Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 33 of 182
Found at i:12793684 original size:29 final size:28
Alignment explanation
Indices: 12793407--12793688 Score: 106
Period size: 29 Copynumber: 9.7 Consensus size: 28
12793397 CGAACTTTCT
* *
12793407 AAAATCCCATTTTTAACCCCGATTTCACCA
1 AAAATTCCA-TTTTAACCCCAATTTCA-CA
*
12793437 AAAATTACCGTTTT-ACCCCAAAACTTTC-C-
1 AAAATT-CCATTTTAACCCC--AA-TTTCACA
* * **
12793466 AAGATCCCATTTTTAACCCTGATTTCACCA
1 AAAATTCCA-TTTTAACCCCAATTTCA-CA
*
12793496 AAAATTACCGTTTT-ACCCTCAAACTTTC-C-
1 AAAATT-CCATTTTAACCC-C-AA-TTTCACA
* * *
12793525 AAAATCCCATTTTAACCTCGATTTCACCA
1 AAAATTCCATTTTAACCCCAATTTCA-CA
*
12793554 AAAATTACCA-TTT-ACCCCTAAACTTT--CT
1 AAAATT-CCATTTTAACCCC--AA-TTTCACA
12793582 AAAA-TCTCATTTTTAACCCCAATTTCACCA
1 AAAATTC-CA-TTTTAACCCCAATTTCA-CA
* *
12793612 AAAGTTACCATTTTACCCCCGAACTTTC-C-
1 AAAATT-CCATTTTAACCCC-AA-TTTCACA
*
12793641 AAAATTCCATTTTTAACCCCAATTCCACA
1 AAAATTCCA-TTTTAACCCCAATTTCACA
12793670 AAAATTGCCATTTT-ACCCC
1 AAAATT-CCATTTTAACCCC
12793689 TAAAAGTCAA
Statistics
Matches: 189, Mismatches: 27, Indels: 74
0.65 0.09 0.26
Matches are distributed among these distances:
26 5 0.03
27 14 0.07
28 33 0.17
29 61 0.32
30 49 0.26
31 14 0.07
32 13 0.07
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAATTCCATTTTAACCCCAATTTCACA
Found at i:12793702 original size:116 final size:117
Alignment explanation
Indices: 12793388--12793702 Score: 404
Period size: 116 Copynumber: 2.7 Consensus size: 117
12793378 GAAATTATAT
* *
12793388 TTTTACCCCCGAACTTTCTAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCGTTTTAC
1 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
* * ** *
12793453 CCC-AAAACTTTCCAAGATCCCATTTTTAACCCTGATTTCACCAAAAATTACCG
66 CCCTAAAA--TTCAAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCA
* * *
12793506 TTTTACCCTCAAACTTTCCAAAATCCCA-TTTTAACCTCGATTTCACCAAAAATTACCA-TTTAC
1 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
* * * *
12793569 CCCTAAACTTTCTAAAATCTCATTTTTAACCCCAATTTCACCAAAAGTTACCA
66 CCCTAAA-ATTCAAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCA
* * * *
12793622 TTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCAATTCCA-CAAAAATTGCCATTTTAC
1 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
*
12793686 CCCTAAAAGTCAAAAAT
66 CCCTAAAATTCAAAAAT
12793703 TACCATTTCG
Statistics
Matches: 170, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
116 88 0.52
117 57 0.34
118 25 0.15
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.32
Consensus pattern (117 bp):
TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
CCCTAAAATTCAAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCA
Found at i:12795233 original size:27 final size:27
Alignment explanation
Indices: 12795189--12795242 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
12795179 GGGGCAAATT
* * *
12795189 GAAGAAATCTAATTTTTTATCCTAACC
1 GAAGAAATCCAATCTTTTACCCTAACC
12795216 GAAGAAATCCAATCTTTTACCCTAACC
1 GAAGAAATCCAATCTTTTACCCTAACC
12795243 AGAGGGTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.31
Consensus pattern (27 bp):
GAAGAAATCCAATCTTTTACCCTAACC
Found at i:12795295 original size:40 final size:40
Alignment explanation
Indices: 12795216--12795437 Score: 193
Period size: 39 Copynumber: 5.6 Consensus size: 40
12795206 TATCCTAACC
** * * *
12795216 GAAGA-AATCCAATCTTTTACCCTAACCAGAGGGTAAGATT
1 GAAGACAATCCAATCTTTTACCCCGATCATAGGG-CAGATT
* * *
12795256 GAAGACCATCCGATCTTTTACCCCGATCATGGGGCAGATT
1 GAAGACAATCCAATCTTTTACCCCGATCATAGGGCAGATT
* ** * *
12795296 GAAGA-AATCCAATATTTTACCCTAATTAAAGGGCAAGATT
1 GAAGACAATCCAATCTTTTACCCCGATCATAGGGC-AGATT
* * *
12795336 GAAGACCATCCGATCTTTTACCCCGATCATAGGGTAGATT
1 GAAGACAATCCAATCTTTTACCCCGATCATAGGGCAGATT
* * * *
12795376 GAA-AAAATCCAATCTTTTACCCTGA-CTTTAGGGTAGATT
1 GAAGACAATCCAATCTTTTACCCCGATC-ATAGGGCAGATT
*
12795415 TAA-ACAATCCAATCTTTTACCCC
1 GAAGACAATCCAATCTTTTACCCC
12795438 TAAAGTTACA
Statistics
Matches: 146, Mismatches: 32, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
38 1 0.01
39 70 0.48
40 33 0.23
41 42 0.29
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (40 bp):
GAAGACAATCCAATCTTTTACCCCGATCATAGGGCAGATT
Found at i:12795297 original size:107 final size:107
Alignment explanation
Indices: 12795110--12795320 Score: 368
Period size: 107 Copynumber: 2.0 Consensus size: 107
12795100 GGGCAGATGA
*
12795110 AAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCGGATCTTTTACCCCGA
1 AAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGA
* * *
12795175 TCATGGGGCAAATTGAAGAAATCTAATTTTTTATCCTAACCG
66 TCATGGGGCAAATTGAAGAAATCCAATATTTTACCCTAACCG
*
12795217 AAGAAATCCAATCTTTTACCCTAACCAGAGGGTAAGATTGAAGACCATCCGATCTTTTACCCCGA
1 AAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGA
*
12795282 TCATGGGGCAGATTGAAGAAATCCAATATTTTACCCTAA
66 TCATGGGGCAAATTGAAGAAATCCAATATTTTACCCTAA
12795321 TTAAAGGGCA
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 98 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (107 bp):
AAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGA
TCATGGGGCAAATTGAAGAAATCCAATATTTTACCCTAACCG
Found at i:12795349 original size:80 final size:80
Alignment explanation
Indices: 12795216--12795398 Score: 294
Period size: 80 Copynumber: 2.3 Consensus size: 80
12795206 TATCCTAACC
* *
12795216 GAAGAAATCCAATCTTTTACCCTAACCAGAGGGTAAGATTGAAGACCATCCGATCTTTTACCCCG
1 GAAGAAATCCAATCTTTTACCCTAACCAAAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCG
*
12795281 ATCATGGGGCAGATT
66 ATCATAGGGCAGATT
* **
12795296 GAAGAAATCCAATATTTTACCCTAATTAAAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCG
1 GAAGAAATCCAATCTTTTACCCTAACCAAAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCG
*
12795361 ATCATAGGGTAGATT
66 ATCATAGGGCAGATT
*
12795376 GAAAAAATCCAATCTTTTACCCT
1 GAAGAAATCCAATCTTTTACCCT
12795399 GACTTTAGGG
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 94 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (80 bp):
GAAGAAATCCAATCTTTTACCCTAACCAAAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCG
ATCATAGGGCAGATT
Found at i:12796418 original size:20 final size:18
Alignment explanation
Indices: 12796379--12796441 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 18
12796369 GTTTAAATAG
12796379 ATTTAAATTTATTATTAA
1 ATTTAAATTTATTATTAA
*
12796397 ATTTAAATTTATTGCTTTAA
1 ATTTAAATTTATT--ATTAA
*
12796417 ATCTAAATTTA--ATTAAA
1 ATTTAAATTTATTATT-AA
12796434 ATTTAAAT
1 ATTTAAAT
12796442 CAATATTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 2 0.05
17 9 0.24
18 13 0.34
20 14 0.37
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (18 bp):
ATTTAAATTTATTATTAA
Found at i:12798740 original size:59 final size:58
Alignment explanation
Indices: 12798453--12798831 Score: 393
Period size: 59 Copynumber: 6.5 Consensus size: 58
12798443 GCTCTCTAGT
* * * *
12798453 CCCTAAACTTTCCAAAATTACATTTTTGACCCTAAAACTT-CCAAAAATTACCATTTTAC
1 CCCTAAACTTTCCAAAATTCCATTTTT-AACCT-CAATTTCCCAAAAATTACCATTTTAC
* * * ** *
12798512 CCATAAACTTTCCAAAATTCCA-TTTTGACCCCGAAACTCCCAAAAATTACC-GTTTAC
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCTC-AATTTCCCAAAAATTACCATTTTAC
12798569 CCCTAAACTTTCCAAAATTCCA-TTTTAACC-CTAATTTCATCC-AAAATT-CCATTTTAC
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCTC-AATTTC--CCAAAAATTACCATTTTAC
* * *
12798626 CCTTAAACTTTCCAAAATTCCA-TTTTAACCTCAAAACTT-CCAAAAATTATCATTTTAC
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCTC--AATTTCCCAAAAATTACCATTTTAC
* * *
12798684 CCCTAAACTTTCCAAAATTTCATTTTTAACCTCGATTTCACCCAAAATTACCATTTTAC
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCTCAATTTC-CCAAAAATTACCATTTTAC
** *
12798743 CCCTAAACTTTCCAAAATTCCATTTTTAACCTTGATTTCACCAAAAA-TACCGTTTTA-
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCTCAATTTC-CCAAAAATTACCATTTTAC
* *
12798800 CCCTCAAACTTTCTAAAATTCTATTTTTAACC
1 CCCT-AAACTTTCCAAAATTCCATTTTTAACC
12798832 CTGAATTTTC
Statistics
Matches: 276, Mismatches: 31, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
56 9 0.03
57 91 0.33
58 81 0.29
59 95 0.34
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (58 bp):
CCCTAAACTTTCCAAAATTCCATTTTTAACCTCAATTTCCCAAAAATTACCATTTTAC
Found at i:12798770 original size:29 final size:28
Alignment explanation
Indices: 12798453--12798768 Score: 279
Period size: 29 Copynumber: 10.9 Consensus size: 28
12798443 GCTCTCTAGT
*
12798453 CCCTAAACTTTCCAAAATTACATTTTTGA-
1 CCCTAAACTTTCCAAAATTCCA-TTTT-AC
12798482 CCCTAAAAC-TTCCAAAAATTACCATTTTAC
1 CCCT-AAACTTTCC-AAAATT-CCATTTTAC
*
12798512 CCATAAACTTTCCAAAATTCCATTTTGAC
1 CCCTAAACTTTCCAAAATTCCATTTT-AC
* * *
12798541 CCCGAAAC-TCCCAAAAATTACC-GTTTAC
1 CCCTAAACTTTCC-AAAATT-CCATTTTAC
*
12798569 CCCTAAACTTTCCAAAATTCCATTTTAA
1 CCCTAAACTTTCCAAAATTCCATTTTAC
*
12798597 CCCT-AATTTCATCCAAAATTCCATTTTAC
1 CCCTAAACTT--TCCAAAATTCCATTTTAC
*
12798626 CCTTAAACTTTCCAAAATTCCATTTTAAC
1 CCCTAAACTTTCCAAAATTCCATTTT-AC
* * *
12798655 CTCAAAAC-TTCCAAAAATTATCATTTTAC
1 CCCTAAACTTTCC-AAAATT-CCATTTTAC
*
12798684 CCCTAAACTTTCCAAAATTTCATTTTTA-
1 CCCTAAACTTTCCAAAATTCCA-TTTTAC
* **
12798712 ACCTCGA-TTTCACCCAAAATTACCATTTTAC
1 CCCTAAACTTT---CCAAAATT-CCATTTTAC
12798743 CCCTAAACTTTCCAAAATTCCATTTT
1 CCCTAAACTTTCCAAAATTCCATTTT
12798769 TAACCTTGAT
Statistics
Matches: 236, Mismatches: 27, Indels: 49
0.76 0.09 0.16
Matches are distributed among these distances:
27 9 0.04
28 67 0.28
29 99 0.42
30 50 0.21
31 8 0.03
32 3 0.01
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.35
Consensus pattern (28 bp):
CCCTAAACTTTCCAAAATTCCATTTTAC
Found at i:12798818 original size:58 final size:58
Alignment explanation
Indices: 12798493--12798831 Score: 381
Period size: 57 Copynumber: 5.8 Consensus size: 58
12798483 CCTAAAACTT
* * * **
12798493 CCAAAAATTACCATTTTACCCATAAACTTTCCAAAATTCCATTTTGACCCCGAAACTC-
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCTCG-ATTTCA
* *
12798551 CCAAAAATTACC-GTTTACCCCTAAACTTTCCAAAATTCCATTTTAACC-CTAATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCTC-GATTTCA
* * *
12798608 TCC-AAAATT-CCATTTTACCCTTAAACTTTCCAAAATTCCATTTTAACCTCAAAACTT--
1 -CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCTC--GATTTCA
* *
12798665 CCAAAAATTATCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCTCGATTTCA
* *
12798724 CCCAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTTGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCTCGATTTCA
* * *
12798783 CCAAAAA-TACCGTTTTA-CCCTCAAACTTTCTAAAATTCTATTTTTAACC
1 CCAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCA-TTTTAACC
12798832 CTGAATTTTC
Statistics
Matches: 246, Mismatches: 23, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
56 8 0.03
57 86 0.35
58 77 0.31
59 75 0.30
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCTCGATTTCA
Found at i:12800697 original size:71 final size:71
Alignment explanation
Indices: 12800620--12800763 Score: 245
Period size: 71 Copynumber: 2.0 Consensus size: 71
12800610 ATAGTGTTGC
* *
12800620 TTTGATTTTGAAGGAGAAAA-GGAGAAAATTGAATTTGATTTGAAAAAGAAAGAACAATGAATGA
1 TTTGATTTTGAAGGA-AAAAGGGAGAAAATTGAATTTAATTTGAAAAAGAAAGAAAAATGAATGA
12800684 AAAGCCA
65 AAAGCCA
*
12800691 TTTGATTTTGAAGGAAAAAGGGAGAAAATTGAATTTAATTTGAAAAAGAAAGAAAAATGGATGAA
1 TTTGATTTTGAAGGAAAAAGGGAGAAAATTGAATTTAATTTGAAAAAGAAAGAAAAATGAATGAA
12800756 AAGCCA
66 AAGCCA
12800762 TT
1 TT
12800764 CCACCCACGT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 4 0.06
71 65 0.94
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.25
Consensus pattern (71 bp):
TTTGATTTTGAAGGAAAAAGGGAGAAAATTGAATTTAATTTGAAAAAGAAAGAAAAATGAATGAA
AAGCCA
Found at i:12810451 original size:19 final size:19
Alignment explanation
Indices: 12810420--12810473 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
12810410 ACATATATAT
*
12810420 TCTCTCTTTATTTTTTTT-
1 TCTCTCTTAATTTTTTTTA
*
12810438 TCTATTCTTAATTTTTTTTA
1 TCT-CTCTTAATTTTTTTTA
12810458 TCTCTC-TAATTTTTTT
1 TCTCTCTTAATTTTTTT
12810474 CCACCTCACC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 13 0.42
19 15 0.48
20 3 0.10
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (19 bp):
TCTCTCTTAATTTTTTTTA
Found at i:12810454 original size:17 final size:19
Alignment explanation
Indices: 12810432--12810474 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
12810422 TCTCTTTATT
12810432 TTTTTTTCTAT-TCT-TAA
1 TTTTTTTCTATCTCTCTAA
12810449 TTTTTTT-TATCTCTCTAA
1 TTTTTTTCTATCTCTCTAA
12810467 TTTTTTTC
1 TTTTTTTC
12810475 CACCTCACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.13
17 10 0.43
18 10 0.43
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTTTCTATCTCTCTAA
Found at i:12813538 original size:22 final size:23
Alignment explanation
Indices: 12813508--12813560 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
12813498 ACTTCCCAAC
*
12813508 ATTTATAATTAA-ATATGCAAAAT
1 ATTT-TAATTAACATATACAAAAT
12813531 ATTTTAA-TAACATATACAAAAT
1 ATTTTAATTAACATATACAAAAT
*
12813553 ACTTTAAT
1 ATTTTAAT
12813561 ACAATTGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 3 0.12
22 19 0.73
23 4 0.15
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTTTAATTAACATATACAAAAT
Found at i:12813561 original size:22 final size:22
Alignment explanation
Indices: 12813520--12813561 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12813510 TTATAATTAA
* *
12813520 ATATGCAAAATATTTTAATAAC
1 ATATACAAAATACTTTAATAAC
12813542 ATATACAAAATACTTTAATA
1 ATATACAAAATACTTTAATA
12813562 CAATTGCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATACAAAATACTTTAATAAC
Found at i:12815285 original size:4 final size:4
Alignment explanation
Indices: 12815263--12815303 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
12815253 TGACTTTGGG
*
12815263 TTTA -TTA TTTGA GTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
12815304 CTATATTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.82
5 3 0.09
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:12815442 original size:59 final size:58
Alignment explanation
Indices: 12815288--12815455 Score: 203
Period size: 59 Copynumber: 2.8 Consensus size: 58
12815278 ATTTATTTAT
* * *
12815288 TTATTTATTTATTTATCTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATA
1 TTATTT-TATATTTATTTATATTTATAAAATAAT-AATAAATAATAAAACAAAATTAATA
* * * * *
12815348 TTATTTTACATTTATTTAT-TTATATTCATACAATAATAAATAATAAAATAAAATTAATA
1 TTATTTTATATTTATTTATATT-TA-TAAAATAATAATAAATAATAAAACAAAATTAATA
12815407 TTATTTTATATTTATTTATATTTATAAAAATAATAATAAATGAATAAAA
1 TTATTTTATATTTATTTATATTTAT-AAAATAATAATAAAT-AATAAAA
12815456 ATAATAAGAA
Statistics
Matches: 91, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
58 3 0.03
59 67 0.74
60 21 0.23
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.45
Consensus pattern (58 bp):
TTATTTTATATTTATTTATATTTATAAAATAATAATAAATAATAAAACAAAATTAATA
Found at i:12816067 original size:40 final size:40
Alignment explanation
Indices: 12815980--12818220 Score: 1291
Period size: 40 Copynumber: 56.5 Consensus size: 40
12815970 CTCTATAGTT
* * * * *
12815980 TTAGGGTTAAAAGTTTAGATTGT-TTCAATTTG-CCTCATGG
1 TTAGGG-TAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAG
* * *
12816020 TTGGGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
12816060 TTAGGGTAAAAGATTGGAT--TCCTTCAATCTGCCC-C-ATG
1 TTAGGGTAAAAGATTGGATGGT-CTTCAATCTGCCCTCTA-G
* * * *
12816098 GTCGAGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAG
1 TTAG-GGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* *
12816139 TTAGGGTAAAAGATTGGATTG-CTTCAATTTGCCC-CATAG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAG
** * *
12816178 TCGGGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* *
12816218 TTAGGGTAAAAGATTGGATTG-CTTCAATCTGCCC-CATGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAG
** * *
12816257 TCGGGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * *
12816297 TTAGGGTAAAAAATTGGATTG-CTTCAATCTGCCC-CATAA
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAG
** * ** *
12816336 TCGGGGTAAGAGATCAGATGGTCTTCAATCTACCCTCTAG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* *
12816376 TTAGGGTAAAAAATTGGATTG-CTTCAATCTGCCC-C-ATG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTA-G
* * * ** * *
12816414 ATTGGGGTAAGAGATGGGATGGTCTTCAATCTGTTCTATAA
1 -TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* *
12816455 TTAGGGTAAAAGATTGGATTG-CTTCAATCTGCCC-CATGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAG
** * * * * * *
12816494 TCGGGGTAAGAGATAGGATGGTCTTCAATCTGTCTTTTGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
** * * *
12816534 TTAAAGTAAAAGATTAGATTG-CTTCAATCTGCCC-CATGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAG
** * * *
12816573 TCGGGGTAAGAGATCT--A--ATCTTCAATCTGTCCTCTAG
1 TTAGGGTAAAAGAT-TGGATGGTCTTCAATCTGCCCTCTAG
* * * *
12816610 TTAGGGTAAAAGATTGGATTG-CTTCAATTTACCC-CACAG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAG
** * *
12816649 TCGGGGTAAGAGATCGGATGGTCTTCAATCTG-CCTC-ATG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTA-G
** * * * * *
12816688 ATCGGGGTAAGAGATCGGATGGTTTTTAATCTGCCCTCTGG
1 -TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * * *
12816729 TTAGGGTAAAAGATTGGATTG-CTTCAATCTATCCC-ATGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCT-GCCCTCTAG
** ** **
12816768 TCGGGGTAAAAGATCAGATGGTCTTCAATAAGCCCTCTAG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* *
12816808 TTAGGGTAAAAGATTGGATTG-CTTCAATTTGCCC-C-A-
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * *
12816844 TGTCGAGGTAAGAGATTGGATGGTCTTTAATCTGCCCTCTAG
1 T-TAG-GGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
** * * ** *
12816886 TTAGGAAAAAAGATTAGATTG-CTTCAAT-TTACCTCATGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAG
*
12816925 TCAGGGTAAAAGATCT-GATGG-CTTCAATCTG-CCTCATAG
1 TTAGGGTAAAAGAT-TGGATGGTCTTCAATCTGCCCTC-TAG
** * *
12816964 TCGGGGTAAGAGATCTGGAT--TACTTCAATCTGCCATCTAG
1 TTAGGGTAAAAGAT-TGGATGGT-CTTCAATCTGCCCTCTAG
* * * *
12817004 TTAGTGTAAAATATCTGAAT--TACTTCAATCTGCCC-CATGG
1 TTAGGGTAAAAGAT-TGGATGGT-CTTCAATCTGCCCTC-TAG
* * * * *
12817044 TTGGGGTAAGAGATCGGATGATCTTCAATCTGCCCTAT-G
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * * * *
12817083 ATAGGGGTAAGAGATCGGATGGTCTTCAATCTACCCTCTAA
1 TTA-GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * * *
12817124 TTAAGGTAAAATATTGGATTG-CTTCAATCTGCCC-CATGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAG
** * * *
12817163 TCGGGGTAAGAGATTGGATGG-CTTTAATCTACCCTCTAG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * *
12817202 TTAGGGTAAAAGATCGGATGGTCTTCAATCTGTCCC-ATGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTG-CCCTCTAG
* * * * * * *
12817242 TCAGGCTAAGAGATCGAATGGTCTTCAATTTACCCTCT-G
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * * * * * *
12817281 TTTGGGGTAAGAGATCGAATGGTCTTCAATATACCCTCTGG
1 -TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
*
12817322 TTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCC-C-ATG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTA-G
* * * *** * ***
12817361 GTCGGCCTAAAAGATCAAATGGTCTTCAATATGTATTCTA-
1 TTAGG-GTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * * * *
12817401 TTCGAGGTAAGAA-ATCGGATGGTCTTCAATCTACCTTCTGG
1 TTAG-GGTAA-AAGATTGGATGGTCTTCAATCTGCCCTCTAG
** * *
12817442 TCGGGGTAAGAGATTGGATGGTCTTCAATCTACCCTCTAG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
*
12817482 TTAGGGTAAAAGATTGGATTG-CTTCAATCTGCCC-C-ATG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTA-G
** * *
12817520 ATCGGGGTAAGAGATTGGATGGTCTTCAATCTGTCCTCTAG
1 -TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* *
12817561 TTAGGGTAACAGATTAGATGGTCTTCAATCTGCCCTCTAG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * *
12817601 TTAGGGTAAAAGATTGGATGGTCTTCAATTTGTCCTCTGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* *
12817641 TTAGGGTAAAAGATTGGATTG-CTTCAATTTG-CCTC-ATG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTA-G
* * * ** * * *
12817679 GTCGGAGTAAGAGATTAAAT-GACTTCAATTTGCCCTCTGG
1 TTAGG-GTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * * *
12817719 TTAGAGTAAAAGATTGAACT-G-CTTTAATTTGCCC-C-ATG
1 TTAGGGTAAAAGATTGGA-TGGTCTTCAATCTGCCCTCTA-G
** * *
12817757 ATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTAG
1 -TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * *
12817798 TTAGGGTAAAAGATTGAATTG-CTTCAATCTG-CCTCATGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAG
** * * * *
12817837 TCGGGGTAAGAGATCGAATGGTCTTCAATCTACCCTCTAG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * * ** *
12817877 TTAAGGTAAAAGGTTAGATTACTTCAATCTCCAATCTGCCC-CATGG
1 TTAGGGTAAAAGATTGGA-T-GGTC--T-T-CAATCTGCCCTC-TAG
* * * ** * * *
12817923 TCAAGGTAAGAGATCAGATGGTCTTCAATCTGCCATTTGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
** * * * * * *
12817963 TCGGGGTAAGAGATCGAATGGTTTTCAATCTACCCTCTAA
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * *
12818003 TTAGGGTAAAAGATTAGATTG-CTTCAATCTGCCC-CATGG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAG
** * *
12818042 TCGGGGTAAGAGATTGGATGG-CTTCAATTTGCCCTCTAG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * * * *
12818081 TTAGGGTAAAATATTAGACT--ACTTCAATCTGCCCCCATGG
1 TTAGGGTAAAAGATTGGA-TGGTCTTCAATCTGCCCTC-TAG
* * *
12818121 TTAGTGTAAAAGATTGGATGGTCTTCAATCTACCCT-TTG
1 TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
* * *
12818160 ATTAAGGTAAAAGATTGAATGGTCTTCAACCTGCCCTCT-G
1 -TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
*
12818200 ATTAGGGTAAACGATTGGATG
1 -TTAGGGTAAAAGATTGGATG
12818221 ACTGTAACTT
Statistics
Matches: 1694, Mismatches: 392, Indels: 230
0.73 0.17 0.10
Matches are distributed among these distances:
36 2 0.00
37 31 0.02
38 55 0.03
39 610 0.36
40 898 0.53
41 58 0.03
42 9 0.01
44 3 0.00
45 3 0.00
46 25 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (40 bp):
TTAGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG
Found at i:12816118 original size:79 final size:79
Alignment explanation
Indices: 12815980--12817956 Score: 1622
Period size: 79 Copynumber: 24.9 Consensus size: 79
12815970 CTCTATAGTT
* * * * * *
12815980 TTAGGGTTAAAAGTTTAGATTGTTTCAATTTGCCTCATGGTTGGGGTAAGAGATCGGATGGTCTT
1 TTAGGG-TAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTT
12816045 CAATCTGCCCTCTAG
65 CAATCTGCCCTCTAG
* *
12816060 TTAGGGTAAAAGATTGGATTCCTTCAATCTGCCCCATGGTCGAGGTAAGAGATCGGATGGTCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
12816125 AATCTGCCCTCTAG
66 AATCTGCCCTCTAG
* *
12816139 TTAGGGTAAAAGATTGGATTGCTTCAATTTGCCCCATAGTCGGGGTAAGAGATCGGATGGTCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
12816204 AATCTGCCCTCTAG
66 AATCTGCCCTCTAG
12816218 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
12816283 AATCTGCCCTCTAG
66 AATCTGCCCTCTAG
* ** *
12816297 TTAGGGTAAAAAATTGGATTGCTTCAATCTGCCCCATAATCGGGGTAAGAGATCAGATGGTCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
*
12816362 AATCTACCCTCTAG
66 AATCTGCCCTCTAG
* * * *
12816376 TTAGGGTAAAAAATTGGATTGCTTCAATCTGCCCCATGATTGGGGTAAGAGATGGGATGGTCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
** * *
12816441 AATCTGTTCTATAA
66 AATCTGCCCTCTAG
*
12816455 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATAGGATGGTCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
* * * *
12816520 AATCTGTCTTTTGG
66 AATCTGCCCTCTAG
** * **
12816534 TTAAAGTAAAAGATTAGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATC---TAATCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
*
12816596 AATCTGTCCTCTAG
66 AATCTGCCCTCTAG
* * **
12816610 TTAGGGTAAAAGATTGGATTGCTTCAATTTACCCCACAGTCGGGGTAAGAGATCGGATGGTCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
12816675 AATCTG-CCTC-ATG
66 AATCTGCCCTCTA-G
** * * * * * ** * * *
12816688 ATCGGGGTAAGAGATCGGATGGTTTTTAATCTGCCCTC-TGGTTAGGGTAAAAGATTGGATTG-C
1 -TTAGGGTAAAAGATTGGATTG-CTTCAATCTGCCC-CATGGTCGGGGTAAGAGATCGGATGGTC
* * *
12816751 TTCAATCTATCCC-ATGG
63 TTCAATCT-GCCCTCTAG
** ** * ** * ** * * *
12816768 TCGGGGTAAAAGATCAGATGGTCTTCAATAAGCCCTC-TAGTTAGGGTAAAAGATTGGATTG-CT
1 TTAGGGTAAAAGATTGGATTG-CTTCAATCTGCCC-CATGGTCGGGGTAAGAGATCGGATGGTCT
*
12816831 TCAATTTGCCC-C-A-
64 TCAATCTGCCCTCTAG
* * * * * ** ** * ** *
12816844 TGTCGAGGTAAGAGATTGGATGGTCTTTAATCTGCCCTC-TAGTTAGGAAAAAAGATTAGATTG-
1 T-TAG-GGTAAAAGATTGGATTG-CTTCAATCTGCCC-CATGGTCGGGGTAAGAGATCGGATGGT
** *
12816907 CTTCAAT-TTACCTCATGG
62 CTTCAATCTGCCCTC-TAG
* * * *
12816925 TCAGGGTAAAAGATCT-GATGGCTTCAATCTGCCTCATAGTCGGGGTAAGAGATCTGGAT--TAC
1 TTAGGGTAAAAGAT-TGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATC-GGATGGT-C
*
12816987 TTCAATCTGCCATCTAG
63 TTCAATCTGCCCTCTAG
* * * * * *
12817004 TTAGTGTAAAATATCTGAATTACTTCAATCTGCCCCATGGTTGGGGTAAGAGATCGGATGATCTT
1 TTAGGGTAAAAGAT-TGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTT
*
12817069 CAATCTGCCCTAT-G
65 CAATCTGCCCTCTAG
* * * * * ** *** * * * *
12817083 ATAGGGGTAAGAGATCGGATGGTCTTCAATCTACCCTC-TAATTAAGGTAAAATATTGGATTG-C
1 TTA-GGGTAAAAGATTGGATTG-CTTCAATCTGCCC-CATGGTCGGGGTAAGAGATCGGATGGTC
*
12817146 TTCAATCTGCCC-CATGG
63 TTCAATCTGCCCTC-TAG
** * * * * * ** *
12817163 TCGGGGTAAGAGATTGGATGGCTTTAATCTACCCTC-TAGTTAGGGTAAAAGATCGGATGGTCTT
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCC-CATGGTCGGGGTAAGAGATCGGATGGTCTT
* *
12817227 CAATCTGTCCC-ATGG
65 CAATCTG-CCCTCTAG
* * * * * * * * * * *
12817242 TCAGGCTAAGAGATCGAATGGTCTTCAATTTACCCTC-TGTTTGGGGTAAGAGATCGAATGGTCT
1 TTAGGGTAAAAGATTGGATTG-CTTCAATCTGCCC-CATGGTCGGGGTAAGAGATCGGATGGTCT
* * *
12817306 TCAATATACCCTCTGG
64 TCAATCTGCCCTCTAG
* * ** * **
12817322 TTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCCCATGGTCGGCCTAAAAGATCAAATGGTCTT
1 TTAGGGTAAAAGATTGGATTG-CTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTT
* ***
12817387 CAATATGTATTCTA-
65 CAATCTGCCCTCTAG
* * * * * *
12817401 TTCGAGGTAAGAA-ATCGGATGGTCTTCAATCTACCTTC-TGGTCGGGGTAAGAGATTGGATGGT
1 TTAG-GGTAA-AAGATTGGATTG-CTTCAATCTGCC-CCATGGTCGGGGTAAGAGATCGGATGGT
*
12817464 CTTCAATCTACCCTCTAG
62 CTTCAATCTGCCCTCTAG
* *
12817482 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
*
12817547 AATCTGTCCTCTAG
66 AATCTGCCCTCTAG
* * * * ** * *
12817561 TTAGGGTAACAGATTAGATGGTCTTCAATCTGCCCTC-TAGTTAGGGTAAAAGATTGGATGGTCT
1 TTAGGGTAAAAGATTGGATTG-CTTCAATCTGCCC-CATGGTCGGGGTAAGAGATCGGATGGTCT
* * *
12817625 TCAATTTGTCCTCTGG
64 TCAATCTGCCCTCTAG
* * * *** *
12817641 TTAGGGTAAAAGATTGGATTGCTTCAATTTGCCTCATGGTCGGAGTAAGAGATTAAAT-GACTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
* *
12817705 AATTTGCCCTCTGG
66 AATCTGCCCTCTAG
* * * * * * *
12817719 TTAGAGTAAAAGATTGAACTGCTTTAATTTGCCCCATGATCGGGGTAAGAGATTGGATGGTCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
*
12817784 AATCTGCCCTTTAG
66 AATCTGCCCTCTAG
* * *
12817798 TTAGGGTAAAAGATTGAATTGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATCGAATGGTCTTC
1 TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
*
12817863 AATCTACCCTCTAG
66 AATCTGCCCTCTAG
* * * * ** *
12817877 TTAAGGTAAAAGGTTAGATTACTTCAATCTCCAATCTGCCCCATGGTCAAGGTAAGAGATCAGAT
1 TTAGGGTAAAAGATTGGA-T--TGC--T-T-CAATCTGCCCCATGGTCGGGGTAAGAGATCGGAT
12817942 GGTCTTCAATCTGCC
59 GGTCTTCAATCTGCC
12817957 ATTTGGTCGG
Statistics
Matches: 1578, Mismatches: 267, Indels: 98
0.81 0.14 0.05
Matches are distributed among these distances:
76 65 0.04
77 6 0.00
78 189 0.12
79 893 0.57
80 365 0.23
81 13 0.01
82 2 0.00
84 1 0.00
85 1 0.00
86 43 0.03
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (79 bp):
TTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTC
AATCTGCCCTCTAG
Found at i:12817410 original size:120 final size:119
Alignment explanation
Indices: 12816012--12817875 Score: 550
Period size: 119 Copynumber: 15.7 Consensus size: 119
12816002 TTTCAATTTG
* * * * * **
12816012 CCTCATGGTTGGGGTAAGAGATCGGATGGTCTTCAATCTGCCCTC-TAGTTAGGGTAAAAGATTG
1 CCTC-TGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCC-CATGGTCAGGCTAAAAGATCA
* * * * *
12816076 GAT--TCCTTCAATCTGCC-CCATGGTCGAGGTAAGAGATCGGATGGTCTTCAATCTGC
64 AATGGT-CTTCAATTTACCTCTAT--TCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
* * * * * * * * **
12816132 CCTCTAGTTAGGGTAAAAGATTGGATTG-CTTCAATTTGCCCCATAGTCGGGGTAAGAGATCGGA
1 CCTCTGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCCCATGGTCAGGCTAAAAGATCAAA
** * * * * *
12816196 TGGTCTTCAATCTGCCCTCTAGTTAG-GGTAAAAGATTGGATTG-CTTCAATCTGC
66 TGGTCTTCAAT-TTACCTCTA-TTCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
** * * * * * **
12816250 CC-CATGGTCGGGGTAAGAGATCGGATGGTCTTCAATCTGCCCTC-TAGTTAGGGTAAAAAATTG
1 CCTC-TGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCC-CATGGTCAGGCTAAAAGATCA
* * * * * * * *
12816313 GATTG-CTTCAATCTGCCCCATAATCGGGGTAAGAGATCAGATGGTCTTCAATCTAC
64 AATGGTCTTCAATTTACCTC-TATTCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
* * * * * ** * * ***
12816369 CCTCTAGTTAGGGTAAAAAATTGGATTG-CTTCAATCTGCCCCATGATTGGGGTAAGAGATGGGA
1 CCTCTGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCCCATGGTCAGGCTAAAAGATCAAA
* * * * * * *
12816433 TGGTCTTCAATCTGT-TCTATAATTAG-GGTAAAAGATTGGATTG-CTTCAATCTGC
66 TGGTCTTCAAT-T-TACCTCT-ATTCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
** * * * *** * * *
12816487 CC-CATGGTCGGGGTAAGAGATAGGATGGTCTTCAATCTGTCTTTTGGTTAAAG-TAAAAGATTA
1 CCTC-TGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCCCATGG-TCAGGCTAAAAGATCA
* * * * * * ** **
12816550 GATTG-CTTCAATCTGCC-CCATGGTCGGGGTAAGAGATC---TAATCTTCAATCTGT
64 AATGGTCTTCAATTTACCTCTAT--TCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
* * * * * ** * * * **
12816603 CCTCTAGTTAGGGTAAAAGATTGGATTG-CTTCAATTTACCCCACAGTCGGGGTAAGAGATCGGA
1 CCTCTGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCCCATGGTCAGGCTAAAAGATCAAA
* * * * * *
12816667 TGGTCTTCAATCTGCCTC-ATGATCGGGGTAAGAGATCGGATGGTTTTTAATCTGC
66 TGGTCTTCAATTTACCTCTAT--TCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
* * ** * * *
12816722 CCTCTGGTTAGGGTAAAAGATTGGATTG-CTTCAATCTATCCCATGGTCGGGGTAAAAGATCAGA
1 CCTCTGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCCCATGGTCAGGCTAAAAGATCAAA
* * * * * * *
12816786 TGGTCTTCAA-TAAGCCCTCTAGTTAG-GGTAAAAGATTGGATTG-CTTCAATTTGC
66 TGGTCTTCAATTTA--CCTCTA-TTCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
* * * * * * ** *
12816840 CC-CAT-G-TCGAGGTAAGAGATTGGATGGTCTTTAATCTGCCCTC-TAGTTAGGAAAAAAGATT
1 CCTC-TGGTTAG-GGTAAAAGATCGGATGGTCTTCAATCTGCCC-CATGGTCAGGCTAAAAGATC
* * * * *
12816901 AGATTG-CTTCAATTTACCTC-ATGGTC-AGGGTAAAAGATCTGATGG-CTTCAATCT-G
63 AAATGGTCTTCAATTTACCTCTAT--TCGA-GGTAAGAGATCGGATGGTCTTCAATCTAC
* ** * * * * *
12816956 CCTCATAGTCGGGGTAAGAGATCTGGAT--TACTTCAATCTGCCATC-TAGTTAGTG-TAAAATA
1 CCTC-TGGTTAGGGTAAAAGATC-GGATGGT-CTTCAATCTGCC-CCATGGTCAG-GCTAAAAGA
* * * * * * * *
12817017 TCTGAAT--TACTTCAATCTGCC-CCATGGTTGGGGTAAGAGATCGGATGATCTTCAATCTGC
61 TC-AAATGGT-CTTCAATTTACCTCTAT--TCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
* * * * * *
12817077 CCTAT-GATAGGGGTAAGAGATCGGATGGTCTTCAATCTACCCTCTAAT--TAAGG-TAAAATAT
1 CCTCTGGTTA-GGGTAAAAGATCGGATGGTCTTCAATCTGCCC-C--ATGGTCAGGCTAAAAGAT
*** * * * * * * *
12817138 TGGATTG-CTTCAATCTGCC-CCATGGTCGGGGTAAGAGATTGGATGG-CTTTAATCTAC
62 CAAATGGTCTTCAATTTACCTCTAT--TCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
* * * *
12817195 CCTCTAGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGTCCCATGGTCAGGCTAAGAGATCGAA
1 CCTCTGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCCCATGGTCAGGCTAAAAGATCAAA
* * * * *
12817260 TGGTCTTCAATTTACCCTCTGTTTGGGGTAAGAGATCGAATGGTCTTCAATATAC
66 TGGTCTTCAATTTA-CCTCTATTCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
12817315 CCTCTGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCCCATGGTC-GGCCTAAAAGATCAA
1 CCTCTGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCCCATGGTCAGG-CTAAAAGATCAA
* *
12817379 ATGGTCTTCAATATGTA-TTCTATTCGAGGTAAGAAATCGGATGGTCTTCAATCTAC
65 ATGGTCTTCAAT-T-TACCTCTATTCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
* ** * * * * * * ***
12817435 CTTCTGGTCGGGGTAAGAGATTGGATGGTCTTCAATCTACCCTC-TAGTTAGGGTAAAAGATTGG
1 CCTCTGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCC-CATGGTCAGGCTAAAAGATCAA
* * * * * * **
12817499 ATTG-CTTCAATCTGCC-CCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTGT
65 ATGGTCTTCAATTTACCTCTAT--TCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
* * ** * * * ***
12817554 CCTCTAGTTAGGGTAACAGATTAGATGGTCTTCAATCTGCCCTC-TAGTTAGGGTAAAAGATTGG
1 CCTCTGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCC-CATGGTCAGGCTAAAAGATCAA
* * * * * * **
12817618 ATGGTCTTCAATTTGTCCTCTGGTTAG-GGTAAAAGATTGGATTG-CTTCAAT-TTG
65 ATGGTCTTCAATTT-ACCTCT-ATTCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
* * *** * * *
12817672 CCTCATGG-TCGGAGTAAGAGATTAAAT-GACTTCAATTTGCCCTC-TGGTTAGAG-TAAAAGAT
1 CCTC-TGGTTAGG-GTAAAAGATCGGATGGTCTTCAATCTGCCC-CATGGTCAG-GCTAAAAGA-
* * * * * * * *
12817733 TGAACT-G-CTTTAATTTGCC-CCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTGC
61 TCAAATGGTCTTCAATTTACCTCTAT--TCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
* * * * * * * * * *
12817791 CCTTTAGTTAGGGTAAAAGATTGAATTG-CTTCAATCTGCCTCATGGTCGGGGTAAGAGATCGAA
1 CCTCTGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCCCATGGTCAGGCTAAAAGATCAAA
*
12817855 TGGTCTTCAATCTACCCTCTA
66 TGGTCTTCAATTTA-CCTCTA
12817876 GTTAAGGTAA
Statistics
Matches: 1339, Mismatches: 299, Indels: 211
0.72 0.16 0.11
Matches are distributed among these distances:
114 4 0.00
115 28 0.02
116 74 0.06
117 100 0.07
118 368 0.27
119 482 0.36
120 253 0.19
121 23 0.02
122 5 0.00
123 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (119 bp):
CCTCTGGTTAGGGTAAAAGATCGGATGGTCTTCAATCTGCCCCATGGTCAGGCTAAAAGATCAAA
TGGTCTTCAATTTACCTCTATTCGAGGTAAGAGATCGGATGGTCTTCAATCTAC
Found at i:12818210 original size:80 final size:80
Alignment explanation
Indices: 12816023--12818220 Score: 989
Period size: 79 Copynumber: 27.7 Consensus size: 80
12816013 CTCATGGTTG
* * * *
12816023 GGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGAT--TCCTTCA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGT-CTTCA
* * * *
12816086 ATCTGCCCCATG-GTC
65 ATCTACCCTATGATTA
* * * * *
12816101 GAGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTG-CTTCA
1 G-GGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCA
* * * **
12816165 ATTTGCCCCAT-AGTCG
65 ATCTACCCTATGA-TTA
* * * * *
12816181 GGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTG-CTTCAA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAA
* * * **
12816245 TCTGCCCCATGGTCG
66 TCTACCCTATGATTA
* * * * * *
12816260 GGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAAATTGGATTG-CTTCAA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAA
* * * **
12816324 TCTGCCCCATAATCG
66 TCTACCCTATGATTA
* * * * * *
12816339 GGGTAAGAGA-TCAGATGGTCTTCAATCTACCCTCTAGTTAGGGTAAAAAATTGGATTG-CTTCA
1 GGGTAAAAGATTGA-ATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCA
* * *
12816402 ATCTGCCCCATGATTG
65 ATCTACCCTATGATTA
* * * ** * ** *
12816418 GGGTAAGAGATGGGATGGTCTTCAATCTGTTCTATAATTAGGGTAAAAGATTGGATTG-CTTCAA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAA
* * * **
12816482 TCTGCCCCATGGTCG
66 TCTACCCTATGATTA
* * * * * * ** * *
12816497 GGGTAAGAGATAGGATGGTCTTCAATCTGTCTTTTGGTTAAAGTAAAAGATTAGATTG-CTTCAA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAA
* * * **
12816561 TCTGCCCCATGGTCG
66 TCTACCCTATGATTA
* * * *
12816576 GGGTAAGAGATCT-AA---TCTTCAATCTGTCCTCTAGTTAGGGTAAAAGATTGGATTG-CTTCA
1 GGGTAAAAGAT-TGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCA
* * * **
12816636 ATTTACCCCA-CAGTCG
65 ATCTACCCTATGA-TTA
* * * * ** * * * *
12816652 GGGTAAGAGATCGGATGGTCTTCAATCTG-CCTCATGATCGGGGTAAGAGATCGGATGGTTTTTA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTC-TGGTTAGGGTAAAAGATTGGATGGTCTTCA
* * *
12816716 ATCTGCCCTCTGGTTA
65 ATCTACCCTATGATTA
* * * * ** **
12816732 GGGTAAAAGATTGGATTG-CTTCAATCTATCCC-ATGGTCGGGGTAAAAGATCAGATGGTCTTCA
1 GGGTAAAAGATTGAATGGTCTTCAATCT-GCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCA
* *
12816795 AT-AAGCCCTCT-AGTTA
65 ATCTA-CCCTATGA-TTA
* * * * * *
12816811 GGGTAAAAGATTGGATTG-CTTCAATTTGCCC-CAT-G-TCGAGGTAAGAGATTGGATGGTCTTT
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTC-TGGTTAG-GGTAAAAGATTGGATGGTCTTC
* *
12816872 AATCTGCCCTCT-AGTTA
64 AATCTACCCTATGA-TTA
** * ** *
12816889 GGAAAAAAGATT-AGATTG-CTTCAAT-TTACCTCATGGTCAGGGTAAAAGATCT-GATGG-CTT
1 GGGTAAAAGATTGA-ATGGTCTTCAATCTGCCCTC-TGGTTAGGGTAAAAGAT-TGGATGGTCTT
* **
12816949 CAATCT-GCCTCAT-AGTCG
63 CAATCTACCCT-ATGA-TTA
* * * * * * *
12816967 GGGTAAGAGATCTGGAT--TACTTCAATCTGCCATCTAGTTAGTGTAAAATATCTGAAT--TACT
1 GGGTAAAAGAT-TGAATGGT-CTTCAATCTGCCCTCTGGTTAGGGTAAAAGAT-TGGATGGT-CT
* * * *
12817028 TCAATCTGCCCCATGGTTG
62 TCAATCTACCCTATGATTA
* * * * * * * *
12817047 GGGTAAGAGATCGGATGATCTTCAATCTGCCCTAT-GATAGGGGTAAGAGATCGGATGGTCTTCA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTA-GGGTAAAAGATTGGATGGTCTTCA
* *
12817111 ATCTACCCTCTAATTA
65 ATCTACCCTATGATTA
* * * * ** * *
12817127 AGGTAAAATATTGGATTG-CTTCAATCTGCCC-CATGGTCGGGGTAAGAGATTGGATGG-CTTTA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTC-TGGTTAGGGTAAAAGATTGGATGGTCTTCA
*
12817189 ATCTACCCTCT-AGTTA
65 ATCTACCCTATGA-TTA
* * * * * * * *
12817205 GGGTAAAAGATCGGATGGTCTTCAATCTGTCCC-ATGGTCAGGCTAAGAGATCGAATGGTCTTCA
1 GGGTAAAAGATTGAATGGTCTTCAATCTG-CCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCA
* * * *
12817269 ATTTACCCTCTGTTTG
65 ATCTACCCTATGATTA
* * * * *
12817285 GGGTAAGAGATCGAATGGTCTTCAATATACCCTCTGGTTAGGGTAAAAGATCGGATGGTCTTCAA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAA
* * * *
12817350 TCTGCCCCATG-GTC
66 TCTACCCTATGATTA
* ** * *** * * *
12817364 GGCCTAAAAGATCAAATGGTCTTCAATATGTATTCT-ATTCGAGGTAAGAA-ATCGGATGGTCTT
1 GG-GTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAG-GGTAA-AAGATTGGATGGTCTT
* * * **
12817427 CAATCTACCTTCTGGTCG
63 CAATCTACCCTATGATTA
* * * * *
12817445 GGGTAAGAGATTGGATGGTCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTGGATTG-CTTCAA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAA
* * **
12817509 TCTGCCCCATGATCG
66 TCTACCCTATGATTA
* * * * * *
12817524 GGGTAAGAGATTGGATGGTCTTCAATCTGTCCTCTAGTTAGGGTAACAGATTAGATGGTCTTCAA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAA
* *
12817589 TCTGCCCTCT-AGTTA
66 TCTACCCTATGA-TTA
* * * *
12817604 GGGTAAAAGATTGGATGGTCTTCAATTTGTCCTCTGGTTAGGGTAAAAGATTGGATTG-CTTCAA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAA
** * *
12817668 T-TTGCCTCATG-GTC
66 TCTACCCT-ATGATTA
* * * * * * *
12817682 GGAGTAAGAGATTAAAT-GACTTCAATTTGCCCTCTGGTTAGAGTAAAAGATTGAACT-G-CTTT
1 GG-GTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGA-TGGTCTTC
* * * **
12817744 AATTTGCCCCATGATCG
64 AATCTACCCTATGATTA
* * * * * *
12817761 GGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTAGTTAGGGTAAAAGATTGAATTG-CTTCAA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAA
* * **
12817825 TCT-GCCTCATGGTCG
66 TCTACCCT-ATGATTA
* * * * * * * **
12817840 GGGTAAGAGATCGAATGGTCTTCAATCTACCCTCTAGTTAAGGTAAAAGGTTAGATTACTTCAAT
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGA-T-GGTC--T
* * * *
12817905 CTCCAATCTGCCCCATGGTCA
62 -T-CAATCTACCCTATGATTA
* * * * * ** * * * *
12817926 AGGTAAGAGA-TCAGATGGTCTTCAATCTGCCATTTGGTCGGGGTAAGAGATCGAATGGTTTTCA
1 GGGTAAAAGATTGA-ATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCA
* *
12817990 ATCTACCCTCTAATTA
65 ATCTACCCTATGATTA
* ** *
12818006 GGGTAAAAGATT-AGATTG-CTTCAATCTGCCC-CATGGTCGGGGTAAGAGATTGGATGG-CTTC
1 GGGTAAAAGATTGA-ATGGTCTTCAATCTGCCCTC-TGGTTAGGGTAAAAGATTGGATGGTCTTC
* * *
12818067 AATTTGCCCTCT-AGTTA
64 AATCTACCCTATGA-TTA
* * * * *
12818084 GGGTAAAATATTAGACT--ACTTCAATCTGCCCCCATGGTTAGTGTAAAAGATTGGATGGTCTTC
1 GGGTAAAAGATT-GAATGGTCTTCAATCTGCCCTC-TGGTTAGGGTAAAAGATTGGATGGTCTTC
*
12818147 AATCTACCCTTTGATTA
64 AATCTACCCTATGATTA
* * * *
12818164 AGGTAAAAGATTGAATGGTCTTCAACCTGCCCTCTGATTAGGGTAAACGATTGGATG
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATG
12818221 ACTGTAACTT
Statistics
Matches: 1710, Mismatches: 320, Indels: 178
0.77 0.14 0.08
Matches are distributed among these distances:
76 62 0.04
77 9 0.01
78 223 0.13
79 913 0.53
80 415 0.24
81 29 0.02
82 2 0.00
84 2 0.00
85 3 0.00
86 50 0.03
87 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (80 bp):
GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCAA
TCTACCCTATGATTA
Found at i:12818558 original size:49 final size:49
Alignment explanation
Indices: 12818494--12818633 Score: 163
Period size: 49 Copynumber: 2.9 Consensus size: 49
12818484 CCTCATCTTC
* *
12818494 AGGGTGTAAGATTCGTCGTTACGGCTCCAATCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCGTCGTTACGGCTTCAATCTTTCCCTTCACATCTCT
* * * * * *
12818543 AGGGTATAAGGTTCGTCGCTACGGGTTCAACCTTTCTCTTCATATCTCT
1 AGGGTATAAGATTCGTCGTTACGGCTTCAATCTTTCCCTTCACATCTCT
* *** *
12818592 AGGGTATCAGATTTACCGTTGCGGCTTCAATCTTTCCCTTCA
1 AGGGTATAAGATTCGTCGTTACGGCTTCAATCTTTCCCTTCA
12818634 AACCTGTAGA
Statistics
Matches: 73, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
49 73 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (49 bp):
AGGGTATAAGATTCGTCGTTACGGCTTCAATCTTTCCCTTCACATCTCT
Found at i:12819557 original size:21 final size:22
Alignment explanation
Indices: 12819517--12819563 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
12819507 GACCTCCTCT
12819517 TTTTCTTTTCTTCTTTTTTTCC
1 TTTTCTTTTCTTCTTTTTTTCC
12819539 TTTTC-TTT-TTCTCTTTTTTCC
1 TTTTCTTTTCTTCT-TTTTTTCC
12819560 TTTT
1 TTTT
12819564 TATTTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTCTTTTCTTCTTTTTTTCC
Found at i:12819564 original size:22 final size:24
Alignment explanation
Indices: 12819515--12819570 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
12819505 TCGACCTCCT
12819515 CTTTTTC-TTTTCTTCTTTTTTTC
1 CTTTTTCTTTTTCTTCTTTTTTTC
12819538 C-TTTTCTTTTTC-TC-TTTTTTC
1 CTTTTTCTTTTTCTTCTTTTTTTC
*
12819559 CTTTTTATTTTT
1 CTTTTTCTTTTT
12819571 TTGGTGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 8 0.27
22 16 0.53
23 6 0.20
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (24 bp):
CTTTTTCTTTTTCTTCTTTTTTTC
Found at i:12833812 original size:200 final size:200
Alignment explanation
Indices: 12833468--12834095 Score: 934
Period size: 200 Copynumber: 3.1 Consensus size: 200
12833458 GAGGCAATCA
* * * * * *
12833468 TCTTCTTGATAAGATACAGAGAAGAACACCAACTCAGCGCCCAAACACGAGTAAATCTTCGGACT
1 TCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTC-AACACGAGTAAATCTTCGAACC
* * *
12833533 GAGCTTCCTGATG-AGACACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCTTGATGAGA
65 CAGCTTCCTGATGAAG-TACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGA
* * * *
12833597 CACAGAGAAGTGGACCAGATTTGTTTTCCTGAGGAGATCGAGAGAAGCGAATTAAAATAAGTGAT
129 CACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACAAGTGAT
12833662 GCGGTTG
194 GCGGTTG
* * *
12833669 TCTTCTTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCAAATCTTCGAACCC
1 TCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAACACGAGTAAATCTTCGAACCC
12833734 AGCTTCCTGATGAAGTACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGACA
66 AGCTTCCTGATGAAGTACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGACA
12833799 CAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACAAGTGATGC
131 CAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACAAGTGATGC
12833864 GGTTG
196 GGTTG
* * *
12833869 TCTTCCTGATGAAATTCAGAGAAGAACACCAACTCAACGCTCAACGCGAGTAAATCTTCGAACCC
1 TCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAACACGAGTAAATCTTCGAACCC
* * * * *
12833934 AGCTTACTGATGAAGTATTGAGAAGTAAGTCGAAGCAATAAAAAGGTTAACTTCCTGATGAGACA
66 AGCTTCCTGATGAAGTACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGACA
* * * *
12833999 CAGAGAAGTGGACTAAATTCGTCTTCCTGAGGAGATCCAGAGAGGCGAATTAAAACAAATGATTG
131 CAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACAAGTGA-TG
**
12834064 CGGTCA
195 CGGTTG
* *
12834070 TCCTCCTGATGAGACACAGAGAAGAA
1 TCTTCCTGATGAGATACAGAGAAGAA
12834096 GGCCAGGTCA
Statistics
Matches: 390, Mismatches: 35, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
200 322 0.83
201 68 0.17
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (200 bp):
TCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTCAACACGAGTAAATCTTCGAACCC
AGCTTCCTGATGAAGTACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGACA
CAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACAAGTGATGC
GGTTG
Found at i:12834570 original size:27 final size:27
Alignment explanation
Indices: 12834540--12834607 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
12834530 CCAAGTCCAT
12834540 TTACAAAGGCCCAAATTGAAGGCCCAA
1 TTACAAAGGCCCAAATTGAAGGCCCAA
* * *
12834567 TTACAAATGCCCAAATTGAGGGCCCAT
1 TTACAAAGGCCCAAATTGAAGGCCCAA
*
12834594 TTACAATGGCCCAA
1 TTACAAAGGCCCAA
12834608 GTAGGTCCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (27 bp):
TTACAAAGGCCCAAATTGAAGGCCCAA
Found at i:12835311 original size:9 final size:9
Alignment explanation
Indices: 12835299--12835385 Score: 59
Period size: 9 Copynumber: 9.1 Consensus size: 9
12835289 ATCCTATTAA
12835299 TAATAATAT
1 TAATAATAT
*
12835308 TAATATTAT
1 TAATAATAT
12835317 TGAATATATCAT
1 T-AATA-AT-AT
*
12835329 TAATAACAT
1 TAATAATAT
*
12835338 TAATTAATAG
1 TAA-TAATAT
*
12835348 TAATAATAA
1 TAATAATAT
12835357 TAATAAATAT
1 TAAT-AATAT
* *
12835367 T-TTAATAA
1 TAATAATAT
12835375 TAATAGATAT
1 TAATA-ATAT
12835385 T
1 T
12835386 TTGGTAATAT
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
8 5 0.08
9 26 0.43
10 21 0.35
11 5 0.08
12 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (9 bp):
TAATAATAT
Found at i:12835394 original size:21 final size:18
Alignment explanation
Indices: 12835351--12835387 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12835341 TTAATAGTAA
12835351 TAATAATAATAAATATTT
1 TAATAATAATAAATATTT
*
12835369 TAATAATAATAGATATTT
1 TAATAATAATAAATATTT
12835387 T
1 T
12835388 GGTAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TAATAATAATAAATATTT
Found at i:12836164 original size:32 final size:33
Alignment explanation
Indices: 12836127--12836228 Score: 99
Period size: 33 Copynumber: 3.2 Consensus size: 33
12836117 TGCACGTTTG
*
12836127 GTCC-TTCCATATTTTTAAATTA-TTTTAATTTA
1 GTCCTTTCCATACTTTT-AATTATTTTTAATTTA
*
12836159 GTCCTTTTCATACTTTTAATTATTTTTAATTTA
1 GTCCTTTCCATACTTTTAATTATTTTTAATTTA
* * *
12836192 G-CC---CAATAATTTTATTTACTTTTTAATTTA
1 GTCCTTTCCATACTTTTAATTA-TTTTTAATTTA
12836222 GTCCTTT
1 GTCCTTT
12836229 GACATTTTGA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
29 11 0.19
30 12 0.21
31 2 0.04
32 11 0.19
33 21 0.37
ACGTcount: A:0.25, C:0.14, G:0.04, T:0.57
Consensus pattern (33 bp):
GTCCTTTCCATACTTTTAATTATTTTTAATTTA
Found at i:12836498 original size:29 final size:29
Alignment explanation
Indices: 12836465--12836636 Score: 108
Period size: 29 Copynumber: 5.9 Consensus size: 29
12836455 CCCTAAACTG
12836465 TTCAAAAATTATCA-TTTTACCCCCGAACT
1 TTCAAAAATTATCATTTTTACCCCCGAA-T
* * *
12836494 TTCAAAAATTCT-ATTTTTAACCTCG-AT
1 TTCAAAAATTATCATTTTTACCCCCGAAT
* *
12836521 TTCACCAAAAATTACCA-TTTTACCCTCGAACT
1 TT---CAAAAATTATCATTTTTACCCCCGAA-T
* * * *
12836553 TTCCAAAATT-CCATTTTTAACCCTG-AT
1 TTCAAAAATTATCATTTTTACCCCCGAAT
*
12836580 TTCACCAAAAATTA-CATTTTTACCCCCGAAA
1 TT---CAAAAATTATCATTTTTACCCCCGAAT
* *
12836611 GTCAAAAATTATCA-TTTCACCCCCGA
1 TTCAAAAATTATCATTTTTACCCCCGA
12836637 GTATCCAAAG
Statistics
Matches: 113, Mismatches: 16, Indels: 29
0.72 0.10 0.18
Matches are distributed among these distances:
27 6 0.05
28 26 0.23
29 37 0.33
30 37 0.33
31 4 0.04
32 3 0.03
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
TTCAAAAATTATCATTTTTACCCCCGAAT
Found at i:12836532 original size:30 final size:31
Alignment explanation
Indices: 12836496--12836601 Score: 111
Period size: 30 Copynumber: 3.6 Consensus size: 31
12836486 CCCGAACTTT
*
12836496 CAAAAATT-CTATTTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTTAACCTCGATTTCAC
*
12836526 CAAAAATTACCA-TTTTACCCTCGAACTTT--C
1 CAAAAATTACCATTTTTAACCTCG-A-TTTCAC
12836556 C-AAAATT-CCATTTTTAACC-CTGATTTCAC
1 CAAAAATTACCATTTTTAACCTC-GATTTCAC
12836585 CAAAAATTA-CATTTTTA
1 CAAAAATTACCATTTTTA
12836602 CCCCCGAAAG
Statistics
Matches: 64, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
27 3 0.05
28 5 0.08
29 16 0.25
30 34 0.53
31 3 0.05
32 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.38
Consensus pattern (31 bp):
CAAAAATTACCATTTTTAACCTCGATTTCAC
Found at i:12836561 original size:59 final size:58
Alignment explanation
Indices: 12836467--12836609 Score: 216
Period size: 59 Copynumber: 2.4 Consensus size: 58
12836457 CTAAACTGTT
*
12836467 CAAAAATTATCATTTTACCCCCGAACTTTCAAAAATTCTATTTTTAA-CCTCGATTTCAC
1 CAAAAATTA-CATTTTACCCCCGAACTTTCAAAAATTCCATTTTTAACCCT-GATTTCAC
* *
12836526 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCTGATTTCAC
1 CAAAAATTA-CATTTTACCCCCGAACTTTCAAAAATTCCATTTTTAACCCTGATTTCAC
12836585 CAAAAATTACATTTTTACCCCCGAA
1 CAAAAATTACA-TTTTACCCCCGAA
12836610 AGTCAAAAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
58 2 0.03
59 72 0.94
60 3 0.04
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.35
Consensus pattern (58 bp):
CAAAAATTACATTTTACCCCCGAACTTTCAAAAATTCCATTTTTAACCCTGATTTCAC
Found at i:12836627 original size:59 final size:59
Alignment explanation
Indices: 12836467--12836627 Score: 204
Period size: 59 Copynumber: 2.7 Consensus size: 59
12836457 CTAAACTGTT
*
12836467 CAAAAATTATCATTTTACCCCCGAACTTTCAAAAA-TTCTATTTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAACTTTCAAAAATTTC-ATTTTTAACCTCGATTTCAC
* * *
12836526 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACC-CTGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAACTTTCAAAAATTTCATTTTTAACCTC-GATTTCAC
**
12836585 CAAAAATTA-CATTTTTACCCCCGAA-AGTCAAAAATTATCATTT
1 CAAAAATTACCA-TTTTACCCCCGAACTTTCAAAAATT-TCATTT
12836628 CACCCCCGAG
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
58 11 0.12
59 76 0.85
60 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCGAACTTTCAAAAATTTCATTTTTAACCTCGATTTCAC
Found at i:12838389 original size:56 final size:58
Alignment explanation
Indices: 12838302--12838410 Score: 161
Period size: 57 Copynumber: 1.9 Consensus size: 58
12838292 TATTTGGGTT
*
12838302 TATTATTTATTTATTTATCTATATTCAT-AAAATAATAAATAAA-AAATAAAAAATTAA
1 TATTATTTATATATTTATCTATATTCATAAAAATAAT-AATAAATAAATAAAAAATTAA
* *
12838359 TATTATTT-TATATTTATTTATATTCATAAAAATAATAATAAATGAATAAAAA
1 TATTATTTATATATTTATCTATATTCATAAAAATAATAATAAATAAATAAAAA
12838411 TAATAGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
56 23 0.49
57 24 0.51
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (58 bp):
TATTATTTATATATTTATCTATATTCATAAAAATAATAATAAATAAATAAAAAATTAA
Found at i:12838411 original size:56 final size:56
Alignment explanation
Indices: 12838302--12838415 Score: 153
Period size: 56 Copynumber: 2.0 Consensus size: 56
12838292 TATTTGGGTT
*
12838302 TATTATTTATTTATTTATCTATATTCATAAAATAATAAATAAAAAATAAAAAATTAA
1 TATTATTTATATATTTATCTATATTCATAAAATAATAAATAAAAAATAAAAAA-TAA
* *
12838359 TATTATTT-TATATTTATTTATATTCATAAAAATAAT-AATAAATGAAT-AAAAATAA
1 TATTATTTATATATTTATCTATATTCAT-AAAATAATAAATAAA-AAATAAAAAATAA
12838414 TA
1 TA
12838416 GAAAAATAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
55 5 0.10
56 28 0.54
57 19 0.37
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.43
Consensus pattern (56 bp):
TATTATTTATATATTTATCTATATTCATAAAATAATAAATAAAAAATAAAAAATAA
Found at i:12844272 original size:20 final size:21
Alignment explanation
Indices: 12844247--12844286 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12844237 ATATGGGAAA
12844247 TCAAATTTAAATT-TAAAATC
1 TCAAATTTAAATTCTAAAATC
*
12844267 TCAAATTTATATTCTAAAAT
1 TCAAATTTAAATTCTAAAAT
12844287 ATAGTATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (21 bp):
TCAAATTTAAATTCTAAAATC
Found at i:12849953 original size:18 final size:18
Alignment explanation
Indices: 12849930--12849967 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
12849920 TAATATAATT
12849930 TTATTCG-GTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
12849948 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
12849966 TT
1 TT
12849968 TCGAAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:12855246 original size:38 final size:38
Alignment explanation
Indices: 12855195--12855269 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
12855185 GAATAACATG
* *
12855195 ATTTTTATACCATTCAAG-CATTAATTGTTAAGAAACTT
1 ATTTTTACACCATT-AAGACATTAATTGATAAGAAACTT
* *
12855233 ATTTTTACACCATTTAGACATTCATTGATAAGAAACT
1 ATTTTTACACCATTAAGACATTAATTGATAAGAAACT
12855270 ATAACTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.06
38 30 0.94
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (38 bp):
ATTTTTACACCATTAAGACATTAATTGATAAGAAACTT
Found at i:12858582 original size:24 final size:24
Alignment explanation
Indices: 12858514--12858574 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
12858504 TGATACATGT
* *
12858514 ATATAAAAATATTTATAAATATCAA
1 ATAT-AAAATATTAATAAATTTCAA
*
12858539 ATAATAAAAT-TAAATAAATTTCAA
1 AT-ATAAAATATTAATAAATTTCAA
12858563 ATATAAAATATT
1 ATATAAAATATT
12858575 CATTAATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
23 7 0.23
24 14 0.47
25 7 0.23
26 2 0.07
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATAAAATATTAATAAATTTCAA
Found at i:12862675 original size:16 final size:15
Alignment explanation
Indices: 12862626--12862676 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 15
12862616 TAACACATGG
*
12862626 ATAAATAATTTAAAA
1 ATAAAAAATTTAAAA
12862641 ATATAAAAATATTCAAAA
1 ATA-AAAAAT-TT-AAAA
12862659 ATAAAAAATTTATAAA
1 ATAAAAAATTTA-AAA
12862675 AT
1 AT
12862677 TCAATAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.13
16 12 0.39
17 8 0.26
18 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAAAAATTTAAAA
Found at i:12864947 original size:23 final size:23
Alignment explanation
Indices: 12864878--12864947 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
12864868 TCATTAACAT
* *
12864878 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCGATTA-A
* *
12864902 TGTTCATGAACATGTTTGTTTAA
1 TGTTCATGAACATGTTCGATTAA
12864925 TGTTCATGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCGATTAA
12864948 ATTAAATGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 22 0.55
24 18 0.45
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (23 bp):
TGTTCATGAACATGTTCGATTAA
Found at i:12864974 original size:23 final size:23
Alignment explanation
Indices: 12864930--12864976 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12864920 TTTAATGTTC
* *
12864930 ATGAACATGTTCGATTAAATTAA
1 ATGAACATATTCGATGAAATTAA
12864953 ATGAACATATTCG-TGAATATTAA
1 ATGAACATATTCGATGAA-ATTAA
12864976 A
1 A
12864977 CAAACAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.34
Consensus pattern (23 bp):
ATGAACATATTCGATGAAATTAA
Found at i:12867845 original size:13 final size:13
Alignment explanation
Indices: 12867810--12867845 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
12867800 TTTTAATAAT
12867810 TTATGTTATTTTA
1 TTATGTTATTTTA
**
12867823 TTATAATATTTTA
1 TTATGTTATTTTA
12867836 TTATGTTATT
1 TTATGTTATT
12867846 GTGTTGTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (13 bp):
TTATGTTATTTTA
Found at i:12867845 original size:26 final size:26
Alignment explanation
Indices: 12867810--12867861 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
12867800 TTTTAATAAT
*
12867810 TTATGTTATTTTATTATAATATTTTA
1 TTATGTTATTGTATTATAATATTTTA
* *
12867836 TTATGTTATTGTGTTGTAATATTTTA
1 TTATGTTATTGTATTATAATATTTTA
12867862 GTCATTGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (26 bp):
TTATGTTATTGTATTATAATATTTTA
Found at i:12870109 original size:17 final size:18
Alignment explanation
Indices: 12870076--12870128 Score: 81
Period size: 17 Copynumber: 3.0 Consensus size: 18
12870066 CAGTCTGGTA
*
12870076 AGTTCATAGTGTAAATCT
1 AGTTCGTAGTGTAAATCT
12870094 AGTTCGTAGT-TAAATCT
1 AGTTCGTAGTGTAAATCT
*
12870111 ATTTCGTAGTGTAAATCT
1 AGTTCGTAGTGTAAATCT
12870129 TACTTAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 16 0.50
18 16 0.50
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (18 bp):
AGTTCGTAGTGTAAATCT
Found at i:12872940 original size:41 final size:42
Alignment explanation
Indices: 12872883--12872976 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 42
12872873 GTATGGTCTT
* * * *
12872883 TGCACTGGGTCGGGTCCAAGTCTGCTAACCAAGC-TTAACCC
1 TGCACTGGGTTGGGTCCAAGTCAGCCAACAAAGCTTTAACCC
* *
12872924 TGCACTGGGTTGGGTCCGAGTCAGCCAACAAAGCTTTAACCT
1 TGCACTGGGTTGGGTCCAAGTCAGCCAACAAAGCTTTAACCC
12872966 TGCACTGGGTT
1 TGCACTGGGTT
12872977 ATGTCGAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 29 0.63
42 17 0.37
ACGTcount: A:0.21, C:0.28, G:0.27, T:0.24
Consensus pattern (42 bp):
TGCACTGGGTTGGGTCCAAGTCAGCCAACAAAGCTTTAACCC
Found at i:12898261 original size:12 final size:12
Alignment explanation
Indices: 12898244--12898277 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
12898234 CCTTCATAGT
12898244 TTTTTAATTTTC
1 TTTTTAATTTTC
12898256 TTTTT-ATTTTC
1 TTTTTAATTTTC
*
12898267 TTTTTAGTTTT
1 TTTTTAATTTT
12898278 GATTTGATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTTAATTTTC
Found at i:12900048 original size:22 final size:22
Alignment explanation
Indices: 12900023--12900064 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12900013 TAATTTTGGG
12900023 TAAACATAAATTAATAAAAAAA
1 TAAACATAAATTAATAAAAAAA
*
12900045 TAAACGTAAATTAATAAAAA
1 TAAACATAAATTAATAAAAA
12900065 TATTAAATTT
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:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAACATAAATTAATAAAAAAA
Found at i:12913556 original size:1 final size:1
Alignment explanation
Indices: 12913550--12913574 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12913540 GTCCTTACAA
12913550 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
12913575 ACGACTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:12916608 original size:18 final size:20
Alignment explanation
Indices: 12916574--12916615 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
12916564 ACAAAAATTA
*
12916574 AAAATATCAAAACAATTTTT
1 AAAATATCAAAACAATTTAT
12916594 AAAAT-TCAAAA-AATTTAT
1 AAAATATCAAAACAATTTAT
12916612 AAAA
1 AAAA
12916616 ATTTCAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 6 0.29
20 5 0.24
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATATCAAAACAATTTAT
Found at i:12916616 original size:19 final size:19
Alignment explanation
Indices: 12916571--12916624 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
12916561 ACAACAAAAA
12916571 TTAAAAATATCAAAACAATT
1 TTAAAAAT-TCAAAACAATT
*
12916591 TTTAAAATTCAAAA-AATT
1 TTAAAAATTCAAAACAATT
12916609 TATAAAAATTTCAAAA
1 T-TAAAAA-TTCAAAA
12916625 TTTATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 5 0.17
19 11 0.37
20 14 0.47
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAAATTCAAAACAATT
Found at i:12916639 original size:24 final size:24
Alignment explanation
Indices: 12916606--12916652 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
12916596 AATTCAAAAA
* *
12916606 ATTTATAAAAATTTCAAAATTTAT
1 ATTTAAAAAAATTTAAAAATTTAT
12916630 ATTTAAAAAAATTTAAAAATTTA
1 ATTTAAAAAAATTTAAAAATTTA
12916653 AAAAATCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTTAAAAAAATTTAAAAATTTAT
Found at i:12916653 original size:18 final size:18
Alignment explanation
Indices: 12916566--12916657 Score: 59
Period size: 18 Copynumber: 5.2 Consensus size: 18
12916556 CTTTCACAAC
*
12916566 AAAAA-TTAAAAATATCAA
1 AAAAATTTAAAAAT-TTAA
* * *
12916584 AACAATTTTTAAAATTCAA
1 AA-AAATTTAAAAATTTAA
*
12916603 AAAATTTATAAAAATTT--
1 AAAAATT-TAAAAATTTAA
* *
12916620 CAAAATTT--ATATTTAA
1 AAAAATTTAAAAATTTAA
12916636 AAAAATTTAAAAATTTAA
1 AAAAATTTAAAAATTTAA
12916654 AAAA
1 AAAA
12916658 TCTAATGAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.09
16 8 0.14
17 5 0.09
18 18 0.31
19 15 0.26
20 7 0.12
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTTAAAAATTTAA
Found at i:12917836 original size:59 final size:58
Alignment explanation
Indices: 12917728--12917933 Score: 220
Period size: 59 Copynumber: 3.5 Consensus size: 58
12917718 GAAGTTTGGG
* * * * * * * *
12917728 AAAATCGGGATCAAAAATGGAATTTTGGGAAGTT-TAGGGGGAAATTGGTAACTCTTAAA
1 AAAATTGGG-TCAAAAATGGAATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTAGA
* *
12917787 AAAATTGGAGTCAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGA
1 AAAATTGG-GTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGA
* * *
12917846 AAAATTAGGGT-TAAAATGAAATTTTTGGAAGTTCGAGGGTAAAATGGCAATTTTTAGA
1 AAAATT-GGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGA
*
12917904 AAATTTGGGGTCAAAAATGGAA-TTTTGGAA
1 AAAATT-GGGTCAAAAATGGAATTTTTGGAA
12917934 AAGTTTGGGG
Statistics
Matches: 125, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
58 60 0.48
59 61 0.49
60 4 0.03
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (58 bp):
AAAATTGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGA
Found at i:12917841 original size:29 final size:28
Alignment explanation
Indices: 12917800--12917900 Score: 116
Period size: 29 Copynumber: 3.5 Consensus size: 28
12917790 ATTGGAGTCA
12917800 AAAATGTAATTTTTGGAAGTTCGAGGGT
1 AAAATGTAATTTTTGGAAGTTCGAGGGT
*
12917828 AAAATGGTAATTTTTGGAAAAATT--AGGGTT
1 AAAAT-GTAATTTTTGG--AAGTTCGAGGG-T
*
12917858 AAAATGAAATTTTTGGAAGTTCGAGGGT
1 AAAATGTAATTTTTGGAAGTTCGAGGGT
*
12917886 AAAATGGCAATTTTT
1 AAAAT-GTAATTTTT
12917901 AGAAAATTTG
Statistics
Matches: 62, Mismatches: 4, Indels: 13
0.78 0.05 0.16
Matches are distributed among these distances:
27 4 0.06
28 11 0.18
29 37 0.60
30 6 0.10
31 4 0.06
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGT
Found at i:12917878 original size:58 final size:59
Alignment explanation
Indices: 12917786--12917933 Score: 203
Period size: 58 Copynumber: 2.5 Consensus size: 59
12917776 TAACTCTTAA
* * *
12917786 AAAAATT-GGAGTCAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGG
1 AAAAATTAGG-GTCAAAAATGAAATTTTTGGAAGTTCGAGGGTAAAATGGCAATTTTTAG
*
12917845 AAAAATTAGGGT-TAAAATGAAATTTTTGGAAGTTCGAGGGTAAAATGGCAATTTTTAG
1 AAAAATTAGGGTCAAAAATGAAATTTTTGGAAGTTCGAGGGTAAAATGGCAATTTTTAG
* * *
12917903 AAAATTTGGGGTCAAAAATGGAA-TTTTGGAA
1 AAAAATTAGGGTCAAAAATGAAATTTTTGGAA
12917934 AAGTTTGGGG
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
58 60 0.76
59 17 0.22
60 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.32
Consensus pattern (59 bp):
AAAAATTAGGGTCAAAAATGAAATTTTTGGAAGTTCGAGGGTAAAATGGCAATTTTTAG
Found at i:12917914 original size:29 final size:28
Alignment explanation
Indices: 12917800--12917943 Score: 114
Period size: 29 Copynumber: 5.0 Consensus size: 28
12917790 ATTGGAGTCA
* * *
12917800 AAAATGTAATTTTTGG-AAGTTCGAGGGT
1 AAAATGGAATTTTTGGAAAATTTG-GGGT
* *
12917828 AAAATGGTAATTTTTGGAAAAATTAGGGTT
1 AAAATGG-AATTTTTGG-AAAATTTGGGGT
* * *
12917858 AAAATGAAATTTTTGG-AAGTTCGAGGGT
1 AAAATGGAATTTTTGGAAAATTTG-GGGT
*
12917886 AAAATGGCAATTTTTAGAAAATTTGGGGT
1 AAAATGG-AATTTTTGGAAAATTTGGGGT
12917915 CAAAAATGGAA-TTTTGGAAAAGTTTGGGG
1 --AAAATGGAATTTTTGGAAAA-TTTGGGG
12917944 GTCAAATTAT
Statistics
Matches: 94, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
27 5 0.05
28 15 0.16
29 39 0.41
30 23 0.24
31 12 0.13
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAAATTTGGGGT
Found at i:12917941 original size:30 final size:32
Alignment explanation
Indices: 12917886--12917949 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
12917876 GTTCGAGGGT
12917886 AAAATGGCAATTTTTAGAAAATTT-GGGGTCA
1 AAAATGGCAATTTTTAGAAAATTTGGGGGTCA
*
12917917 AAAATGG-AA-TTTTGGAAAAGTTTGGGGGTCA
1 AAAATGGCAATTTTTAGAAAA-TTTGGGGGTCA
12917948 AA
1 AA
12917950 TTATGATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 9 0.30
30 5 0.17
31 16 0.53
ACGTcount: A:0.39, C:0.05, G:0.27, T:0.30
Consensus pattern (32 bp):
AAAATGGCAATTTTTAGAAAATTTGGGGGTCA
Found at i:12917961 original size:31 final size:29
Alignment explanation
Indices: 12917886--12917963 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 29
12917876 GTTCGAGGGT
*
12917886 AAAATGGCAATTTTTAGAAAATTTGGGGTCA
1 AAAATGG--ATTTTTGGAAAATTTGGGGTCA
*
12917917 AAAATGGAATTTTGGAAAAGTTTGGGGGTCA
1 AAAATGGATTTTTGGAAAA-TTT-GGGGTCA
*
12917948 AATTAT-GATTTTTGGA
1 AA-AATGGATTTTTGGA
12917964 CAGTTTAGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 10 0.25
30 3 0.08
31 25 0.62
32 2 0.05
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAATGGATTTTTGGAAAATTTGGGGTCA
Found at i:12919171 original size:6 final size:6
Alignment explanation
Indices: 12919160--12919205 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
12919150 TGTTATTTGT
* *
12919160 TATTAA TATTAA TATTAA TATTAA TATTAA TAATACT TATTAA TAT
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTA-A TATTAA TAT
12919206 GTTTTGAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 31 0.89
7 4 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TATTAA
Found at i:12919636 original size:25 final size:25
Alignment explanation
Indices: 12919608--12919667 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
12919598 ATGCAGTGGC
* **
12919608 GGTGATGGTAGAGCAGGTTGAAGCT
1 GGTGATGGCAGAGCAAATTGAAGCT
* *
12919633 GGTGGTGGCAGAGCAAATTGAAGTT
1 GGTGATGGCAGAGCAAATTGAAGCT
*
12919658 GGTGGTGGCA
1 GGTGATGGCA
12919668 CTGTTGGTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.23, C:0.08, G:0.45, T:0.23
Consensus pattern (25 bp):
GGTGATGGCAGAGCAAATTGAAGCT
Found at i:12919912 original size:6 final size:6
Alignment explanation
Indices: 12919895--12919995 Score: 93
Period size: 6 Copynumber: 17.0 Consensus size: 6
12919885 ATTATTCAAA
* * *
12919895 TAAATT TGAATT TAAATT T--ATGA TAAATT TAAATT TCTAATT TAAATT
1 TAAATT TAAATT TAAATT TAAAT-T TAAATT TAAATT T-AAATT TAAATT
* * *
12919943 TAAA-A TAAATT TAAATT TCTAATT TAAATT TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT
12919990 TAAATT
1 TAAATT
12919996 CTGTTGGGTC
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
4 2 0.03
5 9 0.12
6 53 0.70
7 12 0.16
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:12919938 original size:13 final size:13
Alignment explanation
Indices: 12919920--12919973 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 13
12919910 ATTTATGATA
12919920 AATTTAAATTTCT
1 AATTTAAATTTCT
*
12919933 AATTTAAATTTAAAAT
1 AATTTAAATTT---CT
12919949 AAATTTAAATTTCT
1 -AATTTAAATTTCT
12919963 AATTTAAATTT
1 AATTTAAATTT
12919974 AAAATAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 22 0.63
14 1 0.03
16 1 0.03
17 11 0.31
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTTAAATTTCT
Found at i:12919939 original size:30 final size:30
Alignment explanation
Indices: 12919895--12919990 Score: 158
Period size: 30 Copynumber: 3.2 Consensus size: 30
12919885 ATTATTCAAA
* **
12919895 TAAATTT-GAATTTAAATTTATGATAAATT
1 TAAATTTCTAATTTAAATTTAAAATAAATT
12919924 TAAATTTCTAATTTAAATTTAAAATAAATT
1 TAAATTTCTAATTTAAATTTAAAATAAATT
12919954 TAAATTTCTAATTTAAATTTAAAATAAATT
1 TAAATTTCTAATTTAAATTTAAAATAAATT
12919984 TAAATTT
1 TAAATTT
12919991 AAATTCTGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
29 7 0.11
30 56 0.89
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
TAAATTTCTAATTTAAATTTAAAATAAATT
Found at i:12919992 original size:17 final size:17
Alignment explanation
Indices: 12919903--12919993 Score: 90
Period size: 17 Copynumber: 5.8 Consensus size: 17
12919893 AATAAATTTG
**
12919903 AATTTAAATTTATGATA
1 AATTTAAATTTAAAATA
*
12919920 AATTTAAATTT---CT-
1 AATTTAAATTTAAAATA
12919933 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
12919950 AATTTAAATTT---CT-
1 AATTTAAATTTAAAATA
12919963 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
12919980 AATTTAAATTTAAA
1 AATTTAAATTTAAA
12919994 TTCTGTTGGG
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
13 22 0.35
14 2 0.03
16 2 0.03
17 36 0.58
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:12922177 original size:22 final size:23
Alignment explanation
Indices: 12922149--12922191 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
12922139 TGACAATATA
12922149 AAAATT-AAG-ATATCAAATTATC
1 AAAATTAAAGTATAT-AAATTATC
12922171 AAAATTAAAGTATATAAATTA
1 AAAATTAAAGTATATAAATTA
12922192 AATCATAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (23 bp):
AAAATTAAAGTATATAAATTATC
Found at i:12934389 original size:31 final size:31
Alignment explanation
Indices: 12934351--12934413 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
12934341 ATGATCAAAT
12934351 TTTTCTATGTATCTTTAAGGATCTTTAAAAA
1 TTTTCTATGTATCTTTAAGGATCTTTAAAAA
12934382 TTTTCTATGTATCTTTAAGGATCTTTAAAAA
1 TTTTCTATGTATCTTTAAGGATCTTTAAAAA
12934413 T
1 T
12934414 CATATCTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.49
Consensus pattern (31 bp):
TTTTCTATGTATCTTTAAGGATCTTTAAAAA
Found at i:12935341 original size:14 final size:14
Alignment explanation
Indices: 12935322--12935368 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
12935312 AACTTGTTGC
*
12935322 TTTTAATTTTTGTA
1 TTTTAATTTTTATA
12935336 TTTTAA-TTTTATCAA
1 TTTTAATTTTTAT--A
*
12935351 TTTTAATCTTTATA
1 TTTTAATTTTTATA
12935365 TTTT
1 TTTT
12935369 TTTGAATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 5 0.18
14 11 0.39
15 7 0.25
16 5 0.18
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (14 bp):
TTTTAATTTTTATA
Found at i:12937010 original size:2 final size:2
Alignment explanation
Indices: 12937003--12937039 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12936993 GAGGTCTCAA
12937003 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
12937040 AAGAACAAAA
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:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12942922 original size:21 final size:22
Alignment explanation
Indices: 12942882--12942923 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
12942872 TTGATTTGTA
* *
12942882 TATGTTTTTATTTTTTAATTTT
1 TATGATTTTATTTATTAATTTT
12942904 TATGATTTT-TTTATTAATTT
1 TATGATTTTATTTATTAATTT
12942924 ATTCAATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (22 bp):
TATGATTTTATTTATTAATTTT
Found at i:12945807 original size:22 final size:23
Alignment explanation
Indices: 12945776--12945819 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
12945766 GTGACTATGG
12945776 TTTTTGTCCTT-TTTATCTTTCTC
1 TTTTTGTCCTTCTTT-TCTTTCTC
12945799 TTTTT-TCCTTCTTTTCTTTCT
1 TTTTTGTCCTTCTTTTCTTTCT
12945820 TTCTAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTTGTCCTTCTTTTCTTTCTC
Found at i:12947381 original size:2 final size:2
Alignment explanation
Indices: 12947376--12947410 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12947366 TTATGATTTG
12947376 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 T
12947411 TTGTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12951773 original size:15 final size:15
Alignment explanation
Indices: 12951742--12951790 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
12951732 AATTAATTTT
12951742 TTTACTAAATAATAAAA
1 TTTA-TAAA-AATAAAA
* * *
12951759 TTTTTATATATAAAA
1 TTTATAAAAATAAAA
12951774 TTTATAAAAATAAAA
1 TTTATAAAAATAAAA
12951789 TT
1 TT
12951791 AAAAAAGTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 20 0.77
16 3 0.12
17 3 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTATAAAAATAAAA
Found at i:12953952 original size:2 final size:2
Alignment explanation
Indices: 12953909--12953933 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12953899 ATACATTTAC
12953909 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
12953934 ATTTTATTTT
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:12954264 original size:56 final size:57
Alignment explanation
Indices: 12954151--12954261 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
12954141 AATAAAAAAA
*
12954151 TATTTTTTTATTCGTGTTTTTTGATGCTGGCCATTAGCTACCAAACACCCAAAAATT
1 TATTTTTTTATTCGTGTTTTTTGATGCTGGCCATTAGATACCAAACACCCAAAAATT
* * **
12954208 TATTTTTTTATTCGTGTTTTTTGGTGCTTGCCATTAGATGGCAAACACCCAAAA
1 TATTTTTTTATTCGTGTTTTTTGATGCTGGCCATTAGATACCAAACACCCAAAA
12954262 TTTTTGTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.42
Consensus pattern (57 bp):
TATTTTTTTATTCGTGTTTTTTGATGCTGGCCATTAGATACCAAACACCCAAAAATT
Found at i:12955521 original size:18 final size:18
Alignment explanation
Indices: 12955472--12955522 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
12955462 CAAACTAATT
*
12955472 TATAAATATTTC-AAATA
1 TATATATATTTCTAAATA
* *
12955489 TATATGA-AATACTAAATA
1 TATAT-ATATTTCTAAATA
12955507 TATATATATTTCTAAA
1 TATATATATTTCTAAA
12955523 ATTCCCCTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (18 bp):
TATATATATTTCTAAATA
Found at i:12965358 original size:9 final size:10
Alignment explanation
Indices: 12965339--12965381 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
12965329 TCAATTAAAT
12965339 AAATTATTAA
1 AAATTATTAA
*
12965349 AAATTATAAAA
1 AAATTAT-TAA
12965360 AAATTATTTAA
1 AAATTA-TTAA
12965371 AAA-TATTAA
1 AAATTATTAA
12965380 AA
1 AA
12965382 TTTAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 6 0.21
10 9 0.31
11 13 0.45
12 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAATTATTAA
Found at i:12965380 original size:22 final size:21
Alignment explanation
Indices: 12965332--12965381 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
12965322 ATCTGATTCA
*
12965332 ATTAAATAAATTATTAAAAAT
1 ATTAAAAAAATTATTAAAAAT
12965353 -TATAAAAAAATTATTTAAAAAT
1 AT-TAAAAAAATTA-TTAAAAAT
12965375 ATTAAAA
1 ATTAAAA
12965382 TTTAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 10 0.40
22 13 0.52
23 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTAAAAAAATTATTAAAAAT
Found at i:12965381 original size:21 final size:21
Alignment explanation
Indices: 12965332--12965381 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
12965322 ATCTGATTCA
12965332 ATTAAATAAATTATTAAAAATT
1 ATTAAA-AAATTATTAAAAATT
*
12965354 ATAAAAAAATTATTTAAAAA-T
1 ATTAAAAAATTA-TTAAAAATT
12965375 ATTAAAA
1 ATTAAAA
12965382 TTTAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTAAAAAATTATTAAAAATT
Found at i:12965806 original size:23 final size:24
Alignment explanation
Indices: 12965779--12965824 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
12965769 TATCGATAAA
*
12965779 ATGTCTCTTAAATATTAA-AAATT
1 ATGTCGCTTAAATATTAACAAATT
* *
12965802 ATGTCGCTTGATTATTAACAAAT
1 ATGTCGCTTAAATATTAACAAAT
12965825 AGTCATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (24 bp):
ATGTCGCTTAAATATTAACAAATT
Found at i:12968799 original size:31 final size:31
Alignment explanation
Indices: 12968721--12968802 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
12968711 GAATTTGATC
12968721 AAATCAAAA-TCTCATGTATAAAATTGCAAAA
1 AAATCAAAAGT-TCATGTATAAAATTGCAAAA
* **
12968752 AAATCAAAAGTACATGTATAAAATTGCACATT
1 AAATCAAAAGTTCATGTATAAAATTGCA-AAA
*
12968784 AAA-CTAAAGTTCATGTATA
1 AAATCAAAAGTTCATGTATA
12968803 GTTTTGAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
31 39 0.89
32 5 0.11
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (31 bp):
AAATCAAAAGTTCATGTATAAAATTGCAAAA
Found at i:12970231 original size:19 final size:19
Alignment explanation
Indices: 12970191--12970232 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
12970181 AAATTTAGCC
* *
12970191 TAAATAGAATCATATAACA
1 TAAATAGAATAATATAAAA
12970210 TAAATA-AATAATATAAAAA
1 TAAATAGAATAATAT-AAAA
12970229 TAAA
1 TAAA
12970233 ATCAGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (19 bp):
TAAATAGAATAATATAAAA
Found at i:12973180 original size:14 final size:14
Alignment explanation
Indices: 12973158--12973200 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
12973148 ACTCACTTAT
12973158 ATTAATTTTTTTTA
1 ATTAATTTTTTTTA
*
12973172 ATT-ATTTTTATATA
1 ATTAATTTTT-TTTA
12973186 ATTAATTTTTTTTA
1 ATTAATTTTTTTTA
12973200 A
1 A
12973201 ATTGAGGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 6 0.24
14 13 0.52
15 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTAATTTTTTTTA
Found at i:12975227 original size:13 final size:12
Alignment explanation
Indices: 12975185--12975225 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
12975175 TTTAAAAATA
12975185 AAAATAATTTTT
1 AAAATAATTTTT
12975197 AAAATAATTATTT
1 AAAATAATT-TTT
*
12975210 CAAATAATTTTT
1 AAAATAATTTTT
12975222 AAAA
1 AAAA
12975226 ATGTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
AAAATAATTTTT
Found at i:12978379 original size:13 final size:13
Alignment explanation
Indices: 12978361--12978390 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
12978351 CCTTTGACAA
12978361 TGCACACGCATTT
1 TGCACACGCATTT
12978374 TGCACACGCATTT
1 TGCACACGCATTT
12978387 TGCA
1 TGCA
12978391 TACACAGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (13 bp):
TGCACACGCATTT
Found at i:12983973 original size:32 final size:32
Alignment explanation
Indices: 12983937--12984000 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
12983927 TTTTCTTCTA
*
12983937 TTTAATTTCAATCAATCCTTTCTCTTT-TTTTC
1 TTTAATCTCAATCAATCCTTTCT-TTTATTTTC
* *
12983969 TTTAATCTCAATCCATCTTTTCTTTTATTTTC
1 TTTAATCTCAATCAATCCTTTCTTTTATTTTC
12984001 CCTAAATCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 3 0.11
32 25 0.89
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (32 bp):
TTTAATCTCAATCAATCCTTTCTTTTATTTTC
Found at i:12985038 original size:22 final size:23
Alignment explanation
Indices: 12984997--12985040 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
12984987 TTAACAAGTT
**
12984997 TTTTGCATAATTTTTTAAAAATG
1 TTTTGCATAATTTTAGAAAAATG
12985020 TTTT-CATAATTTTAGAAAAAT
1 TTTTGCATAATTTTAGAAAAAT
12985041 AAATTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (23 bp):
TTTTGCATAATTTTAGAAAAATG
Found at i:12990748 original size:51 final size:51
Alignment explanation
Indices: 12990664--12990838 Score: 287
Period size: 51 Copynumber: 3.4 Consensus size: 51
12990654 TAAATGAAAG
* *
12990664 GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAATCCTTTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTAAA
* *
12990715 GGTCCGATGACTAAGTGTCATCATGAGTGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTAAA
* *
12990766 GGTCCGATGACTAAGTGCCATCATGAATAAATGAATCCTTTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTAAA
*
12990817 GGCCCGATGACTAAGTGTCATC
1 GGTCCGATGACTAAGTGTCATC
12990839 GTGAATTTAT
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 114 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.30
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTAAA
Found at i:12991658 original size:21 final size:21
Alignment explanation
Indices: 12991615--12991674 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
12991605 TAGATGCATG
* *
12991615 ACATGTATAGGTAGAAATTAT
1 ACATGTATCGGTAGAAATAAT
* *
12991636 ACTTGTATCGGTAGAACTAAT
1 ACATGTATCGGTAGAAATAAT
* *
12991657 ACAAGTACCGGTAGAAAT
1 ACATGTATCGGTAGAAAT
12991675 CTGCACTGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (21 bp):
ACATGTATCGGTAGAAATAAT
Found at i:13001491 original size:9 final size:9
Alignment explanation
Indices: 13001479--13001544 Score: 55
Period size: 9 Copynumber: 7.0 Consensus size: 9
13001469 TTTAGAATTT
13001479 TTTTTTTAA
1 TTTTTTTAA
13001488 -TTTTTTATA
1 TTTTTTTA-A
*
13001497 TGTTCTTTAGA
1 T-TTTTTTA-A
13001508 -TTTTTTAA
1 TTTTTTTAA
13001516 TATTTTTTAAA
1 T-TTTTTT-AA
*
13001527 TTTTTATAA
1 TTTTTTTAA
13001536 TTTTTTTAA
1 TTTTTTTAA
13001545 AATATAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
8 8 0.17
9 17 0.37
10 11 0.24
11 10 0.22
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.70
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:13001511 original size:19 final size:18
Alignment explanation
Indices: 13001479--13001541 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 18
13001469 TTTAGAATTT
*
13001479 TTTTTTTAATTTTTTATA
1 TTTTTTAAATTTTTTATA
*
13001497 TGTTCTTTAGATTTTTTAATA
1 T-TT-TTTAAATTTTTT-ATA
13001518 TTTTTTAAA-TTTTTATAA
1 TTTTTTAAATTTTTTAT-A
13001536 TTTTTT
1 TTTTTT
13001542 TAAAATATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 2 0.05
18 13 0.34
19 7 0.18
20 12 0.32
21 4 0.11
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTTTAAATTTTTTATA
Found at i:13001542 original size:19 final size:20
Alignment explanation
Indices: 13001480--13001545 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 20
13001470 TTAGAATTTT
* *
13001480 TTTTTTAATTTTTTAT-ATG
1 TTTTTTAAATTTTTATAATA
* *
13001499 TTCTTTAGATTTTT-TAATA
1 TTTTTTAAATTTTTATAATA
13001518 TTTTTTAAATTTTTATAAT-
1 TTTTTTAAATTTTTATAATA
13001537 TTTTTTAAA
1 TTTTTTAAA
13001546 ATATAAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.03
19 34 0.87
20 4 0.10
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTTTTAAATTTTTATAATA
Found at i:13001583 original size:19 final size:19
Alignment explanation
Indices: 13001552--13001602 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
13001542 TAAAATATAA
*
13001552 ATTTTGAAATTTTCATAAA-T
1 ATTTTG-AATTTT-AAAAATT
13001572 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATT
*
13001591 ATTGTGAATTTT
1 ATTTTGAATTTT
13001603 GTTTGTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 18 0.64
20 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:13006618 original size:6 final size:7
Alignment explanation
Indices: 13006600--13006624 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13006590 ATTCAATAAT
13006600 GAAAAAA
1 GAAAAAA
13006607 GAAAAAA
1 GAAAAAA
13006614 GAAAAAA
1 GAAAAAA
13006621 GAAA
1 GAAA
13006625 TAAAAGAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:13007362 original size:58 final size:59
Alignment explanation
Indices: 13007285--13007421 Score: 145
Period size: 58 Copynumber: 2.3 Consensus size: 59
13007275 ATTATGAATA
*
13007285 TAAAACAA-TCAACAAATTTAACTCTT-AAAATTTACAAAATTTAT-TTTAATTTGAATTT
1 TAAAA-AATTCAATAAATTTAAC-CTTCAAAATTTACAAAATTTATATTTAATTTGAATTT
* * * * *
13007343 TAAAAAATTCAATAAATTTAACCTTCGAGATTTATAAAATTTATCAATTTAGTTTTAATTT
1 TAAAAAATTCAATAAATTTAACCTTCAAAATTTACAAAATTTAT--ATTTAATTTGAATTT
**
13007404 TAAAATTTTCAATAAATT
1 TAAAAAATTCAATAAATT
13007422 AAATTTTGAT
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
57 5 0.08
58 33 0.50
61 28 0.42
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (59 bp):
TAAAAAATTCAATAAATTTAACCTTCAAAATTTACAAAATTTATATTTAATTTGAATTT
Found at i:13007765 original size:21 final size:21
Alignment explanation
Indices: 13007739--13007780 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
13007729 AATCAAATTG
13007739 GGATTTTTAGTTTTAGTTTTA
1 GGATTTTTAGTTTTAGTTTTA
* *
13007760 GGATTTTTATTTTTATTTTTA
1 GGATTTTTAGTTTTAGTTTTA
13007781 TTTATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (21 bp):
GGATTTTTAGTTTTAGTTTTA
Found at i:13007859 original size:16 final size:16
Alignment explanation
Indices: 13007838--13007870 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13007828 TGGGTTTGTA
13007838 TATATTGGATTAGGTT
1 TATATTGGATTAGGTT
*
13007854 TATATTGGATTGGGTT
1 TATATTGGATTAGGTT
13007870 T
1 T
13007871 GGGTGGATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (16 bp):
TATATTGGATTAGGTT
Found at i:13014686 original size:149 final size:148
Alignment explanation
Indices: 13014508--13014810 Score: 597
Period size: 149 Copynumber: 2.0 Consensus size: 148
13014498 AACCTGAAAC
13014508 ATTGTAATATATATATATATATATGAATAAAAAGCTATTTAAAAATTCAAAACATTACATCAATC
1 ATTGTAATATATATATATATATATGAATAAAAAGCTATTTAAAAATTCAAAACATTACATCAATC
13014573 AGCATAAACAAATACATAACAATATAATTGATTTTAATCAATACAAAAATGATATAAACTATCAT
66 AGCATAAACAAATACATAACAATATAATTGATTTTAATCAATACAAAAATGATATAAACTATCAT
13014638 GGGAAGAAGGGCATTAAT
131 GGGAAGAAGGGCATTAAT
13014656 ATTGTATATATATATATATATATATGAATAAAAAGCTATTTAAAAATTCAAAACATTACATCAAT
1 ATTGTA-ATATATATATATATATATGAATAAAAAGCTATTTAAAAATTCAAAACATTACATCAAT
13014721 CAGCATAAACAAATACATAACAATATAATTGATTTTAATCAATACAAAAATGATATAAACTATCA
65 CAGCATAAACAAATACATAACAATATAATTGATTTTAATCAATACAAAAATGATATAAACTATCA
13014786 TGGGAAGAAGGGCATTAAT
130 TGGGAAGAAGGGCATTAAT
13014805 ATTGTA
1 ATTGTA
13014811 GTTGAAGCTG
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
148 6 0.04
149 148 0.96
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (148 bp):
ATTGTAATATATATATATATATATGAATAAAAAGCTATTTAAAAATTCAAAACATTACATCAATC
AGCATAAACAAATACATAACAATATAATTGATTTTAATCAATACAAAAATGATATAAACTATCAT
GGGAAGAAGGGCATTAAT
Found at i:13019146 original size:29 final size:29
Alignment explanation
Indices: 13019109--13019318 Score: 133
Period size: 29 Copynumber: 7.2 Consensus size: 29
13019099 TCAAAATGCG
* *
13019109 ATTTTTGGATGCTCGAGGGTAAAATAGTA
1 ATTTTTGGATGTTCGGGGGTAAAATAGTA
* *
13019138 ATTTTTGGAAGTTTTGGGGGTAAAATAGTA
1 ATTTTTGGATG-TTCGGGGGTAAAATAGTA
* *
13019168 ATTTTTGAATGTTCGGGGGTAAAA-ACTTA
1 ATTTTTGGATGTTCGGGGGTAAAATA-GTA
* * *
13019197 ATTTTTGGAAAGTT-TGGGGTCAAAAATA-CA
1 ATTTTTGG-ATGTTCGGGGGT--AAAATAGTA
* * * *
13019227 ATTTTAGGAAGTTTGGGGGTAAAATGGTA
1 ATTTTTGGATGTTCGGGGGTAAAATAGTA
* * **
13019256 ATTTTTGGAAGTTTGGGGACAAAA-ATGTA
1 ATTTTTGGATGTTCGGGGGTAAAATA-GTA
* * * *
13019285 ATTTTTGTGAAGTTCGGAGGTTAAAT-GTG
1 ATTTTTG-GATGTTCGGGGGTAAAATAGTA
13019314 ATTTT
1 ATTTT
13019319 GGAAAAATTC
Statistics
Matches: 144, Mismatches: 26, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
28 6 0.04
29 80 0.56
30 53 0.37
31 4 0.03
32 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.38
Consensus pattern (29 bp):
ATTTTTGGATGTTCGGGGGTAAAATAGTA
Found at i:13019161 original size:30 final size:29
Alignment explanation
Indices: 13019125--13019298 Score: 178
Period size: 29 Copynumber: 5.9 Consensus size: 29
13019115 GGATGCTCGA
13019125 GGGTAAAATAGTAATTTTTGGAAGTTTTGG
1 GGGTAAAATAGTAATTTTTGGAAG-TTTGG
*
13019155 GGGTAAAATAGTAATTTTT-GAATGTTCGG
1 GGGTAAAATAGTAATTTTTGGAA-GTTTGG
*
13019184 GGGTAAAA-ACTTAATTTTTGGAAAGTTT-G
1 GGGTAAAATA-GTAATTTTTGG-AAGTTTGG
* *
13019213 GGGTCAAAAATA-CAATTTTAGGAAGTTTGG
1 GGGT--AAAATAGTAATTTTTGGAAGTTTGG
*
13019243 GGGTAAAATGGTAATTTTTGGAAGTTTGG
1 GGGTAAAATAGTAATTTTTGGAAGTTTGG
**
13019272 GGACAAAA-ATGTAATTTTTGTGAAGTT
1 GGGTAAAATA-GTAATTTTTG-GAAGTT
13019299 CGGAGGTTAA
Statistics
Matches: 122, Mismatches: 11, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
28 6 0.05
29 66 0.54
30 43 0.35
31 6 0.05
32 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.37
Consensus pattern (29 bp):
GGGTAAAATAGTAATTTTTGGAAGTTTGG
Found at i:13019297 original size:59 final size:58
Alignment explanation
Indices: 13019125--13019322 Score: 192
Period size: 59 Copynumber: 3.4 Consensus size: 58
13019115 GGATGCTCGA
**
13019125 GGGTAAAATAGTAATTTTTGGAAGTTTTGGGGGTAAAATAGTAA-TTTT-TGAATGTTCGG
1 GGGTAAAATAGTAATTTTTGGAAG-TTTGGGGCAAAAAT-GTAATTTTTGTGAA-GTTCGG
* ** * *
13019184 GGGTAAAA-ACTTAATTTTTGGAAAGTTTGGGGTCAAAAATACAATTTTAG-GAAGTTTGG
1 GGGTAAAATA-GTAATTTTTGG-AAGTTTGGGG-CAAAAATGTAATTTTTGTGAAGTTCGG
*
13019243 GGGTAAAATGGTAATTTTTGGAAGTTTGGGGACAAAAATGTAATTTTTGTGAAGTTCGG
1 GGGTAAAATAGTAATTTTTGGAAGTTTGGGG-CAAAAATGTAATTTTTGTGAAGTTCGG
* * *
13019302 AGGTTAAAT-GTGA-TTTTGGAA
1 GGGTAAAATAGTAATTTTTGGAA
13019323 AAATTCAAGG
Statistics
Matches: 115, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
57 8 0.07
58 28 0.24
59 65 0.57
60 14 0.12
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.36
Consensus pattern (58 bp):
GGGTAAAATAGTAATTTTTGGAAGTTTGGGGCAAAAATGTAATTTTTGTGAAGTTCGG
Found at i:13019365 original size:30 final size:29
Alignment explanation
Indices: 13019125--13019389 Score: 145
Period size: 30 Copynumber: 9.0 Consensus size: 29
13019115 GGATGCTCGA
*
13019125 GGGTAAAATAGTAATTTTTGG-AAGTTTTGG
1 GGGTAAAATA-TAATTTTTGGAAAG-TTTAG
* **
13019155 GGGTAAAATAGTAATTTTT-GAATGTTCGG
1 GGGTAAAATA-TAATTTTTGGAAAGTTTAG
13019184 GGGTAAAA-ACTTAATTTTTGGAAAGTTT-G
1 GGGTAAAATA--TAATTTTTGGAAAGTTTAG
* * *
13019213 GGGTCAAAAATACAATTTTAGG-AAGTTTGG
1 GGGT--AAAATATAATTTTTGGAAAGTTTAG
*
13019243 GGGTAAAATGGTAATTTTTGG-AAGTTT-G
1 GGGTAAAAT-ATAATTTTTGGAAAGTTTAG
* * *
13019271 GGGACAAAAATGTAATTTTTGTG-AAG-TTCG
1 GGG--TAAAATATAATTTTTG-GAAAGTTTAG
* * * * * *
13019301 GAGGTTAAATGTGA-TTTTGGAAAAATTCAA
1 G-GGTAAAATATAATTTTTGG-AAAGTTTAG
13019331 GGGTCAAAATATAATTTTTGGAAAGTTTAG
1 GGGT-AAAATATAATTTTTGGAAAGTTTAG
* * *
13019361 GGGTCAAAATATGATTTTTAGACAGTTTA
1 GGGT-AAAATATAATTTTTGGAAAGTTTA
13019390 TGGACTTTTT
Statistics
Matches: 190, Mismatches: 27, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
27 1 0.01
28 15 0.08
29 70 0.37
30 91 0.48
31 12 0.06
32 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
GGGTAAAATATAATTTTTGGAAAGTTTAG
Found at i:13020460 original size:6 final size:6
Alignment explanation
Indices: 13020449--13020492 Score: 52
Period size: 6 Copynumber: 6.7 Consensus size: 6
13020439 ACTTTACTAT
13020449 TATTAA TATTAA TTATTATTA TATTTAA TATTAA TATTAA TATT
1 TATTAA TATTAA -TATTA--A TA-TTAA TATTAA TATTAA TATT
13020493 CATTCAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 20 0.59
7 8 0.24
8 2 0.06
9 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
TATTAA
Found at i:13022084 original size:40 final size:38
Alignment explanation
Indices: 13022016--13022150 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
13022006 ACCAGAATGG
* *
13022016 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
13022056 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
13022093 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
13022134 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
13022151 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:13022148 original size:41 final size:38
Alignment explanation
Indices: 13022048--13022151 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
13022038 TTCGAAGCAA
* *
13022048 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
13022085 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
13022123 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
13022152 CTCGAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:13023074 original size:13 final size:12
Alignment explanation
Indices: 13023004--13023085 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 12
13022994 CATATACATA
*
13023004 TATATATATTAGT
1 TATA-ATATTAAT
*
13023017 TAATAATAATAA-
1 T-ATAATATTAAT
*
13023029 TATAATACTAAT
1 TATAATATTAAT
*
13023041 TA-AATAATAATT
1 TATAATATTAA-T
*
13023053 TATATTATTATAT
1 TATAATATTA-AT
13023066 TATAATATTAAT
1 TATAATATTAAT
13023078 TAATAATA
1 T-ATAATA
13023086 AATTAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 16 0.29
12 9 0.16
13 27 0.48
14 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (12 bp):
TATAATATTAAT
Found at i:13028214 original size:40 final size:38
Alignment explanation
Indices: 13028146--13028280 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
13028136 ACCAGAATGG
* *
13028146 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
13028186 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
13028223 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
13028264 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
13028281 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:13028278 original size:41 final size:38
Alignment explanation
Indices: 13028178--13028281 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
13028168 TTCGAAGCAA
* *
13028178 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
13028215 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
13028253 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
13028282 CTCGAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:13029204 original size:13 final size:12
Alignment explanation
Indices: 13029134--13029215 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 12
13029124 CATATACATA
*
13029134 TATATATATTAGT
1 TATA-ATATTAAT
*
13029147 TAATAATAATAA-
1 T-ATAATATTAAT
*
13029159 TATAATACTAAT
1 TATAATATTAAT
*
13029171 TA-AATAATAATT
1 TATAATATTAA-T
*
13029183 TATATTATTATAT
1 TATAATATTA-AT
13029196 TATAATATTAAT
1 TATAATATTAAT
13029208 TAATAATA
1 T-ATAATA
13029216 AATTAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 16 0.29
12 9 0.16
13 27 0.48
14 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (12 bp):
TATAATATTAAT
Found at i:13029587 original size:6 final size:6
Alignment explanation
Indices: 13029576--13029623 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
13029566 GGCTTTCATC
** * *
13029576 ATTTAA ATTTAA AAATAA ATTTAA ACTTAT A-TTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
13029623 A
1 A
13029624 ATAAACTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
5 4 0.12
6 30 0.88
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:13029613 original size:17 final size:17
Alignment explanation
Indices: 13029576--13029651 Score: 89
Period size: 17 Copynumber: 4.4 Consensus size: 17
13029566 GGCTTTCATC
*
13029576 ATTTAAATTTAAAAATAA
1 ATTTAAACTT-AAAATAA
* *
13029594 ATTTAAACTTATATTAA
1 ATTTAAACTTAAAATAA
*
13029611 ATTTAAATTTAAAATAA
1 ATTTAAACTTAAAATAA
* *
13029628 ACTTAATCTTAAAATAA
1 ATTTAAACTTAAAATAA
13029645 ATTTAAA
1 ATTTAAA
13029652 AAATGATTTA
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
17 38 0.81
18 9 0.19
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAAACTTAAAATAA
Found at i:13029645 original size:28 final size:28
Alignment explanation
Indices: 13029597--13029652 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
13029587 AAAATAAATT
*
13029597 TAAACTTATATTAAATTTAAATTTAAAA
1 TAAACTTATATTAAATATAAATTTAAAA
*
13029625 TAAACTTAATCTTAAA-ATAAATTTAAAA
1 TAAACTT-ATATTAAATATAAATTTAAAA
13029653 AATGATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (28 bp):
TAAACTTATATTAAATATAAATTTAAAA
Found at i:13029646 original size:34 final size:35
Alignment explanation
Indices: 13029576--13029651 Score: 109
Period size: 34 Copynumber: 2.2 Consensus size: 35
13029566 GGCTTTCATC
* * *
13029576 ATTTAAATTTAAAAATAAATTTAAACTTATATTAA
1 ATTTAAATTTAAAAATAAACTTAAACTTAAAATAA
*
13029611 ATTTAAATTT-AAAATAAACTTAATCTTAAAATAA
1 ATTTAAATTTAAAAATAAACTTAAACTTAAAATAA
13029645 ATTTAAA
1 ATTTAAA
13029652 AAATGATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 27 0.73
35 10 0.27
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (35 bp):
ATTTAAATTTAAAAATAAACTTAAACTTAAAATAA
Found at i:13030771 original size:18 final size:18
Alignment explanation
Indices: 13030741--13030792 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
13030731 AAAATTTTAA
*
13030741 AAAAATTCA-AAAAAAT-
1 AAAATTTCATAAAAAATC
*
13030757 AAAATATTTATAAAAATATC
1 AAAAT-TTCATAAAAA-ATC
13030777 AAAATTTCATAAAAAA
1 AAAATTTCATAAAAAA
13030793 ATTTAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 4 0.14
17 3 0.10
18 6 0.21
19 11 0.38
20 5 0.17
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATTTCATAAAAAATC
Found at i:13030771 original size:19 final size:19
Alignment explanation
Indices: 13030749--13030794 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
13030739 AAAAAAATTC
*
13030749 AAAAAAAT-AAAATATTTAT
1 AAAAAAATCAAAAT-TTCAT
*
13030768 AAAAATATCAAAATTTCAT
1 AAAAAAATCAAAATTTCAT
13030787 AAAAAAAT
1 AAAAAAAT
13030795 TTAAAAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAAAATCAAAATTTCAT
Found at i:13038055 original size:18 final size:18
Alignment explanation
Indices: 13038034--13038078 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
13038024 ATTTAATGTA
*
13038034 AATATATATAATTAATAT
1 AATATATATAATTAACAT
* *
13038052 AATATTTTTAATTAACAT
1 AATATATATAATTAACAT
*
13038070 ATTATATAT
1 AATATATAT
13038079 CCGAACCAAG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
AATATATATAATTAACAT
Found at i:13045634 original size:31 final size:31
Alignment explanation
Indices: 13045596--13045656 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
13045586 AATAGCTTAA
13045596 TGACTTAAATAAAAACTTTTGAATAATTTAG
1 TGACTTAAATAAAAACTTTTGAATAATTTAG
**
13045627 TGACTTAAATAAAATTTTTTGAATAATTTA
1 TGACTTAAATAAAAACTTTTGAATAATTTA
13045657 ATAATCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAATTTAG
Found at i:13045674 original size:31 final size:31
Alignment explanation
Indices: 13045592--13045677 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 31
13045582 ACTTAATAGC
* * **
13045592 TTAATGACTTAAATAAAAACTTTTGAATAAT
1 TTAATGAATCAAATAAAATTTTTTGAATAAT
* * *
13045623 TTAGTGACTTAAATAAAATTTTTTGAATAAT
1 TTAATGAATCAAATAAAATTTTTTGAATAAT
*
13045654 TTAAT-AATCAAATTATAATTTTTT
1 TTAATGAATCAAA-TAAAATTTTTT
13045678 AAATTAAATG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 5 0.11
31 42 0.89
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (31 bp):
TTAATGAATCAAATAAAATTTTTTGAATAAT
Found at i:13052179 original size:23 final size:22
Alignment explanation
Indices: 13052147--13052245 Score: 101
Period size: 23 Copynumber: 4.4 Consensus size: 22
13052137 GTTGGGGAAA
13052147 CAGTAAGCACACACAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
*
13052169 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAAGCACACACAGTGCAAT
* * * *
13052192 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGTGC-AAT
*
13052215 CAGTAAGCACACA-AGGTGCGAAA
1 CAGTAAGCACACACA-GTGC-AAT
13052238 CAGTAAGC
1 CAGTAAGC
13052246 GCGCTAGCGT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
22 17 0.26
23 48 0.74
ACGTcount: A:0.38, C:0.26, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGTAAGCACACACAGTGCAAT
Found at i:13058019 original size:23 final size:24
Alignment explanation
Indices: 13057966--13058019 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
13057956 AAGGTAATTT
13057966 TTTTAATATACTGGTATACTTACA
1 TTTTAATATACTGGTATACTTACA
** *
13057990 TGATAATAT-CTGTTCATA-TTACA
1 TTTTAATATACTGGT-ATACTTACA
13058013 TTTTAAT
1 TTTTAAT
13058020 CCTTTGATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.48
Consensus pattern (24 bp):
TTTTAATATACTGGTATACTTACA
Done.