
613079 TTC
1 TTC
613082 AGAAACTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.46
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTAAGT
Found at i:613651 original size:21 final size:21
Alignment explanation
Indices: 613558--613651 Score: 73
Period size: 21 Copynumber: 4.5 Consensus size: 21
613548 CTGACTCACT
*
613558 TGTCATCGTTCAAGAGGCCTC
1 TGTCATCGTTCAAGAGGCCCC
* *
613579 T-CCTATCATTCAAGAGGCCCC
1 TGTC-ATCGTTCAAGAGGCCCC
* ** *
613600 TATCATCCCTCAAGAGTCCCC
1 TGTCATCGTTCAAGAGGCCCC
** * *
613621 TCCCACCGTTCAAGAGGCCAC
1 TGTCATCGTTCAAGAGGCCCC
613642 TGTCATCGTT
1 TGTCATCGTT
613652 TGAAGAGGTC
Statistics
Matches: 54, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
20 1 0.02
21 52 0.96
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (21 bp):
TGTCATCGTTCAAGAGGCCCC
Found at i:613676 original size:43 final size:42
Alignment explanation
Indices: 613558--613679 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 42
613548 CTGACTCACT
* * *
613558 TGTCATCGTTCAAGAGG-CCTCTCCTATCATTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGGTCC-CTCCCACCATTCAAGAGGCCAC
* ** *
613600 TATCATCCCTCAAGA-GTCCCCTCCCACCGTTCAAGAGGCCAC
1 TGTCATCGTTCAAGAGGT-CCCTCCCACCATTCAAGAGGCCAC
*
613642 TGTCATCGTTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TGTCATCG-TTCAAGAGGTCCCTCCCACCATTCAAGAG
613680 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
41 1 0.02
42 36 0.56
43 25 0.39
44 2 0.03
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TGTCATCGTTCAAGAGGTCCCTCCCACCATTCAAGAGGCCAC
Found at i:615227 original size:20 final size:20
Alignment explanation
Indices: 615202--615279 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
615192 AGGTACACTT
*
615202 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
* *
615222 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAA
*
615242 TCGCAATGCGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
* *
615262 TCGTAACGCGAAAGTCAA
1 TCGCAACGCGAAACTCAA
615280 TTCGCGTTGC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:615246 original size:40 final size:40
Alignment explanation
Indices: 615202--615279 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
615192 AGGTACACTT
* *
615202 TCGCAACGCTAAA-CTCAAAATCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAAGC-CAAAATCGCAACGCGAAAGTCAAAA
* *
615242 TCGCAATGCGAAAGCCAAAATCGTAACGCGAAAGTCAA
1 TCGCAACGCGAAAGCCAAAATCGCAACGCGAAAGTCAA
615280 TTCGCGTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (40 bp):
TCGCAACGCGAAAGCCAAAATCGCAACGCGAAAGTCAAAA
Found at i:615343 original size:20 final size:20
Alignment explanation
Indices: 615269--615434 Score: 166
Period size: 20 Copynumber: 8.7 Consensus size: 20
615259 AAATCGTAAC
*
615269 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
615288 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
615308 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
615322 GCGATAGTCAAATTCCCGTT
1 GCGATAGTCAAATTCGCGTT
*
615342 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
615362 ACGATAGTCAAATTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
615382 ACGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
615402 GCAATAGTCAAATTCACGTT
1 GCGATAGTCAAATTCGCGTT
*
615422 GCGATATTCAAAT
1 GCGATAGTCAAAT
615435 GAATGTGTAA
Statistics
Matches: 122, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
14 10 0.08
16 1 0.01
18 1 0.01
19 8 0.07
20 102 0.84
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:615628 original size:18 final size:18
Alignment explanation
Indices: 615605--615639 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
615595 AAGCCGGTTG
*
615605 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
615623 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
615640 GTCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:617915 original size:24 final size:24
Alignment explanation
Indices: 617888--617941 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
617878 TTGAAACATC
617888 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
617912 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
617936 ATCAAA
1 ATCAAA
617942 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:617955 original size:24 final size:24
Alignment explanation
Indices: 617888--617955 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
617878 TTGAAACATC
* * *
617888 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
617912 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
617936 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
617956 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:618618 original size:17 final size:17
Alignment explanation
Indices: 618596--618633 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
618586 CGGATGGGGA
618596 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
618613 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
618630 AGGA
1 AGGA
618634 ACGGATGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.37, T:0.32
Consensus pattern (17 bp):
AGGATGTCGTTGGATAT
Found at i:618642 original size:22 final size:20
Alignment explanation
Indices: 618593--618643 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 20
618583 TGCCGGATGG
618593 GGAAGGATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
618613 ---AGGATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
618630 AGGAACGGATGTCG
1 -GGAA-GGATGTCG
618644 CCAGAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 17 0.65
21 1 0.04
22 8 0.31
ACGTcount: A:0.25, C:0.08, G:0.39, T:0.27
Consensus pattern (20 bp):
GGAAGGATGTCGTTGGATAT
Found at i:618805 original size:20 final size:20
Alignment explanation
Indices: 618780--618846 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
618770 GAAATTCAGT
*
618780 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAAAATCGC
* * *
618800 GTTGCGAT-TTACATATTCGC
1 GTTGCGATAGT-CAAAATCGC
* *
618820 ATTGCGATAGTTAAAATCGC
1 GTTGCGATAGTCAAAATCGC
618840 GTTGCGA
1 GTTGCGA
618847 ATCTGGAAAC
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
19 1 0.03
20 34 0.94
21 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (20 bp):
GTTGCGATAGTCAAAATCGC
Found at i:629086 original size:17 final size:17
Alignment explanation
Indices: 629064--629100 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
629054 CATAAATGTT
629064 AAACG-AATATATTTATC
1 AAACGAAATATATTTA-C
629081 AAACGAAATATATTTAC
1 AAACGAAATATATTTAC
629098 AAA
1 AAA
629101 TGTAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (17 bp):
AAACGAAATATATTTAC
Found at i:631346 original size:11 final size:11
Alignment explanation
Indices: 631332--631385 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
631322 AAATTTGAAA
631332 AAAAATAAAAG
1 AAAAATAAAAG
*
631343 AAAAATCAAAG
1 AAAAATAAAAG
* **
631354 ATATAATGTAAG
1 A-AAAATAAAAG
631366 -AAAATAAAAG
1 AAAAATAAAAG
631376 AAAAATAAAA
1 AAAAATAAAA
631386 AATATTGAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
10 7 0.21
11 20 0.59
12 7 0.21
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAG
Found at i:631562 original size:18 final size:18
Alignment explanation
Indices: 631532--631567 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
631522 AATTTTAAAC
631532 ATATATAATTTATTCAAA
1 ATATATAATTTATTCAAA
631550 ATATGATAA-TTATTCAAA
1 ATAT-ATAATTTATTCAAA
631568 GTTCCTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (18 bp):
ATATATAATTTATTCAAA
Found at i:634141 original size:3 final size:3
Alignment explanation
Indices: 634133--634187 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
634123 TAGTTTACCC
634133 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
634180 TTA TTA TT
1 TTA TTA TT
634188 CTACCTTCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:634893 original size:13 final size:13
Alignment explanation
Indices: 634875--634899 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
634865 ACATTAAAGA
634875 TTTTGAGATTTTT
1 TTTTGAGATTTTT
634888 TTTTGAGATTTT
1 TTTTGAGATTTT
634900 ATAATTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (13 bp):
TTTTGAGATTTTT
Found at i:645123 original size:18 final size:18
Alignment explanation
Indices: 645100--645135 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
645090 ATCCCATGCA
645100 ATACGTACAGCAGTATGG
1 ATACGTACAGCAGTATGG
645118 ATACGTACAGCAGTATGG
1 ATACGTACAGCAGTATGG
645136 CTGTTAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (18 bp):
ATACGTACAGCAGTATGG
Found at i:645190 original size:18 final size:18
Alignment explanation
Indices: 645167--645203 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
645157 CAGCTATCCG
645167 AGATAATTGACATGGGGA
1 AGATAATTGACATGGGGA
645185 AGATAATTGACATGGGGA
1 AGATAATTGACATGGGGA
645203 A
1 A
645204 ATACCAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.32, T:0.22
Consensus pattern (18 bp):
AGATAATTGACATGGGGA
Found at i:653777 original size:19 final size:19
Alignment explanation
Indices: 653753--653869 Score: 79
Period size: 19 Copynumber: 6.5 Consensus size: 19
653743 AAATTTAGTT
653753 TTTATATTAATTATAATTC
1 TTTATATTAATTATAATTC
**
653772 TTTATATTTTTTATAATTC
1 TTTATATTAATTATAATTC
* *
653791 -TTATATT-A-TA-ATTTG
1 TTTATATTAATTATAATTC
* * *
653806 TATATTATAAATT-TGATT-
1 TTTA-TATTAATTATAATTC
*
653824 TTTATATTAATTCA-AATTA
1 TTTATATTAATT-ATAATTC
*
653843 TTTATATTATTTATAATTC
1 TTTATATTAATTATAATTC
653862 -TTATATTA
1 TTTATATTA
653870 TAAATTTTAT
Statistics
Matches: 75, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
15 3 0.04
16 4 0.05
17 10 0.13
18 23 0.31
19 35 0.47
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTATATTAATTATAATTC
Found at i:653820 original size:15 final size:14
Alignment explanation
Indices: 653782--653820 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
653772 TTTATATTTT
653782 TTATAATTCT-TATA
1 TTATAATT-TGTATA
653796 TTATAATTTGTATA
1 TTATAATTTGTATA
653810 TTATAAATTTG
1 TTAT-AATTTG
653821 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 16 0.70
15 6 0.26
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (14 bp):
TTATAATTTGTATA
Found at i:653826 original size:71 final size:70
Alignment explanation
Indices: 653742--653885 Score: 213
Period size: 71 Copynumber: 2.0 Consensus size: 70
653732 TTATGATAAT
* *
653742 TAAATTTAGTTTTTATATTAATT-ATAATTCTTTATATTTTTTATAATTCTTATATTAT-AATTT
1 TAAATTTAGTTTTTATATTAATTCA-AATTATTTATATTATTTATAATTCTTATATTATAAATTT
653805 GTATATTA
65 -TAT-TTA
653813 TAAATTT-GATTTTTATATTAATTCAAATTATTTATATTATTTATAATTCTTATATTATAAATTT
1 TAAATTTAG-TTTTTATATTAATTCAAATTATTTATATTATTTATAATTCTTATATTATAAATTT
653877 TATTTA
65 TATTTA
653883 TAA
1 TAA
653886 TCACTAAATT
Statistics
Matches: 68, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
70 7 0.10
71 55 0.81
72 6 0.09
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (70 bp):
TAAATTTAGTTTTTATATTAATTCAAATTATTTATATTATTTATAATTCTTATATTATAAATTTT
ATTTA
Found at i:654229 original size:15 final size:15
Alignment explanation
Indices: 654209--654239 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
654199 TTATCTCAGA
654209 TCTTATAGGTAAGGT
1 TCTTATAGGTAAGGT
*
654224 TCTTATAGTTAAGGT
1 TCTTATAGGTAAGGT
654239 T
1 T
654240 TTACAAGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (15 bp):
TCTTATAGGTAAGGT
Found at i:656240 original size:10 final size:10
Alignment explanation
Indices: 656203--656246 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
656193 AATCATATTA
656203 ATTTTTTTGT
1 ATTTTTTTGT
* *
656213 AATTTTTTGG
1 ATTTTTTTGT
*
656223 ATTTTTTTTT
1 ATTTTTTTGT
*
656233 ATTTTTTTAT
1 ATTTTTTTGT
656243 ATTT
1 ATTT
656247 GTAAAATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (10 bp):
ATTTTTTTGT
Found at i:656240 original size:20 final size:20
Alignment explanation
Indices: 656203--656239 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
656193 AATCATATTA
656203 ATTTTTTTGTAATTTTTTGG
1 ATTTTTTTGTAATTTTTTGG
*
656223 ATTTTTTT-TTATTTTTT
1 ATTTTTTTGTAATTTTTT
656240 TATATTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (20 bp):
ATTTTTTTGTAATTTTTTGG
Found at i:656624 original size:18 final size:19
Alignment explanation
Indices: 656600--656642 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
656590 AAAAGGTAAA
*
656600 ATTTATCGGATATATTTTT
1 ATTTATCAGATATATTTTT
656619 -TTTATCAGATATATTTTT
1 ATTTATCAGATATATTTTT
656637 ATTTAT
1 ATTTAT
656643 GTCACATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (19 bp):
ATTTATCAGATATATTTTT
Found at i:656793 original size:21 final size:21
Alignment explanation
Indices: 656766--656813 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
656756 GGTCGAAAAA
*
656766 AATATTTTAAATATTATTATT
1 AATATTTTAAATATTAATATT
* * *
656787 AGTATTTTTATTATTAATATT
1 AATATTTTAAATATTAATATT
656808 AATATT
1 AATATT
656814 AATATTTCTT
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:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
AATATTTTAAATATTAATATT
Found at i:658032 original size:28 final size:27
Alignment explanation
Indices: 658000--658057 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
657990 AATAAACTAT
658000 TTATAATTAATATTAAAATAAGTATATA
1 TTATAATTAATATTAAAATAAGTA-ATA
* *
658028 TTATAATTAATATTAATATAATTAATA
1 TTATAATTAATATTAAAATAAGTAATA
658055 TTA
1 TTA
658058 ATATTAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TTATAATTAATATTAAAATAAGTAATA
Found at i:658073 original size:16 final size:16
Alignment explanation
Indices: 658003--658077 Score: 72
Period size: 15 Copynumber: 5.0 Consensus size: 16
657993 AAACTATTTA
*
658003 TAATTAATATTAA-AA
1 TAATTAATATTAATAT
* *
658018 TAAGT-ATA-TATTA-
1 TAATTAATATTAATAT
658031 TAATTAATATTAATA-
1 TAATTAATATTAATAT
658046 TAATTAATATTAATAT
1 TAATTAATATTAATAT
658062 TAACTT-ATATTAATAT
1 TAA-TTAATATTAATAT
658078 AATATAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
13 6 0.12
14 7 0.14
15 23 0.45
16 13 0.25
17 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (16 bp):
TAATTAATATTAATAT
Found at i:658094 original size:7 final size:7
Alignment explanation
Indices: 658082--658107 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
658072 TAATATAATA
658082 TAATTTG
1 TAATTTG
658089 TAATTTG
1 TAATTTG
658096 TAATTTG
1 TAATTTG
658103 TAATT
1 TAATT
658108 AATATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (7 bp):
TAATTTG
Found at i:658144 original size:31 final size:31
Alignment explanation
Indices: 658106--658166 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
658096 TAATTTGTAA
658106 TTAATATTAATATAAAATATA-GTCTATAAAG
1 TTAATATTAATATAAAATATATGT-TATAAAG
*
658137 TTAATATTAATATAAACTATATGTTATAAA
1 TTAATATTAATATAAAATATATGTTATAAA
658167 TTATATAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (31 bp):
TTAATATTAATATAAAATATATGTTATAAAG
Found at i:658184 original size:14 final size:14
Alignment explanation
Indices: 658167--658228 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
658157 ATGTTATAAA
658167 TTATATAGTATAGT
1 TTATATAGTATAGT
* *
658181 TTATAAACTATAGT
1 TTATATAGTATAGT
* *
658195 TAATATAATTAATA-T
1 TTATAT-AGT-ATAGT
*
658210 TAATATAGTATAGT
1 TTATATAGTATAGT
658224 TTATA
1 TTATA
658229 AACTATATAC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 3 0.08
14 23 0.61
15 9 0.24
16 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (14 bp):
TTATATAGTATAGT
Found at i:658218 original size:43 final size:40
Alignment explanation
Indices: 658169--658259 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 40
658159 GTTATAAATT
*
658169 ATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTATA--TAATAT-ATTAATATAA
*
658212 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
1 ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
658252 ATTATAGT
1 A-TATAGT
658260 TAAGATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 10 0.22
41 11 0.24
43 24 0.53
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (40 bp):
ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
Found at i:658222 original size:29 final size:29
Alignment explanation
Indices: 658189--658281 Score: 78
Period size: 29 Copynumber: 3.0 Consensus size: 29
658179 GTTTATAAAC
658189 TATAGTTAATATAATTAATATTAATATAG
1 TATAGTTAATATAATTAATATTAATATAG
* * *
658218 TATAGTTTATAAACTATATACTATATTAATATAAAT
1 TATAGTTAATATA--AT-TA--ATATTAATAT--AG
* *
658254 TATAGTTAAGATAATTAACATTAATATA
1 TATAGTTAATATAATTAATATTAATATA
658282 AACTATATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
29 12 0.24
31 11 0.22
32 2 0.04
33 2 0.04
34 12 0.24
36 11 0.22
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (29 bp):
TATAGTTAATATAATTAATATTAATATAG
Found at i:658312 original size:20 final size:21
Alignment explanation
Indices: 658271--658312 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
658261 AAGATAATTA
658271 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
658293 ACATTAATATAAAC-TATAGT
1 ACATTAATATAAACATATAGT
658313 TTACAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:658329 original size:21 final size:21
Alignment explanation
Indices: 658300--658352 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
658290 AGTACATTAA
* *
658300 TATAAACTATAGTTTACAAAT
1 TATAAACTATAGGTTACAAAG
* *
658321 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTACAAAG
658342 TATAAACTATA
1 TATAAACTATA
658353 TAGTACACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (21 bp):
TATAAACTATAGGTTACAAAG
Found at i:658418 original size:17 final size:17
Alignment explanation
Indices: 658396--658453 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
658386 GTTTATATTT
*
658396 TATATATACTAATGAAC
1 TATATATACTAATGAAA
**
658413 TATATA-A-TATAT-AGT
1 TATATATACTA-ATGAAA
658428 TTATATATACTAATGAAA
1 T-ATATATACTAATGAAA
658446 TATATATA
1 TATATATA
658454 ATGTATAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 4 0.12
16 8 0.25
17 16 0.50
18 4 0.12
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (17 bp):
TATATATACTAATGAAA
Found at i:658418 original size:33 final size:33
Alignment explanation
Indices: 658378--658472 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 33
658368 GTTTACATAT
* * *
658378 ACTATATAGTTTATATTTTATATATACTAATGA
1 ACTATATAATATATAGTTTATATATACTAATGA
658411 ACTATATAATATATAGTTTATATATACTAATGAA
1 ACTATATAATATATAGTTTATATATACTAATG-A
* *
658445 ATATATATAATGTATAGTTTATATATAC
1 A-CTATATAATATATAGTTTATATATAC
658473 CATATAGTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 29 0.53
34 2 0.04
35 24 0.44
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.45
Consensus pattern (33 bp):
ACTATATAATATATAGTTTATATATACTAATGA
Found at i:658436 original size:18 final size:18
Alignment explanation
Indices: 658363--658486 Score: 81
Period size: 18 Copynumber: 6.7 Consensus size: 18
658353 TAGTACACTA
* *
658363 ATATAGTTTACATATACT
1 ATATAGTTTATATATAAT
*
658381 ATATAGTTTATATTTTATAT
1 ATATAGTTTATA-TATA-AT
* **
658401 ATACTAATGAACTATATAAT
1 ATA-TAGTTTA-TATATAAT
*
658421 ATATAGTTTATATATACT
1 ATATAGTTTATATATAAT
**
658439 A-AT-GAAATATATATAAT
1 ATATAG-TTTATATATAAT
* **
658456 GTATAGTTTATATATACC
1 ATATAGTTTATATATAAT
658474 ATATAGTTTATAT
1 ATATAGTTTATAT
658487 GCACTATAGT
Statistics
Matches: 79, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
16 1 0.01
17 11 0.14
18 41 0.52
19 8 0.10
20 9 0.11
21 7 0.09
22 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (18 bp):
ATATAGTTTATATATAAT
Found at i:658561 original size:49 final size:47
Alignment explanation
Indices: 658508--658700 Score: 156
Period size: 51 Copynumber: 3.8 Consensus size: 47
658498 TAAATTATTT
* *
658508 TATATAGTATATAAATATCAACTATAGTATACAGTTTATATGATTTTTA
1 TATATAGTATATAAATATCAACTATAGTATATA-TTTATAT-ATTTTAA
* *
658557 TATATAGTTCATATGTAAATTATACTA-TATAGTATATATACTT-TATATATATAA
1 TATATAG-T-ATA--TAAA-TAT-CAACTATAGTATATAT--TTATATAT-TTTAA
* * * *
658611 TATATAGTATATAAATATAAACTATAGTATATATATAGGTCATATGTAAA
1 TATATAGTATATAAATATCAACTATAGTATATATTTA--T-ATATTTTAA
*
658661 CTATATAGTATATAAATATCAACTATAGTATATATATATA
1 -TATATAGTATATAAATATCAACTATAGTATATATTTATA
658701 GGTCATATGT
Statistics
Matches: 118, Mismatches: 11, Indels: 31
0.74 0.07 0.19
Matches are distributed among these distances:
47 1 0.01
48 2 0.02
49 23 0.19
50 8 0.07
51 43 0.36
52 3 0.03
53 8 0.07
54 26 0.22
55 4 0.03
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (47 bp):
TATATAGTATATAAATATCAACTATAGTATATATTTATATATTTTAA
Found at i:658594 original size:2 final size:2
Alignment explanation
Indices: 658577--658647 Score: 54
Period size: 2 Copynumber: 33.0 Consensus size: 2
658567 ATATGTAAAT
*
658577 TA TA CTA TA TA GTA TA TA TA CTT TA TA TA TA TA -A TA TA TA GTA
1 TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* *
658620 TA TA AA TA TA AA CTA TA GTA TA TA TA TA
1 TA TA TA TA TA TA -TA TA -TA TA TA TA TA
658648 GGTCATATGT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
1 1 0.02
2 45 0.80
3 10 0.18
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:658623 original size:20 final size:20
Alignment explanation
Indices: 658577--658647 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
658567 ATATGTAAAT
*
658577 TATACTATATAGT-ATATATAC
1 TATA-TATATA-TAATATATAG
*
658598 TTTATATATATAATATATAG
1 TATATATATATAATATATAG
*
658618 TATATAAATATAA-ACTATAG
1 TATATATATATAATA-TATAG
658638 TATATATATA
1 TATATATATA
658648 GGTCATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 2 0.05
20 38 0.88
21 3 0.07
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (20 bp):
TATATATATATAATATATAG
Found at i:658695 original size:53 final size:53
Alignment explanation
Indices: 658611--658951 Score: 294
Period size: 53 Copynumber: 6.3 Consensus size: 53
658601 ATATATATAA
*
658611 TATATAGTATATAAATATAAACTATAG--TATATATATAGGTCATATGTAAAC
1 TATATAGTATATAAATATCAACTATAGTATATATATATAGGTCATATGTAAAC
658662 TATATAGTATATAAATATCAACTATAGTATATATATATAGGTCATATGTAAAC
1 TATATAGTATATAAATATCAACTATAGTATATATATATAGGTCATATGTAAAC
* * ** *
658715 TATATAGTTTATATATAT-AGTTCATATGTA-A-A-CTAT-GGTTCATATGTAAATATC
1 TATATAGTATATAAATATCAACT-ATA-GTATATATATATAGG-TCATATGT-AA-A-C
* * * *
658769 AACTATAGTTTATATGTAAACTAT--AGT-TAGTATATAAACTATATAGTTTATATGTAAAC
1 TA-TATAG--TATA--TAAA-TATCAACTATAGTATAT--A-TATATAGGTCATATGTAAAC
* * *
658828 TATAGTTCA-TATATAATTATCAACTTTAG--TATATATATAGTTCATATGTAAAC
1 TATA--T-AGTATATAAATATCAACTATAGTATATATATATAGGTCATATGTAAAC
658881 TATATAGTATATAAATATCAACTATAGTATATATATATAGGTCATATGTAAAC
1 TATATAGTATATAAATATCAACTATAGTATATATATATAGGTCATATGTAAAC
* *
658934 TATATAGTTTATATATAT
1 TATATAGTATATAAATAT
658952 AGTTCATATG
Statistics
Matches: 237, Mismatches: 23, Indels: 58
0.75 0.07 0.18
Matches are distributed among these distances:
50 3 0.01
51 56 0.24
52 5 0.02
53 107 0.45
54 6 0.03
55 8 0.03
56 9 0.04
57 8 0.03
58 9 0.04
59 6 0.03
60 6 0.03
61 3 0.01
62 10 0.04
63 1 0.00
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (53 bp):
TATATAGTATATAAATATCAACTATAGTATATATATATAGGTCATATGTAAAC
Found at i:658721 original size:33 final size:33
Alignment explanation
Indices: 658684--658750 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
658674 AAATATCAAC
658684 TATAGTATATATATATAGGTCATATGTAAACTA
1 TATAGTATATATATATAGGTCATATGTAAACTA
* *
658717 TATAGTTTATATATATAGTTCATATGTAAACTA
1 TATAGTATATATATATAGGTCATATGTAAACTA
658750 T
1 T
658751 GGTTCATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.43
Consensus pattern (33 bp):
TATAGTATATATATATAGGTCATATGTAAACTA
Found at i:658728 original size:20 final size:20
Alignment explanation
Indices: 658728--659032 Score: 103
Period size: 18 Copynumber: 16.2 Consensus size: 20
658718 ATAGTTTATA
*
658728 TATATAGTTCATATGTAAAC
1 TATATAGTTTATATGTAAAC
* *
658748 --TATGGTTCATATGTAAATATC
1 TATATAGTTTATATGT-AA-A-C
*
658769 AACTATAGTTTATATGTAAAC
1 TA-TATAGTTTATATGTAAAC
*
658790 --TATAG-TTAGTATATAAAC
1 TATATAGTTTA-TATGTAAAC
658808 TATATAGTTTATATGTAAAC
1 TATATAGTTTATATGTAAAC
* *
658828 --TATAGTTCATATAT-AA-
1 TATATAGTTTATATGTAAAC
** *
658844 T-TATCAACTT-TA-GTATA-
1 TATAT-AGTTTATATGTAAAC
*
658861 TATATAGTTCATATGTAAAC
1 TATATAGTTTATATGTAAAC
658881 TATATAG--TATA--TAAA-
1 TATATAGTTTATATGTAAAC
*
658896 TATCA-A--CTATA-GTATATA-
1 TAT-ATAGTTTATATGTA-A-AC
* *
658914 TATATAGGTCATATGTAAAC
1 TATATAGTTTATATGTAAAC
* * *
658934 TATATAGTTTATATATATAG
1 TATATAGTTTATATGTAAAC
* * * *
658954 T-TCATA-TGTAAATATCAAC
1 TAT-ATAGTTTATATGTAAAC
658973 --TATAGTTTATATGTAAAC
1 TATATAGTTTATATGTAAAC
*
658991 --TATAG-TTAGTATATAAAC
1 TATATAGTTTA-TATGTAAAC
659009 TATATAGTTTATATGTAAAC
1 TATATAGTTTATATGTAAAC
659029 TATA
1 TATA
659033 GTTCATATAT
Statistics
Matches: 217, Mismatches: 35, Indels: 66
0.68 0.11 0.21
Matches are distributed among these distances:
15 8 0.04
16 8 0.04
17 22 0.10
18 76 0.35
19 16 0.07
20 61 0.28
21 11 0.05
22 1 0.00
23 2 0.01
24 12 0.06
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.42
Consensus pattern (20 bp):
TATATAGTTTATATGTAAAC
Found at i:658792 original size:18 final size:18
Alignment explanation
Indices: 658764--659130 Score: 165
Period size: 18 Copynumber: 20.2 Consensus size: 18
658754 TCATATGTAA
*
658764 ATATCAACTATAGTTTAT
1 ATATAAACTATAGTTTAT
*
658782 ATGTAAACTATAG-TTAGT
1 ATATAAACTATAGTTTA-T
658800 ATATAAACTATATAGTTTAT
1 ATATAAAC--TATAGTTTAT
* *
658820 ATGTAAACTATAGTTCAT
1 ATATAAACTATAGTTTAT
* *
658838 ATAT-AATTATCAACTTTAGT
1 ATATAAACTAT--AGTTTA-T
*
658858 ATAT--A-TATAGTTCAT
1 ATATAAACTATAGTTTAT
* *
658873 ATGTAAACTATATAGTATATAA
1 ATATAAAC--TATAGT-T-TAT
*
658895 ATATCAACTATAG--TAT
1 ATATAAACTATAGTTTAT
* *
658911 ATAT--A-TATAGGTCAT
1 ATATAAACTATAGTTTAT
*
658926 ATGTAAACTATATAGTTTAT
1 ATATAAAC--TATAGTTTAT
** * *
658946 ATATATAGTTCATA-TGTAA
1 ATATA-AACT-ATAGTTTAT
*
658965 ATATCAACTATAGTTTAT
1 ATATAAACTATAGTTTAT
*
658983 ATGTAAACTATAG-TTAGT
1 ATATAAACTATAGTTTA-T
659001 ATATAAACTATATAGTTTAT
1 ATATAAAC--TATAGTTTAT
* *
659021 ATGTAAACTATAGTTCAT
1 ATATAAACTATAGTTTAT
*
659039 ATATAAA-TATCAACCTTTAGT
1 ATATAAACTAT--A-GTTTA-T
* *
659060 ATATATA-TATAGTTCAT
1 ATATAAACTATAGTTTAT
* *
659077 ATGTAAACTATAGTTCAT
1 ATATAAACTATAGTTTAT
* * *
659095 ATATATAGTATA---TAA
1 ATATAAACTATAGTTTAT
659110 ATATAAACTATAGTTTAT
1 ATATAAACTATAGTTTAT
659128 ATA
1 ATA
659131 AATAGTATAT
Statistics
Matches: 261, Mismatches: 52, Indels: 72
0.68 0.14 0.19
Matches are distributed among these distances:
13 5 0.02
14 1 0.00
15 20 0.08
16 10 0.04
17 25 0.10
18 100 0.38
19 15 0.06
20 60 0.23
21 18 0.07
22 7 0.03
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (18 bp):
ATATAAACTATAGTTTAT
Found at i:658836 original size:80 final size:75
Alignment explanation
Indices: 658705--658863 Score: 210
Period size: 80 Copynumber: 2.1 Consensus size: 75
658695 TATATAGGTC
* * *
658705 ATATGTAAACTATATAGTTTATATATATAGTTCATATGTAAACTATGGTTCATATGTAAATATCA
1 ATATGTAAACTATATAGTTTAAATATATAGTTCATATGTAAACTATAGTTCATATATAAATATCA
*
658770 ACTATAGTTT
66 ACTATAGTAT
* *
658780 ATATGTAAACTATAGTTAGTATATAAACTATATAGTTTATATGTAAACTATAGTTCATATATAAT
1 ATATGTAAACTATA--TAGT-T-TAAA-TATATAGTTCATATGTAAACTATAGTTCATATATAAA
*
658845 TATCAACTTTAGTAT
61 TATCAACTATAGTAT
658860 ATAT
1 ATAT
658864 ATAGTTCATA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
75 14 0.19
77 4 0.06
78 1 0.01
79 3 0.04
80 50 0.69
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (75 bp):
ATATGTAAACTATATAGTTTAAATATATAGTTCATATGTAAACTATAGTTCATATATAAATATCA
ACTATAGTAT
Found at i:658915 original size:24 final size:24
Alignment explanation
Indices: 658825--658917 Score: 66
Period size: 24 Copynumber: 3.8 Consensus size: 24
658815 TTTATATGTA
*
658825 AACTATAGT-TCATATATAATTATC
1 AACTATAGTAT-ATATATAAATATC
* * *
658849 AACTTTAGTATATATATAGTTCATATGTA
1 AACTATAGTATATATATA----A-ATATC
*
658878 AACTATA-TA-GTATATAAATATC
1 AACTATAGTATATATATAAATATC
658900 AACTATAGTATATATATA
1 AACTATAGTATATATATA
658918 TAGGTCATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
22 10 0.19
23 3 0.06
24 21 0.40
25 1 0.02
27 6 0.12
28 3 0.06
29 8 0.15
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (24 bp):
AACTATAGTATATATATAAATATC
Found at i:658940 original size:33 final size:33
Alignment explanation
Indices: 658903--658965 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
658893 AAATATCAAC
658903 TATAGTATATATATATAGGTCATATGTAAACTA
1 TATAGTATATATATATAGGTCATATGTAAACTA
* *
658936 TATAGTTTATATATATAGTTCATATGTAAA
1 TATAGTATATATATATAGGTCATATGTAAA
658966 TATCAACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (33 bp):
TATAGTATATATATATAGGTCATATGTAAACTA
Found at i:658984 original size:33 final size:33
Alignment explanation
Indices: 658892--658984 Score: 82
Period size: 33 Copynumber: 2.7 Consensus size: 33
658882 ATATAGTATA
658892 TAAATATCAACTATAGTATATATATATAGGTCATATG
1 TAAATATCAACTATAG--T-T-TATATAGGTCATATG
* * * *
658929 TAAACTAT-ATAGTTTA-TATATATAGTTCATATG
1 TAAA-TATCA-ACTATAGTTTATATAGGTCATATG
658962 TAAATATCAACTATAGTTTATAT
1 TAAATATCAACTATAGTTTATAT
658985 GTAAACTATA
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
32 7 0.16
33 25 0.56
35 1 0.02
37 5 0.11
38 7 0.16
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (33 bp):
TAAATATCAACTATAGTTTATATAGGTCATATG
Found at i:659021 original size:38 final size:38
Alignment explanation
Indices: 658916--659088 Score: 139
Period size: 38 Copynumber: 4.6 Consensus size: 38
658906 AGTATATATA
* *
658916 TATAGGTCATATGTAAACTATATAGTTTATA--T--A-
1 TATAGTTCATATATAAACTATATAGTTTATATGTAAAC
* *
658949 TATAGTTCATATGTAAATATCAACTATAGTTTATATGTAAAC
1 TATAGTTCATATAT-AA-A-CTA-TATAGTTTATATGTAAAC
658991 TATAGTT-AGTATATAAACTATATAGTTTATATGTAAAC
1 TATAGTTCA-TATATAAACTATATAGTTTATATGTAAAC
* * *
659029 TATAGTTCATATATAAA-TATCA-ACCTTTAGTATATATA-
1 TATAGTTCATATATAAACTAT-ATA-GTTTA-TATGTAAAC
*
659067 TATAGTTCATATGTAAACTATA
1 TATAGTTCATATATAAACTATA
659089 GTTCATATAT
Statistics
Matches: 117, Mismatches: 8, Indels: 25
0.78 0.05 0.17
Matches are distributed among these distances:
33 13 0.11
34 2 0.02
35 1 0.01
36 2 0.02
37 15 0.13
38 55 0.47
39 13 0.11
40 1 0.01
41 4 0.03
42 11 0.09
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (38 bp):
TATAGTTCATATATAAACTATATAGTTTATATGTAAAC
Found at i:659035 original size:219 final size:218
Alignment explanation
Indices: 658618--659045 Score: 623
Period size: 219 Copynumber: 2.0 Consensus size: 218
658608 TAATATATAG
658618 TATATAAATATAAACTATAGTATATATATAGGTCATATGTAAACTATATAGTATATAAATATCAA
1 TATATAAATATAAACTATAGTATATATATAGGTCATATGTAAACTATATAGTATATAAATATCAA
658683 CTATAGTATATATATATAGGTCATATGTAAACTATATAGTTTATATATATAGTTCATATGTAAAC
66 CTATAGTATATATATATAGGTCATATGTAAACTATATAGTTTATATATATAGTTCATATGTAAAC
*** * *
658748 TATGGTTCATATGTAAATATCAACTATAGTTTATATGTAAACTATAGTTAGTATATAAACTATAT
131 TATAACTCATATGTAAATATAAACTATAGTTTATATATAAACTATAGTTAGTATATAAAC-ATAT
* *
658813 AGTTTATATGTAAACTATAGTTCA
195 AGTTCATATATAAACTATAGTTCA
* * * *
658837 TATATAATTATCAACTTTAGTATATATATAGTTCATATGTAAACTATATAGTATATAAATATCAA
1 TATATAAATATAAACTATAGTATATATATAGGTCATATGTAAACTATATAGTATATAAATATCAA
658902 CTATAGTATATATATATAGGTCATATGTAAACTATATAGTTTATATATATAGTTCATATGTAAA-
66 CTATAGTATATATATATAGGTCATATGTAAACTATATAGTTTATATATATAGTTCATATGTAAAC
* * * *
658966 TATCAACT-ATAGTTTATATGTAAACTATAG-TTAGTATATAAACTATATAGTTTA-TATGTAAA
131 TAT-AACTCATA-TGTAAATATAAACTATAGTTTA-TATATAAAC--TATAG-TTAGTATATAAA
659028 C-TATAGTTCATATATAAA
190 CATATAGTTCATATATAAA
659046 TATCAACCTT
Statistics
Matches: 188, Mismatches: 15, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
218 9 0.05
219 163 0.87
221 13 0.07
222 3 0.02
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (218 bp):
TATATAAATATAAACTATAGTATATATATAGGTCATATGTAAACTATATAGTATATAAATATCAA
CTATAGTATATATATATAGGTCATATGTAAACTATATAGTTTATATATATAGTTCATATGTAAAC
TATAACTCATATGTAAATATAAACTATAGTTTATATATAAACTATAGTTAGTATATAAACATATA
GTTCATATATAAACTATAGTTCA
Found at i:659117 original size:33 final size:32
Alignment explanation
Indices: 659038--659188 Score: 132
Period size: 33 Copynumber: 4.6 Consensus size: 32
659028 CTATAGTTCA
* *
659038 TATATAAATATCAACCTTTAGTATATATATATAG
1 TATATAAATAT-AAACTATAGT-TATATATATAG
*
659072 T-TCAT--ATGTAAACTATAGTTCATATATATAG
1 TAT-ATAAATATAAACTATAGTT-ATATATATAG
*
659103 TATATAAATATAAACTATAGTTTATATAAATAG
1 TATATAAATATAAACTATAG-TTATATATATAG
* *
659136 TATATAAATATAAA-TATAAATTATAGTATGTAG
1 TATATAAATATAAACTAT-AGTTATA-TATATAG
659169 TTTATATAAATATAAA-TATA
1 --TATATAAATATAAACTATA
659189 AACCCTAAAT
Statistics
Matches: 99, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
30 1 0.01
31 21 0.21
32 12 0.12
33 42 0.42
34 6 0.06
35 17 0.17
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (32 bp):
TATATAAATATAAACTATAGTTATATATATAG
Found at i:659151 original size:39 final size:35
Alignment explanation
Indices: 659104--659191 Score: 104
Period size: 35 Copynumber: 2.4 Consensus size: 35
659094 TATATATAGT
659104 ATATAAATATAAACTATAGTTTATATAAATAGTATATAA
1 ATATAAATATAAACTATAG--TATAT-AAT-GTATATAA
* * * *
659143 ATATAAATATAAATTATAGTATGTAGTTTATATAA
1 ATATAAATATAAACTATAGTATATAATGTATATAA
659178 ATATAAATATAAAC
1 ATATAAATATAAAC
659192 CCTAAATCCC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
35 20 0.45
36 2 0.05
37 4 0.09
39 18 0.41
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (35 bp):
ATATAAATATAAACTATAGTATATAATGTATATAA
Found at i:659253 original size:14 final size:13
Alignment explanation
Indices: 659220--659258 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
659210 ATCCATAATC
*
659220 CCTAAACTATAAA
1 CCTAAACCATAAA
659233 CCTTAAACCATAAA
1 CC-TAAACCATAAA
659247 CTCTAAACCATA
1 C-CTAAACCATA
659259 TATACTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 2 0.09
14 20 0.87
15 1 0.04
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (13 bp):
CCTAAACCATAAA
Found at i:659457 original size:2 final size:2
Alignment explanation
Indices: 659450--659502 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
659440 TTATACATGG
* *
659450 TA TA TA TA -A TT TA TA CA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
659490 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
659503 TAGTTGTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:659462 original size:20 final size:20
Alignment explanation
Indices: 659427--659497 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
659417 TATAAACTTT
*
659427 ATAGTAT-TATAGTTTATAC
1 ATAGTATATATAATTTATAC
*
659446 ATGGTATATATAATTTATAC
1 ATAGTATATATAATTTATAC
* * *
659466 ATAATATATATATATATATAT
1 ATAGTATATATA-ATTTATAC
659487 ATA-TATATATA
1 ATAGTATATATA
659498 TATATTAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 6 0.14
20 29 0.66
21 9 0.20
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (20 bp):
ATAGTATATATAATTTATAC
Found at i:659930 original size:208 final size:208
Alignment explanation
Indices: 659572--660123 Score: 813
Period size: 208 Copynumber: 2.6 Consensus size: 208
659562 TATTTTTCAT
* *
659572 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAATTTTTTATTTTTAATTTCATATTTGTTCAAT
1 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
* *
659637 TTAGTCCTCCACATTTTATTTGCATCA-GAAATTGATTCATACTTATTACTTATTTCTATTTATT
66 TTAGTCCTCCAAATTTTATTTGCAT-ATGAAATTGATCCATACTTATTACTTATTTCTATTT-TT
* *
659701 AATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACACTTTTGTATTAATTTCAAC-CTCAA
129 AATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACACTTTTGTATTAATTTAAACACACAA
*
659765 TTTAAAATTATTTTG
194 TTTAAAATTATTTCG
* * *
659780 ATTTGATCCCTTTTGCGTTGTTTAGTTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAAT
1 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
* *
659845 TTAGTCCTCCAAATTTTATTTGCATATGAAATTAACCCATACTTATTACTTATTTCTATTTTTAA
66 TTAGTCCTCCAAATTTTATTTGCATATGAAATTGATCCATACTTATTACTTATTTCTATTTTT-A
* **
659910 ATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTAAACATCACAA
130 ATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACACTTTTGTATTAATTTAAACA-CACAA
659975 TTTAAAATTATTTCG
194 TTTAAAATTATTTCG
*
659990 ATTTGATCCCTCATCAATATGTGTTGTTTAATTAATTTAAATTTTTATTTGTAATTTCATATTTG
1 ATTTGATCCCT--T---T-TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTG
* * *
660055 TTCAATTTAGTCCTCTAAATTCTATTTGCATATGAAATTGATCCATACTT-TTCACTTAATTCTA
60 TTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGATCCATACTTATT-ACTTATTTCTA
660119 TTTTT
124 TTTTT
660124 GTTGAGTTAA
Statistics
Matches: 309, Mismatches: 24, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
207 3 0.01
208 170 0.55
210 29 0.09
212 1 0.00
215 3 0.01
216 103 0.33
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.51
Consensus pattern (208 bp):
ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
TTAGTCCTCCAAATTTTATTTGCATATGAAATTGATCCATACTTATTACTTATTTCTATTTTTAA
TTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACACTTTTGTATTAATTTAAACACACAATT
TAAAATTATTTCG
Found at i:663620 original size:21 final size:21
Alignment explanation
Indices: 663538--663621 Score: 73
Period size: 21 Copynumber: 3.9 Consensus size: 21
663528 CAGAACCCCA
*
663538 GGGGGGTATCGATTCCC-C-T
1 GGGGGGGATCGATTCCCTCAT
* *
663557 GTGGGGGGAATCGGTTCCCCTTCAA
1 G-GGGGGG-ATCGATT-CCC-TCAT
* *
663582 AGGGGGAATCGATTCCCTCAT
1 GGGGGGGATCGATTCCCTCAT
663603 GGGGGGGATCGATTCCCTC
1 GGGGGGGATCGATTCCCTC
663622 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
19 1 0.02
20 5 0.10
21 26 0.52
22 6 0.12
23 6 0.12
24 6 0.12
ACGTcount: A:0.15, C:0.25, G:0.36, T:0.24
Consensus pattern (21 bp):
GGGGGGGATCGATTCCCTCAT
Found at i:696750 original size:15 final size:15
Alignment explanation
Indices: 696727--696776 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
696717 CATTATCTTG
*
696727 TAATTGAAAATAGAA
1 TAATAGAAAATAGAA
696742 TAATAGAAAATAG-A
1 TAATAGAAAATAGAA
* *
696756 GAATATACAAATA-AA
1 TAATAGA-AAATAGAA
696771 TAATAG
1 TAATAG
696777 TATAGGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 6 0.21
15 22 0.79
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.24
Consensus pattern (15 bp):
TAATAGAAAATAGAA
Found at i:702763 original size:13 final size:13
Alignment explanation
Indices: 702742--702775 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
702732 ATATTATAGA
*
702742 ATAAAAATAAATT
1 ATAAAAATAAAAT
*
702755 ATTAAAATAAAAT
1 ATAAAAATAAAAT
702768 ATAAAAAT
1 ATAAAAAT
702776 TATCTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAAAAATAAAAT
Found at i:702765 original size:19 final size:22
Alignment explanation
Indices: 702741--702786 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 22
702731 TATATTATAG
702741 AATAAAA-AT-AAATTAT-TAA
1 AATAAAATATAAAATTATCTAA
702760 AATAAAATATAAAAATTATCTAA
1 AATAAAATAT-AAAATTATCTAA
702783 AATA
1 AATA
702787 TATCAAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.30
20 2 0.09
22 7 0.30
23 7 0.30
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
AATAAAATATAAAATTATCTAA
Found at i:704802 original size:2 final size:2
Alignment explanation
Indices: 704795--704826 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
704785 GCAGTGCAAC
704795 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
704827 GTTATTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:704891 original size:23 final size:21
Alignment explanation
Indices: 704848--704900 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
704838 GATTTTTTGA
*
704848 TTTTGTTATTTTTTTTACTTT
1 TTTTGTTATTTCTTTTACTTT
*
704869 CTTTTGTTATTTCCTTTTCCTTT
1 -TTTTGTTATTT-CTTTTACTTT
704892 TCTTTGTTA
1 T-TTTGTTA
704901 CATTATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.08, C:0.13, G:0.06, T:0.74
Consensus pattern (21 bp):
TTTTGTTATTTCTTTTACTTT
Found at i:704994 original size:15 final size:17
Alignment explanation
Indices: 704974--705005 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
704964 CATAATATAA
704974 TAAATT-CAAG-TAGAT
1 TAAATTGCAAGATAGAT
704989 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
705006 AAAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:705555 original size:19 final size:20
Alignment explanation
Indices: 705520--705560 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
705510 TTATTATGAA
*
705520 TTGTAATTTTCTTA-TTTAT
1 TTGTAATTTTCTAATTTTAT
705539 TTGT-ATTTTCGTAATTTTAT
1 TTGTAATTTTC-TAATTTTAT
705559 TT
1 TT
705561 ATGAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 6 0.32
19 6 0.32
20 7 0.37
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (20 bp):
TTGTAATTTTCTAATTTTAT
Found at i:712655 original size:2 final size:2
Alignment explanation
Indices: 712648--712684 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
712638 AAATTAAAGT
712648 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
712685 TCTATAGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:719771 original size:22 final size:22
Alignment explanation
Indices: 719728--719772 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
719718 CATTGCATAA
719728 AAATTAAACAGTTATAAATCCTG
1 AAATTAAACAG-TATAAATCCTG
*
719751 AAATTAAATCAG-ATAACTCCTG
1 AAATTAAA-CAGTATAAATCCTG
719773 TAACTCCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 8 0.40
24 3 0.15
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.29
Consensus pattern (22 bp):
AAATTAAACAGTATAAATCCTG
Found at i:720729 original size:31 final size:31
Alignment explanation
Indices: 720694--720756 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
720684 AGTTTGGTGA
*
720694 ATTCAATATGTCCTTCTCACCAGGAACTCCC
1 ATTCAATATGTCATTCTCACCAGGAACTCCC
*
720725 ATTCAATATGTCATTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACCAGGAACTCCC
720756 A
1 A
720757 AACTCTTGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.32, G:0.10, T:0.30
Consensus pattern (31 bp):
ATTCAATATGTCATTCTCACCAGGAACTCCC
Found at i:722149 original size:14 final size:14
Alignment explanation
Indices: 722132--722161 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
722122 TACCATTGTT
722132 CTCATATAGATCTC
1 CTCATATAGATCTC
*
722146 CTCATCTAGATCTC
1 CTCATATAGATCTC
722160 CT
1 CT
722162 TTCAAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (14 bp):
CTCATATAGATCTC
Found at i:725613 original size:22 final size:22
Alignment explanation
Indices: 725572--725616 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
725562 CATTGCATAA
725572 AAATTAAACAGTTATAACTCCTG
1 AAATTAAACAG-TATAACTCCTG
725595 AAATTAAATCAG-ATAACTCCTG
1 AAATTAAA-CAGTATAACTCCTG
725617 TAACTCCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 8 0.38
24 3 0.14
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (22 bp):
AAATTAAACAGTATAACTCCTG
Found at i:726574 original size:13 final size:13
Alignment explanation
Indices: 726558--726583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
726548 TAGAATAGAT
726558 ATTATTTTGTAAA
1 ATTATTTTGTAAA
726571 ATTATTTTGTAAA
1 ATTATTTTGTAAA
726584 TCACTTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATTATTTTGTAAA
Found at i:727142 original size:43 final size:44
Alignment explanation
Indices: 727090--727176 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
727080 TGGTGTTTTA
* * * *
727090 TCCCAAAAACGCCGCTAAATGTTCTGACATATAGTGGCGTTTGT
1 TCCCAAAAACACAGCTAAATGTTATGACATATAGTGGCATTTGT
*
727134 TCCC-AAAACACAGCTAAATGTTATGTCATATAGTGGCATTTGT
1 TCCCAAAAACACAGCTAAATGTTATGACATATAGTGGCATTTGT
727177 GAATGTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 34 0.89
44 4 0.11
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (44 bp):
TCCCAAAAACACAGCTAAATGTTATGACATATAGTGGCATTTGT
Found at i:728868 original size:41 final size:40
Alignment explanation
Indices: 728823--729035 Score: 191
Period size: 41 Copynumber: 5.2 Consensus size: 40
728813 TGAATCACTT
* *
728823 AAACGCCACTAATGTTCGAGTATTTAACGGCGTTTGTCTAA
1 AAACGCCACTAAAGTTCGAGT-TTTAGCGGCGTTTGTCTAA
* * *
728864 AAACGCCACTAAAGTAT-GAGTCTATAGCGGCGTTTATATAA
1 AAACGCCACTAAAGT-TCGAGT-TTTAGCGGCGTTTGTCTAA
* * * *
728905 AAACGCCGCTAAA-TTACTAGTATTT-GCGGCGTTTTTGCTTA
1 AAACGCCACTAAAGTT-CGAGT-TTTAGCGGCGTTTGT-CTAA
* *
728946 AAACGTCACTAAAGTTCCAGGTTTTAGCGGCGTTTGTC-AA
1 AAACGCCACTAAAGTTCGA-GTTTTAGCGGCGTTTGTCTAA
* * *
728986 AAACACCACTAAAGTACAAGGTTTTAGCGGCGTTTGTCTAA
1 AAACGCCACTAAAGTTCGA-GTTTTAGCGGCGTTTGTCTAA
*
729027 AAATGCCAC
1 AAACGCCAC
729036 ATATGTATCC
Statistics
Matches: 140, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
39 1 0.01
40 46 0.33
41 78 0.56
42 15 0.11
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (40 bp):
AAACGCCACTAAAGTTCGAGTTTTAGCGGCGTTTGTCTAA
Found at i:732213 original size:2 final size:2
Alignment explanation
Indices: 732206--732241 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
732196 ATAAAAATGC
732206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
732242 AGGAAGGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:739662 original size:15 final size:14
Alignment explanation
Indices: 739635--739666 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
739625 TAATTCACAC
739635 ATATTTTTAATATA
1 ATATTTTTAATATA
739649 ATATTTTT-ATAT-
1 ATATTTTTAATATA
739661 ATATTT
1 ATATTT
739667 AATTTATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 4 0.22
14 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATTTTTAATATA
Found at i:740826 original size:20 final size:21
Alignment explanation
Indices: 740801--740846 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
740791 AAATATGAGA
740801 TTTTTTATA-CTTTTAAGGAT
1 TTTTTTATATCTTTTAAGGAT
*
740821 TTTTTTATATTTTTTAAGGAT
1 TTTTTTATATCTTTTAAGGAT
740842 TTTTT
1 TTTTT
740847 AAAAGTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (21 bp):
TTTTTTATATCTTTTAAGGAT
Found at i:740843 original size:11 final size:11
Alignment explanation
Indices: 740811--740848 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
740801 TTTTTTATAC
740811 TTTTAAGGATT
1 TTTTAAGGATT
* *
740822 TTTTTA-TATT
1 TTTTAAGGATT
740832 TTTTAAGGATT
1 TTTTAAGGATT
740843 TTTTAA
1 TTTTAA
740849 AAGTAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (11 bp):
TTTTAAGGATT
Found at i:740847 original size:20 final size:19
Alignment explanation
Indices: 740799--740847 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
740789 GGAAATATGA
740799 GATTTTTTATACTTTTAAG
1 GATTTTTTATACTTTTAAG
*
740818 GATTTTTTTATATTTTTTAAG
1 GA-TTTTTTATA-CTTTTAAG
740839 GATTTTTTA
1 GATTTTTTA
740848 AAAGTAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.07
20 16 0.59
21 9 0.33
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.63
Consensus pattern (19 bp):
GATTTTTTATACTTTTAAG
Found at i:742841 original size:60 final size:60
Alignment explanation
Indices: 742717--742830 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
742707 TGATCTCCTG
* * *
742717 ACTATAGGGTGATGCTTTGTTGAGTATCTCGACTATTAAAAGTTATAAAATGGTCCTTCA
1 ACTATAGGATGATGCTTTATTGAGTATCTCGACTATTAAAAGTTACAAAATGGTCCTTCA
* *
742777 ACTATAGGATGTTGCTTTATTGAGTCATCT-TACTATTAAAAGTTACAAAATGGT
1 ACTATAGGATGATGCTTTATTGAGT-ATCTCGACTATTAAAAGTTACAAAATGGT
742831 TACCTAACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 44 0.92
61 4 0.08
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (60 bp):
ACTATAGGATGATGCTTTATTGAGTATCTCGACTATTAAAAGTTACAAAATGGTCCTTCA
Found at i:744479 original size:19 final size:19
Alignment explanation
Indices: 744441--744479 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
744431 ATTTTAAGTT
*
744441 ATTCAAATCATATTTTAAA
1 ATTCAAATCATATTTAAAA
**
744460 ATTCAAATTTTATTTAAAA
1 ATTCAAATCATATTTAAAA
744479 A
1 A
744480 AATTTCGACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTCAAATCATATTTAAAA
Found at i:748963 original size:13 final size:13
Alignment explanation
Indices: 748945--748972 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
748935 TGGTTTACAG
748945 TACTTGACTGCAT
1 TACTTGACTGCAT
748958 TACTTGACTGCAT
1 TACTTGACTGCAT
748971 TA
1 TA
748973 ATACACTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (13 bp):
TACTTGACTGCAT
Found at i:750559 original size:8 final size:8
Alignment explanation
Indices: 750546--750586 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
750536 CTCATTTTCA
750546 GAGAATTT
1 GAGAATTT
750554 GAGAATTT
1 GAGAATTT
*
750562 -AGAGTTT
1 GAGAATTT
*
750569 GGGAATTT
1 GAGAATTT
750577 GAGAATTT
1 GAGAATTT
750585 GA
1 GA
750587 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:750860 original size:128 final size:128
Alignment explanation
Indices: 750659--751412 Score: 1215
Period size: 128 Copynumber: 5.9 Consensus size: 128
750649 ATCGGAGTAT
750659 TATTCACATGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
* *
750723 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATATATATCAATACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
750786 TATTCACATGAAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
750851 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *** * * * * *
750914 AAGGGACATGAAGGCGCGTTCCCAGGGGCACGCCTTCCATTATTTTGCCATAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
**
750979 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
751042 TATTCACATGAAGGCACGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
751107 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * * *
751170 -AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGCCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
* **
751234 ATTGCCCTATTATGTCACTCATGTCCCTCAGGGACACCCGATATATCAGTACCTATTATTTCAC
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
751298 TATTCACATGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
751363 TTGCCCTATTATGTCACTTATGTCCCTCGGGGACACTAGATATATCAGTA
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
751413 AATCAGGTAA
Statistics
Matches: 568, Mismatches: 56, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
127 29 0.05
128 538 0.95
129 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (128 bp):
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
Found at i:751874 original size:33 final size:34
Alignment explanation
Indices: 751813--751912 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
751803 AAATTTAATG
*
751813 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
751847 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
751880 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
751913 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:752453 original size:21 final size:21
Alignment explanation
Indices: 752423--752516 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
752413 TATGGTATAA
*
752423 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
752444 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
752465 AACCCTGCAGGCTCA-GAATGT
1 AACCCTGCGGGCT-AGGAATGT
*
752486 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
752507 AACCCTGCGG
1 AACCCTGCGG
752517 AGATGGCATA
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
20 3 0.05
21 58 0.89
22 4 0.06
ACGTcount: A:0.22, C:0.28, G:0.32, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:752546 original size:21 final size:21
Alignment explanation
Indices: 752520--752567 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
752510 CCTGCGGAGA
*
752520 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
752541 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
752562 GGGCAT
1 TGGCAT
752568 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:754338 original size:19 final size:18
Alignment explanation
Indices: 754290--754377 Score: 55
Period size: 17 Copynumber: 5.1 Consensus size: 18
754280 TTCTAAATAA
* *
754290 ATAATAATT-ATATAAAT
1 ATAATATTTAATAAAAAT
*
754307 ATTAT-TTTAATAAAAAT
1 ATAATATTTAATAAAAAT
754324 ATAATATTTACAT--AAAT
1 ATAATATTTA-ATAAAAAT
*
754341 ATAATA-AT-ATAAAAAAT
1 ATAATATTTAAT-AAAAAT
754358 AATAACTATTTAA-AAAAAT
1 -ATAA-TATTTAATAAAAAT
754377 A
1 A
754378 CTAACATAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 19
0.69 0.08 0.24
Matches are distributed among these distances:
14 2 0.04
16 3 0.05
17 29 0.53
18 9 0.16
19 10 0.18
20 1 0.02
21 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATATTTAATAAAAAT
Found at i:754371 original size:18 final size:17
Alignment explanation
Indices: 754318--754374 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 17
754308 TTATTTTAAT
754318 AAAAAT-ATAATATTTA
1 AAAAATAATAATATTTA
754334 CATAAATATAATAATA--TA
1 -A-AAA-ATAATAATATTTA
754352 AAAAATAATAACTATTTA
1 AAAAATAATAA-TATTTA
754370 AAAAA
1 AAAAA
754375 ATACTAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
15 7 0.21
16 5 0.15
17 2 0.06
18 12 0.35
19 2 0.06
20 6 0.18
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAAATAATAATATTTA
Found at i:754387 original size:34 final size:34
Alignment explanation
Indices: 754318--754389 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
754308 TTATTTTAAT
* *
754318 AAAAATATAATATTTACATAAATATAATAATATA
1 AAAAATATAATATTTACATAAAAATAATAACATA
*
754352 AAAAATAATAACTATTTA-A-AAAAATACTAACATA
1 AAAAAT-ATAA-TATTTACATAAAAATAATAACATA
754386 AAAA
1 AAAA
754390 TAAATTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 22 0.67
35 5 0.15
36 6 0.18
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (34 bp):
AAAAATATAATATTTACATAAAAATAATAACATA
Found at i:762818 original size:2 final size:2
Alignment explanation
Indices: 762811--762844 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
762801 TATTACATAC
762811 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
762845 GAAATAAGAT
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:763035 original size:17 final size:19
Alignment explanation
Indices: 763002--763036 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
762992 TATTTTCACT
763002 TATATAATAATTCAAAATC
1 TATATAATAATTCAAAATC
763021 TATATAA-AATT-AAAAT
1 TATATAATAATTCAAAAT
763037 AAATTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 4 0.25
19 7 0.44
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
TATATAATAATTCAAAATC
Found at i:763794 original size:4 final size:4
Alignment explanation
Indices: 763785--763809 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
763775 GTCAACTTTA
763785 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
763810 TTTGTTTGTG
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:764415 original size:25 final size:26
Alignment explanation
Indices: 764367--764416 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
764357 GATGATGATA
764367 ATAAATATTCTATAATTTAAAAAATT
1 ATAAATATTCTATAATTTAAAAAATT
*
764393 ATAAAT-TTCATATATTTTAAAAAA
1 ATAAATATTC-TATAATTTAAAAAA
764417 AATATTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (26 bp):
ATAAATATTCTATAATTTAAAAAATT
Found at i:765618 original size:16 final size:16
Alignment explanation
Indices: 765599--765632 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
765589 CAATATACGA
765599 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
765615 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
765631 AT
1 AT
765633 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:765707 original size:16 final size:18
Alignment explanation
Indices: 765675--765708 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
765665 TATTAATGTA
765675 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
765693 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
765709 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:766381 original size:130 final size:130
Alignment explanation
Indices: 766177--766424 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
766167 AATTTTCTTC
* * * *
766177 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTGACACATGTCTGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
766242 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
766307 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
766372 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
766425 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:766875 original size:35 final size:35
Alignment explanation
Indices: 766825--766900 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
766815 AATTGAATTG
* *
766825 AATTGAATTATTTTGGAATTTAGGGTTTAGAATAA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATAA
* *
766860 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATAA
766895 AATTGA
1 AATTGA
766901 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATAA
Found at i:770717 original size:15 final size:15
Alignment explanation
Indices: 770694--770756 Score: 117
Period size: 15 Copynumber: 4.2 Consensus size: 15
770684 CGTAGGACTC
770694 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
770709 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
770724 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
770739 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
770754 CTA
1 CTA
770757 TTATACCCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.32, C:0.33, G:0.21, T:0.14
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:770883 original size:29 final size:29
Alignment explanation
Indices: 770841--770918 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
770831 TTTCATATGT
770841 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
770869 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
770898 TCATGTAGCTCATGTCATTTC
1 TCATGTAGCTCATGTCATTTC
770919 ATATCATGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.14
29 42 0.86
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:770947 original size:12 final size:12
Alignment explanation
Indices: 770930--770975 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
770920 TATCATGTTC
*
770930 TCATATCACAGG
1 TCATATCACAGA
*
770942 TCATATCACATA
1 TCATATCACAGA
*
770954 TCATATCACATA
1 TCATATCACAGA
*
770966 GCATATCACA
1 TCATATCACA
770976 TGAACATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (12 bp):
TCATATCACAGA
Found at i:770961 original size:24 final size:24
Alignment explanation
Indices: 770930--770976 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
770920 TATCATGTTC
*
770930 TCATATCACA-GGTCATATCACATA
1 TCATATCACATAG-CATATCACATA
770954 TCATATCACATAGCATATCACAT
1 TCATATCACATAGCATATCACAT
770977 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (24 bp):
TCATATCACATAGCATATCACATA
Found at i:770976 original size:12 final size:12
Alignment explanation
Indices: 770943--770976 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
770933 TATCACAGGT
*
770943 CATATCACATAT
1 CATATCACATAG
770955 CATATCACATAG
1 CATATCACATAG
770967 CATATCACAT
1 CATATCACAT
770977 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (12 bp):
CATATCACATAG
Found at i:771393 original size:64 final size:63
Alignment explanation
Indices: 771285--771509 Score: 231
Period size: 64 Copynumber: 3.5 Consensus size: 63
771275 TAATGAAGGT
* ** ** * * **
771285 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGTATTCGATGTATT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGT-TTCACTATTAATGGG
*
771349 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAATGGG
* * **
771413 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT-TTCACTATTAATGGG
**
771476 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
771510 ATTCATACAA
Statistics
Matches: 139, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
63 6 0.04
64 130 0.94
65 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAATGGG
Found at i:777683 original size:15 final size:15
Alignment explanation
Indices: 777659--777750 Score: 139
Period size: 15 Copynumber: 6.1 Consensus size: 15
777649 GTAGGACTCT
*
777659 TACATCCCGAATGAC
1 TACATCCCGAAGGAC
*
777674 TACCTCCCGAAGGAC
1 TACATCCCGAAGGAC
*
777689 TACGTCCCGAAGGAC
1 TACATCCCGAAGGAC
777704 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
777719 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
* *
777734 TACGTCCCGAAAGAC
1 TACATCCCGAAGGAC
777749 TA
1 TA
777751 TTATACCCTC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 71 1.00
ACGTcount: A:0.32, C:0.34, G:0.20, T:0.15
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:777714 original size:45 final size:45
Alignment explanation
Indices: 777659--777750 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
777649 GTAGGACTCT
* * *
777659 TACATCCCGAATGACTACCTCCCGAAGGACTACGTCCCGAAGGAC
1 TACATCCCGAAGGACTACATCCCGAAGGACTACGTCCCGAAAGAC
777704 TACATCCCGAAGGACTACATCCCGAAGGACTACGTCCCGAAAGAC
1 TACATCCCGAAGGACTACATCCCGAAGGACTACGTCCCGAAAGAC
777749 TA
1 TA
777751 TTATACCCTC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.34, G:0.20, T:0.15
Consensus pattern (45 bp):
TACATCCCGAAGGACTACATCCCGAAGGACTACGTCCCGAAAGAC
Found at i:777881 original size:29 final size:29
Alignment explanation
Indices: 777835--777912 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
777825 TTTCATATGT
777835 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
777863 TCATGTAGCTCGTGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
777892 TCATGTAGCTCATGTCATTTC
1 TCATGTAGCTCATGTCATTTC
777913 ATATCATATT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.15
29 40 0.85
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:777941 original size:12 final size:12
Alignment explanation
Indices: 777924--777967 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
777914 TATCATATTC
*
777924 TCATATCACAGG
1 TCATATCACAGA
*
777936 TCATATCACATA
1 TCATATCACAGA
*
777948 TCATATCACATA
1 TCATATCACAGA
*
777960 GCATATCA
1 TCATATCA
777968 TATGAACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.30
Consensus pattern (12 bp):
TCATATCACAGA
Found at i:778389 original size:18 final size:18
Alignment explanation
Indices: 778362--778400 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
778352 TGCACTCCTT
*
778362 ATGCATCGATGTGCA-TCG
1 ATGCACCGAT-TGCATTCG
778380 ATGCACCGATTGCATTCG
1 ATGCACCGATTGCATTCG
778398 ATG
1 ATG
778401 TTTCACTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (18 bp):
ATGCACCGATTGCATTCG
Done.