Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 28 of 106
Found at i:5231672 original size:16 final size:17
Alignment explanation
Indices: 5231605--5231667 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
5231595 GGCAAGTACT
*
5231605 AAATGGAAAGTTTACTAA
1 AAATAGAAAG-TTACTAA
* *
5231623 AAATAG-CAGTTATTAA
1 AAATAGAAAGTTACTAA
*
5231639 AAATAGCAAGTTACTAA
1 AAATAGAAAGTTACTAA
5231656 AAATAGAAAGTT
1 AAATAGAAAGTT
5231668 GTAAATCCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 12 0.32
17 21 0.55
18 5 0.13
ACGTcount: A:0.52, C:0.06, G:0.14, T:0.27
Consensus pattern (17 bp):
AAATAGAAAGTTACTAA
Found at i:5234297 original size:21 final size:20
Alignment explanation
Indices: 5234273--5234313 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
5234263 ATCAAGTAAA
*
5234273 AATTAATGAAGTAAGTCATAT
1 AATTAATCAAGTAAGT-ATAT
5234294 AATTAATCAAGTAAGTATAT
1 AATTAATCAAGTAAGTATAT
5234314 GATAATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (20 bp):
AATTAATCAAGTAAGTATAT
Found at i:5234886 original size:10 final size:10
Alignment explanation
Indices: 5234853--5234886 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5234843 TTTCCCTCTT
5234853 TTTTATTTCA
1 TTTTATTTCA
*
5234863 TTTCATTTCA
1 TTTTATTTCA
*
5234873 TTTTATTTTA
1 TTTTATTTCA
5234883 TTTT
1 TTTT
5234887 TGCTCTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTATTTCA
Found at i:5234909 original size:17 final size:17
Alignment explanation
Indices: 5234873--5234919 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 17
5234863 TTTCATTTCA
5234873 TTTTATTTTATTTTTGCTC
1 TTTT-TTTT-TTTTTGCTC
5234892 TTTTCTTTTTTTTT-CTC
1 TTTT-TTTTTTTTTGCTC
5234909 TTTTTTTTTTT
1 TTTTTTTTTTT
5234920 CACTTTATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 7 0.26
17 7 0.26
18 5 0.19
19 8 0.30
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.83
Consensus pattern (17 bp):
TTTTTTTTTTTTTGCTC
Found at i:5234915 original size:15 final size:16
Alignment explanation
Indices: 5234878--5234919 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
5234868 TTTCATTTTA
*
5234878 TTTTATTTTTGCTCTT
1 TTTTTTTTTTGCTCTT
*
5234894 TTCTTTTTTTTTCTCTT
1 TT-TTTTTTTTGCTCTT
5234911 TTTTTTTTT
1 TTTTTTTTT
5234920 CACTTTATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTTGCTCTT
Found at i:5239539 original size:25 final size:25
Alignment explanation
Indices: 5239511--5239571 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
5239501 TTCTAGTGCC
5239511 ATTAAGA-TTCCATAATCCAAGTGAA
1 ATTAAGAGTT-CATAATCCAAGTGAA
* *
5239536 ATTAGGAGTTCTTAATCCAAGTGAA
1 ATTAAGAGTTCATAATCCAAGTGAA
* *
5239561 CTTATGAGTTC
1 ATTAAGAGTTC
5239572 TTATATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (25 bp):
ATTAAGAGTTCATAATCCAAGTGAA
Found at i:5239572 original size:25 final size:25
Alignment explanation
Indices: 5239523--5239574 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
5239513 TAAGATTCCA
5239523 TAATCCAAGTGAAATTAGGAGTTCT
1 TAATCCAAGTGAAATTAGGAGTTCT
* *
5239548 TAATCCAAGTGAACTTATGAGTTCT
1 TAATCCAAGTGAAATTAGGAGTTCT
5239573 TA
1 TA
5239575 TATAAATAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (25 bp):
TAATCCAAGTGAAATTAGGAGTTCT
Found at i:5245280 original size:21 final size:21
Alignment explanation
Indices: 5245254--5245294 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5245244 AAAATTAACG
5245254 ATTAAAAATTAGAATAAAAAA
1 ATTAAAAATTAGAATAAAAAA
* * *
5245275 ATTAAAGATTGGAATTAAAA
1 ATTAAAAATTAGAATAAAAA
5245295 TTAAATAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (21 bp):
ATTAAAAATTAGAATAAAAAA
Found at i:5252995 original size:52 final size:52
Alignment explanation
Indices: 5252938--5253042 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
5252928 TATCTCTTGG
5252938 AAAGCTTTAAGTGTGGTTAAATGAAACTAGATATAAAGAAAACAAAGATTGA
1 AAAGCTTTAAGTGTGGTTAAATGAAACTAGATATAAAGAAAACAAAGATTGA
*
5252990 AAAGCTTTAAGTGTGGTTAAATGAAACTAGATCTAAAGAAAACAAAGATTGA
1 AAAGCTTTAAGTGTGGTTAAATGAAACTAGATATAAAGAAAACAAAGATTGA
5253042 A
1 A
5253043 CACTTGAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.25
Consensus pattern (52 bp):
AAAGCTTTAAGTGTGGTTAAATGAAACTAGATATAAAGAAAACAAAGATTGA
Found at i:5266376 original size:21 final size:20
Alignment explanation
Indices: 5266311--5266380 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 20
5266301 AAATCCAAAA
*
5266311 AAGGGATCGATCCCCCCACA-T
1 AAGGGATCGAT-CCCCCA-AGG
* *
5266332 AGGGGATCGATCACCC-AGG
1 AAGGGATCGATCCCCCAAGG
5266351 CAAGGGATCGATCCCCTCAAGG
1 -AAGGGATCGATCCCC-CAAGG
5266373 AAGGGATC
1 AAGGGATC
5266381 AATCGGGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 1 0.03
20 17 0.43
21 19 0.47
22 3 0.08
ACGTcount: A:0.29, C:0.30, G:0.29, T:0.13
Consensus pattern (20 bp):
AAGGGATCGATCCCCCAAGG
Found at i:5267327 original size:472 final size:473
Alignment explanation
Indices: 5266437--5267384 Score: 1530
Period size: 472 Copynumber: 2.0 Consensus size: 473
5266427 GAACCAATTG
5266437 ATCCCTTCAAGAAAGGATCAATCGATTTTGGGCATGAAAACCTCCAACGGCTACTTTTTCATCTT
1 ATCCCTTCAAGAAAGGATCAATCGATTTTGGGCATGAAAACCTCCAACGGCTACTTTTTCATCTT
* * * *
5266502 TTAAATAGGCATTTCTTCACTCCAAGCTTTCCCAACGGCTAGTTCCTCAATTTCTCTATAAATTG
66 TCAAAGAGGCATTTCTTCACTCCAAGCTTTCCCAACGGCTAGTTCCTCAATTTCTATATAAATTC
** ** *
5266567 GGCACTCCAACGTACCAAAACAAAAGAAAAATCAAGATGAATCAAGAGAGCAAGAGTTAACAAGC
131 AACACTCCAACACACCAAAACAAAAGAAAAATCAAGATGAATCAAGAGAGCAAGAGCTAACAAGC
5266632 AATATTTTCTTTTTCTCAAATAATCAAGAGTTCTTAGAGCTTCAAAGTCTATATCCTTACATTCA
196 AATATTTTCTTTTTCTCAAATAATCAAGAGTTCTTAGAGCTTCAAAGTCTATATCCTTACATTCA
*
5266697 TTGTATCCAAATCATTTTTTTGTTATTCATTTATCTTTTTCTTGTCTATACTTTTGTGTACTTCA
261 TTGTATCCAAATCATCTTTTTGTTATTCATTTATCTTTTTCTTGTCTATACTTTTGTGTACTTCA
*
5266762 AATAGCAAACACCCAACCATTGAGAGGTTCTTAGAGTTTGCAAAACACTTCATTTTTTTTATTTT
326 AATAGCAAACACCCAACCATTAAGAGGTTCTTAGAGTTTGCAAAACACTTCATTTTTTTTATTTT
* *
5266827 GTGAGTTTATAAGTTTAAAGGGGAGGATAACCCTTAAGAGTTTATTATGTTGAGTTTGTAGAGCT
391 GTAAGTTTATAAGCTTAAAGGGGAGGATAACCCTTAAGAGTTTATTATGTTGAGTTTGTAGAGCT
5266892 TAGAGAAGCTTGGTTGTA
456 TAGAGAAGCTTGGTTGTA
* * * * *
5266910 ATCCC-TCAAGAAGGGATTAATC-AGTTTTGGGCGTGAAGACCTCCAATGGCTACTTTTTCATCA
1 ATCCCTTCAAGAAAGGATCAATCGA-TTTTGGGCATGAAAACCTCCAACGGCTACTTTTTCATC-
* * * *
5266973 TTTCAACGA-GCATTTCTTCACTCCAAGCTTTCCCAATGGCTAGTTCTTCAATTTTTATATAAAT
64 TTTCAAAGAGGCATTTCTTCACTCCAAGCTTTCCCAACGGCTAGTTCCTCAATTTCTATATAAAT
*
5267037 TCAACACTCCAACACACCGAAAA-AAAAGAAAAATCAAGATGAATCAAGAGAGCAAGAGCTAATA
129 TCAACACTCCAACACACC-AAAACAAAAGAAAAATCAAGATGAATCAAGAGAGCAAGAGCTAACA
* * * *
5267101 AGCAATATTTTCTTTTTCTCAAGTAATTAATAGTTTTTAGAGCTTCAAAGTCTATATCCTTACAT
193 AGCAATATTTTCTTTTTCTCAAATAATCAAGAGTTCTTAGAGCTTCAAAGTCTATATCCTTACAT
5267166 TCATTGTATCCAAATCATCTTTTTGTTATTCATTTATCTTTTTCTTGTCTATACTTTTGTGTACT
258 TCATTGTATCCAAATCATCTTTTTGTTATTCATTTATCTTTTTCTTGTCTATACTTTTGTGTACT
* *
5267231 TCAAATTTGCAAACACCCAAGCATTAAGAGGTTCTTAGAGTTTGCAAAACACTTCA-TTTTTTTA
323 TCAAA-TAGCAAACACCCAACCATTAAGAGGTTCTTAGAGTTTGCAAAACACTTCATTTTTTTTA
* *
5267295 TTTTGTAAGTTTGTAAGCTT-AAGAGGGAGGATAACCCTTAAGAGTTTATTGTGTTGAGTTTGTA
387 TTTTGTAAGTTTATAAGCTTAAAG-GGGAGGATAACCCTTAAGAGTTTATTATGTTGAGTTTGTA
5267359 GAGCTTAGAGAAGCTTGGTTGTA
451 GAGCTTAGAGAAGCTTGGTTGTA
5267382 ATC
1 ATC
5267385 TTCAACACTT
Statistics
Matches: 439, Mismatches: 31, Indels: 11
0.91 0.06 0.02
Matches are distributed among these distances:
471 4 0.01
472 373 0.85
473 62 0.14
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (473 bp):
ATCCCTTCAAGAAAGGATCAATCGATTTTGGGCATGAAAACCTCCAACGGCTACTTTTTCATCTT
TCAAAGAGGCATTTCTTCACTCCAAGCTTTCCCAACGGCTAGTTCCTCAATTTCTATATAAATTC
AACACTCCAACACACCAAAACAAAAGAAAAATCAAGATGAATCAAGAGAGCAAGAGCTAACAAGC
AATATTTTCTTTTTCTCAAATAATCAAGAGTTCTTAGAGCTTCAAAGTCTATATCCTTACATTCA
TTGTATCCAAATCATCTTTTTGTTATTCATTTATCTTTTTCTTGTCTATACTTTTGTGTACTTCA
AATAGCAAACACCCAACCATTAAGAGGTTCTTAGAGTTTGCAAAACACTTCATTTTTTTTATTTT
GTAAGTTTATAAGCTTAAAGGGGAGGATAACCCTTAAGAGTTTATTATGTTGAGTTTGTAGAGCT
TAGAGAAGCTTGGTTGTA
Found at i:5268182 original size:25 final size:25
Alignment explanation
Indices: 5268153--5268211 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
5268143 TGAAACATAA
5268153 GAAAATGATTTCAAAATTGAATATT
1 GAAAATGATTTCAAAATTGAATATT
5268178 GAAAATGATTTCAAAATTGAATATT
1 GAAAATGATTTCAAAATTGAATATT
5268203 GAAAATGAT
1 GAAAATGAT
5268212 CTTTTGATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.34
Consensus pattern (25 bp):
GAAAATGATTTCAAAATTGAATATT
Found at i:5271873 original size:40 final size:40
Alignment explanation
Indices: 5271828--5271909 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
5271818 AGTTGAGTTG
* *
5271828 TGTTGGATTAGGATACATAAAGTGAGGGGGAGTTTTGCCA
1 TGTTGGATTAGGATACACAAAGTAAGGGGGAGTTTTGCCA
* *
5271868 TGTTGGATTAGGATGCACAAATTAAGGGGGAGTTTTGCCA
1 TGTTGGATTAGGATACACAAAGTAAGGGGGAGTTTTGCCA
5271908 TG
1 TG
5271910 CGTTGTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.27, C:0.09, G:0.34, T:0.30
Consensus pattern (40 bp):
TGTTGGATTAGGATACACAAAGTAAGGGGGAGTTTTGCCA
Found at i:5277548 original size:16 final size:17
Alignment explanation
Indices: 5277527--5277563 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5277517 CTCTAATAAA
*
5277527 AATTTC-TAGAAACTAT
1 AATTTCTTAAAAACTAT
5277543 AATTTCTTAAAAACTAT
1 AATTTCTTAAAAACTAT
5277560 AATT
1 AATT
5277564 ATTAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.41
Consensus pattern (17 bp):
AATTTCTTAAAAACTAT
Found at i:5277568 original size:16 final size:17
Alignment explanation
Indices: 5277536--5277568 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5277526 AAATTTCTAG
*
5277536 AAACTATAATTTCTTAA
1 AAACTATAATTTATTAA
5277553 AAACTATAA-TTATTAA
1 AAACTATAATTTATTAA
5277569 TAAATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
AAACTATAATTTATTAA
Found at i:5281940 original size:2 final size:2
Alignment explanation
Indices: 5281933--5281957 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5281923 TAGATCTTTA
5281933 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
5281958 AATGGAAGCT
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:5283737 original size:14 final size:14
Alignment explanation
Indices: 5283718--5283757 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5283708 TTCTTTCTTT
*
5283718 TTCTTTATTTTCCA
1 TTCTTTCTTTTCCA
**
5283732 TTCTTTCTTTTCTT
1 TTCTTTCTTTTCCA
5283746 TTCTTTCTTTTC
1 TTCTTTCTTTTC
5283758 AACTCAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCTTTCTTTTCCA
Found at i:5283739 original size:28 final size:27
Alignment explanation
Indices: 5283704--5283757 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
5283694 TAAATCATTG
5283704 ATTCTTC-TTTCTTTTTCTTTATTTTCC
1 ATTCTTCTTTTC-TTTTCTTTATTTTCC
*
5283731 ATTCTTTCTTTTCTTTTCTTTCTTTTC
1 ATTC-TTCTTTTCTTTTCTTTATTTTC
5283758 AACTCAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 16 0.67
29 4 0.17
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (27 bp):
ATTCTTCTTTTCTTTTCTTTATTTTCC
Found at i:5288485 original size:34 final size:32
Alignment explanation
Indices: 5288416--5288478 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
5288406 CCTTTTTTAG
* *
5288416 TAACTATATAATTTTGTTACAAAAATCTTATA
1 TAACTAAATAATTTTGTTACAAAAATATTATA
*
5288448 TAACTAAATTATTTTCGTTACATAAAATATT
1 TAACTAAATAATTTT-GTTACA-AAAATATT
5288479 TCATAACGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 13 0.50
33 6 0.23
34 7 0.27
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (32 bp):
TAACTAAATAATTTTGTTACAAAAATATTATA
Found at i:5288573 original size:103 final size:103
Alignment explanation
Indices: 5288431--5288699 Score: 303
Period size: 103 Copynumber: 2.6 Consensus size: 103
5288421 ATATAATTTT
* * *
5288431 GTTACAAAAA-TCTTATA-TAACTAA-ATTATTTTCGTTACATAAAATATTTCATAACGATTAAA
1 GTTATAAAAACTCTTA-AGTAAC-AATATTATTTTGGTTACATAAAATATTTCATAACAATTAAA
* *
5288493 TATTTTTTCTTAAAC-CCTTTTTCAACAACCATAAGAGTTG
64 TATTGTTTCTTAAACTCC-TTTTCAACAACCATAAAAGTTG
* * **
5288533 GTTATAAAAACTCTTAAGTAACAATATTATTATGGTTACATAATATATTTTGTAACAATTAAATA
1 GTTATAAAAACTCTTAAGTAACAATATTATTTTGGTTACATAAAATATTTCATAACAATTAAATA
* ** **
5288598 TTGTTTGTTAAACTCCTTTTCAGTAATTATAAAAGTTG
66 TTGTTTCTTAAACTCCTTTTCAACAACCATAAAAGTTG
** * * * *
5288636 GTTATAAAAACTCTTAAGTAATTATATTATTTTGATTACATAACATATGTCATAAAAATTAAAT
1 GTTATAAAAACTCTTAAGTAACAATATTATTTTGGTTACATAAAATATTTCATAACAATTAAAT
5288700 GTCATTTTAA
Statistics
Matches: 140, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
102 12 0.09
103 126 0.90
104 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (103 bp):
GTTATAAAAACTCTTAAGTAACAATATTATTTTGGTTACATAAAATATTTCATAACAATTAAATA
TTGTTTCTTAAACTCCTTTTCAACAACCATAAAAGTTG
Found at i:5289439 original size:17 final size:17
Alignment explanation
Indices: 5289419--5289470 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
5289409 TTTCCTTTTA
5289419 TTGTAGTTCTACTTTCC
1 TTGTAGTTCTACTTTCC
* **
5289436 TTGT--TT-TCCTTTTA
1 TTGTAGTTCTACTTTCC
5289450 TTGTAGTTCTACTTTCC
1 TTGTAGTTCTACTTTCC
5289467 TTGT
1 TTGT
5289471 TTTCCTTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 2 0.08
17 13 0.50
ACGTcount: A:0.10, C:0.19, G:0.12, T:0.60
Consensus pattern (17 bp):
TTGTAGTTCTACTTTCC
Found at i:5289444 original size:31 final size:31
Alignment explanation
Indices: 5289409--5289479 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
5289399 TTTTCTATCC
5289409 TTTCCTTTTATTGTAGTTCTACTTTCCTTGT
1 TTTCCTTTTATTGTAGTTCTACTTTCCTTGT
5289440 TTTCCTTTTATTGTAGTTCTACTTTCCTTGT
1 TTTCCTTTTATTGTAGTTCTACTTTCCTTGT
5289471 TTTCCTTTT
1 TTTCCTTTT
5289480 TGGAAACTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.08, C:0.20, G:0.08, T:0.63
Consensus pattern (31 bp):
TTTCCTTTTATTGTAGTTCTACTTTCCTTGT
Found at i:5296307 original size:16 final size:16
Alignment explanation
Indices: 5296257--5296308 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
5296247 TTCTATATAT
* *
5296257 TTTCATGCAATTTACA
1 TTTCTTGCAATTTAAA
*
5296273 TTGCTTGCAATTTAAA
1 TTTCTTGCAATTTAAA
5296289 TTTCTTGCAATTTAAA
1 TTTCTTGCAATTTAAA
5296305 TTTC
1 TTTC
5296309 ATGTTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (16 bp):
TTTCTTGCAATTTAAA
Found at i:5297896 original size:60 final size:60
Alignment explanation
Indices: 5297777--5297906 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 60
5297767 TTTTAGCAAG
* * * * * *
5297777 GGATTATTCAAGGTATTTTTTACTAAAAACACCTTGAATAATCCCTATATAAATTAGAGA
1 GGATTATTCAAGGTATGTTCTACCAAAAACACCTTGAATAATCCCTAAAAAAATAAGAGA
* * *
5297837 GGATTATTTAAGGTGTGTTCTACCAAAAACACCTTGAATAAT-CC-AAAAAAATGCA-AGA
1 GGATTATTCAAGGTATGTTCTACCAAAAACACCTTGAATAATCCCTAAAAAAAT-AAGAGA
5297895 -GATTATTCAAGG
1 GGATTATTCAAGG
5297907 CGTTAATGCC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
57 11 0.18
58 9 0.15
59 3 0.05
60 37 0.62
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (60 bp):
GGATTATTCAAGGTATGTTCTACCAAAAACACCTTGAATAATCCCTAAAAAAATAAGAGA
Found at i:5298442 original size:61 final size:60
Alignment explanation
Indices: 5298377--5298520 Score: 157
Period size: 60 Copynumber: 2.4 Consensus size: 60
5298367 AAGTTTTTAT
*
5298377 AAAAGACTATTCAAGGCATTTTCTGGCCA-AAAACACATTCAATAATT-TCAAAAAAAATAGA
1 AAAAGACTATTAAAGGCATTTT-TGG-CAGAAAACACATTCAATAATTCTCAAAAAAAATA-A
* * * * * *
5298438 AAAAGACTATTAAAAGCATTTTTTGCAGAAAACATATTGAATAATTCTCCAAAAAATTAA
1 AAAAGACTATTAAAGGCATTTTTGGCAGAAAACACATTCAATAATTCTCAAAAAAAATAA
* * *
5298498 AAAAAATTATTTAAGGCATTTTT
1 AAAAGACTATTAAAGGCATTTTT
5298521 AACCAGAAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
59 2 0.03
60 38 0.54
61 30 0.43
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (60 bp):
AAAAGACTATTAAAGGCATTTTTGGCAGAAAACACATTCAATAATTCTCAAAAAAAATAA
Found at i:5299964 original size:34 final size:34
Alignment explanation
Indices: 5299916--5299994 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
5299906 CTAAATGACA
* * **
5299916 AAATGTAGCGGTGTTTTCTACTATAAATGCCACT
1 AAATTTAGTGGTGTTTTCTACTATAAACACCACT
* *
5299950 AAATTTAGTGGTGTTTTCTATTATAAACACCTCT
1 AAATTTAGTGGTGTTTTCTACTATAAACACCACT
5299984 AAATTTAGTGG
1 AAATTTAGTGG
5299995 CATTTTATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (34 bp):
AAATTTAGTGGTGTTTTCTACTATAAACACCACT
Found at i:5302431 original size:20 final size:19
Alignment explanation
Indices: 5302382--5302454 Score: 53
Period size: 21 Copynumber: 3.6 Consensus size: 19
5302372 AGCCTTACCC
5302382 GATCGATCCCTT-CCTTGAAGG
1 GATCGATCCCTTGCC-TG--GG
*
5302403 GATCAATCCCTTGCCTGGG
1 GATCGATCCCTTGCCTGGG
5302422 TGATCGATCCCCTATG--TGGGG
1 -GATCGAT-CCCT-TGCCT-GGG
5302443 GATCGATCCCTT
1 GATCGATCCCTT
5302455 TTGGATTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
18 1 0.02
19 6 0.13
20 14 0.31
21 20 0.44
22 4 0.09
ACGTcount: A:0.16, C:0.29, G:0.26, T:0.29
Consensus pattern (19 bp):
GATCGATCCCTTGCCTGGG
Found at i:5305989 original size:116 final size:115
Alignment explanation
Indices: 5305828--5306054 Score: 445
Period size: 116 Copynumber: 2.0 Consensus size: 115
5305818 TGTAGTAATT
5305828 TTCAAATCTCACACTTTACAATTTTCAGAGATATGCATACTTGCATCAAGAAATTATAAAATAAT
1 TTCAAATCTCACACTTTACAATTTTCAGAGATATGCATACTTGCATCAAGAAATTATAAAATAAT
5305893 CTTAAAAAATTTCTCAAATTAATAACTATGCATTATACTAGCAATTCATA
66 CTTAAAAAATTTCTCAAATTAATAACTATGCATTATACTAGCAATTCATA
5305943 TTCAAATCTCACACTTATACAATTTTCAGAGATATGCATACTTGCATCAAGAAATTATAAAATAA
1 TTCAAATCTCACACTT-TACAATTTTCAGAGATATGCATACTTGCATCAAGAAATTATAAAATAA
5306008 TCTTAAAAAATTTCTCAAATTAATAACTATGCATTATACTAGCAATT
65 TCTTAAAAAATTTCTCAAATTAATAACTATGCATTATACTAGCAATT
5306055 ATCAATGCAA
Statistics
Matches: 111, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
115 16 0.14
116 95 0.86
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (115 bp):
TTCAAATCTCACACTTTACAATTTTCAGAGATATGCATACTTGCATCAAGAAATTATAAAATAAT
CTTAAAAAATTTCTCAAATTAATAACTATGCATTATACTAGCAATTCATA
Found at i:5306484 original size:20 final size:20
Alignment explanation
Indices: 5306459--5306497 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5306449 ATGTAACCAA
*
5306459 AAATAACTAACTTGTAACTG
1 AAATAACTAACTTCTAACTG
*
5306479 AAATAACTACCTTCTAACT
1 AAATAACTAACTTCTAACT
5306498 TCCAAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
AAATAACTAACTTCTAACTG
Found at i:5309611 original size:23 final size:22
Alignment explanation
Indices: 5309568--5309638 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
5309558 TTTATCTAAT
*
5309568 TAAAAAAT-GAAAAACAAAAAAA
1 TAAAAAATGGACAAAC-AAAAAA
*
5309590 TAAAAAATGGACAAAGATAAAAA
1 TAAAAAATGGACAAACA-AAAAA
* *
5309613 CGAAAAAA-GGACAAATAAAAAA
1 -TAAAAAATGGACAAACAAAAAA
5309635 TAAA
1 TAAA
5309639 GAAAAAGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
21 3 0.07
22 14 0.34
23 18 0.44
24 6 0.15
ACGTcount: A:0.75, C:0.06, G:0.10, T:0.10
Consensus pattern (22 bp):
TAAAAAATGGACAAACAAAAAA
Found at i:5310074 original size:15 final size:15
Alignment explanation
Indices: 5310056--5310089 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5310046 TAAAACAAAC
5310056 AAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAGG
*
5310071 AAAAAATAAAAAAGG
1 AAAAAAAAAAAAAGG
5310086 AAAA
1 AAAA
5310090 TGAAGCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAAAAGG
Found at i:5311014 original size:13 final size:13
Alignment explanation
Indices: 5310996--5311035 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
5310986 AATTTAACTT
*
5310996 AAAAAATCATAAA
1 AAAAAATAATAAA
5311009 AAAAAATAATAAA
1 AAAAAATAATAAA
* *
5311022 ATAAAATAAGAAA
1 AAAAAATAATAAA
5311035 A
1 A
5311036 TAATAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.15
Consensus pattern (13 bp):
AAAAAATAATAAA
Found at i:5311717 original size:16 final size:17
Alignment explanation
Indices: 5311681--5311725 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
5311671 GGGTCTCACT
5311681 TAAAAATT-TTAAATGGA
1 TAAAAATTATTAAAT-GA
5311698 -AAAAATTATTAAAT-A
1 TAAAAATTATTAAATGA
5311713 TAAAAA-TATTAAA
1 TAAAAATTATTAAA
5311726 AAACAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.31
16 12 0.46
17 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (17 bp):
TAAAAATTATTAAATGA
Found at i:5311717 original size:17 final size:17
Alignment explanation
Indices: 5311682--5311723 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5311672 GGTCTCACTT
*
5311682 AAAAATT-TTAAATGGA
1 AAAAATTATTAAATAGA
*
5311698 AAAAATTATTAAATATA
1 AAAAATTATTAAATAGA
5311715 AAAATATTA
1 AAAA-ATTA
5311724 AAAAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 7 0.32
17 11 0.50
18 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
AAAAATTATTAAATAGA
Found at i:5311998 original size:18 final size:19
Alignment explanation
Indices: 5311959--5312000 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
5311949 AACGAAATTG
*
5311959 AAAAAATAAAATATCTAGA
1 AAAAAATAAAACATCTAGA
*
5311978 AAAAAATAAAACATTTA-A
1 AAAAAATAAAACATCTAGA
5311996 AAAAA
1 AAAAA
5312001 CAAAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAAAATAAAACATCTAGA
Found at i:5317617 original size:2 final size:2
Alignment explanation
Indices: 5317610--5317634 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5317600 ACATTTTCCT
5317610 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
5317635 TTTCTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5328195 original size:32 final size:32
Alignment explanation
Indices: 5328159--5328221 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
5328149 GTGTCCTTAA
* * *
5328159 GATTTTTAGGACTTTGGATTTCATGGATTTTG
1 GATTTTGAGGACTTTGGATTTAAGGGATTTTG
*
5328191 GATTTTGAGGAGTTTGGATTTAAGGGATTTT
1 GATTTTGAGGACTTTGGATTTAAGGGATTTT
5328222 AAAAATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.21, C:0.03, G:0.29, T:0.48
Consensus pattern (32 bp):
GATTTTGAGGACTTTGGATTTAAGGGATTTTG
Found at i:5328206 original size:16 final size:16
Alignment explanation
Indices: 5328159--5328211 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
5328149 GTGTCCTTAA
*
5328159 GATTTTTAGGACTTTG
1 GATTTTCAGGACTTTG
*
5328175 GA-TTTCATGGATTTTG
1 GATTTTCA-GGACTTTG
* *
5328191 GATTTTGAGGAGTTTG
1 GATTTTCAGGACTTTG
5328207 GATTT
1 GATTT
5328212 AAGGGATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 4 0.13
16 23 0.74
17 4 0.13
ACGTcount: A:0.19, C:0.04, G:0.28, T:0.49
Consensus pattern (16 bp):
GATTTTCAGGACTTTG
Found at i:5329339 original size:6 final size:6
Alignment explanation
Indices: 5329324--5329369 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
5329314 CTATGTTATT
*
5329324 TTTTTGG TTTTTG TTTCTG TTTTTG TGTTTT- TTTTT- TTTTTG TTTT
1 TTTTT-G TTTTTG TTTTTG TTTTTG T-TTTTG TTTTTG TTTTTG TTTT
5329370 GCGTTTCTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 9 0.26
6 17 0.49
7 9 0.26
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:5342271 original size:20 final size:20
Alignment explanation
Indices: 5342229--5342274 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
5342219 TTAAGCTCCA
*
5342229 AACATAAAATTTGGGAGTGC
1 AACATAAAATTTGGGAGTCC
*
5342249 AACATAAAATTT-TGAGTACC
1 AACATAAAATTTGGGAGT-CC
5342269 AACATA
1 AACATA
5342275 GAAAGTGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (20 bp):
AACATAAAATTTGGGAGTCC
Found at i:5345469 original size:3 final size:3
Alignment explanation
Indices: 5345456--5345491 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
5345446 TAGATGAGGG
5345456 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
5345492 GCCTGTAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:5346822 original size:117 final size:118
Alignment explanation
Indices: 5346697--5346934 Score: 388
Period size: 118 Copynumber: 2.0 Consensus size: 118
5346687 ACGGTTGTAA
* * *
5346697 TATCCTTCTCCCACC-TTGTTTTTGCCAGCATTTATGTCTTTTGGAAAGGCCGCCAAAAGTGGCC
1 TATCCTTCTCCCACCTTTGTTTTTGCCAGCATTTATGTCTTTTGGAAAAGCCACCAAAAGCGGCC
* * *
5346761 TGCAAACGTGGTTCCTTTTTCCAAAAGGGTTCTACTTTAAGTGTACGAGTCTT
66 TACAAACGTGGTTCCTTTTTCCAAAAGGGTTCTACTGTAAGTATACGAGTCTT
* *
5346814 TATCCTTCTTCCACCTTTGTTTTTGCCAGCATTTATGTCTTTTGGAAAAGCCACCAAAAGCGGTC
1 TATCCTTCTCCCACCTTTGTTTTTGCCAGCATTTATGTCTTTTGGAAAAGCCACCAAAAGCGGCC
*
5346879 TACAAACGTGGTTCCTTTTTCCAAAATGGTTCTACTGTAAGTATACGAGTCTT
66 TACAAACGTGGTTCCTTTTTCCAAAAGGGTTCTACTGTAAGTATACGAGTCTT
5346932 TAT
1 TAT
5346935 ATATACATAT
Statistics
Matches: 111, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
117 14 0.13
118 97 0.87
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (118 bp):
TATCCTTCTCCCACCTTTGTTTTTGCCAGCATTTATGTCTTTTGGAAAAGCCACCAAAAGCGGCC
TACAAACGTGGTTCCTTTTTCCAAAAGGGTTCTACTGTAAGTATACGAGTCTT
Found at i:5353508 original size:7 final size:8
Alignment explanation
Indices: 5353471--5353527 Score: 71
Period size: 8 Copynumber: 7.0 Consensus size: 8
5353461 TAATGGATGA
5353471 AAAAAATG
1 AAAAAATG
5353479 AAAAAAATG
1 -AAAAAATG
5353488 AAAAAATG
1 AAAAAATG
5353496 AAAAAA-G
1 AAAAAATG
*
5353503 AAAAAATT
1 AAAAAATG
*
5353511 AAAAAGTGG
1 AAAAAAT-G
5353520 AAAAAATG
1 AAAAAATG
5353528 TAAGAGTAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
7 7 0.17
8 21 0.50
9 14 0.33
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:5353515 original size:9 final size:9
Alignment explanation
Indices: 5353467--5353501 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
5353457 TTAATAATGG
5353467 ATGAAAAAA
1 ATGAAAAAA
5353476 ATGAAAAAA
1 ATGAAAAAA
5353485 ATG-AAAAA
1 ATGAAAAAA
5353493 ATGAAAAAA
1 ATGAAAAAA
5353502 GAAAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
ATGAAAAAA
Found at i:5354987 original size:38 final size:38
Alignment explanation
Indices: 5354935--5355007 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
5354925 AGTCATGAGC
*
5354935 CTCTTTTTAAAGGAG-TCTTATTTATTTTTCAAAGTTAT
1 CTCTGTTTAAAGGAGCT-TTATTTATTTTTCAAAGTTAT
* *
5354973 CTCTGTTTAGAGGAGCTTTATTTATTTTTCGAAGT
1 CTCTGTTTAAAGGAGCTTTATTTATTTTTCAAAGT
5355008 CGTTGAGCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
38 30 0.97
39 1 0.03
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (38 bp):
CTCTGTTTAAAGGAGCTTTATTTATTTTTCAAAGTTAT
Found at i:5355026 original size:43 final size:43
Alignment explanation
Indices: 5354930--5355550 Score: 448
Period size: 43 Copynumber: 14.5 Consensus size: 43
5354920 TCAAAAGTCA
* * *
5354930 TGAGCCTCTTTTTAAAGGAGTCTTATTTATTTTTCAAA---GT
1 TGAGCCTCTGTTTAGAGGAGCCTTATTTATTTTTCAAAGTTGT
* * * *
5354970 T-A-TCTCTGTTTAGAGGAGCTTTATTTATTTTTCGAAGTCGT
1 TGAGCCTCTGTTTAGAGGAGCCTTATTTATTTTTCAAAGTTGT
* * * * * *
5355011 TGAGCTTTTTTTTAGAAGAGCTTTATTTATTTTTTAAAAGTTG-
1 TGAGCCTCTGTTTAGAGGAGCCTTATTTA-TTTTTCAAAGTTGT
* * * * *
5355054 TGAGCCTCTGTTTAAAGAAACCTTGTTTAGTTTTCAAAAGTTGT
1 TGAGCCTCTGTTTAGAGGAGCCTTATTTATTTTTC-AAAGTTGT
* * * *
5355098 TAAGTCTCTGTTTAGAGGAGCTTTATTT-TCTTTTCAAAGTCGT
1 TGAGCCTCTGTTTAGAGGAGCCTTATTTAT-TTTTCAAAGTTGT
* * *
5355141 TAAGCCTCTGTTTAGAGGAGCCTTATTTATTTTTTAAAGTCGT
1 TGAGCCTCTGTTTAGAGGAGCCTTATTTATTTTTCAAAGTTGT
* * * ** * *
5355184 TGAGCCTCTATTTAAAGAAGTTTTATTCAGTTTTCAAAGTTGT
1 TGAGCCTCTGTTTAGAGGAGCCTTATTTATTTTTCAAAGTTGT
* * **
5355227 TGAGCCTCTGTTTAGAGGAGCCTTATTCAGTTTTCAAAAGTCAT
1 TGAGCCTCTGTTTAGAGGAGCCTTATTTATTTTTC-AAAGTTGT
* * * * * * **
5355271 TAAGCCTATGCTTAGATGAGCTTTATTTACTTTTCAAAGTCAT
1 TGAGCCTCTGTTTAGAGGAGCCTTATTTATTTTTCAAAGTTGT
* ** ** * **
5355314 TGAACCTCTACTTAGAAAAGCCTTATTTAGTTTTCAAAAGTTAC
1 TGAGCCTCTGTTTAGAGGAGCCTTATTTATTTTTC-AAAGTTGT
* * * * **
5355358 TAAGCCTTTATTTAGGGGAGCCTTATTTATTTTTCAAAGTCAT
1 TGAGCCTCTGTTTAGAGGAGCCTTATTTATTTTTCAAAGTTGT
* * * * * *
5355401 GGAGCTTTTGTTTGGAAGAGCCTTATTTACTTTTCAAAGTTGT
1 TGAGCCTCTGTTTAGAGGAGCCTTATTTATTTTTCAAAGTTGT
* * * *
5355444 TGAGCCTTTGCTTAGAGGAGCCTTATTTAGTTTACAAAAGTTGT
1 TGAGCCTCTGTTTAGAGGAGCCTTATTTATTTTTC-AAAGTTGT
* * * *
5355488 TAAGCTTCTATTTA-AGGAAGTCTTATTTATTTTTCAAAGTTGT
1 TGAGCCTCTGTTTAGAGG-AGCCTTATTTATTTTTCAAAGTTGT
* * *
5355531 GGAGCTTCTATTTAGAGGAG
1 TGAGCCTCTGTTTAGAGGAG
5355551 TTTTTATGTT
Statistics
Matches: 458, Mismatches: 108, Indels: 27
0.77 0.18 0.05
Matches are distributed among these distances:
38 28 0.06
39 1 0.00
40 1 0.00
41 3 0.01
42 5 0.01
43 282 0.62
44 138 0.30
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.43
Consensus pattern (43 bp):
TGAGCCTCTGTTTAGAGGAGCCTTATTTATTTTTCAAAGTTGT
Found at i:5355121 original size:130 final size:130
Alignment explanation
Indices: 5354973--5355546 Score: 557
Period size: 130 Copynumber: 4.4 Consensus size: 130
5354963 TCAAAGTTAT
* * * *
5354973 CTCTGTTTAGAGGAGCTTTATTTATTTTTCGAAGTCGTTGAGCTTTTTTTTAGAAGAGCTTTATT
1 CTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTTGAGCTTCTGTTTAGAAGAGCCTTATT
* * ** * *
5355038 TATTTTTTAAAAGTTG-TGAGCCTCTGTTTAAAGAAACCTTGTTTAGTTTTCAAAAGTTGTTAAG
66 TA-CTTTTCAAAGTTGTTGAGCCTCTACTTAAAGAAGCCTTATTTAGTTTTCAAAAGTTGTTAAG
*
5355102 T
130 C
* * *
5355103 CTCTGTTTAGAGGAGCTTTATTT-TCTTTTCAAAGTCGTTAAGCCTCTGTTTAGAGGAGCCTTAT
1 CTCTGTTTAGAGGAGCTTTATTTAT-TTTTCAAAGTCGTTGAGCTTCTGTTTAGAAGAGCCTTAT
* * * * ** * *
5355167 TTATTTTTTAAAGTCGTTGAGCCTCTATTTAAAGAAGTTTTATTCAGTTTTC-AAAGTTGTTGAG
65 TTACTTTTCAAAGTTGTTGAGCCTCTACTTAAAGAAGCCTTATTTAGTTTTCAAAAGTTGTTAAG
5355231 C
130 C
* * * * * * * * * *
5355232 CTCTGTTTAGAGGAGCCTTATTCAGTTTTCAAAAGTCATTAAGCCTATGCTTAGATGAGCTTTAT
1 CTCTGTTTAGAGGAGCTTTATTTATTTTTC-AAAGTCGTTGAGCTTCTGTTTAGAAGAGCCTTAT
** * **
5355297 TTACTTTTCAAAGTCATTGAACCTCTACTTAGAA-AAGCCTTATTTAGTTTTCAAAAGTTACTAA
65 TTACTTTTCAAAGTTGTTGAGCCTCTACTTA-AAGAAGCCTTATTTAGTTTTCAAAAGTTGTTAA
5355361 GC
129 GC
* * * * * * * *
5355363 CTTTATTTAGGGGAGCCTTATTTATTTTTCAAAGTCATGGAGCTTTTGTTTGGAAGAGCCTTATT
1 CTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTTGAGCTTCTGTTTAGAAGAGCCTTATT
* * * * *
5355428 TACTTTTCAAAGTTGTTGAGCCTTTGCTTAGAGGAGCCTTATTTAGTTTACAAAAGTTGTTAAGC
66 TACTTTTCAAAGTTGTTGAGCCTCTACTTAAAGAAGCCTTATTTAGTTTTCAAAAGTTGTTAAGC
* * * * *
5355493 TTCTATTTA-AGGAAG-TCTTATTTATTTTTCAAAGTTGTGGAGCTTCTATTTAGA
1 CTCTGTTTAGAGG-AGCT-TTATTTATTTTTCAAAGTCGTTGAGCTTCTGTTTAGA
5355547 GGAGTTTTTA
Statistics
Matches: 367, Mismatches: 68, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
129 52 0.14
130 278 0.76
131 37 0.10
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.43
Consensus pattern (130 bp):
CTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTTGAGCTTCTGTTTAGAAGAGCCTTATT
TACTTTTCAAAGTTGTTGAGCCTCTACTTAAAGAAGCCTTATTTAGTTTTCAAAAGTTGTTAAGC
Found at i:5355122 original size:87 final size:86
Alignment explanation
Indices: 5354932--5355550 Score: 393
Period size: 87 Copynumber: 7.2 Consensus size: 86
5354922 AAAAGTCATG
* * * * * *
5354932 AGCCTCTTTTTAAAGGAG-TCTTATTTATTTTTCAAAG-T-T-A-TCTCTGTTTAGAGGAGCTTT
1 AGCCTCTGTTTAGAGGAGCT-TTATTTATTTTTCAAAGTTGTGAGCCTCTGTTTAAAGAAGCCTT
* * * *
5354992 ATTTATTTTTC-GAAGTCGTTG
65 ATTTAGTTTTCAAAAGTTGTTA
* * * * * *
5355013 AGCTTTTTTTTAGAAGAGCTTTATTTATTTTTTAAAAGTTGTGAGCCTCTGTTTAAAGAAACCTT
1 AGCCTCTGTTTAGAGGAGCTTTATTTA-TTTTTCAAAGTTGTGAGCCTCTGTTTAAAGAAGCCTT
*
5355078 GTTTAGTTTTCAAAAGTTGTTA
65 ATTTAGTTTTCAAAAGTTGTTA
* * * * *
5355100 AGTCTCTGTTTAGAGGAGCTTTATTT-TCTTTTCAAAGTCGTTAAGCCTCTGTTTAGAGGAGCCT
1 AGCCTCTGTTTAGAGGAGCTTTATTTAT-TTTTCAAAGTTG-TGAGCCTCTGTTTAAAGAAGCCT
** * *
5355164 TATTTA-TTTTTTAAAGTCGTTG
64 TATTTAGTTTTCAAAAGTTGTTA
* * * * * * * *
5355186 AGCCTCTATTTAAAGAAGTTTTATTCAGTTTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCCTT
1 AGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTTG-TGAGCCTCTGTTTAAAGAAGCCTT
* **
5355251 ATTCAGTTTTCAAAAGTCATTA
65 ATTTAGTTTTCAAAAGTTGTTA
* * * * * **
5355273 AGCCTATGCTTAGATGAGCTTTATTTACTTTTCAAAGTCAT-TGAACCTCTACTTAGAA-AAGCC
1 AGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGT--TGTGAGCCTCTGTTTA-AAGAAGCC
**
5355336 TTATTTAGTTTTCAAAAGTTACTA
63 TTATTTAGTTTTCAAAAGTTGTTA
* * * * * * *
5355360 AGCCTTTATTTAGGGGAGCCTTATTTATTTTTCAAAGTCATG-GAGCTTTTGTTTGGAAG-AGCC
1 AGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGT--TGTGAGCCTCTGTTT-AAAGAAGCC
* *
5355423 TTATTTACTTTTC-AAAGTTGTTG
63 TTATTTAGTTTTCAAAAGTTGTTA
* * * * * * * * * *
5355446 AGCCTTTGCTTAGAGGAGCCTTATTTAGTTTACAAAAGTTGTTAAGCTTCTATTTAAGGAAGTCT
1 AGCCTCTGTTTAGAGGAGCTTTATTTATTTTTC-AAAGTTG-TGAGCCTCTGTTTAAAGAAGCCT
* **
5355511 TATTTATTTTTC-AAAGTTGTGG
64 TATTTAGTTTTCAAAAGTTGTTA
* *
5355533 AGCTTCTATTTAGAGGAG
1 AGCCTCTGTTTAGAGGAG
5355551 TTTTTATGTT
Statistics
Matches: 421, Mismatches: 96, Indels: 36
0.76 0.17 0.07
Matches are distributed among these distances:
81 21 0.05
82 10 0.02
83 1 0.00
84 1 0.00
85 4 0.01
86 142 0.34
87 240 0.57
88 1 0.00
89 1 0.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (86 bp):
AGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTTGTGAGCCTCTGTTTAAAGAAGCCTTA
TTTAGTTTTCAAAAGTTGTTA
Found at i:5357457 original size:117 final size:116
Alignment explanation
Indices: 5357289--5357508 Score: 275
Period size: 117 Copynumber: 1.9 Consensus size: 116
5357279 ACATTCCTTG
* * *
5357289 GGTGATCGATCCTCTATGTGGGGGAATCAATCCCTTTTATTACTTTTCAAAC-CATGATAGCATT
1 GGTGATCGATCCCCTATGTGGGGGAATCAATCCCTTTTATGAATTTTCAAACTCAT-ATAGCATT
5357353 CTGCCAAGAAAAATAGATCGATCCCTTTT-AGGGAGGGATCGATCCCATGCTTA
65 CTGCCAA-AAAAATAGATCGAT-CCTTTTAAGGGAGGGATCGATCCCATGCTTA
* * * * * *
5357406 GGTGATCGATCCCCTATGTAGGGGG-ATCGATCTCTTTTGTGAATTTTCAAACTCATTTTGCTTT
1 GGTGATCGATCCCCTATGT-GGGGGAATCAATCCCTTTTATGAATTTTCAAACTCATATAGCATT
***
5357470 CTGTGTAAAAAATAGATCGATCCTTTTAAGGGAGGGATC
65 CTGCCAAAAAAATAGATCGATCCTTTTAAGGGAGGGATC
5357509 AATCGGGTAA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
115 6 0.07
116 25 0.28
117 49 0.56
118 8 0.09
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (116 bp):
GGTGATCGATCCCCTATGTGGGGGAATCAATCCCTTTTATGAATTTTCAAACTCATATAGCATTC
TGCCAAAAAAATAGATCGATCCTTTTAAGGGAGGGATCGATCCCATGCTTA
Found at i:5358423 original size:174 final size:172
Alignment explanation
Indices: 5358175--5358491 Score: 440
Period size: 174 Copynumber: 1.8 Consensus size: 172
5358165 CTAATTACCC
* * * *
5358175 AAGGATGATATTCTTAGAAATTTCAAATTGTAAATTTCTATGAAATCTTTAGGTGAGAAATTTCT
1 AAGGATGAGATTCTTAAAAATTTCAAATGGTAAATTTCTAAGAAATCTTTAGGTGAGAAATTTCT
* * * ** *
5358240 CTAAATTTGTCTCAAATGGTGAAATAATTTAGATGAAGTTTTAATAAAAGTAATTG-TATTCTTT
66 CTAAATTTGTCTCAAATGATGAAAGAATTTAAATGAAACTTTAA-AAAA-TAATTGATATTATTT
5358304 TTCAAATAAAAAAATTTTGGTTGAAAAATATTTGACAATTATCT
129 TTCAAATAAAAAAATTTTGGTTGAAAAATATTTGACAATTATCT
*
5358348 AAGGGTGAGATTCTTAAAAATTTCAAATGGTAAATTATCTAAGAAATCTTTAGGTGAGAAATTT-
1 AAGGATGAGATTCTTAAAAATTTCAAATGGTAAATT-TCTAAGAAATCTTTAGGTGAGAAATTTC
* *
5358412 TTTAAAATTTGTCTCAAATGATGGAAGAATTTAAATGAAACTTTAAAAAATAATTGTCATATTAT
65 TCT-AAATTTGTCTCAAATGATGAAAGAATTTAAATGAAACTTTAAAAAATAATTG--ATATTAT
*
5358477 TTTTTAAATAAAAAA
127 TTTTCAAATAAAAAA
5358492 CAAAAAAAAA
Statistics
Matches: 125, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
172 6 0.05
173 38 0.30
174 62 0.50
175 19 0.15
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (172 bp):
AAGGATGAGATTCTTAAAAATTTCAAATGGTAAATTTCTAAGAAATCTTTAGGTGAGAAATTTCT
CTAAATTTGTCTCAAATGATGAAAGAATTTAAATGAAACTTTAAAAAATAATTGATATTATTTTT
CAAATAAAAAAATTTTGGTTGAAAAATATTTGACAATTATCT
Found at i:5358599 original size:47 final size:46
Alignment explanation
Indices: 5358493--5358599 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 46
5358483 AATAAAAAAC
* *
5358493 AAAAAAAAAGAATTTCTAAATAGACCCAAATGGTAAAAAATTTAGA
1 AAAAAAAAAAAAATTCTAAATAGACCCAAATGGTAAAAAATTTAGA
** * * *
5358539 AATTAAAAAAAAATTCTAAATTGATCCAAATGGTGAAAAATTTA-A
1 AAAAAAAAAAAAATTCTAAATAGACCCAAATGGTAAAAAATTTAGA
5358584 ATAAAAATAAAAAAAT
1 A-AAAAA-AAAAAAAT
5358600 AAAAATAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
45 2 0.04
46 40 0.80
47 8 0.16
ACGTcount: A:0.61, C:0.07, G:0.08, T:0.24
Consensus pattern (46 bp):
AAAAAAAAAAAAATTCTAAATAGACCCAAATGGTAAAAAATTTAGA
Found at i:5358601 original size:14 final size:14
Alignment explanation
Indices: 5358582--5358608 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5358572 TGAAAAATTT
5358582 AAATAAAAATAAAA
1 AAATAAAAATAAAA
5358596 AAATAAAAATAAA
1 AAATAAAAATAAA
5358609 TCTGAGCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AAATAAAAATAAAA
Found at i:5360945 original size:13 final size:13
Alignment explanation
Indices: 5360927--5360953 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5360917 ATTTCTGGTA
5360927 ATTTTTCTTTTTC
1 ATTTTTCTTTTTC
5360940 ATTTTTCTTTTTC
1 ATTTTTCTTTTTC
5360953 A
1 A
5360954 AAAGACAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTTTCTTTTTC
Found at i:5363108 original size:7 final size:7
Alignment explanation
Indices: 5363097--5363131 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
5363087 TGAAGAAGTT
*
5363097 TACTTCT
1 TACTTCC
5363104 TACTTCC
1 TACTTCC
5363111 TACTTCC
1 TACTTCC
5363118 TACTTCC
1 TACTTCC
5363125 TACTTCC
1 TACTTCC
5363132 GATCCTAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.14, C:0.40, G:0.00, T:0.46
Consensus pattern (7 bp):
TACTTCC
Found at i:5364611 original size:21 final size:22
Alignment explanation
Indices: 5364573--5364624 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
5364563 CCTGAAATTA
5364573 ATAAAATATTATTTTTTTAAAT
1 ATAAAATATTATTTTTTTAAAT
5364595 ATAAAATATTA-TTTTTTAAAT
1 ATAAAATATTATTTTTTTAAAT
5364616 AT-AAATATT
1 ATAAAATATT
5364625 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 12 0.40
22 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAAAATATTATTTTTTTAAAT
Found at i:5364633 original size:30 final size:30
Alignment explanation
Indices: 5364597--5364657 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5364587 TTTTAAATAT
* * * *
5364597 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATCATTATATAAATATAAATAATTA
*
5364627 AAAATATCATTATATAAATATATATAATTA
1 AAAATATCATTATATAAATATAAATAATTA
5364657 A
1 A
5364658 TTAATTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATATCATTATATAAATATAAATAATTA
Found at i:5376775 original size:45 final size:45
Alignment explanation
Indices: 5376721--5376813 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
5376711 TAATGTGAAC
* * *
5376721 ATAATTAGCTATTGCCTAAGGTCAT-GGGATTTACATGTAAACATA
1 ATAATTAGCTATTGCATAAAGTCATAAGG-TTTACATGTAAACATA
* * *
5376766 ATAATTAGCTGTTGCATAAAGTCATAAGGTTTGCATGTGAACATA
1 ATAATTAGCTATTGCATAAAGTCATAAGGTTTACATGTAAACATA
5376811 ATA
1 ATA
5376814 TTCATAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 39 0.95
46 2 0.05
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (45 bp):
ATAATTAGCTATTGCATAAAGTCATAAGGTTTACATGTAAACATA
Found at i:5377652 original size:66 final size:66
Alignment explanation
Indices: 5377546--5377680 Score: 234
Period size: 66 Copynumber: 2.0 Consensus size: 66
5377536 TTTTTACTAT
*
5377546 CTTAAACATAAAAGATGATGAAGCTCTATTACTTTTAGGTAGACCTTTCCTATTCACTGCCAAAG
1 CTTAAACATAAAAGATGATGAAGCTCTATTACTTTTAGGTAAACCTTTCCTATTCACTGCCAAAG
5377611 C
66 C
* * *
5377612 CTTAAACATAGAGGATGATGAAGCTCTATTACTTTTAGGTAAACCTTTCCTATTCACTGCCCAAG
1 CTTAAACATAAAAGATGATGAAGCTCTATTACTTTTAGGTAAACCTTTCCTATTCACTGCCAAAG
5377677 C
66 C
5377678 CTT
1 CTT
5377681 GATAGATATG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (66 bp):
CTTAAACATAAAAGATGATGAAGCTCTATTACTTTTAGGTAAACCTTTCCTATTCACTGCCAAAG
C
Found at i:5395448 original size:21 final size:21
Alignment explanation
Indices: 5395424--5395471 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
5395414 GGACTCTAAG
5395424 TAGGCTTAGAATAACTATGAC
1 TAGGCTTAGAATAACTATGAC
5395445 TAGGCTTAGAATAACTATGAC
1 TAGGCTTAGAATAACTATGAC
5395466 TAGGCT
1 TAGGCT
5395472 CAATGGGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (21 bp):
TAGGCTTAGAATAACTATGAC
Found at i:5398242 original size:22 final size:22
Alignment explanation
Indices: 5398208--5398271 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
5398198 AAATAATTTT
* *
5398208 TTTTTTATATTTTTAAAATCAA
1 TTTTTAATTTTTTTAAAATCAA
5398230 TTTTTAATTTTTTT-AAATCAA
1 TTTTTAATTTTTTTAAAATCAA
*
5398251 TATTTCAATTTTTTTAGAAAT
1 T-TTTTAATTTTTTTA-AAAT
5398272 TTTTCAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 8 0.22
22 24 0.67
24 4 0.11
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTTAATTTTTTTAAAATCAA
Found at i:5398276 original size:20 final size:21
Alignment explanation
Indices: 5398217--5398278 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
5398207 TTTTTTTATA
*
5398217 TTTTTAAAATCAATTTTT-AAT
1 TTTTTTAAA-CAATTTTTCAAT
*
5398238 TTTTTTAAATCAATATTTCAAT
1 TTTTTTAAA-CAATTTTTCAAT
*
5398260 TTTTTTAGA-AATTTTTCAA
1 TTTTTTAAACAATTTTTCAA
5398279 AATTTTCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 9 0.25
21 16 0.44
22 11 0.31
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTTTAAACAATTTTTCAAT
Found at i:5398855 original size:37 final size:35
Alignment explanation
Indices: 5398797--5398870 Score: 87
Period size: 37 Copynumber: 2.1 Consensus size: 35
5398787 AATATATATT
5398797 TTTTATAAAAACACAAAAATTAA-AAATATAGAAAA
1 TTTTATAAAAACACAAAAATTAAGAAATA-AGAAAA
** *
5398832 TTTTATAAAAATTTCAAAGAATTAAGAAATAATAAAA
1 TTTTATAAAAA-CACAAA-AATTAAGAAATAAGAAAA
5398869 TT
1 TT
5398871 AAATATTTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 11 0.33
36 4 0.12
37 13 0.39
38 5 0.15
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (35 bp):
TTTTATAAAAACACAAAAATTAAGAAATAAGAAAA
Found at i:5399023 original size:17 final size:17
Alignment explanation
Indices: 5399003--5399045 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
5398993 AAAAAAAATT
5399003 AAAATATTCAATTTAAA
1 AAAATATTCAATTTAAA
* *
5399020 AAAATA-TGATTTTAAA
1 AAAATATTCAATTTAAA
5399036 AAAA-ATTCAA
1 AAAATATTCAA
5399046 ACCATATGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
15 1 0.05
16 14 0.67
17 6 0.29
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATATTCAATTTAAA
Found at i:5400058 original size:43 final size:43
Alignment explanation
Indices: 5400006--5400096 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 43
5399996 GAGGGATAGA
*
5400006 TTTTA-TTTTTAAATTATGTTCTAAGTAAGACAGAAGGATAAAT
1 TTTTATTTTTTAAATTATGTTCTAAATAAGACAGAAGGA-AAAT
* *
5400049 TTTTATTTTTTAAATTATGTTTTAAATAAGAGAGAAGGAAAAT
1 TTTTATTTTTTAAATTATGTTCTAAATAAGACAGAAGGAAAAT
5400092 TTTTA
1 TTTTA
5400097 CACCAAATTG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 14 0.32
44 30 0.68
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (43 bp):
TTTTATTTTTTAAATTATGTTCTAAATAAGACAGAAGGAAAAT
Found at i:5400258 original size:13 final size:13
Alignment explanation
Indices: 5400242--5400266 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5400232 AGATATATAT
5400242 ATAAATAAATAAA
1 ATAAATAAATAAA
5400255 ATAAATAAATAA
1 ATAAATAAATAA
5400267 TAAAATATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAAATAAATAAA
Found at i:5407972 original size:26 final size:26
Alignment explanation
Indices: 5407943--5408007 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
5407933 CAAGTTAAAC
*
5407943 TAAGTGCATCAGAATGGTTGCATGTT
1 TAAGTGCATCAGAATGGTTGCATATT
*
5407969 TAAGTGCATCAGAATGGTTGCCTATT
1 TAAGTGCATCAGAATGGTTGCATATT
*
5407995 TCAGTGCAATCAG
1 TAAGTGC-ATCAG
5408008 TGTTAAACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 30 0.86
27 5 0.14
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (26 bp):
TAAGTGCATCAGAATGGTTGCATATT
Found at i:5421540 original size:19 final size:19
Alignment explanation
Indices: 5421502--5421540 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5421492 TGTCATGCTT
**
5421502 TTTAACAGGCAATATCACA
1 TTTAACAGGCAATAAAACA
5421521 TTTAACAGGCAATAAAACA
1 TTTAACAGGCAATAAAACA
5421540 T
1 T
5421541 GTATGTAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (19 bp):
TTTAACAGGCAATAAAACA
Found at i:5422064 original size:17 final size:17
Alignment explanation
Indices: 5422025--5422085 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
5422015 TTTTATCTTT
* *
5422025 ATAATTTATT-ATCAAA
1 ATAATTAATTAATAAAA
*
5422041 ATTATTAATTAATAAAA
1 ATAATTAATTAATAAAA
* * *
5422058 ATAATTAAATATTAATA
1 ATAATTAATTAATAAAA
*
5422075 ATAATTTATTA
1 ATAATTAATTA
5422086 TAATAATTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
16 8 0.23
17 27 0.77
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATTAATTAATAAAA
Found at i:5422157 original size:21 final size:22
Alignment explanation
Indices: 5422120--5422193 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 22
5422110 TATTTTAATT
**
5422120 AATATTAATTTCTTAAA-ACAA
1 AATATTAATTTAATAAATACAA
**
5422141 AATATTAATTTAATAAATTTAA
1 AATATTAATTTAATAAATACAA
* * **
5422163 AATGTTAATTTAAT-CATATTA
1 AATATTAATTTAATAAATACAA
5422184 AATATTAATT
1 AATATTAATT
5422194 AACAATATTT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
21 28 0.65
22 15 0.35
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (22 bp):
AATATTAATTTAATAAATACAA
Found at i:5422223 original size:41 final size:40
Alignment explanation
Indices: 5422168--5422396 Score: 171
Period size: 41 Copynumber: 5.7 Consensus size: 40
5422158 TTTAAAATGT
* *
5422168 TAATTTAATCATATTAAATATTAATTAACAATATTTTATA
1 TAATTTAATAATATTAAATATTAATTAATAATATTTTATA
* *
5422208 TGAATTTAATAATATTCAATATTAATT--TAATATTATTAAA
1 T-AATTTAATAATATTAAATATTAATTAATAATATT-TTATA
* * * *
5422248 TTAGTATTTAGT-ATATTAAGTATTATTTAATAATATTATATA
1 -TA--ATTTAATAATATTAAATATTAATTAATAATATTTTATA
* * * * **
5422290 TTATTGAACAATATTAAATATTAATTTAATAATACTAAATA
1 TAATTTAATAATATTAAATATTAA-TTAATAATATTTTATA
* * * *
5422331 TTCAATTTCATAATATTAAA-AATATTTAATATTATTTTA-A
1 -T-AATTTAATAATATTAAATATTAATTAATAATATTTTATA
* *
5422371 TAATATATTAATATTAAATATTAATT
1 TAATTTAATAATATTAAATATTAATT
5422397 TAAATATATT
Statistics
Matches: 144, Mismatches: 33, Indels: 25
0.71 0.16 0.12
Matches are distributed among these distances:
38 14 0.10
39 16 0.11
40 19 0.13
41 62 0.43
42 13 0.09
43 20 0.14
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (40 bp):
TAATTTAATAATATTAAATATTAATTAATAATATTTTATA
Found at i:5422241 original size:11 final size:11
Alignment explanation
Indices: 5422141--5422242 Score: 56
Period size: 11 Copynumber: 9.6 Consensus size: 11
5422131 CTTAAAACAA
5422141 AATATTAATTT
1 AATATTAATTT
5422152 AATA--AATTT
1 AATATTAATTT
*
5422161 AAAATGTTAATTT
1 --AATATTAATTT
*
5422174 AATCA-T-ATTA
1 AAT-ATTAATTT
5422184 AATATTAA-TT
1 AATATTAATTT
* *
5422194 AACAAT-ATTT
1 AATATTAATTT
* *
5422204 TATATGAATTT
1 AATATTAATTT
* *
5422215 AATAAT-ATTC
1 AATATTAATTT
5422225 AATATTAATTT
1 AATATTAATTT
5422236 AATATTA
1 AATATTA
5422243 TTAAATTAGT
Statistics
Matches: 65, Mismatches: 16, Indels: 20
0.64 0.16 0.20
Matches are distributed among these distances:
9 7 0.11
10 24 0.37
11 29 0.45
13 5 0.08
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (11 bp):
AATATTAATTT
Found at i:5422343 original size:22 final size:21
Alignment explanation
Indices: 5422140--5422413 Score: 219
Period size: 21 Copynumber: 13.3 Consensus size: 21
5422130 TCTTAAAACA
5422140 AAATATTAATTTAATAA-ATTT
1 AAATATTAATTTAATAATA-TT
* *
5422161 AAAATGTTAATTTAATCATATT
1 -AAATATTAATTTAATAATATT
*
5422183 AAATATTAA-TTAACAATATT
1 AAATATTAATTTAATAATATT
** *
5422203 TTATATGAATTTAATAATATT
1 AAATATTAATTTAATAATATT
* *
5422224 CAATATTAATTTAATATTATT
1 AAATATTAATTTAATAATATT
* *
5422245 AAATTAGT-ATTTAGT-ATATT
1 AAA-TATTAATTTAATAATATT
*
5422265 AAGTATT-ATTTAATAATATT
1 AAATATTAATTTAATAATATT
* * *
5422285 ATATATT-ATTGAACAATATT
1 AAATATTAATTTAATAATATT
*
5422305 AAATATTAATTTAATAATACT
1 AAATATTAATTTAATAATATT
*
5422326 AAATATTCAATTTCATAATATT
1 AAATATT-AATTTAATAATATT
* *
5422348 AAA-AAT-ATTTAATATTATT
1 AAATATTAATTTAATAATATT
* * * *
5422367 --TTAATAATATATTAATATT
1 AAATATTAATTTAATAATATT
5422386 AAATATTAATTTAA-ATATATT
1 AAATATTAATTTAATA-ATATT
*
5422407 TAATATT
1 AAATATT
5422414 GAATATTTTT
Statistics
Matches: 199, Mismatches: 42, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
18 3 0.02
19 30 0.15
20 49 0.25
21 81 0.41
22 35 0.18
23 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (21 bp):
AAATATTAATTTAATAATATT
Found at i:5422401 original size:12 final size:13
Alignment explanation
Indices: 5422375--5422403 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5422365 TTTTAATAAT
5422375 ATATTAATATTAA
1 ATATTAATATTAA
5422388 ATATTAAT-TTAA
1 ATATTAATATTAA
5422400 ATAT
1 ATAT
5422404 ATTTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTAATATTAA
Found at i:5422406 original size:102 final size:101
Alignment explanation
Indices: 5422173--5422413 Score: 251
Period size: 102 Copynumber: 2.4 Consensus size: 101
5422163 AATGTTAATT
* * * * *
5422173 TAATCATATTAAATATTAA-TTAACAATATTTTATATGAATTTAATAATATTCAATATTAATTTA
1 TAATAATATTAAATATTAATTTAACAATATTTAATATTAATTTAATAATACTAAATATTAATTTA
* * * *
5422237 ATATTATTAAATTAGTATTTAGTATATTAAGTATTATT
66 ATAATATTAAA-TAATATTTAATATATTAAGTA-TATA
* * *
5422275 TAATAATATTATATATT-ATTGAACAATATTAAATATTAATTTAATAATACTAAATATTCAATTT
1 TAATAATATTAAATATTAATTTAACAATATTTAATATTAATTTAATAATACTAAATATT-AATTT
*
5422339 CATAATATTAAA-AATATTTAATATTATTTTAA-TA-ATA
65 AATAATATTAAATAATATTTAATA-TA--TTAAGTATATA
*
5422376 TATTAATATTAAATATTAATTTAA-ATATATTTAATATT
1 TAATAATATTAAATATTAATTTAACA-ATATTTAATATT
5422414 GAATATTTTT
Statistics
Matches: 115, Mismatches: 17, Indels: 14
0.79 0.12 0.10
Matches are distributed among these distances:
101 28 0.24
102 66 0.57
103 17 0.15
104 4 0.03
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (101 bp):
TAATAATATTAAATATTAATTTAACAATATTTAATATTAATTTAATAATACTAAATATTAATTTA
ATAATATTAAATAATATTTAATATATTAAGTATATA
Found at i:5422420 original size:41 final size:40
Alignment explanation
Indices: 5422140--5422420 Score: 131
Period size: 41 Copynumber: 6.8 Consensus size: 40
5422130 TCTTAAAACA
* * *
5422140 AAATATTAATTTAATAAATTTAAAATGTTAAT-TTAATCATATT
1 AAATATTAATTTAATATATTTAATAT-TGAATATT-A--ATATT
* * *
5422183 AAATATTAA-TTAACAATATTTTATA-TGAATTTAATAATATT
1 AAATATTAATTTAA-TATATTTAATATTGAA--TATTAATATT
* *
5422224 CAATATTAATTTAATAT-TATTAA-ATT-AGTATTTAGTATATT
1 AAATATTAATTTAATATAT-TTAATATTGAATA-TTA--ATATT
* *
5422265 AAGTATT-ATTTAATAATATTATATATTATTG-A-A-CAATATT
1 AAATATTAATTTAAT-ATATT-TA-A-TATTGAATATTAATATT
* * * *
5422305 AAATATTAATTTAATAATACTAAATATTCAATTTCATAATATT
1 AAATATTAATTTAAT-ATATTTAATATTGAATAT--TAATATT
* *
5422348 AAA-AAT-ATTTAATATTATTTTAATAAT--ATATTAATATT
1 AAATATTAATTTAATA-TA-TTTAATATTGAATATTAATATT
5422386 AAATATTAATTTAAATATATTTAATATTGAATATT
1 AAATATTAATTT-AATATATTTAATATTGAATATT
5422421 TTTATAATAA
Statistics
Matches: 180, Mismatches: 28, Indels: 62
0.67 0.10 0.23
Matches are distributed among these distances:
38 16 0.09
39 14 0.08
40 32 0.18
41 65 0.36
42 20 0.11
43 28 0.16
44 2 0.01
45 3 0.02
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (40 bp):
AAATATTAATTTAATATATTTAATATTGAATATTAATATT
Found at i:5422443 original size:29 final size:29
Alignment explanation
Indices: 5422351--5422444 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
5422341 TAATATTAAA
*
5422351 AATATTTAATATTATTT-TAATAATATATT
1 AATATTGAATATTATTTATAATAATAT-TT
*
5422380 AATATTAAATATTAATTTA-AAT-ATATTT
1 AATATTGAATATT-ATTTATAATAATATTT
*
5422408 AATATTGAATATT-TTTATAATAACATCTT
1 AATATTGAATATTATTTATAATAATAT-TT
5422437 AATATTGA
1 AATATTGA
5422445 TAACTAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
26 4 0.07
27 3 0.05
28 17 0.30
29 26 0.46
30 7 0.12
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
AATATTGAATATTATTTATAATAATATTT
Found at i:5422453 original size:57 final size:59
Alignment explanation
Indices: 5422351--5422491 Score: 146
Period size: 57 Copynumber: 2.4 Consensus size: 59
5422341 TAATATTAAA
* * *
5422351 AATATTTAATATTATTT-TAATAATATATTAATATTAAATATTAATTT-A-AATATATTT
1 AATATTGAATATT-TTTATAATAACATATTAATATTAAATACTAATTTAATAATATATTT
* * *
5422408 AATATTGAATATTTTTATAATAACATCTTAATATT-GATAACTAATTTAATAATATTTTT
1 AATATTGAATATTTTTATAATAACATATTAATATTAAAT-ACTAATTTAATAATATATTT
*
5422467 ATATTATTGAATTAATTTTATAATA
1 A-A-TATTGAA-TATTTTTATAATA
5422492 TTTTACAATT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
56 5 0.07
57 35 0.50
58 1 0.01
59 9 0.13
60 1 0.01
61 7 0.10
62 12 0.17
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (59 bp):
AATATTGAATATTTTTATAATAACATATTAATATTAAATACTAATTTAATAATATATTT
Found at i:5422586 original size:28 final size:28
Alignment explanation
Indices: 5422522--5422590 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
5422512 TTTTTTAAAA
** *
5422522 TTTTAATATTAATTGAATAATATTTTCAT
1 TTTTAATATT-ATCAAATAATATTTTAAT
** *
5422551 ACTAAATATTATCAAATAATATTTTAAT
1 TTTTAATATTATCAAATAATATTTTAAT
5422579 TTTTAATATTAT
1 TTTTAATATTAT
5422591 TTTAACAGTA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
28 24 0.77
29 7 0.23
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (28 bp):
TTTTAATATTATCAAATAATATTTTAAT
Found at i:5422713 original size:30 final size:28
Alignment explanation
Indices: 5422648--5422738 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 28
5422638 ATTTTCTCAT
*
5422648 TATTTTAACA-TTAATATTAATTTAATAA
1 TATTTTAAAATTTAATATTAATTT-ATAA
5422676 T-TCTTTAAAATTTTAATATTAAGTTTATAA
1 TAT-TTTAAAA-TTTAATATTAA-TTTATAA
* * *
5422706 TATTTTAATATTAAATAATAATTTTATAA
1 TATTTTAAAATTTAATATTAA-TTTATAA
5422735 TATT
1 TATT
5422739 ATAATATTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
27 1 0.02
28 7 0.13
29 20 0.38
30 21 0.40
31 4 0.08
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (28 bp):
TATTTTAAAATTTAATATTAATTTATAA
Found at i:5422732 original size:29 final size:29
Alignment explanation
Indices: 5422648--5422747 Score: 105
Period size: 29 Copynumber: 3.4 Consensus size: 29
5422638 ATTTTCTCAT
* *
5422648 TATTTTAACATT-AATATTAATTTAATAA
1 TATTTTAATATTAAATATTAATTTTATAA
* * *
5422676 T-TCTTTAAAATTTTAATATTAAGTTTATAA
1 TAT-TTTAATA-TTAAATATTAATTTTATAA
*
5422706 TATTTTAATATTAAATAATAATTTTATAA
1 TATTTTAATATTAAATATTAATTTTATAA
*
5422735 TATTATAATATTA
1 TATTTTAATATTA
5422748 TTTGAATAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.02
28 7 0.12
29 30 0.50
30 21 0.35
31 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (29 bp):
TATTTTAATATTAAATATTAATTTTATAA
Found at i:5422734 original size:8 final size:8
Alignment explanation
Indices: 5422700--5422748 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
5422690 AATATTAAGT
5422700 TTATAATA
1 TTATAATA
*
5422708 TTTTAATA
1 TTATAATA
5422716 TTA-AATA
1 TTATAATA
*
5422723 --ATAATT
1 TTATAATA
5422729 TTATAATA
1 TTATAATA
5422737 TTATAATA
1 TTATAATA
5422745 TTAT
1 TTAT
5422749 TTGAATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 1 0.03
6 3 0.09
7 4 0.12
8 26 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTATAATA
Found at i:5422735 original size:21 final size:22
Alignment explanation
Indices: 5422685--5422744 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
5422675 ATTCTTTAAA
* *
5422685 ATTTTAATATTA-AGTTTATAAT
1 ATTTTAATATTATA-ATAATAAT
5422707 ATTTTAATATTA-AATAATAAT
1 ATTTTAATATTATAATAATAAT
5422728 -TTTATAATATTATAATA
1 ATTT-TAATATTATAATA
5422745 TTATTTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.09
21 14 0.41
22 17 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTTAATATTATAATAATAAT
Found at i:5422744 original size:51 final size:49
Alignment explanation
Indices: 5422658--5422779 Score: 131
Period size: 51 Copynumber: 2.4 Consensus size: 49
5422648 TATTTTAACA
* *
5422658 TTAATATTAATTTAATAATTCTTTAAAATTTTAATATTAAGTTT-ATAATATT
1 TTAATATTAA-ATAATAATT-TTTAAAATTATAATATT-A-TTTAATAATATT
*
5422710 TTAATATTAAATAATAATTTTATAATATTATAATATTATTTGAATAATATT
1 TTAATATTAAATAATAATTTT-TAAAATTATAATATTATTT-AATAATATT
* *
5422761 TT-GTATTAAATATTAATTT
1 TTAATATTAAATAATAATTT
5422780 AATGAGATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
49 3 0.05
50 18 0.29
51 31 0.50
52 10 0.16
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (49 bp):
TTAATATTAAATAATAATTTTTAAAATTATAATATTATTTAATAATATT
Found at i:5422789 original size:28 final size:29
Alignment explanation
Indices: 5422735--5422790 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
5422725 AATTTTATAA
*
5422735 TATTATAATATTATTTGAATAATATTTTG
1 TATTATAATATTATTTGAATAAGATTTTG
*
5422764 TATTA-AATATTAATTT-AATGAGATTTT
1 TATTATAATATT-ATTTGAATAAGATTTT
5422791 AATGTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (29 bp):
TATTATAATATTATTTGAATAAGATTTTG
Found at i:5422843 original size:27 final size:27
Alignment explanation
Indices: 5422807--5422888 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
5422797 ATTTTAAATT
*
5422807 ATTTATTTAATTTATATAA-TATTTTA
1 ATTTATTTAATTTATATAATTATTATA
* *
5422833 CTATTATTTAA-TTATTTAATTATTATA
1 AT-TTATTTAATTTATATAATTATTATA
*
5422860 ATTTAATTTAATTAATATAAATTAATTAT
1 ATTT-ATTTAATTTATAT-AATT-ATTAT
5422889 CTAATTAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
26 10 0.23
27 21 0.48
28 4 0.09
29 4 0.09
30 5 0.11
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTTATTTAATTTATATAATTATTATA
Found at i:5422846 original size:8 final size:8
Alignment explanation
Indices: 5422835--5422873 Score: 51
Period size: 8 Copynumber: 4.5 Consensus size: 8
5422825 ATATTTTACT
5422835 ATTATTTA
1 ATTATTTA
5422843 ATTATTTA
1 ATTATTTA
5422851 ATTATTATA
1 ATTATT-TA
5422860 ATTTAATTTA
1 A-TT-ATTTA
5422870 ATTA
1 ATTA
5422874 ATATAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 15 0.54
9 5 0.18
10 5 0.18
11 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATTATTTA
Found at i:5422868 original size:19 final size:18
Alignment explanation
Indices: 5422835--5422886 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
5422825 ATATTTTACT
5422835 ATTATT-TAATT-ATTTA
1 ATTATTATAATTAATTTA
5422851 ATTATTATAATTTAATTTA
1 ATTATTATAA-TTAATTTA
*
5422870 ATTAATATAAATTAATT
1 ATTATTAT-AATTAATT
5422887 ATCTAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 6 0.19
17 3 0.10
18 2 0.06
19 18 0.58
20 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTATAATTAATTTA
Found at i:5423827 original size:29 final size:29
Alignment explanation
Indices: 5423785--5423841 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
5423775 CATTTTGATT
*
5423785 TATTATTATATAATAAATTAATAAATAAG
1 TATTATCATATAATAAATTAATAAATAAG
5423814 TATTATCATATAATAAATTAATAAATAA
1 TATTATCATATAATAAATTAATAAATAA
5423842 ATTTTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (29 bp):
TATTATCATATAATAAATTAATAAATAAG
Found at i:5423848 original size:29 final size:29
Alignment explanation
Indices: 5423785--5423848 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
5423775 CATTTTGATT
* *
5423785 TATTATTATATAATAAATTAATAAATAAG
1 TATTATCATATAATAAATTAATAAATAAA
5423814 TATTATCATATAATAAATTAATAAATAAA
1 TATTATCATATAATAAATTAATAAATAAA
*
5423843 TTTTAT
1 TATTAT
5423849 TTTAATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
TATTATCATATAATAAATTAATAAATAAA
Found at i:5424460 original size:12 final size:13
Alignment explanation
Indices: 5424443--5424472 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
5424433 ATAAATTTAT
5424443 TATATTTTAA-AA
1 TATATTTTAATAA
5424455 TATATTTTAATAA
1 TATATTTTAATAA
5424468 TATAT
1 TATAT
5424473 ATATGAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATTTTAATAA
Found at i:5424855 original size:71 final size:69
Alignment explanation
Indices: 5424769--5424917 Score: 187
Period size: 71 Copynumber: 2.1 Consensus size: 69
5424759 TTTTATACTA
* * *
5424769 TGATAATATTAATAAATATTAACAATTTAATTT-TGATTTTGCTATAATATAAGTAAAATTTGGT
1 TGATAATAATAATAAATAATAACAATTTAATTTAT-ATTTT-CTATAATATAAATAAAATTT-G-
5424833 ATA-CTTT
62 ATACCTTT
* * *
5424840 TGATAATAATGATAAATAATAACAATTTAATTTATATTTTTTATACTATAAATAAAATTTGATAC
1 TGATAATAATAATAAATAATAACAATTTAATTTATATTTTCTATAATATAAATAAAATTTGATAC
5424905 CTTT
66 CTTT
5424909 TGAT-ATAAT
1 TGATAATAAT
5424918 TTTGATTTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
68 8 0.11
69 9 0.13
70 17 0.24
71 35 0.50
72 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.46
Consensus pattern (69 bp):
TGATAATAATAATAAATAATAACAATTTAATTTATATTTTCTATAATATAAATAAAATTTGATAC
CTTT
Found at i:5424926 original size:47 final size:49
Alignment explanation
Indices: 5424867--5424971 Score: 110
Period size: 48 Copynumber: 2.2 Consensus size: 49
5424857 AATAACAATT
* * *
5424867 TAATTTAT-ATTTTTTAT-ACTATAAATAAAA-TTTGATACCTTTTGATA
1 TAATTT-TGATTTTTAATAACTATAAATAAAATTTTAATAACTTTTGATA
* **
5424914 TAATTTTGA-TTTTAATAACTTTTGATAAAATTTTAATAACTTTTGATA
1 TAATTTTGATTTTTAATAACTATAAATAAAATTTTAATAACTTTTGATA
*
5424962 CAATTTTGAT
1 TAATTTTGAT
5424972 AACCGTCAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
46 7 0.15
47 17 0.36
48 23 0.49
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (49 bp):
TAATTTTGATTTTTAATAACTATAAATAAAATTTTAATAACTTTTGATA
Found at i:5424941 original size:10 final size:10
Alignment explanation
Indices: 5424923--5424974 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 10
5424913 ATAATTTTGA
*
5424923 TTTTAATAAC
1 TTTTGATAAC
*
5424933 TTTTGATAAAA
1 TTTTGAT-AAC
*
5424944 TTTTAATAAC
1 TTTTGATAAC
*
5424954 TTTTGATACAA
1 TTTTGATA-AC
5424965 TTTTGATAAC
1 TTTTGATAAC
5424975 CGTCAATATT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (10 bp):
TTTTGATAAC
Found at i:5424948 original size:21 final size:21
Alignment explanation
Indices: 5424922--5424974 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
5424912 TATAATTTTG
5424922 ATTTTAATAACTTTTGATAAA
1 ATTTTAATAACTTTTGATAAA
*
5424943 ATTTTAATAACTTTTGATACA
1 ATTTTAATAACTTTTGATAAA
*
5424964 ATTTTGATAAC
1 ATTTTAATAAC
5424975 CGTCAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (21 bp):
ATTTTAATAACTTTTGATAAA
Found at i:5425101 original size:22 final size:22
Alignment explanation
Indices: 5425054--5425107 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
5425044 TGATATGGTT
*
5425054 TTAATAACATTTTGGTAACTTA
1 TTAATAACATTTTGATAACTTA
*
5425076 -TAATATACTTTTTGATAA-TTA
1 TTAATA-ACATTTTGATAACTTA
5425097 TTAATAA-ATTT
1 TTAATAACATTT
5425108 GTATCATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 3 0.11
21 9 0.33
22 15 0.56
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (22 bp):
TTAATAACATTTTGATAACTTA
Found at i:5425508 original size:44 final size:43
Alignment explanation
Indices: 5425381--5425517 Score: 134
Period size: 44 Copynumber: 3.1 Consensus size: 43
5425371 TAATACTATT
5425381 TTATCAATAATTTACTA-TAAGTTATAAATGATATATATTACTAAA
1 TTATCAATAA-TTACTACTAAGTTATAAATGAT-T-TATTACTAAA
* * * ** * *
5425426 TTATCAATTAATTACTACTAAATTAGT-ATTTAGGTATTATTAAT
1 TTATCAA-TAATTACTACTAAGTTA-TAAATGATTTATTACTAAA
*
5425470 TTATGAATAATTCACTACTAAGTTATAAATGATTTATTACTAAA
1 TTATCAATAATT-ACTACTAAGTTATAAATGATTTATTACTAAA
5425514 TTAT
1 TTAT
5425518 TGATGATTTC
Statistics
Matches: 72, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
43 6 0.08
44 40 0.56
45 13 0.18
46 12 0.17
47 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (43 bp):
TTATCAATAATTACTACTAAGTTATAAATGATTTATTACTAAA
Found at i:5425510 original size:22 final size:22
Alignment explanation
Indices: 5425485--5425605 Score: 75
Period size: 22 Copynumber: 5.5 Consensus size: 22
5425475 AATAATTCAC
5425485 TACTAAGTTATAAATGATTTAT
1 TACTAAGTTATAAATGATTTAT
* ** **
5425507 TACTAAATTATTGATGATTTCC
1 TACTAAGTTATAAATGATTTAT
* * *
5425529 TACTACGTTACT-AATTATTAAT
1 TACTAAGTTA-TAAATGATTTAT
*
5425551 TA-TAAAGTTATAACTGATTTAT
1 TACT-AAGTTATAAATGATTTAT
* * * * *
5425573 TATTAATTTATCAATAATTTAC
1 TACTAAGTTATAAATGATTTAT
*
5425595 TACAAAGTTAT
1 TACTAAGTTAT
5425606 CATAATTAAC
Statistics
Matches: 71, Mismatches: 24, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
21 2 0.03
22 67 0.94
23 2 0.03
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (22 bp):
TACTAAGTTATAAATGATTTAT
Found at i:5425553 original size:88 final size:89
Alignment explanation
Indices: 5425380--5425545 Score: 210
Period size: 88 Copynumber: 1.9 Consensus size: 89
5425370 TTAATACTAT
* *
5425380 TTTATCAATAATTTACTATAAGTTATAAATGATATATATTACTAAATTATCAATTAATTACTACT
1 TTTATCAATAATTCACTATAAGTTATAAATGATATATATTACTAAATTATCAATGAATTACTACT
* *
5425445 AAATTAGTATTTAGGTATTATTAA
66 AAATTACTAATTAGGTATTATTAA
* ** * *
5425469 TTTATGAATAATTCACTACTAAGTTATAAATGAT-T-TATTACTAAATTATTGATGATTTCCTAC
1 TTTATCAATAATTCACTA-TAAGTTATAAATGATATATATTACTAAATTATCAATGAATTACTAC
**
5425532 TACGTTACTAATTA
65 TAAATTACTAATTA
5425546 TTAATTATAA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
88 33 0.51
89 17 0.26
90 15 0.23
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.45
Consensus pattern (89 bp):
TTTATCAATAATTCACTATAAGTTATAAATGATATATATTACTAAATTATCAATGAATTACTACT
AAATTACTAATTAGGTATTATTAA
Found at i:5425904 original size:22 final size:24
Alignment explanation
Indices: 5425879--5425936 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 24
5425869 CTCATAATTT
5425879 ACTATTAAGTTATC-ACTGA-TTA-
1 ACTATTAAGTTATCGA-TGATTTAC
*
5425901 ACTATTAAATT-TCGATGATTTAC
1 ACTATTAAGTTATCGATGATTTAC
5425924 ACTATTAAGTTAT
1 ACTATTAAGTTAT
5425937 ATTAATTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 5 0.17
22 14 0.47
23 10 0.33
24 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (24 bp):
ACTATTAAGTTATCGATGATTTAC
Found at i:5425964 original size:45 final size:42
Alignment explanation
Indices: 5425852--5425993 Score: 117
Period size: 44 Copynumber: 3.2 Consensus size: 42
5425842 AAGTTATTCC
* * *
5425852 TAATTTA-TATTAAATTACTC-ATAATTTACTATTAAGTTATCAC
1 TAATTTACTATTAAATT--TCAATGATTAACTATTAAGTTAT-AT
* * *
5425895 TGATTAACTATTAAATTTCGATGATTTACACTATTAAGTTATAT
1 TAATTTACTATTAAATTTCAATGA-TTA-ACTATTAAGTTATAT
* * *
5425939 TAATTTACTTTTAAACTTTCAATGATTAACTACTAAATTATTAT
1 TAATTTACTATTAAA-TTTCAATGATTAACTATTAAGTTA-TAT
5425983 TAATTTTACTA
1 TAA-TTTACTA
5425994 CTAAGTTATT
Statistics
Matches: 80, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
42 2 0.03
43 18 0.22
44 33 0.41
45 27 0.34
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (42 bp):
TAATTTACTATTAAATTTCAATGATTAACTATTAAGTTATAT
Found at i:5426092 original size:23 final size:22
Alignment explanation
Indices: 5426061--5426132 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
5426051 TAACTTATTG
* *
5426061 TTAAGTTATCACTAATTTACTA
1 TTAAGTTATCAATGATTTACTA
* *
5426083 TTAAGGTTATTAATGATTTATTA
1 TTAA-GTTATCAATGATTTACTA
*
5426106 TTAAGTTATCAATGATTAACTA
1 TTAAGTTATCAATGATTTACTA
5426128 TTAAG
1 TTAAG
5426133 CTTTTATTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 24 0.57
23 18 0.43
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.46
Consensus pattern (22 bp):
TTAAGTTATCAATGATTTACTA
Found at i:5426152 original size:45 final size:45
Alignment explanation
Indices: 5426055--5426172 Score: 123
Period size: 45 Copynumber: 2.6 Consensus size: 45
5426045 TGAAATTAAC
* * * *
5426055 TTATTGTTAAGTTATCACTAATTTACTATTAAGGTTATTAATGAT
1 TTATTATTAAGTTATCAATGATTTACTATTAAGCTTATTAATGAT
* * *
5426100 TTATTATTAAGTTATCAATGATTAACTATTAAGCTT-TTATTTGTT
1 TTATTATTAAGTTATCAATGATTTACTATTAAGCTTATTA-ATGAT
* *
5426145 TTTTTATTAACG-TATCATTGATTTACTA
1 TTATTATTAA-GTTATCAATGATTTACTA
5426173 ATATCTTATT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
44 3 0.05
45 57 0.93
46 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.09, T:0.52
Consensus pattern (45 bp):
TTATTATTAAGTTATCAATGATTTACTATTAAGCTTATTAATGAT
Found at i:5426467 original size:22 final size:22
Alignment explanation
Indices: 5426442--5426497 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
5426432 GTTATTAGTG
**
5426442 ATTTACTGTTAAACTATCAATA
1 ATTTACTACTAAACTATCAATA
* *
5426464 ATTTATTACTAAACTATCAATG
1 ATTTACTACTAAACTATCAATA
*
5426486 ATTTATTACTAA
1 ATTTACTACTAA
5426498 TTTATGAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (22 bp):
ATTTACTACTAAACTATCAATA
Found at i:5426507 original size:22 final size:22
Alignment explanation
Indices: 5426464--5426610 Score: 72
Period size: 22 Copynumber: 6.7 Consensus size: 22
5426454 ACTATCAATA
** *
5426464 ATTTATTACTAAACTATCAATG
1 ATTTATTACTAATTTATGAATG
5426486 ATTTATTACTAATTTATGAATG
1 ATTTATTACTAATTTATGAATG
* * * * *
5426508 ATTTGTCATTAAATTATCAATG
1 ATTTATTACTAATTTATGAATG
* *
5426530 ATTTCTATTA--AATTAATG-ATA
1 A-TT-TATTACTAATTTATGAATG
* ** *
5426551 ATCTACCACTAAGTTATTG-ATG
1 ATTTATTACTAATTTA-TGAATG
5426573 ATTTATTA-TAAATTTAT-AATTG
1 ATTTATTACT-AATTTATGAA-TG
*
5426595 ATTTACTACTAATTTA
1 ATTTATTACTAATTTA
5426611 CTAAAAAGTT
Statistics
Matches: 91, Mismatches: 25, Indels: 18
0.68 0.19 0.13
Matches are distributed among these distances:
19 3 0.03
20 1 0.01
21 10 0.11
22 71 0.78
23 3 0.03
24 3 0.03
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (22 bp):
ATTTATTACTAATTTATGAATG
Found at i:5426670 original size:22 final size:22
Alignment explanation
Indices: 5426645--5426731 Score: 63
Period size: 22 Copynumber: 4.1 Consensus size: 22
5426635 AAATTACTGC
* *
5426645 TAAATTATCATTAATTTGCAAT
1 TAAATTATCAGTAATTTACAAT
* *
5426667 TAAATTATTAGTAATTTACTAT
1 TAAATTATCAGTAATTTACAAT
* * *
5426689 TAAGTTATC---AATTTATAAC
1 TAAATTATCAGTAATTTACAAT
* * *
5426708 TAAATTATCAATGATTTACTAT
1 TAAATTATCAGTAATTTACAAT
5426730 TA
1 TA
5426732 TATTTTTATA
Statistics
Matches: 48, Mismatches: 14, Indels: 6
0.71 0.21 0.09
Matches are distributed among these distances:
19 15 0.31
22 33 0.69
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (22 bp):
TAAATTATCAGTAATTTACAAT
Found at i:5426767 original size:21 final size:23
Alignment explanation
Indices: 5426718--5426768 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
5426708 TAAATTATCA
*
5426718 ATGATTTACTATTATATTTTTAT
1 ATGATTTACTATTATATTGTTAT
*
5426741 AT-ATTTACTA-TATGTTGTTAT
1 ATGATTTACTATTATATTGTTAT
5426762 -TGATTTA
1 ATGATTTA
5426769 GTACTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.04
21 14 0.56
22 8 0.32
23 2 0.08
ACGTcount: A:0.29, C:0.04, G:0.08, T:0.59
Consensus pattern (23 bp):
ATGATTTACTATTATATTGTTAT
Found at i:5426944 original size:65 final size:66
Alignment explanation
Indices: 5426875--5427020 Score: 150
Period size: 65 Copynumber: 2.2 Consensus size: 66
5426865 TATGCGTGAC
* * * * *
5426875 TTACTATTAAGTTATCACTAATTAACTATTAAGCTATCGATGATTTATTATTAAACTAT-ATTGA
1 TTACTATTAAGTTATCAATAATTAACTATTAAACTATCAATGATTTATTACTAAACTATCATTAA
5426939 T
66 T
* * * * * * * * *
5426940 TTACTTTTAAATTTTTAATGATTAACTATTAAATTATTAATTATTTATTACTAAATTATCATTAA
1 TTACTATTAAGTTATCAATAATTAACTATTAAACTATCAATGATTTATTACTAAACTATCATTAA
5427005 T
66 T
*
5427006 TTACTACTAAGTTAT
1 TTACTATTAAGTTAT
5427021 TTATAATTTA
Statistics
Matches: 62, Mismatches: 18, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
65 46 0.74
66 16 0.26
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.49
Consensus pattern (66 bp):
TTACTATTAAGTTATCAATAATTAACTATTAAACTATCAATGATTTATTACTAAACTATCATTAA
T
Found at i:5426971 original size:22 final size:22
Alignment explanation
Indices: 5426815--5426998 Score: 86
Period size: 22 Copynumber: 8.5 Consensus size: 22
5426805 TCAATTTATC
* * *
5426815 ATTAAATTATTTATGGTTCACT
1 ATTAAATTATTAATGATTAACT
* * *
5426837 ACTAAATTATTACTGATTTA-T
1 ATTAAATTATTAATGATTAACT
***
5426858 ATTAAATTATGCGTGACTT-ACT
1 ATTAAATTATTAATGA-TTAACT
* * * *
5426880 ATTAAGTTATCACTAATTAACT
1 ATTAAATTATTAATGATTAACT
** ** * *
5426902 ATTAAGCTATCGATGATTTATT
1 ATTAAATTATTAATGATTAACT
* * *
5426924 ATTAAACTA-TATTGATTTACT
1 ATTAAATTATTAATGATTAACT
* *
5426945 TTTAAATTTTTAATGATTAACT
1 ATTAAATTATTAATGATTAACT
* * *
5426967 ATTAAATTATTAATTATTTATT
1 ATTAAATTATTAATGATTAACT
*
5426989 ACTAAATTAT
1 ATTAAATTAT
5426999 CATTAATTTA
Statistics
Matches: 122, Mismatches: 36, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
21 30 0.25
22 92 0.75
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTAAATTATTAATGATTAACT
Found at i:5427132 original size:22 final size:22
Alignment explanation
Indices: 5426875--5427125 Score: 110
Period size: 22 Copynumber: 11.7 Consensus size: 22
5426865 TATGCGTGAC
*
5426875 TTACTATTAAGTTATCACTAAT
1 TTACTATTAAGTTATCATTAAT
* * *
5426897 TAACTATTAAGCTATCGA-TGAT
1 TTACTATTAAGTTATC-ATTAAT
* ** *
5426919 TTATTATTAAACTAT-ATTGAT
1 TTACTATTAAGTTATCATTAAT
* * * * * *
5426940 TTACTTTTAAATTTTTAATGAT
1 TTACTATTAAGTTATCATTAAT
* * *
5426962 TAACTATTAAATTATTAATT-AT
1 TTACTATTAAGTTA-TCATTAAT
* * *
5426984 TTATTACTAAATTATCATTAAT
1 TTACTATTAAGTTATCATTAAT
* *
5427006 TTACTACTAAGTTAT-TTATAAT
1 TTACTATTAAGTTATCAT-TAAT
* *
5427028 TTACTACT--GTCA--ATTAA-
1 TTACTATTAAGTTATCATTAAT
* * *
5427045 TTACTATTAAGCTGA-AATTGAT
1 TTACTATTAAG-TTATCATTAAT
* * *
5427067 TTACTAATAAGTTATTACT-AT
1 TTACTATTAAGTTATCATTAAT
5427088 TTACTATTAAGTTATCATTAAT
1 TTACTATTAAGTTATCATTAAT
*
5427110 TTATTATTAAGTTATC
1 TTACTATTAAGTTATC
5427126 GATAATTAAA
Statistics
Matches: 180, Mismatches: 36, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
17 7 0.04
18 3 0.02
19 2 0.01
20 6 0.03
21 44 0.24
22 114 0.63
23 4 0.02
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (22 bp):
TTACTATTAAGTTATCATTAAT
Found at i:5427728 original size:6 final size:6
Alignment explanation
Indices: 5427717--5427757 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
5427707 TAGTTAAAGA
5427717 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
5427758 AGAAAGGAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:5427891 original size:59 final size:57
Alignment explanation
Indices: 5427793--5428208 Score: 471
Period size: 59 Copynumber: 7.0 Consensus size: 57
5427783 CTTGTGTAGA
*
5427793 GAAAATTGATACTTTCAACTTTTCCCCAAAAAACATTTTTTTTGAAATTTATTTTTAAG
1 GAAAATTGATACTTTCAACTTTT-CCC-AAAAATATTTTTTTTGAAATTTATTTTTAAG
* * **
5427852 GAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTTTTAAAACTTTCATTTTCGAG
1 GAAAATTGATACTTTCAAC-TTTTCCCAAAAATA-TTTTTTTTGAAA-TTT-ATTTTTAAG
* *
5427913 GAAAATTGATACTTTCAACTTTTTCTCAAAAATCCTTTTTCTTTTGAAAATTTATTTTTAAG
1 GAAAATTGATACTTTCAAC-TTTTCCCAAAAAT--ATTTT-TTTTG-AAATTTATTTTTAAG
* *
5427975 GAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTATTTCTAAG
1 GAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTTGAAATTTATTTTTAAG
* * *
5428032 GAAAATTGATACTTTTAACTTTTTCCTAAAAATA-TTTTTTGGAAATTTTGATTTTTAAG
1 GAAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTTTGAAA-TTT-ATTTTTAAG
* *
5428091 AAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTAGAAATTT-TGATTTTAAG
1 GAAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTTTGAAATTTAT--TTTTAAG
5428149 GAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTTGATTTTTA
1 GAAAATTGATACTTTCAACTTTTCCC-AAAAATA-TTTTTTTT-GAAA-TTT-ATTTTTA
5428209 TTTAAAGAAA
Statistics
Matches: 311, Mismatches: 24, Indels: 41
0.83 0.06 0.11
Matches are distributed among these distances:
56 1 0.00
57 53 0.17
58 64 0.21
59 77 0.25
60 13 0.04
61 46 0.15
62 46 0.15
63 7 0.02
64 4 0.01
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.47
Consensus pattern (57 bp):
GAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTGAAATTTATTTTTAAG
Found at i:5428240 original size:8 final size:7
Alignment explanation
Indices: 5428216--5428287 Score: 53
Period size: 7 Copynumber: 10.3 Consensus size: 7
5428206 TTATTTAAAG
5428216 AAAATATA
1 AAAATA-A
*
5428224 ATAATAA
1 AAAATAA
*
5428231 AAATTAA
1 AAAATAA
5428238 AAAAT-A
1 AAAATAA
5428244 AAAATAAA
1 AAAAT-AA
5428252 AAAATAA
1 AAAATAA
5428259 AAAA-AA
1 AAAATAA
*
5428265 GTAAAA-CA
1 --AAAATAA
5428273 AAAAT-A
1 AAAATAA
5428279 AAAATAA
1 AAAATAA
5428286 AA
1 AA
5428288 TTAAGATAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
6 18 0.34
7 19 0.36
8 16 0.30
ACGTcount: A:0.81, C:0.01, G:0.01, T:0.17
Consensus pattern (7 bp):
AAAATAA
Found at i:5428243 original size:14 final size:14
Alignment explanation
Indices: 5428216--5428282 Score: 73
Period size: 14 Copynumber: 4.7 Consensus size: 14
5428206 TTATTTAAAG
* *
5428216 AAAATATAATAATA
1 AAAATAAAAAAATA
*
5428230 AAAATTAAAAAATA
1 AAAATAAAAAAATA
5428244 AAAATAAAAAAATA
1 AAAATAAAAAAATA
*
5428258 AAAA-AAAGTAAAACA
1 AAAATAAA--AAAATA
5428273 AAAATAAAAA
1 AAAATAAAAA
5428283 TAAAATTAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
13 3 0.07
14 30 0.67
15 9 0.20
16 3 0.07
ACGTcount: A:0.81, C:0.01, G:0.01, T:0.16
Consensus pattern (14 bp):
AAAATAAAAAAATA
Found at i:5428244 original size:20 final size:20
Alignment explanation
Indices: 5428216--5428253 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5428206 TTATTTAAAG
* *
5428216 AAAATATAATAATAAAAATT
1 AAAAAATAAAAATAAAAATT
5428236 AAAAAATAAAAATAAAAA
1 AAAAAATAAAAATAAAAA
5428254 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAAATAAAAATAAAAATT
Found at i:5428246 original size:6 final size:6
Alignment explanation
Indices: 5428216--5428302 Score: 65
Period size: 6 Copynumber: 14.3 Consensus size: 6
5428206 TTATTTAAAG
*
5428216 AAAATAT AATAAT AAAAATT AAAAAAT AAAAAT AAAAA- AATAAA- AAAAAGT
1 AAAA-AT AAAAAT AAAAA-T -AAAAAT AAAAAT AAAAAT AA-AAAT AAAAA-T
* * *
5428267 -AAAAC AAAAAT AAAAAT -AAAAT TAAGAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
5428303 TATTAAATAA
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
5 10 0.15
6 46 0.70
7 5 0.08
8 5 0.08
ACGTcount: A:0.78, C:0.01, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:5428264 original size:23 final size:24
Alignment explanation
Indices: 5428223--5428313 Score: 78
Period size: 27 Copynumber: 3.6 Consensus size: 24
5428213 AAGAAAATAT
*
5428223 AATAATAAAAAT-TAAAAAATAAA
1 AATAATAAAAATAAAAAAAATAAA
5428246 AATAA-AAAAATAAAAAAAAGTAAAA
1 AATAATAAAAATAAAAAAAA-T-AAA
* *
5428271 CAAAAATAAAAATAAAATTAAGATAAA
1 -AATAATAAAAATAAAA--AAAATAAA
*
5428298 AATAATATTAAATAAA
1 AATAATA-AAAATAAA
5428314 CCTAATCTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
22 6 0.11
23 11 0.20
24 1 0.02
25 3 0.05
26 10 0.18
27 20 0.36
28 1 0.02
29 3 0.05
ACGTcount: A:0.77, C:0.01, G:0.02, T:0.20
Consensus pattern (24 bp):
AATAATAAAAATAAAAAAAATAAA
Found at i:5428296 original size:17 final size:16
Alignment explanation
Indices: 5428226--5428313 Score: 65
Period size: 17 Copynumber: 5.4 Consensus size: 16
5428216 AAAATATAAT
*
5428226 AATAAAAATTAAA--A
1 AATAAAAATAAAATTA
*
5428240 AATAAAAATAAAAAAATA
1 AATAAAAAT--AAAATTA
**
5428258 AA-AAAAAGTAAAACAAA
1 AATAAAAA-TAAAA-TTA
5428275 AATAAAAATAAAATTA
1 AATAAAAATAAAATTA
*
5428291 AGATAAAAATAATATTA
1 A-ATAAAAATAAAATTA
5428308 AATAAA
1 AATAAA
5428314 CCTAATCTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
14 9 0.15
16 14 0.23
17 29 0.48
18 9 0.15
ACGTcount: A:0.77, C:0.01, G:0.02, T:0.19
Consensus pattern (16 bp):
AATAAAAATAAAATTA
Found at i:5429234 original size:17 final size:17
Alignment explanation
Indices: 5429203--5429240 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
5429193 AAGAAAAAAA
5429203 ATAATGATAATAATCAG
1 ATAATGATAATAATCAG
5429220 ATAATCGATAA-AATCAG
1 ATAAT-GATAATAATCAG
5429237 ATAA
1 ATAA
5429241 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.26
Consensus pattern (17 bp):
ATAATGATAATAATCAG
Found at i:5429344 original size:25 final size:22
Alignment explanation
Indices: 5429300--5429344 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 22
5429290 AAGATAAAAA
*
5429300 ATAATAAAAAATAAATTATAAT
1 ATAATAAAAAATAAACTATAAT
5429322 ATAATAATAAATATATAACTATA
1 ATAATAA-AAA-ATA-AACTATA
5429345 TAAAAATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 3 0.16
24 3 0.16
25 6 0.32
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATAAAAAATAAACTATAAT
Found at i:5429624 original size:1 final size:1
Alignment explanation
Indices: 5429618--5429658 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
5429608 AACATTGTCA
* * *
5429618 TTTTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5429659 AACCCAAAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (1 bp):
T
Done.