Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 132 of 279
Found at i:42406768 original size:5 final size:5
Alignment explanation
Indices: 42406758--42406800 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
42406748 ATAAATAAGA
42406758 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATA
42406801 ACTAAACTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:42410403 original size:43 final size:43
Alignment explanation
Indices: 42410345--42410539 Score: 284
Period size: 43 Copynumber: 4.5 Consensus size: 43
42410335 CATTATAACA
* *
42410345 TGCTAGGCTCAAAGGCCCGAATACACATCACCGGCACGAAACC
1 TGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAACC
* *
42410388 TGCTAGGCACGAAGGCCCGAATACACATCACCGGTACGAAGCC
1 TGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAACC
* * *
42410431 TGCTAGGCACGAAGGCTCGAATACACATCACCAGCACGAAGCC
1 TGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAACC
* * *
42410474 TGCTAGGCATGAAGGGCCGAATACACATCACCGGCAC-AAAGCA
1 TGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAA-CC
42410517 TGCTAGGCACGAAGGCCCGAATA
1 TGCTAGGCACGAAGGCCCGAATA
42410540 TAGTACCAGC
Statistics
Matches: 136, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
42 2 0.01
43 134 0.99
ACGTcount: A:0.32, C:0.31, G:0.25, T:0.12
Consensus pattern (43 bp):
TGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAACC
Found at i:42412544 original size:19 final size:20
Alignment explanation
Indices: 42412515--42412558 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
42412505 CTAGTAAATT
42412515 TAAAGATAAAACCAAAAGTG
1 TAAAGATAAAACCAAAAGTG
*
42412535 TAAA-ATAAAACCGAAAGTG
1 TAAAGATAAAACCAAAAGTG
42412554 TAAAG
1 TAAAG
42412559 GTTTAAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.59, C:0.09, G:0.16, T:0.16
Consensus pattern (20 bp):
TAAAGATAAAACCAAAAGTG
Found at i:42415712 original size:22 final size:23
Alignment explanation
Indices: 42415686--42415730 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
42415676 ACCTGATCAG
42415686 AATACGACACAT-AAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
42415708 AATACGACACATAAAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
42415731 TCAGTAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTGA
Found at i:42415965 original size:28 final size:29
Alignment explanation
Indices: 42415933--42416019 Score: 124
Period size: 28 Copynumber: 3.1 Consensus size: 29
42415923 AAAACACACC
*
42415933 AGTATAATCC-TCCAAAACACACCAGTAT
1 AGTATAATCCATCCAAAACACACCAGAAT
* *
42415961 AGTATAATCCTTCC-AGACACACCAGAAT
1 AGTATAATCCATCCAAAACACACCAGAAT
*
42415989 AATATAATCCATCCAAAACACACCAGAAT
1 AGTATAATCCATCCAAAACACACCAGAAT
42416018 AG
1 AG
42416020 CACAAAGTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
28 34 0.67
29 17 0.33
ACGTcount: A:0.45, C:0.28, G:0.08, T:0.20
Consensus pattern (29 bp):
AGTATAATCCATCCAAAACACACCAGAAT
Found at i:42416190 original size:16 final size:15
Alignment explanation
Indices: 42416169--42416212 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
42416159 CACTTTCCAG
42416169 TTTCAATCAATACACA
1 TTTCAATCAAT-CACA
*
42416185 TTTCAATTAATCACA
1 TTTCAATCAATCACA
42416200 TATTCATATCAAT
1 T-TTCA-ATCAAT
42416213 TTCATCACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 14 0.58
17 5 0.21
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (15 bp):
TTTCAATCAATCACA
Found at i:42424411 original size:20 final size:21
Alignment explanation
Indices: 42424374--42424422 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
42424364 AATTTTAATT
**
42424374 AAAATTATTATATTACAATAA
1 AAAATTATTATAAAACAATAA
42424395 AAAATTATT-TAAAACAATAA
1 AAAATTATTATAAAACAATAA
42424415 ATAAATTA
1 A-AAATTA
42424423 AAATTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATTATTATAAAACAATAA
Found at i:42424827 original size:26 final size:24
Alignment explanation
Indices: 42424766--42424831 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 24
42424756 CTAACTTAGG
42424766 TTTGAATGT-ATTTTGATTACGTT
1 TTTGAATGTAATTTTGATTACGTT
* *
42424789 TAT-AATGATTAATTTTTATTATCGTT
1 TTTGAATG--TAATTTTGATTA-CGTT
42424815 ATTTGAATGTAATTTTG
1 -TTTGAATGTAATTTTG
42424832 TAATTGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
22 4 0.12
23 2 0.06
24 1 0.03
25 9 0.27
26 11 0.33
27 2 0.06
28 4 0.12
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (24 bp):
TTTGAATGTAATTTTGATTACGTT
Found at i:42428533 original size:34 final size:34
Alignment explanation
Indices: 42428490--42428559 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
42428480 AAGGAAAAAA
42428490 ATAGAATAAAAATTAAAAACAACAATCATAGCTT
1 ATAGAATAAAAATTAAAAACAACAATCATAGCTT
42428524 ATAGAATAAAAATTAAAAACAACAATCATAGCTT
1 ATAGAATAAAAATTAAAAACAACAATCATAGCTT
42428558 AT
1 AT
42428560 CTTCAAGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.59, C:0.11, G:0.06, T:0.24
Consensus pattern (34 bp):
ATAGAATAAAAATTAAAAACAACAATCATAGCTT
Found at i:42432169 original size:19 final size:20
Alignment explanation
Indices: 42432115--42432171 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
42432105 TGTCATATTA
* *
42432115 TTTTTTATATATTTATATTG
1 TTTTTTATATAATTATATAG
*
42432135 TTTTATTTTAATAATTA-ATAG
1 TTTT-TTAT-ATAATTATATAG
42432156 TTTTTTATATAATTAT
1 TTTTTTATATAATTAT
42432172 CTTAACTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 7 0.23
20 7 0.23
21 10 0.33
22 6 0.20
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTTTTATATAATTATATAG
Found at i:42438613 original size:24 final size:24
Alignment explanation
Indices: 42438581--42438653 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 24
42438571 TAAGTGATCA
42438581 TTATTTCTCATGTTCTTTTACCTT
1 TTATTTCTCATGTTCTTTTACCTT
* *
42438605 TTATTTCTCATCCTTTGCCCTTTACCTT
1 TTATTTCTCAT--GTT--CTTTTACCTT
42438633 TTATTTCTCATGTTCTTTTAC
1 TTATTTCTCATGTTCTTTTAC
42438654 TCTCTTATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
24 17 0.41
26 4 0.10
28 20 0.49
ACGTcount: A:0.12, C:0.25, G:0.04, T:0.59
Consensus pattern (24 bp):
TTATTTCTCATGTTCTTTTACCTT
Found at i:42443223 original size:19 final size:19
Alignment explanation
Indices: 42443180--42443216 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
42443170 TCCAAACACT
42443180 AGAAAAGTAAATCATTTTC
1 AGAAAAGTAAATCATTTTC
42443199 AGAAAAGTAAATCATTTT
1 AGAAAAGTAAATCATTTT
42443217 TCAAAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (19 bp):
AGAAAAGTAAATCATTTTC
Found at i:42446828 original size:6 final size:6
Alignment explanation
Indices: 42446817--42446883 Score: 98
Period size: 6 Copynumber: 11.2 Consensus size: 6
42446807 AAATAGTTTA
*
42446817 CAATTC CAATTC CAATTC CAATCC CAATTC CAATTC CAATTC CAATTC
1 CAATTC CAATTC CAATTC CAATTC CAATTC CAATTC CAATTC CAATTC
* * *
42446865 CCATTC CCATTC CCATTC C
1 CAATTC CAATTC CAATTC C
42446884 CCTTCCTCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.31
Consensus pattern (6 bp):
CAATTC
Found at i:42447303 original size:12 final size:12
Alignment explanation
Indices: 42447286--42447312 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42447276 CCTACAAAAA
42447286 TATTTCCCCTTT
1 TATTTCCCCTTT
42447298 TATTTCCCCTTT
1 TATTTCCCCTTT
42447310 TAT
1 TAT
42447313 CTTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.11, C:0.30, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTTCCCCTTT
Found at i:42451217 original size:21 final size:21
Alignment explanation
Indices: 42451191--42451231 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42451181 ATCTGCTCAA
* *
42451191 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
42451212 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
42451232 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:42455997 original size:21 final size:21
Alignment explanation
Indices: 42455971--42456011 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42455961 ATCTGCTCAA
* *
42455971 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
42455992 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
42456012 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:42465656 original size:2 final size:2
Alignment explanation
Indices: 42465649--42465702 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
42465639 CAGCACTACT
42465649 TC TC TC TC 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
*
42465691 TT TC TC TC TC TC
1 TC TC TC TC TC TC
42465703 ATGCATGCTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:42467096 original size:10 final size:10
Alignment explanation
Indices: 42467083--42467144 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
42467073 AATATTAAAA
42467083 AATAATTTTT
1 AATAATTTTT
*
42467093 AAT-ATATTT
1 AATAATTTTT
42467102 AA-ATATTTTT
1 AATA-ATTTTT
42467112 -ATAATTTTT
1 AATAATTTTT
*
42467121 AAAATATTTTT
1 AATA-ATTTTT
*
42467132 AATGATTTTT
1 AATAATTTTT
42467142 AAT
1 AAT
42467145 TTTGAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
9 14 0.33
10 20 0.48
11 8 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
AATAATTTTT
Found at i:42467105 original size:20 final size:21
Alignment explanation
Indices: 42467082--42467143 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 21
42467072 AAATATTAAA
42467082 AAATAATTTTTAAT-ATATTT
1 AAATAATTTTTAATAATATTT
*
42467102 AAAT-ATTTTT-ATAATTTTT
1 AAATAATTTTTAATAATATTT
* *
42467121 AAA-ATATTTTTAATGATTTTT
1 AAATA-ATTTTTAATAATATTT
42467142 AA
1 AA
42467144 TTTTGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 2 0.06
19 14 0.39
20 10 0.28
21 10 0.28
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AAATAATTTTTAATAATATTT
Found at i:42467144 original size:28 final size:27
Alignment explanation
Indices: 42467085--42467181 Score: 97
Period size: 28 Copynumber: 3.4 Consensus size: 27
42467075 TATTAAAAAA
* *
42467085 TAATTTTTAATATA-TTTAAATATTTTT
1 TAATTTTTAAAATATTTTTAATA-TTTT
42467112 ATAATTTTTAAAATATTTTTAATGATTTT
1 -TAATTTTTAAAATATTTTTAAT-ATTTT
*
42467141 TAATTTTGAAAAATAATTTTTATATATTTT
1 TAATTTT-TAAAAT-ATTTTTA-ATATTTT
*
42467171 TAAATTTTAAA
1 TAATTTTTAAA
42467182 TTTTAAAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
28 20 0.34
29 18 0.31
30 19 0.32
31 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
TAATTTTTAAAATATTTTTAATATTTT
Found at i:42467184 original size:38 final size:40
Alignment explanation
Indices: 42467112--42467197 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 40
42467102 AAATATTTTT
* *
42467112 ATAATTTTTAAAATATTTTTAATGATTTTTAATTTTGAAAA
1 ATAATTTTTAAAATATTTTTAA-GATTTTAAATTTTAAAAA
*
42467153 ATAATTTTT-ATATATTTTTAA-ATTTTAAATTTTAAAAA
1 ATAATTTTTAAAATATTTTTAAGATTTTAAATTTTAAAAA
42467191 ATTAATT
1 A-TAATT
42467198 AAATGTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
38 16 0.39
39 5 0.12
40 11 0.27
41 9 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (40 bp):
ATAATTTTTAAAATATTTTTAAGATTTTAAATTTTAAAAA
Found at i:42468483 original size:21 final size:19
Alignment explanation
Indices: 42468458--42468511 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 19
42468448 TTTTTTAAAT
42468458 TATAAAAATAATTTAAAAAA
1 TATAAAAATAATTT-AAAAA
*
42468478 TAATAAAAAT-GTTTAAAAA
1 T-ATAAAAATAATTTAAAAA
42468497 TATAAAAATATATTT
1 TATAAAAATA-ATTT
42468512 TTAATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 8 0.28
19 6 0.21
20 7 0.24
21 8 0.28
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
TATAAAAATAATTTAAAAA
Found at i:42470750 original size:15 final size:16
Alignment explanation
Indices: 42470732--42470764 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42470722 TTTATTTTTA
*
42470732 TTTTATTTTTTAC-TT
1 TTTTACTTTTTACGTT
42470747 TTTTACTTTTTACGTT
1 TTTTACTTTTTACGTT
42470763 TT
1 TT
42470765 CTTGTGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTACTTTTTACGTT
Found at i:42472544 original size:10 final size:10
Alignment explanation
Indices: 42472529--42472574 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
42472519 TAATCTTAGG
42472529 ATTTAT-TTT
1 ATTTATCTTT
42472538 CATTTATCTTT
1 -ATTTATCTTT
*
42472549 AATTATCTTT
1 ATTTATCTTT
42472559 ATTTAT-TTGT
1 ATTTATCTT-T
42472569 ATTTAT
1 ATTTAT
42472575 GTTTTAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:42476500 original size:25 final size:25
Alignment explanation
Indices: 42476315--42476499 Score: 293
Period size: 25 Copynumber: 7.4 Consensus size: 25
42476305 GACCTCAGCA
* *
42476315 TGCTCTCTGATTATTAGCACGTCAG
1 TGCTCTCTGAATATTAGCACGCCAG
*
42476340 TGCTCTCTGAATATTAGCATGCCAG
1 TGCTCTCTGAATATTAGCACGCCAG
42476365 TGCTCTCTGAATATTAGCACGCCAG
1 TGCTCTCTGAATATTAGCACGCCAG
42476390 TGCTCTCTGAATATTAGCACGCCAG
1 TGCTCTCTGAATATTAGCACGCCAG
42476415 TGCTCTCTGAATATTAGCACGCCAG
1 TGCTCTCTGAATATTAGCACGCCAG
42476440 TGCTCTCT-AATTATTAGCACGCCAG
1 TGCTCTCTGAA-TATTAGCACGCCAG
* *
42476465 TGTTCTCTG-ATATTTAGCACGTCAG
1 TGCTCTCTGAATA-TTAGCACGCCAG
42476490 TGCTCTCTGA
1 TGCTCTCTGA
42476500 TTAGCACATT
Statistics
Matches: 149, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.03
25 145 0.97
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.32
Consensus pattern (25 bp):
TGCTCTCTGAATATTAGCACGCCAG
Found at i:42476543 original size:22 final size:21
Alignment explanation
Indices: 42476478--42476544 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 21
42476468 TCTCTGATAT
*
42476478 TTAGCACGTCAGTGCTCTCTG
1 TTAGCACTTCAGTGCTCTCTG
*
42476499 ATTAGCACATT-TGTGCTCTCTG
1 -TTAGCAC-TTCAGTGCTCTCTG
42476521 TGTAGCACTTCAGTGCTCTCTG
1 T-TAGCACTTCAGTGCTCTCTG
42476543 TT
1 TT
42476545 CATTAGTGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 4 0.10
22 34 0.87
23 1 0.03
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (21 bp):
TTAGCACTTCAGTGCTCTCTG
Found at i:42490240 original size:51 final size:51
Alignment explanation
Indices: 42490095--42490299 Score: 313
Period size: 51 Copynumber: 4.0 Consensus size: 51
42490085 NNNNNNNNNN
* * * *
42490095 AAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGAC
1 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGAT
* *
42490146 AAATGATAAGTGGTAGC-TTAGCTACTCTTATCTGATCAGTGACAAGTGAT
1 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGAT
*
42490196 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAGTGAT
1 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGAT
* * *
42490247 AAGTGATAAGTGATAGTTTTAGCTATACTTATCTGATCAGTGACAAGTGAT
1 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGAT
42490298 AA
1 AA
42490300 ATGTGATCAG
Statistics
Matches: 141, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
50 45 0.32
51 96 0.68
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (51 bp):
AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGAT
Found at i:42495622 original size:30 final size:30
Alignment explanation
Indices: 42495588--42495648 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
42495578 TCCTTAACTC
42495588 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
42495618 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
42495648 A
1 A
42495649 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:42497272 original size:10 final size:10
Alignment explanation
Indices: 42497259--42497300 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
42497249 TAATATTAGG
42497259 ATTTATTTTT
1 ATTTATTTTT
*
42497269 ATTTATCTTT
1 ATTTATTTTT
*
42497279 ATTTATTTGT
1 ATTTATTTTT
42497289 ATTTATCTTTT
1 ATTTAT-TTTT
42497300 A
1 A
42497301 GAATTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
10 23 0.85
11 4 0.15
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:42497284 original size:20 final size:20
Alignment explanation
Indices: 42497259--42497298 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
42497249 TAATATTAGG
*
42497259 ATTTATTTTTATTTATCTTT
1 ATTTATTTGTATTTATCTTT
42497279 ATTTATTTGTATTTATCTTT
1 ATTTATTTGTATTTATCTTT
42497299 TAGAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (20 bp):
ATTTATTTGTATTTATCTTT
Found at i:42502904 original size:28 final size:28
Alignment explanation
Indices: 42502851--42502934 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
42502841 CACTTTGTGC
42502851 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
42502880 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
42502908 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
42502935 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:42502946 original size:23 final size:24
Alignment explanation
Indices: 42502855--42502948 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 24
42502845 TTGTGCTATT
42502855 CTGGTGTGTTTTGGATGGATTATATTA
1 CTGGTGTGTTTTGGA-GGA-TATA-TA
*
42502882 TTCTGGTGTGTTTGGGAGGATTATATGATA
1 --CTGGTGTGTTTTGGAGG---ATAT-ATA
42502912 CTGGTGTGTTTTGGAGGAT-TATA
1 CTGGTGTGTTTTGGAGGATATATA
42502935 CTGGTGTGTTTTGG
1 CTGGTGTGTTTTGG
42502949 TTGGACATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
23 17 0.29
24 1 0.02
25 2 0.03
28 18 0.31
29 14 0.24
30 5 0.08
31 2 0.03
ACGTcount: A:0.16, C:0.04, G:0.34, T:0.46
Consensus pattern (24 bp):
CTGGTGTGTTTTGGAGGATATATA
Found at i:42503169 original size:23 final size:23
Alignment explanation
Indices: 42503139--42503225 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 23
42503129 GCTTTACTGA
*
42503139 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTTATGTGTCGTATT
* *
42503162 TCAGGCACCTTGTGTGTCGCA--
1 TCAGGCACCTTATGTGTCGTATT
* **
42503183 GCAGGCACCTCGTGTGTCG--TT
1 TCAGGCACCTTATGTGTCGTATT
42503204 TCAGGCA-CTTATGTGTCGTATT
1 TCAGGCACCTTATGTGTCGTATT
42503226 CTGATCAGGT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
20 9 0.17
21 23 0.44
22 2 0.04
23 18 0.35
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (23 bp):
TCAGGCACCTTATGTGTCGTATT
Found at i:42506625 original size:19 final size:19
Alignment explanation
Indices: 42506601--42506645 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
42506591 AAATGAATCG
42506601 GTAACTCCAGTAATGCTCC
1 GTAACTCCAGTAATGCTCC
*
42506620 GTAACTCCGGTAATGCTCC
1 GTAACTCCAGTAATGCTCC
42506639 GTAACTC
1 GTAACTC
42506646 TATTCTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
GTAACTCCAGTAATGCTCC
Found at i:42513818 original size:23 final size:23
Alignment explanation
Indices: 42513786--42513846 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
42513776 CCAAAAATAT
* * ** *
42513786 AAAATCATAAATTAACATATAAC
1 AAAATTATAATTTAACAGTTAAA
42513809 AAAATTATAATTTAACAGTTAAA
1 AAAATTATAATTTAACAGTTAAA
42513832 AAAATTATAATTTAA
1 AAAATTATAATTTAA
42513847 TTTTAAACCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAATTATAATTTAACAGTTAAA
Found at i:42516506 original size:2 final size:2
Alignment explanation
Indices: 42516499--42516534 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
42516489 CAGCACTACT
42516499 TC 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
42516535 ATGCATGCTA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:42517063 original size:17 final size:17
Alignment explanation
Indices: 42517041--42517074 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42517031 ATCCACTAAT
*
42517041 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
42517058 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
42517075 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:42521702 original size:17 final size:17
Alignment explanation
Indices: 42521680--42521713 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42521670 ATCCACTAAT
*
42521680 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
42521697 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
42521714 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:42531048 original size:237 final size:234
Alignment explanation
Indices: 42530756--42531955 Score: 954
Period size: 237 Copynumber: 4.9 Consensus size: 234
42530746 CATTCTTATC
* * * * *
42530756 ATATATTATTGTTTATTGTTATATTGGTTGAAATATGTTTTAAGTCCCTATACTTTTTGTACATT
1 ATATATTATTATATATTATTATATTGGTTGAAATATGCTTTAAGTCCCTATACTTTTCGTACATT
* * * *
42530821 TGATAGTTAGCCATCCTATTATATTACATAATGTTATATCATATCATATAATATATAATACATTA
66 TGAAAGTTAGCC-TCCTACTATATTACATAATGCTATATCATATCATATAATATATAATATA-TA
* * *
42530886 ATAGTTTATACATATGCATCAATGATTAAACATTATAATATCATATAGTATTATACATTTTATTA
129 ATA-TTTAT--ATATGCATCAATGATTAAACATTATAATATCATGTAATACTATACATTTTATTA
* * *
42530951 TGATTTATAATATAATAATAGTTATACATAATAGTAGTACA-TT
191 TAATCTATAATATAATAATAGTTATATATAATAGTAGTACATTT
42530994 ATATATTA-T-TATATTATTATATTGGTTGAAATATGCTTTTAAGTCCCTATACTTTTCGTACAT
1 ATATATTATTATATATTATTATATTGGTTGAAATATGC-TTTAAGTCCCTATACTTTTCGTACAT
* * * * **
42531057 TTGAAAGTTAGCTCTCTTATTATATTACATAATGCTATATCATACCATGTGGTATATAATATATT
65 TTGAAAGTTAGC-CTCCTACTATATTACATAATGCTATATCATATCATATAATATATAATATA-T
*
42531122 AATAGTTTATATATGCATCAATGATTAAACA-TATAATATCATGTAATACTATATATTTTATTAT
128 AATA-TTTATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATACATTTTATTAT
*
42531186 AATTTATAATATAATAATAGTTATATATAATAGTAGTACATTAT
192 AATCTATAATATAATAATAGTTATATATAATAGTAGTACATT-T
** ** *
42531230 ATATAAATTATTATACATTATTGTTTATTATTATTCTAATTGAAATATGCTCCAAGTCCTTATAC
1 ATAT--ATTATTAT--A-TA----TTATTA-TA-T-TGGTTGAAATATGCTTTAAGTCCCTATAC
* * * * * *
42531295 TTTTCGTACATCTAAAAGTTAACCCTTCTACTATATTATATATTGCTATATCATATAGCATATAA
54 TTTTCGTACATTTGAAAGTT-AGCCTCCTACTATATTACATAATGCTATATCATAT--CATATAA
* * * * * *
42531360 CATAT--TA-ATAAT-TTTGTATATGCATCAATGATTGAACATTAAAATATTATGTAATTTTCTA
116 TATATAATATATAATATTTATATATGCATCAATGATTAAACATTATAATATCATGTAA--TACTA
42531421 T-C-TTTTATTATAATCTATAATATAATAATA-TTAATATATAATAGTAGTATACATTATTT
179 TACATTTTATTATAATCTATAATATAATAATAGTT-ATATATAATAGTAG--TAC---ATTT
* * * * ** * * *
42531480 ATTACATATTATTGTTTATTATTATAGTGGTTGAAATTTGCTTTAAGTTTCTATGC-TTTCATGC
1 A-T--ATATTATTATATATTATTATATTGGTTGAAATATGCTTTAAGTCCCTATACTTTTCGTAC
* * * *
42531544 ATTTGGAAGTTAGCCTTCCTACTATATTATATAATGCTATATCATATCACATATTAATATTTTAT
63 ATTTGAAAGTTAGCC-TCCTACTATATTACATAATGCTATATCATAT--CATA-TAATATATAAT
* * * * * **
42531609 ATAT-ATGTATATATATGTATAAATGATT-AACATTATAATATCATGTAATACCATATTTTTTAT
124 ATATAATATTTATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATACATTTTAT
* * *
42531672 TATAATCTATATTATATTAATAGTTATATATAATAGTAGTCCATTAT
189 TATAATCTATAATATAATAATAGTTATATATAATAGTAGTACATT-T
* * * * **
42531719 ATATTACTTATTGTTGTATATTATTGTTTATTGTTACAATAGTTAAAATATGTTTTAAGTCTTTA
1 ATA-TA-TTA---TTATATATTA-T-TATATTG--------GTTGAAATATGCTTTAAGTCCCTA
* * * ** * ** *
42531784 TATTTTTCATACATTTGAAAGTTAACCCTATTACTATATTATATAATATTATATCATATCATAAA
51 TACTTTTCGTACATTTGAAAGTT-AGCCTCCTACTATATTACATAATGCTATATCATATCATATA
* * * * * * * *
42531849 ATATATTAATGGTTTATATATATATATATGTATCGATAATTAAACATTACAATATCATGTAATAT
115 ATATA-TAAT-ATATA-ATATTTATATATGCATCAATGATTAAACATTATAATATCATGTAATAC
* *
42531914 TATATC-TTTTACTATAATCTATATTATAATAATAGTTATATA
177 TATA-CATTTTATTATAATCTATAATATAATAATAGTTATATA
42531956 CATGTTAATA
Statistics
Matches: 785, Mismatches: 111, Indels: 116
0.78 0.11 0.11
Matches are distributed among these distances:
234 67 0.09
235 22 0.03
236 30 0.04
237 93 0.12
238 20 0.03
239 6 0.01
240 48 0.06
241 41 0.05
242 2 0.00
243 71 0.09
244 27 0.03
245 26 0.03
246 54 0.07
247 10 0.01
248 13 0.02
249 64 0.08
250 23 0.03
251 41 0.05
252 44 0.06
253 25 0.03
254 58 0.07
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (234 bp):
ATATATTATTATATATTATTATATTGGTTGAAATATGCTTTAAGTCCCTATACTTTTCGTACATT
TGAAAGTTAGCCTCCTACTATATTACATAATGCTATATCATATCATATAATATATAATATATAAT
ATTTATATATGCATCAATGATTAAACATTATAATATCATGTAATACTATACATTTTATTATAATC
TATAATATAATAATAGTTATATATAATAGTAGTACATTT
Found at i:42531215 original size:16 final size:17
Alignment explanation
Indices: 42531189--42531222 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
42531179 TTATTATAAT
42531189 TTATAATATAATAATAG
1 TTATAATATAATAATAG
*
42531206 TTAT-ATATAATAGTAG
1 TTATAATATAATAATAG
42531222 T
1 T
42531223 ACATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (17 bp):
TTATAATATAATAATAG
Found at i:42531636 original size:489 final size:480
Alignment explanation
Indices: 42530861--42531955 Score: 1190
Period size: 489 Copynumber: 2.2 Consensus size: 480
42530851 ATGTTATATC
* * * * *
42530861 ATATCATATAATATATAATACATTAATAGTTTATACATATGCATCAATGATTAAACATTATAATA
1 ATATCATAT-ACATATAATATATTAATAATTT-TATATATGCATCAATGATTAAACATTAAAATA
* * * * *
42530926 TCATATAGTATTATA-CATTTTATTATGATTTATAATATAATAATAGTTATACATAATAGTAGTA
64 TCATGTAATATTATATC-TTTTATTATAATCTATAATATAATAATAGTTATATATAATAGTAGTA
* *
42530990 CATTATATATTATTATATTATTATATTGGTTGAAATATGCTTTTAAGTCCCTATACTTTTCGTAC
128 CATTATATATTATTATATTATTATAGTGGTTGAAATATGCTTTTAAGTCCCTATACTTTTCATAC
* * *
42531055 ATTTGAAAGTTAGCTCTCTTATTATATTACATAATGCTATATCATACCATGTGGTATATAATATA
193 ATTTGAAAGTTAGCTCTCCTACTATATTACATAATGCTATATCATACCATAT-GTATATAATATA
* * *
42531120 TTAATAGTTTATATATGCATCAATGATTAAACA-TATAATATCATGTAATACTATATATTTTATT
257 TTAATAGTATATATATGCATAAATGATT-AACATTATAATATCATGTAATACCATATATTTTATT
*
42531184 ATAATTTATAATATAATAATAGTTATATATAATAGTAGTACATTATATA-TA-AATTATTATACA
321 ATAATCTATAATATAATAATAGTTATATATAATAGTAGTACATTATATATTACAATTATTATACA
*** * *
42531247 TTATTGTTTATTATTATTCTAATTGAAATATGCTCCAAGTCCTTATACTTTTCGTACATCTAAAA
386 TTATTGTTTATTATTACAATAATTAAAATATGCTCCAAGTCCTTATACTTTTCATACATCTAAAA
* *
42531312 GTTAACCCT-TCTACTATATTATATATTGCT
451 GTTAACCCTAT-TACTATATTATATAATACT
* * *
42531342 ATATCATATAGCATATAACATATTAATAATTTTGTATATGCATCAATGATTGAACATTAAAATAT
1 ATATCATATA-CATATAATATATTAATAATTTTATATATGCATCAATGATTAAACATTAAAATAT
* * *
42531407 TATGTAATTTTCTATCTTTTATTATAATCTATAATATAATAATA-TTAATATATAATAGTAGTAT
65 CATGTAATATTATATCTTTTATTATAATCTATAATATAATAATAGTT-ATATATAATAGTAG--T
* * ** *
42531471 ACATTATTTATTACATATTATTGTTTATTATTATAGTGGTTGAAATTTGC-TTTAAGTTTCTATG
127 AC---A-TTA-T--ATATTA-T-TATATTATTATAGTGGTTGAAATATGCTTTTAAGTCCCTATA
* * *
42531535 C-TTTCATGCATTTGGAAGTTAGC-CTTCCTACTATATTATATAATGCTATATCATATCACATAT
183 CTTTTCATACATTTGAAAGTTAGCTC-TCCTACTATATTACATAATGCTATATCATA-C-CATAT
* * *
42531598 -TA-ATATTTTA-TATATATGTATATATATGTATAAATGATTAACATTATAATATCATGTAATAC
245 GTATATAATATATTA-ATA-GTATATATATGCATAAATGATTAACATTATAATATCATGTAATAC
* * * *
42531660 CATATTTTTTATTATAATCTATATTATATTAATAGTTATATATAATAGTAGTCCATTATATATTA
308 CATATATTTTATTATAATCTATAATATAATAATAGTTATATATAATAGTAGTACATTATATATTA
* * * * * * * ** * *
42531725 CTTATTGTTGTATATTATTGTTTATTGTTACAATAGTTAAAATATGTTTTAAGTCTTTATATTTT
373 C-AATTATTATACATTATTGTTTATTATTACAATAATTAAAATATGCTCCAAGTCCTTATACTTT
* * *
42531790 TCATACATTTGAAAGTTAACCCTATTACTATATTATATAATATT
437 TCATACATCTAAAAGTTAACCCTATTACTATATTATATAATACT
* * * * *
42531834 ATATCATAT-CATAAAATATATTAATGGTTTATATATATATATATGTATCGATAATTAAACATTA
1 ATATCATATACATATAATATATTAA-----TA-AT-TTTATATATGCATCAATGATTAAACATTA
* * *
42531898 CAATATCATGTAATATTATATCTTTTACTATAATCTATATTATAATAATAGTTATATA
59 AAATATCATGTAATATTATATCTTTTATTATAATCTATAATATAATAATAGTTATATA
42531956 CATGTTAATA
Statistics
Matches: 507, Mismatches: 75, Indels: 48
0.80 0.12 0.08
Matches are distributed among these distances:
479 2 0.00
480 78 0.15
481 27 0.05
482 3 0.01
485 1 0.00
486 3 0.01
487 3 0.01
488 14 0.03
489 147 0.29
490 29 0.06
491 28 0.06
492 93 0.18
493 1 0.00
495 2 0.00
496 2 0.00
497 72 0.14
498 2 0.00
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (480 bp):
ATATCATATACATATAATATATTAATAATTTTATATATGCATCAATGATTAAACATTAAAATATC
ATGTAATATTATATCTTTTATTATAATCTATAATATAATAATAGTTATATATAATAGTAGTACAT
TATATATTATTATATTATTATAGTGGTTGAAATATGCTTTTAAGTCCCTATACTTTTCATACATT
TGAAAGTTAGCTCTCCTACTATATTACATAATGCTATATCATACCATATGTATATAATATATTAA
TAGTATATATATGCATAAATGATTAACATTATAATATCATGTAATACCATATATTTTATTATAAT
CTATAATATAATAATAGTTATATATAATAGTAGTACATTATATATTACAATTATTATACATTATT
GTTTATTATTACAATAATTAAAATATGCTCCAAGTCCTTATACTTTTCATACATCTAAAAGTTAA
CCCTATTACTATATTATATAATACT
Found at i:42533301 original size:66 final size:66
Alignment explanation
Indices: 42533195--42533326 Score: 246
Period size: 66 Copynumber: 2.0 Consensus size: 66
42533185 GAGTTAAATC
* *
42533195 TAGTTTTTCCGAGTCAAAACATGTAAAGGGATTTTATATTATGTATATAACTATATATACCTGGA
1 TAGTTTTTCCGAGTCAAAACATGTAAACGGATTATATATTATGTATATAACTATATATACCTGGA
42533260 T
66 T
42533261 TAGTTTTTCCGAGTCAAAACATGTAAACGGATTATATATTATGTATATAACTATATATACCTGGA
1 TAGTTTTTCCGAGTCAAAACATGTAAACGGATTATATATTATGTATATAACTATATATACCTGGA
42533326 T
66 T
42533327 ACGGAGATAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (66 bp):
TAGTTTTTCCGAGTCAAAACATGTAAACGGATTATATATTATGTATATAACTATATATACCTGGA
T
Found at i:42536704 original size:16 final size:18
Alignment explanation
Indices: 42536683--42536719 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
42536673 TTAATCAAAT
42536683 AAGTTTAG-AAAAAA-AA
1 AAGTTTAGCAAAAAAGAA
*
42536699 AAGTTTGGCAAAAAAGAA
1 AAGTTTAGCAAAAAAGAA
42536717 AAG
1 AAG
42536720 ATATACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.62, C:0.03, G:0.19, T:0.16
Consensus pattern (18 bp):
AAGTTTAGCAAAAAAGAA
Found at i:42543835 original size:20 final size:20
Alignment explanation
Indices: 42543810--42543848 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42543800 TGCTGGAACT
* *
42543810 TGCATTTTGGCTTTTTTTAG
1 TGCATTTTAGCTTGTTTTAG
42543830 TGCATTTTAGCTTGTTTTA
1 TGCATTTTAGCTTGTTTTA
42543849 TTTGTTTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.10, G:0.18, T:0.59
Consensus pattern (20 bp):
TGCATTTTAGCTTGTTTTAG
Found at i:42546188 original size:16 final size:16
Alignment explanation
Indices: 42546167--42546201 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
42546157 TATTAAATGA
42546167 TATAAAACATTTTTGG
1 TATAAAACATTTTTGG
42546183 TATAAAACATTTTTGG
1 TATAAAACATTTTTGG
42546199 TAT
1 TAT
42546202 GGTTAGAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (16 bp):
TATAAAACATTTTTGG
Found at i:42546257 original size:27 final size:27
Alignment explanation
Indices: 42546219--42546272 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
42546209 GACTATCAAA
42546219 CCAAAAGTTCATTATCTAACAGTTGTC
1 CCAAAAGTTCATTATCTAACAGTTGTC
42546246 CCAAAAGTTCATTATCTAACAGTTGTC
1 CCAAAAGTTCATTATCTAACAGTTGTC
42546273 AAAATTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (27 bp):
CCAAAAGTTCATTATCTAACAGTTGTC
Found at i:42546680 original size:10 final size:9
Alignment explanation
Indices: 42546628--42546949 Score: 133
Period size: 10 Copynumber: 34.7 Consensus size: 9
42546618 CCAACAAATG
42546628 AATTTTTAT
1 AATTTTTAT
*
42546637 ATATTTTTTT
1 A-ATTTTTAT
*
42546647 TATATTTTATT
1 AAT-TTTTA-T
**
42546658 AAAATTTAT
1 AATTTTTAT
42546667 -ATTTTTAAT
1 AATTTTT-AT
*
42546676 AATTTATTAG
1 AATTT-TTAT
*
42546686 AACTTATTAT
1 AA-TTTTTAT
*
42546696 GATTTTTTAT
1 -AATTTTTAT
*
42546706 AAGTTTTAT
1 AATTTTTAT
*
42546715 AATTATTGAT
1 AATT-TTTAT
42546725 AA-TTTTAT
1 AATTTTTAT
42546733 AA-TTTTAT
1 AATTTTTAT
42546741 AA--TTTAT
1 AATTTTTAT
*
42546748 -ATTTTATTT
1 AATTTT-TAT
42546757 GAATTTTTAT
1 -AATTTTTAT
42546767 -ATTTTTAT
1 AATTTTTAT
* *
42546775 GATATTTAT
1 AATTTTTAT
*
42546784 TATTTTTAT
1 AATTTTTAT
* *
42546793 AATATTTAC
1 AATTTTTAT
*
42546802 AAATTTTAT
1 AATTTTTAT
** *
42546811 AAGTTCATAGA
1 AA-TTTTTA-T
* *
42546822 AAGTTTTAA
1 AATTTTTAT
42546831 ATATTTTTA-
1 A-ATTTTTAT
42546840 ACATGTTTTAT
1 A-AT-TTTTAT
*
42546851 -TTTTTTAT
1 AATTTTTAT
* *
42546859 AATTAATTAG
1 AATT-TTTAT
42546869 AATTTTTAT
1 AATTTTTAT
*
42546878 AATATTTAT
1 AATTTTTAT
42546887 AAGTTTTTAT
1 AA-TTTTTAT
42546897 GAATTTTTAT
1 -AATTTTTAT
* *
42546907 TAGTTTTAT
1 AATTTTTAT
42546916 AATTTTTTAT
1 AA-TTTTTAT
*
42546926 AA-TATTAT
1 AATTTTTAT
*
42546934 AAGTTTATAT
1 AA-TTTTTAT
42546944 AATTTT
1 AATTTT
42546950 GTAATATTTT
Statistics
Matches: 232, Mismatches: 54, Indels: 54
0.68 0.16 0.16
Matches are distributed among these distances:
6 1 0.00
7 5 0.02
8 41 0.18
9 79 0.34
10 90 0.39
11 16 0.07
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.60
Consensus pattern (9 bp):
AATTTTTAT
Found at i:42546692 original size:26 final size:26
Alignment explanation
Indices: 42546642--42546692 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
42546632 TTTATATATT
* * *
42546642 TTTTTTATATTTTATTAAAATTTATA
1 TTTTTAATAATTTATTAAAACTTATA
*
42546668 TTTTTAATAATTTATTAGAACTTAT
1 TTTTTAATAATTTATTAAAACTTAT
42546693 TATGATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTTTAATAATTTATTAAAACTTATA
Found at i:42546748 original size:7 final size:8
Alignment explanation
Indices: 42546700--42546812 Score: 77
Period size: 9 Copynumber: 13.0 Consensus size: 8
42546690 TATTATGATT
42546700 TTTTATAA
1 TTTTATAA
42546708 GTTTTATAA
1 -TTTTATAA
42546717 TTATTGATAA
1 TT-TT-ATAA
42546727 TTTTATAA
1 TTTTATAA
42546735 TTTTATAA
1 TTTTATAA
42546743 -TTTAT-A
1 TTTTATAA
42546749 TTTTATTTGAA
1 TTTTA--T-AA
*
42546760 TTTTTATAT
1 -TTTTATAA
*
42546769 TTTTATGA
1 TTTTATAA
*
42546777 TATTTATTAT
1 T-TTTA-TAA
42546787 TTTTATAA
1 TTTTATAA
*
42546795 TATTTACAAA
1 T-TTTA-TAA
42546805 TTTTATAA
1 TTTTATAA
42546813 GTTCATAGAA
Statistics
Matches: 84, Mismatches: 8, Indels: 25
0.72 0.07 0.21
Matches are distributed among these distances:
6 1 0.01
7 9 0.11
8 26 0.31
9 30 0.36
10 12 0.14
11 1 0.01
12 5 0.06
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.61
Consensus pattern (8 bp):
TTTTATAA
Found at i:42546765 original size:19 final size:20
Alignment explanation
Indices: 42546743--42546793 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
42546733 AATTTTATAA
*
42546743 TTTATATTTTATTTGA-ATT
1 TTTATATTTTATATGATATT
42546762 TTTATATTTT-TATGATATT
1 TTTATATTTTATATGATATT
42546781 TATTAT-TTTTATA
1 T-TTATATTTTATA
42546794 ATATTTACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 4 0.14
19 18 0.64
20 6 0.21
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTATATTTTATATGATATT
Found at i:42546893 original size:18 final size:18
Alignment explanation
Indices: 42546853--42546958 Score: 67
Period size: 18 Copynumber: 5.8 Consensus size: 18
42546843 TGTTTTATTT
* *
42546853 TTTTATAATTAATTAGAA
1 TTTTATAATTATTTATAA
42546871 TTTTTATAA-TATTTATAA
1 -TTTTATAATTATTTATAA
*
42546889 GTTTTTATGAATT-TTTATTAG
1 --TTTTAT-AATTATTTA-TAA
*
42546910 TTTTATAATTTTTTATAA
1 TTTTATAATTATTTATAA
* *
42546928 TATTATAAGTT-TATATAA
1 TTTTATAA-TTATTTATAA
*
42546946 TTTTGTAA-TATTT
1 TTTTATAATTATTT
42546959 TATTTTTTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.01
17 2 0.03
18 32 0.45
19 27 0.38
20 6 0.08
21 3 0.04
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTTATAATTATTTATAA
Found at i:42546893 original size:19 final size:19
Alignment explanation
Indices: 42546852--42546918 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
42546842 ATGTTTTATT
* *
42546852 TTTTTATAATTAATTAGAA-
1 TTTTTATAA-TATTTATAAG
42546871 TTTTTATAATATTTATAAG
1 TTTTTATAATATTTATAAG
* *
42546890 TTTTTATGAATTTTTATTAG
1 TTTTTAT-AATATTTATAAG
42546910 -TTTTATAAT
1 TTTTTATAAT
42546919 TTTTTATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 10 0.24
19 22 0.52
20 10 0.24
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (19 bp):
TTTTTATAATATTTATAAG
Found at i:42546914 original size:29 final size:28
Alignment explanation
Indices: 42546845--42546949 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 28
42546835 TTTTAACATG
* *
42546845 TTTTATT-TTTTTATAATTAATTA-GAAT
1 TTTTATTAGTTTTATAATT-TTTATGAAT
*
42546872 TTTTA-TAATATTTATAAGTTTTTATGAAT
1 TTTTATTAGT-TTTATAA-TTTTTATGAAT
42546901 TTTTATTAGTTTTATAATTTTTTAT-AA-
1 TTTTATTAGTTTTATAA-TTTTTATGAAT
* *
42546928 TATTATAAGTTTATATAATTTT
1 TTTTATTAGTTT-TATAATTTT
42546950 GTAATATTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
26 1 0.02
27 20 0.30
28 17 0.26
29 25 0.38
30 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (28 bp):
TTTTATTAGTTTTATAATTTTTATGAAT
Found at i:42546922 original size:19 final size:19
Alignment explanation
Indices: 42546699--42546927 Score: 80
Period size: 18 Copynumber: 12.5 Consensus size: 19
42546689 TTATTATGAT
42546699 TTTTTATAAG-TTTTATAA
1 TTTTTATAAGTTTTTATAA
*
42546717 TTATTGATAA--TTTTATAA
1 TT-TTTATAAGTTTTTATAA
42546735 -TTTTATAA---TTTAT-A
1 TTTTTATAAGTTTTTATAA
*
42546749 TTTTATTTGAA-TTTTTAT-A
1 TTTT-TAT-AAGTTTTTATAA
* * *
42546768 TTTTTATGA-TATTTATTA
1 TTTTTATAAGTTTTTATAA
* *
42546786 TTTTTATAA-TATTTACAA
1 TTTTTATAAGTTTTTATAA
* ** *
42546804 ATTTTATAAGTTCATAGAAA
1 TTTTTATAAGTTTTTA-TAA
* *
42546824 GTTTTA-AATATTTTTA-ACA
1 TTTTTATAA-GTTTTTATA-A
*
42546843 TGTTTTAT--TTTTTTATAA
1 T-TTTTATAAGTTTTTATAA
* *
42546861 TTAATTAGAA-TTTTTATAA
1 TT-TTTATAAGTTTTTATAA
*
42546880 TATTTATAAGTTTTTATGAA
1 TTTTTATAAGTTTTTAT-AA
*
42546900 TTTTTATTAG-TTTTATAA
1 TTTTTATAAGTTTTTATAA
42546918 TTTTTTATAA
1 -TTTTTATAA
42546928 TATTATAAGT
Statistics
Matches: 163, Mismatches: 28, Indels: 39
0.71 0.12 0.17
Matches are distributed among these distances:
14 1 0.01
15 8 0.05
16 8 0.05
17 11 0.07
18 55 0.34
19 54 0.33
20 26 0.16
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTTATAAGTTTTTATAA
Found at i:42547397 original size:9 final size:9
Alignment explanation
Indices: 42547380--42547433 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
42547370 ATATATTACC
*
42547380 AATTCAGTT
1 AATTTAGTT
42547389 AATTTAGTT
1 AATTTAGTT
42547398 AATTTCAGTT
1 AATTT-AGTT
42547408 AA-TT--TT
1 AATTTAGTT
*
42547414 AATTTGGTT
1 AATTTAGTT
*
42547423 AATTCAGTT
1 AATTTAGTT
42547432 AA
1 AA
42547434 ATGAACATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 4 0.11
7 2 0.05
9 26 0.68
10 6 0.16
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (9 bp):
AATTTAGTT
Found at i:42547409 original size:10 final size:10
Alignment explanation
Indices: 42547382--42547412 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
42547372 ATATTACCAA
42547382 TTCAGTTAAT
1 TTCAGTTAAT
42547392 TT-AGTTAAT
1 TTCAGTTAAT
42547401 TTCAGTTAAT
1 TTCAGTTAAT
42547411 TT
1 TT
42547413 TAATTTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (10 bp):
TTCAGTTAAT
Found at i:42547417 original size:25 final size:24
Alignment explanation
Indices: 42547387--42547433 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
42547377 ACCAATTCAG
42547387 TTAATTTAGTTAATTTCAGTTAATT
1 TTAATTTAGTTAA-TTCAGTTAATT
*
42547412 TTAATTTGGTTAATTCAGTTAA
1 TTAATTTAGTTAATTCAGTTAA
42547434 ATGAACATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (24 bp):
TTAATTTAGTTAATTCAGTTAATT
Found at i:42551594 original size:2 final size:2
Alignment explanation
Indices: 42551587--42551613 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42551577 TTCTCTGCAA
42551587 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
42551614 TTTGAAGCGT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:42565092 original size:2 final size:2
Alignment explanation
Indices: 42565087--42565115 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42565077 TCTACATTGA
42565087 CT CT 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 CT CT C
42565116 GTTTTTGATG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:42568998 original size:28 final size:28
Alignment explanation
Indices: 42568958--42569013 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
42568948 TGTGGGGCAT
42568958 AGCTTGTTATGAATGAGGAGACGAAAAA
1 AGCTTGTTATGAATGAGGAGACGAAAAA
42568986 AGCTTGTTATGAATGAGGAGACGAAAAA
1 AGCTTGTTATGAATGAGGAGACGAAAAA
42569014 GTAGTTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.29, T:0.21
Consensus pattern (28 bp):
AGCTTGTTATGAATGAGGAGACGAAAAA
Found at i:42597114 original size:44 final size:44
Alignment explanation
Indices: 42597062--42597156 Score: 147
Period size: 44 Copynumber: 2.2 Consensus size: 44
42597052 ATTCATAGAT
*
42597062 AAAA-TAATATTAAAATAACCTACACTAATTAAAATTTAAGTAA
1 AAAATTAATATTAAAATAACCTACACTAATTAAAATTTAAATAA
* **
42597105 AAATTTAATATTAAAATAATTTACACTAATTAAAATTTAAATAA
1 AAAATTAATATTAAAATAACCTACACTAATTAAAATTTAAATAA
42597149 AAAATTAA
1 AAAATTAA
42597157 AAATATAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 3 0.07
44 43 0.93
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.34
Consensus pattern (44 bp):
AAAATTAATATTAAAATAACCTACACTAATTAAAATTTAAATAA
Found at i:42614774 original size:48 final size:48
Alignment explanation
Indices: 42614718--42614811 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
42614708 AGGGAATTCT
* * *
42614718 GTTGAATCCTTTATTGTTGCG-AATT-GAGCTAACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTG-GAAATTAG-GCTAACTTAGGCATTTTTACG
*
42614766 GTTGAATCCATTATTGGTGGAAATTAGGCTGACTTAGGCATTTTTA
1 GTTGAATCCATTATTGGTGGAAATTAGGCTAACTTAGGCATTTTTA
42614812 AGCCAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 1 0.03
48 38 0.95
49 1 0.03
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGGAAATTAGGCTAACTTAGGCATTTTTACG
Found at i:42617290 original size:48 final size:48
Alignment explanation
Indices: 42617234--42617327 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
42617224 AGGGAATTCT
* * *
42617234 GTTGAATCCTTTATTGTTGCG-AATT-GAGCTAACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTG-GAAATTAG-GCTAACTTAGGCATTTTTACG
*
42617282 GTTGAATCCATTATTGGTGGAAATTAGGCTGACTTAGGCATTTTTA
1 GTTGAATCCATTATTGGTGGAAATTAGGCTAACTTAGGCATTTTTA
42617328 AGCCAAAGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 1 0.03
48 38 0.95
49 1 0.03
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGGAAATTAGGCTAACTTAGGCATTTTTACG
Found at i:42618138 original size:4 final size:4
Alignment explanation
Indices: 42618129--42618154 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
42618119 CAAGAAGGAC
42618129 GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GT
42618155 CATTCAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:42620180 original size:5 final size:5
Alignment explanation
Indices: 42620170--42620209 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
42620160 TCATAGTGAA
*
42620170 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAA ATAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAA
42620210 AACACAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:42623161 original size:20 final size:20
Alignment explanation
Indices: 42623098--42623183 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
42623088 ATATAAAAAT
* *
42623098 ATATATTATATATTATATTA
1 ATATATAATATATAATATTA
*
42623118 AT-T-TAATATTTAAGTATTA
1 ATATATAATATATAA-TATTA
*
42623137 ATATATAATATATCATATTA
1 ATATATAATATATAATATTA
* *
42623157 TTATATTATATATAATA-TA
1 ATATATAATATATAATATTA
42623176 ATATATAA
1 ATATATAA
42623184 AACATAAGTA
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
18 7 0.13
19 16 0.30
20 22 0.42
21 8 0.15
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (20 bp):
ATATATAATATATAATATTA
Found at i:42623183 original size:7 final size:7
Alignment explanation
Indices: 42623095--42623183 Score: 64
Period size: 7 Copynumber: 13.3 Consensus size: 7
42623085 TTAATATAAA
42623095 AATATAT
1 AATATAT
*
42623102 ATTATAT
1 AATATAT
*
42623109 ATTATATT
1 AATATA-T
42623117 AAT-T-T
1 AATATAT
*
42623122 AATATTT
1 AATATAT
42623129 AAGTAT-T
1 AA-TATAT
42623136 AATATAT
1 AATATAT
42623143 AATATAT
1 AATATAT
*
42623150 CATAT-T
1 AATATAT
*
42623156 ATTATAT
1 AATATAT
*
42623163 TATATAT
1 AATATAT
42623170 -A-ATAT
1 AATATAT
42623175 AATATAT
1 AATATAT
42623182 AA
1 AA
42623184 AACATAAGTA
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
5 8 0.12
6 10 0.15
7 43 0.64
8 6 0.09
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (7 bp):
AATATAT
Found at i:42624408 original size:22 final size:22
Alignment explanation
Indices: 42624379--42624435 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
42624369 TAGCACGTTA
42624379 AGTGCTCTCTGTTTAGCAC-AT
1 AGTGCTCTCTGTTTAGCACTAT
* *
42624400 ATGTGCTCTCTGTATAGCACTTT
1 A-GTGCTCTCTGTTTAGCACTAT
42624423 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
42624436 CATTTGTGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 28 0.90
23 2 0.06
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (22 bp):
AGTGCTCTCTGTTTAGCACTAT
Found at i:42641380 original size:29 final size:30
Alignment explanation
Indices: 42641323--42641390 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
42641313 CACGCTTAAA
* * *
42641323 ATATTTGCACTATTAGTCCTCCAACTTTTC
1 ATATTTACACTATTAATCCTCCAAATTTTC
* *
42641353 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTCCAAATTTTC
42641382 AGTATTTAC
1 A-TATTTAC
42641391 TCTTGGGCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.46
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTCCAAATTTTC
Found at i:42643179 original size:7 final size:7
Alignment explanation
Indices: 42643129--42643221 Score: 65
Period size: 7 Copynumber: 14.1 Consensus size: 7
42643119 ATATAAAAAT
*
42643129 ATATATG
1 ATATATA
*
42643136 ATATATT
1 ATATATA
42643143 ATAT-TA
1 ATATATA
42643149 AT-T-TA
1 ATATATA
*
42643154 ATATTTA
1 ATATATA
42643161 AGTAT-TA
1 A-TATATA
42643168 ATATATA
1 ATATATA
*
42643175 ATATATC
1 ATATATA
42643182 ATAT-T-
1 ATATATA
42643187 AT-TATA
1 ATATATA
*
42643193 TTATATA
1 ATATATA
* *
42643200 TTATATT
1 ATATATA
42643207 ATATATA
1 ATATATA
42643214 ATATATA
1 ATATATA
42643221 A
1 A
42643222 AACATAAGTA
Statistics
Matches: 72, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
4 1 0.01
5 8 0.11
6 9 0.12
7 51 0.71
8 3 0.04
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (7 bp):
ATATATA
Found at i:42643179 original size:39 final size:38
Alignment explanation
Indices: 42643128--42643219 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 38
42643118 AATATAAAAA
* *
42643128 TATATATGATATATTATATTAATT-TA-ATAT-TTAAGTAT
1 TATATATAATATATCATATT-ATTATATATATATT-A-TAT
42643166 TAATATATAATATATCATATTATTATATTATATATTATAT
1 T-ATATATAATATATCATATTATTATA-TATATATTATAT
42643206 TATATATAATATAT
1 TATATATAATATAT
42643220 AAAACATAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
38 4 0.09
39 32 0.68
40 4 0.09
41 5 0.11
42 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (38 bp):
TATATATAATATATCATATTATTATATATATATTATAT
Found at i:42644439 original size:22 final size:22
Alignment explanation
Indices: 42644411--42644466 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
42644401 AGCACGTTAA
42644411 GTGCTCTCTGTTTAGCACATAT-
1 GTGCTCTCTGTTTAGCAC-TATC
* *
42644433 GTGCTCTCTGTATAGCACTTTC
1 GTGCTCTCTGTTTAGCACTATC
42644455 GTGCTCTCTGTT
1 GTGCTCTCTGTT
42644467 CATTTGTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.43
Consensus pattern (22 bp):
GTGCTCTCTGTTTAGCACTATC
Found at i:42650300 original size:22 final size:22
Alignment explanation
Indices: 42650272--42650313 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
42650262 ATAGCTAATG
42650272 GAATTTATTCTAAAATTAAAAA
1 GAATTTATTCTAAAATTAAAAA
*
42650294 GAATTTATTTTAAAATTAAA
1 GAATTTATTCTAAAATTAAA
42650314 GCATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
GAATTTATTCTAAAATTAAAAA
Found at i:42654406 original size:56 final size:56
Alignment explanation
Indices: 42654320--42654448 Score: 195
Period size: 56 Copynumber: 2.3 Consensus size: 56
42654310 CGGCTGTGTC
* * *
42654320 AGTCAGTATGCTCACACAGCCTAGCACACGGGCGTGTGGCTTGGCCGTGTGACCTA
1 AGTCAGTATACTCACACAGCCTAGCACACGGGCGTATGGCTTGGCCGTGTGACCCA
* * *
42654376 AGTCAGTATACTCATACAGTCTAGCACACGGGCGTATGGTTTGGCCGTGTGACCCA
1 AGTCAGTATACTCACACAGCCTAGCACACGGGCGTATGGCTTGGCCGTGTGACCCA
*
42654432 AGTTAGTATACTCACAC
1 AGTCAGTATACTCACAC
42654449 GGGCATGGAC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 65 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.24
Consensus pattern (56 bp):
AGTCAGTATACTCACACAGCCTAGCACACGGGCGTATGGCTTGGCCGTGTGACCCA
Found at i:42655769 original size:19 final size:19
Alignment explanation
Indices: 42655742--42655802 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
42655732 CTTGTTAATG
*
42655742 GTGTTTGATTAGTGGAATT
1 GTGTCTGATTAGTGGAATT
* *
42655761 GTGTCTGATTAATGGAACT
1 GTGTCTGATTAGTGGAATT
* * *
42655780 GCGTGTGATTAGTAGAATT
1 GTGTCTGATTAGTGGAATT
42655799 GTGT
1 GTGT
42655803 ATGCATGAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.23, C:0.05, G:0.31, T:0.41
Consensus pattern (19 bp):
GTGTCTGATTAGTGGAATT
Found at i:42660043 original size:2 final size:2
Alignment explanation
Indices: 42660036--42660060 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42660026 AACGAAATTA
42660036 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
42660061 AATGCAATTA
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:42662358 original size:19 final size:18
Alignment explanation
Indices: 42662331--42662370 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
42662321 TCTCATTTTA
*
42662331 TCATTTCATATTTCATTTC
1 TCATCTCATA-TTCATTTC
42662350 TCATCTCATATTCATTTC
1 TCATCTCATATTCATTTC
42662368 TCA
1 TCA
42662371 ACTTTGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.53
Consensus pattern (18 bp):
TCATCTCATATTCATTTC
Found at i:42669451 original size:29 final size:30
Alignment explanation
Indices: 42669389--42669451 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
42669379 AATTATATTT
* * *
42669389 TTATAATTTTTAAATGATTAAATCAAAATC
1 TTATAATTTTTAAAGGATAAAATCAAAATA
* *
42669419 TTATCATTTTTAAAGGATAAAAT-ATAATA
1 TTATAATTTTTAAAGGATAAAATCAAAATA
42669448 TTAT
1 TTAT
42669452 TATTAATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (30 bp):
TTATAATTTTTAAAGGATAAAATCAAAATA
Found at i:42671452 original size:30 final size:28
Alignment explanation
Indices: 42671384--42671439 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
42671374 AACAATAATG
* *
42671384 TAAGTGACTAAAATGTAAAATTTTAAACA
1 TAAGTGACTAAAATCT-AAATTTAAAACA
42671413 TAAGTGACTAAAATCT-AATTTAAAACA
1 TAAGTGACTAAAATCTAAATTTAAAACA
42671440 AATAAAGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.40
29 15 0.60
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (28 bp):
TAAGTGACTAAAATCTAAATTTAAAACA
Found at i:42672852 original size:3 final size:3
Alignment explanation
Indices: 42672844--42672880 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
42672834 GAGATCATCT
42672844 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42672881 TTAAAAGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42686520 original size:46 final size:46
Alignment explanation
Indices: 42686340--42686522 Score: 231
Period size: 46 Copynumber: 4.0 Consensus size: 46
42686330 TTATCTTTGA
* * * * **
42686340 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
* *
42686387 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * * **
42686433 CACGTTGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
*
42686479 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
42686523 ATCAGAGAGC
Statistics
Matches: 117, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
46 85 0.73
47 32 0.27
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:42686627 original size:54 final size:54
Alignment explanation
Indices: 42686561--42686805 Score: 490
Period size: 54 Copynumber: 4.5 Consensus size: 54
42686551 TCCTTACAGT
42686561 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
42686615 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
42686669 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
42686723 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
42686777 GGGATTACCAGTCCAGGCTAAATCCCCTG
1 GGGATTACCAGTCCAGGCTAAATCCCCTG
42686806 CAACGACAAT
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 191 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (54 bp):
GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
Found at i:42690987 original size:21 final size:21
Alignment explanation
Indices: 42690963--42691034 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
42690953 CCATGGTATC
42690963 TTTCAACCATGGTCTTGTTCA
1 TTTCAACCATGGTCTTGTTCA
* * * *
42690984 TTTCATATCACGTTGCCATGGTATC-
1 TTTCA-A-C-CATGGTC-TTGT-TCA
42691009 TTTCAACCATGGTCTTGTTCA
1 TTTCAACCATGGTCTTGTTCA
42691030 TTTCA
1 TTTCA
42691035 TATCACGTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
20 2 0.05
21 13 0.35
22 5 0.14
23 2 0.05
24 5 0.14
25 8 0.22
26 2 0.05
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (21 bp):
TTTCAACCATGGTCTTGTTCA
Found at i:42691013 original size:46 final size:46
Alignment explanation
Indices: 42690904--42691317 Score: 578
Period size: 46 Copynumber: 9.0 Consensus size: 46
42690894 TTTGACATGA
* * * * * ** * *
42690904 TGCCATAGTGTCTCTCAACTATGGTCTTACTCATTTTTTTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
42690951 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*** *
42690997 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
42691043 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
42691089 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
42691135 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
42691181 TGCCATGGTATCTTTCAACCACGGTCTTACACATTTC-TAATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT-ATCAGGT
*
42691227 TGCCATGGTATCTTTCAATCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
42691273 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGG
42691318 GAGCACACTC
Statistics
Matches: 340, Mismatches: 25, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.00
46 311 0.91
47 28 0.08
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:42720691 original size:23 final size:21
Alignment explanation
Indices: 42720643--42720709 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
42720633 TTAGTATTTA
* *
42720643 TTAATTTTTTTATTTTAAAAT
1 TTAAATTTTTTAGTTTAAAAT
42720664 TTAAATTTTTTAGTTTAAAAT
1 TTAAATTTTTTAGTTTAAAAT
** *
42720685 TACTAAATTTTAAAGGTTAAAAT
1 T--TAAATTTTTTAGTTTAAAAT
42720708 TT
1 TT
42720710 TTATTATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 21 0.54
23 18 0.46
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (21 bp):
TTAAATTTTTTAGTTTAAAAT
Found at i:42734939 original size:16 final size:16
Alignment explanation
Indices: 42734910--42734979 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
42734900 TTTGGTTCGC
*
42734910 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
* *
42734926 CGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
* *
42734942 TGTAATTGATTAAAGG
1 TGTAATGGATTAGAGG
42734958 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
42734974 TGTAAT
1 TGTAAT
42734980 AGCAAATCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.33, C:0.01, G:0.33, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:42735024 original size:45 final size:44
Alignment explanation
Indices: 42734958--42735048 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
42734948 TGATTAAAGG
* * *
42734958 TGTAATGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAAAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
42735003 TGTAATGGAATAAAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAAAGGCGTAATAGAAATCAACTGTTTGGTTGAA
42735047 TG
1 TG
42735049 GAATAGAGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAAAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:42735228 original size:16 final size:17
Alignment explanation
Indices: 42735191--42735228 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
42735181 ATTTAATCAT
42735191 ATTTAAACATAATTATA
1 ATTTAAACATAATTATA
*
42735208 A-TTAAATAT-ATTATA
1 ATTTAAACATAATTATA
42735223 ATTTAA
1 ATTTAA
42735229 TAAAATTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 11 0.58
17 1 0.05
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTTAAACATAATTATA
Found at i:42735264 original size:22 final size:21
Alignment explanation
Indices: 42735174--42735460 Score: 92
Period size: 22 Copynumber: 14.0 Consensus size: 21
42735164 ATTATCAATA
* *
42735174 ATAA-ATAATTTAATCATATT
1 ATAATATAATTTAATAAAATT
* *
42735194 -TAAACATAATTATAATTAAA-T
1 AT-AATATAATT-TAATAAAATT
*
42735215 ATATTATAATTTAATAAAATT
1 ATAATATAATTTAATAAAATT
* * *
42735236 CTTATATGAATTTACTAAAATT
1 ATAATAT-AATTTAATAAAATT
**
42735258 ATAATAT-A--TAATAGTA-T
1 ATAATATAATTTAATAAAATT
*
42735275 AAAATATAATTTAAAATAATAATT
1 ATAATATAATTT--AATAA-AATT
42735299 ATTAAATATAATTTAATAAAA--
1 A-T-AATATAATTTAATAAAATT
42735320 A-AATATAATTTAATAAAATT
1 ATAATATAATTTAATAAAATT
* * *
42735340 CTTA-AT-A-TTAA-AATATT
1 ATAATATAATTTAATAAAATT
* * * *
42735357 CTTATATGAATTTACTAAAATC
1 ATAATAT-AATTTAATAAAATT
*
42735379 ATAATAT-ATAATACTATAAAA-T
1 ATAATATAAT-TTA--ATAAAATT
* ** **
42735401 ATAATCTAAAATAATTATTATT
1 ATAATATAATTTAA-TAAAATT
*
42735423 A-AATATAATTTAATATAA--
1 ATAATATAATTTAATAAAATT
42735441 AT-ATATAATTTAATAAAATT
1 ATAATATAATTTAATAAAATT
42735461 CTTAGTATTA
Statistics
Matches: 197, Mismatches: 38, Indels: 64
0.66 0.13 0.21
Matches are distributed among these distances:
17 16 0.08
18 45 0.23
19 2 0.01
20 21 0.11
21 38 0.19
22 49 0.25
23 9 0.05
24 7 0.04
26 10 0.05
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (21 bp):
ATAATATAATTTAATAAAATT
Found at i:42735298 original size:13 final size:12
Alignment explanation
Indices: 42735274--42735314 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
42735264 TATAATAGTA
42735274 TAAAATATAATT
1 TAAAATATAATT
42735286 TAAAATAATAATT
1 TAAAAT-ATAATT
*
42735299 ATTAAATATAATT
1 -TAAAATATAATT
42735312 TAA
1 TAA
42735315 TAAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:42735323 original size:18 final size:18
Alignment explanation
Indices: 42735302--42735337 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
42735292 AATAATTATT
42735302 AAATATAATTTAATAAAA
1 AAATATAATTTAATAAAA
42735320 AAATATAATTTAATAAAA
1 AAATATAATTTAATAAAA
42735338 TTCTTAATAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATAATTTAATAAAA
Found at i:42735448 original size:18 final size:17
Alignment explanation
Indices: 42735425--42735459 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
42735415 TTATTATTAA
42735425 ATATAATTTAATATAAAT
1 ATATAATTTAATA-AAAT
42735443 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42735460 TCTTAGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42735518 original size:61 final size:60
Alignment explanation
Indices: 42735229--42735520 Score: 192
Period size: 59 Copynumber: 4.8 Consensus size: 60
42735219 TATAATTTAA
* * *
42735229 TAAA-ATTCTTATATGAATTTACTAAAATTATAATATATAATAGTATAAAA-T-ATAAT-T
1 TAAATATTCTTATA-GAATTTACTAAAATCATAATATATAATACTATAAAATTCTTAATAT
** * * ** * * * *
42735286 TAAAATAATAATTATTA-AATATAATTTAATAAAAAAATATAAT-TTAATAAAATTCTTAATAT
1 T-AAAT-ATTCTTA-TAGAATTTACTAAAATCATAATATATAATACT-ATAAAATTCTTAATAT
* *
42735348 TAAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-T-ATAATCT
1 T-AAATATTCTTATA-GAATTTACTAAAATCATAATATATAATACTATAAAATTCTTAATAT
* * * * ** * *
42735408 AAAATAATTATTATTA-AATATAATTTAAT-ATAAATATATAAT-TTAATAAAATTCTTAGTAT
1 TAAAT-ATTCTTA-TAGAATTTACTAAAATCAT-AATATATAATACT-ATAAAATTCTTAATAT
42735469 TAAATATTCTTATACGAATTTACTAAAATCATAATATATAATACTATAAAAT
1 TAAATATTCTTATA-GAATTTACTAAAATCATAATATATAATACTATAAAAT
42735521 ATAATCTAAA
Statistics
Matches: 174, Mismatches: 40, Indels: 38
0.69 0.16 0.15
Matches are distributed among these distances:
57 1 0.01
58 7 0.04
59 56 0.32
60 26 0.15
61 48 0.28
62 35 0.20
63 1 0.01
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (60 bp):
TAAATATTCTTATAGAATTTACTAAAATCATAATATATAATACTATAAAATTCTTAATAT
Found at i:42735557 original size:121 final size:120
Alignment explanation
Indices: 42735229--42735536 Score: 528
Period size: 121 Copynumber: 2.6 Consensus size: 120
42735219 TATAATTTAA
* * *
42735229 TAAA-ATTCTTATATGAATTTACTAAAATTATAATATATAATAGTATAAAATATAATTTAAAATA
1 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAAATA
*
42735293 ATAATTATTAAATATAATTTAATAAAAAAATATAATTTAATAAAATTCTTAATAT
66 ATTATTATTAAATATAATTTAATAAAAAAATATAATTTAATAAAATTCTTAATAT
42735348 TAAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAAAT
1 T-AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAAAT
* * *
42735413 AATTATTATTAAATATAATTTAATATAAATATATAATTTAATAAAATTCTTAGTAT
65 AATTATTATTAAATATAATTTAATAAAAAAATATAATTTAATAAAATTCTTAATAT
*
42735469 TAAATATTCTTATACGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAAATA
1 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAAATA
42735534 ATT
66 ATT
42735537 GATTTTGTGG
Statistics
Matches: 179, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
119 1 0.01
120 69 0.39
121 109 0.61
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (120 bp):
TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAAATA
ATTATTATTAAATATAATTTAATAAAAAAATATAATTTAATAAAATTCTTAATAT
Found at i:42737037 original size:13 final size:13
Alignment explanation
Indices: 42737021--42737050 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42737011 TAGACCAAGC
42737021 TTTTCAAAAGCAT
1 TTTTCAAAAGCAT
*
42737034 TTTTCATAAGCAT
1 TTTTCAAAAGCAT
42737047 TTTT
1 TTTT
42737051 TTGCAGCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (13 bp):
TTTTCAAAAGCAT
Found at i:42739269 original size:14 final size:14
Alignment explanation
Indices: 42739250--42739276 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42739240 GTATGGTCAG
42739250 ATATGTCGTTTCAC
1 ATATGTCGTTTCAC
42739264 ATATGTCGTTTCA
1 ATATGTCGTTTCA
42739277 ATCAGCTGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (14 bp):
ATATGTCGTTTCAC
Found at i:42743742 original size:19 final size:19
Alignment explanation
Indices: 42743714--42743750 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42743704 CTTTGAGTAG
*
42743714 AAACCAAAAACTTTAACAC
1 AAACCAAAAACTTCAACAC
*
42743733 AAACCTAAAACTTCAACA
1 AAACCAAAAACTTCAACA
42743751 ATAACAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (19 bp):
AAACCAAAAACTTCAACAC
Found at i:42746504 original size:15 final size:15
Alignment explanation
Indices: 42746466--42746521 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
42746456 ACAAAACAAT
* *
42746466 AATATAAATGACTAA
1 AATATAAATAATTAA
* *
42746481 AATAT-AATATTTCA
1 AATATAAATAATTAA
42746495 AATATAAATAATTAA
1 AATATAAATAATTAA
42746510 AATATAATATAA
1 AATATAA-ATAA
42746522 GACAAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 10 0.30
15 19 0.58
16 4 0.12
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.34
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:42748837 original size:18 final size:18
Alignment explanation
Indices: 42748816--42748851 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42748806 TATTTAAATT
* *
42748816 AAAATTTCAAAATTCAAA
1 AAAATTTAAAAAATCAAA
42748834 AAAATTTAAAAAATCAAA
1 AAAATTTAAAAAATCAAA
42748852 TTAAAATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATTTAAAAAATCAAA
Found at i:42758032 original size:89 final size:89
Alignment explanation
Indices: 42757880--42758048 Score: 250
Period size: 89 Copynumber: 1.9 Consensus size: 89
42757870 CATGGCCATC
42757880 GTGCTTACTACCAAGGCTTGAAAATCTCCTCTAGACTTAATGAACTCATACTTCAAAGCTCAATC
1 GTGCTTACTACCAAGGCTTGAAAATCTCCTCTAGACTTAATGAACTCATACTTCAAAGCTCAATC
42757945 AAGTATATATTCTTGTAATTTATT
66 AAGTATATATTCTTGTAATTTATT
* * * * *
42757969 GTGCTTACTACCAAGGCTTGAAAATTTCCTCTAGA-TTCAATGGATTCATACTTTAAAGTTCAAT
1 GTGCTTACTACCAAGGCTTGAAAATCTCCTCTAGACTT-AATGAACTCATACTTCAAAGCTCAAT
* * *
42758033 CATGTTTTTATTCTTG
65 CAAGTATATATTCTTG
42758049 AATCCTTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 2 0.03
89 69 0.97
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (89 bp):
GTGCTTACTACCAAGGCTTGAAAATCTCCTCTAGACTTAATGAACTCATACTTCAAAGCTCAATC
AAGTATATATTCTTGTAATTTATT
Found at i:42760155 original size:52 final size:48
Alignment explanation
Indices: 42760093--42760285 Score: 196
Period size: 47 Copynumber: 4.0 Consensus size: 48
42760083 GAAATGTGAT
* *
42760093 TTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATC-GAG---TGTGATATGTGC
* *
42760145 TTCCGTATAAGACCATATCCGGGATATGGCATCG-GTGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * *
42760192 TACTGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTG-
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * * * *
42760238 ATCCGTGTAAGACCATGGCTGGGCTATGGCCTCG-GTATGTGATATGTG
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAG--TGTGATATGTG
42760286 ACTATGTGCA
Statistics
Matches: 122, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
46 26 0.21
47 54 0.44
48 11 0.09
50 1 0.01
51 1 0.01
52 29 0.24
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (48 bp):
TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
Found at i:42760273 original size:93 final size:97
Alignment explanation
Indices: 42760097--42760304 Score: 228
Period size: 93 Copynumber: 2.1 Consensus size: 97
42760087 TGTGATTTCC
* * *
42760097 GTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGCTTCCGTATAAGACCATA
1 GTATAAGACCATAGCTGGGATATGGCATC-GAG--ATGTGATATGTGCATCCGTATAAGACCATA
*
42760162 TCCGGGATATGGCATCGG-TGTGATATGTG-CTACT
63 GCCGGGATATGGCATCGGATGTGATATGTGACTA-T
* * * *
42760196 GTATAAGACCATATCTGGGATATGGCATC-AG-TGTGATATGTG-ATCCGTGTAAGACCATGGCT
1 GTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATATGTGCATCCGTATAAGACCATAGCC
* *
42760258 GGGCTATGGCCTCGGTATGTGATATGTGACTAT
66 GGGATATGGCATCGG-ATGTGATATGTGACTAT
**
42760291 GTGCAAGACCATAG
1 GTATAAGACCATAG
42760305 TTTTACTATG
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
93 28 0.30
94 11 0.12
95 23 0.25
96 3 0.03
97 2 0.02
99 26 0.28
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (97 bp):
GTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATATGTGCATCCGTATAAGACCATAGCC
GGGATATGGCATCGGATGTGATATGTGACTAT
Found at i:42762282 original size:13 final size:14
Alignment explanation
Indices: 42762261--42762293 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
42762251 TATAATATTT
42762261 AAAAA-TATTT-AA
1 AAAAATTATTTCAA
42762273 AAAAATTATTTCAA
1 AAAAATTATTTCAA
42762287 AAAAATT
1 AAAAATT
42762294 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 5 0.26
14 9 0.47
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAATTATTTCAA
Found at i:42762305 original size:11 final size:11
Alignment explanation
Indices: 42762254--42762305 Score: 54
Period size: 10 Copynumber: 4.6 Consensus size: 11
42762244 TAAATTATAT
42762254 AATATTT-AAA
1 AATATTTAAAA
42762264 AATATTTAAAAA
1 AATATTT-AAAA
42762276 AATTATTTCAAAA
1 AA-TATTT-AAAA
42762289 AA-ATTTAAAA
1 AATATTTAAAA
*
42762299 TATATTT
1 AATATTT
42762306 TCTAAATATC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 12 0.33
11 8 0.22
12 5 0.14
13 11 0.31
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATTTAAAA
Found at i:42768691 original size:36 final size:36
Alignment explanation
Indices: 42768648--42768723 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
42768638 GCTTATAGGA
42768648 ATAAATAATAATTTTAACCTTTATAATGTATTTTAT
1 ATAAATAATAATTTTAACCTTTATAATGTATTTTAT
42768684 ATAAATAATAATTTTAACCTTTATAATGTATTTTAT
1 ATAAATAATAATTTTAACCTTTATAATGTATTTTAT
42768720 ATAA
1 ATAA
42768724 TATTTATATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (36 bp):
ATAAATAATAATTTTAACCTTTATAATGTATTTTAT
Found at i:42784371 original size:23 final size:22
Alignment explanation
Indices: 42784345--42784393 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
42784335 CGACTAAATC
* *
42784345 AATACATAGCATAATAAGATTTA
1 AATACATA-CATAATAAAATTAA
* *
42784368 AATATATACATTATAAAATTAA
1 AATACATACATAATAAAATTAA
42784390 AATA
1 AATA
42784394 ATTTTACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (22 bp):
AATACATACATAATAAAATTAA
Found at i:42789649 original size:32 final size:32
Alignment explanation
Indices: 42789613--42789673 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
42789603 AGGCTGAACT
42789613 GAAGCTCATAAGAGCTAAAC-AGAAACCCAACG
1 GAAGCTCATAAGAGCTAAACGA-AAACCCAACG
** *
42789645 GAAGCTTGTAAGAGCTGAACGAAAACCCA
1 GAAGCTCATAAGAGCTAAACGAAAACCCA
42789674 TAAGGGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 24 0.96
33 1 0.04
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.11
Consensus pattern (32 bp):
GAAGCTCATAAGAGCTAAACGAAAACCCAACG
Found at i:42789677 original size:21 final size:21
Alignment explanation
Indices: 42789653--42789713 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
42789643 CGGAAGCTTG
42789653 TAAGAGCTGAACGAAAACCCA
1 TAAGAGCTGAACGAAAACCCA
* * * * *
42789674 TAAGGGTTAAAC-AGAAGCTCA
1 TAAGAGCTGAACGA-AAACCCA
*
42789695 AAAGAGCTGAACGAAAACC
1 TAAGAGCTGAACGAAAACC
42789714 TATTAGGGTT
Statistics
Matches: 27, Mismatches: 11, Indels: 4
0.64 0.26 0.10
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.11
Consensus pattern (21 bp):
TAAGAGCTGAACGAAAACCCA
Found at i:42792984 original size:2 final size:2
Alignment explanation
Indices: 42792977--42793002 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42792967 TTACTCCCAA
42792977 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
42793003 ACACACACAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:42796651 original size:34 final size:34
Alignment explanation
Indices: 42796613--42796677 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
42796603 TTCGGTCAAT
* *
42796613 TTTAGTCTATGTATTTTTTAAATTTTAAAATACA
1 TTTAGTCTATGTAATATTTAAATTTTAAAATACA
* **
42796647 TTTAGTCTTTGTAATATTTGTATTTTAAAAT
1 TTTAGTCTATGTAATATTTAAATTTTAAAAT
42796678 TTCATTCCTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (34 bp):
TTTAGTCTATGTAATATTTAAATTTTAAAATACA
Found at i:42803735 original size:21 final size:22
Alignment explanation
Indices: 42803718--42803759 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
42803708 ACCTAAATTT
42803718 TTAAA-TTTAAAAAATAAATAA
1 TTAAATTTTAAAAAATAAATAA
*
42803739 TTAAATTTTTAAAAATAAATA
1 TTAAATTTTAAAAAATAAATA
42803760 TATAGAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TTAAATTTTAAAAAATAAATAA
Found at i:42807239 original size:20 final size:21
Alignment explanation
Indices: 42807205--42807258 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
42807195 TGATGATATT
*
42807205 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
42807226 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
42807246 TTTTATTATTTTA
1 TTATATTATTTTA
42807259 TTATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:42807264 original size:11 final size:11
Alignment explanation
Indices: 42807248--42807275 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
42807238 ATGAGATATT
42807248 TTATTATTTTA
1 TTATTATTTTA
42807259 TTATTATTTTA
1 TTATTATTTTA
42807270 TTATTA
1 TTATTA
42807276 ATTATTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:42809021 original size:25 final size:25
Alignment explanation
Indices: 42808993--42809067 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
42808983 AGATGCTTGA
42808993 GATTGCATGTTATTGATGTGAATAT
1 GATTGCATGTTATTGATGTGAATAT
*
42809018 GATTTGAATG-TA--GATGCT---TGA-
1 GA-TTGCATGTTATTGATG-TGAAT-AT
42809039 GATTGCATGTTATTGATGTGAATAT
1 GATTGCATGTTATTGATGTGAATAT
42809064 GATT
1 GATT
42809068 TGAATGTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 20
0.63 0.03 0.33
Matches are distributed among these distances:
20 6 0.16
21 5 0.13
22 2 0.05
23 8 0.21
24 2 0.05
25 9 0.24
26 6 0.16
ACGTcount: A:0.28, C:0.04, G:0.25, T:0.43
Consensus pattern (25 bp):
GATTGCATGTTATTGATGTGAATAT
Found at i:42809035 original size:46 final size:46
Alignment explanation
Indices: 42808982--42809074 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
42808972 ATTATATTCT
42808982 TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
1 TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
42809028 TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
1 TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
42809074 T
1 T
42809075 TCATTGTATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.28, C:0.04, G:0.26, T:0.42
Consensus pattern (46 bp):
TAGATGCTTGAGATTGCATGTTATTGATGTGAATATGATTTGAATG
Found at i:42819172 original size:17 final size:17
Alignment explanation
Indices: 42819150--42819182 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42819140 TAATTAATTA
*
42819150 ATTATATTTTATTTATT
1 ATTATATTATATTTATT
42819167 ATTATATTATATTTAT
1 ATTATATTATATTTAT
42819183 CTTATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATATTATATTTATT
Found at i:42822086 original size:18 final size:19
Alignment explanation
Indices: 42822052--42822087 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42822042 TTAGTCTCTC
*
42822052 TCAAAATAATTTTTAAAAT
1 TCAAAATAATTTATAAAAT
42822071 TCAAAAT-ATTTATAAAA
1 TCAAAATAATTTATAAAA
42822088 ATTATAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
TCAAAATAATTTATAAAAT
Found at i:42822088 original size:19 final size:19
Alignment explanation
Indices: 42822052--42822090 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42822042 TTAGTCTCTC
*
42822052 TCAAAATAATTTTTAAAAT
1 TCAAAATAATTTTAAAAAT
42822071 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTT-TAAAAAT
42822090 T
1 T
42822091 ATAACATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TCAAAATAATTTTAAAAAT
Found at i:42823422 original size:18 final size:16
Alignment explanation
Indices: 42823394--42823428 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
42823384 CTAACGGCGG
42823394 AAATAATATTTATATTA
1 AAATAATATTTAT-TTA
42823411 AAATATATATTTATTTA
1 AAATA-ATATTTATTTA
42823428 A
1 A
42823429 CAATTATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATAATATTTATTTA
Found at i:42823590 original size:20 final size:19
Alignment explanation
Indices: 42823545--42823599 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
42823535 TTTAATGGAA
*
42823545 AATATTTTTAATTAATTATAT
1 AATA-TTTT-ATTTATTATAT
*
42823566 TATATTTTATTTATTATTAT
1 AATATTTTATTTATTA-TAT
*
42823586 AATATTATATTTAT
1 AATATTTTATTTAT
42823600 CCTATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 7 0.24
20 19 0.66
21 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATATTTTATTTATTATAT
Done.