Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 89 of 171
Found at i:29066735 original size:21 final size:21
Alignment explanation
Indices: 29066709--29066755 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
29066699 TTAGGGTCCA
* *
29066709 ATTGCCCTGGAGGAGTAGAGT
1 ATTGCCCGGGAGGAGTAAAGT
29066730 ATTGCCCGGGAGGAGTAAAGT
1 ATTGCCCGGGAGGAGTAAAGT
29066751 ATTGC
1 ATTGC
29066756 GGTGGCTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23
Consensus pattern (21 bp):
ATTGCCCGGGAGGAGTAAAGT
Found at i:29068993 original size:36 final size:37
Alignment explanation
Indices: 29068953--29069023 Score: 94
Period size: 36 Copynumber: 1.9 Consensus size: 37
29068943 ATCCAAATTA
29068953 AAATTATTA-ATT-TTTTCATTTAAAT-AAAAAATATTT
1 AAATTATTATATTATTTT--TTTAAATCAAAAAATATTT
*
29068989 AAATTATTATATTATTTTTTTAAATCAATAAATAT
1 AAATTATTATATTATTTTTTTAAATCAAAAAATAT
29069024 GAACAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
36 16 0.52
37 11 0.35
38 4 0.13
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (37 bp):
AAATTATTATATTATTTTTTTAAATCAAAAAATATTT
Found at i:29069114 original size:95 final size:94
Alignment explanation
Indices: 29069006--29069273 Score: 409
Period size: 95 Copynumber: 2.9 Consensus size: 94
29068996 TATATTATTT
*
29069006 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAATAACAAAATAAAAT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTAC-TACTAACAACAAAATAAAAT
***
29069071 TACTAACTA-ATTTTTTTAAACATTATTAAA
65 TACTAACTACA-AAATTTAAACATTATTAAA
* *
29069101 TTTTAAATCAATAAATATAAACAATGTTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
29069166 ACTAACTAGCAAAATTTAAACATTATTAAA
66 ACTAACTA-CAAAATTTAAACATTATTAAA
*
29069196 TTTTAAATTAATAAATATGAACAATATTTTTTAC-T--TACTACTACTAACAACAAAATAAAATT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
29069258 ACTAACTAGCAAAATT
66 ACTAACTA-CAAAATT
29069274 AAATTAAAAT
Statistics
Matches: 162, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
92 43 0.27
94 29 0.18
95 89 0.55
96 1 0.01
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (94 bp):
TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
ACTAACTACAAAATTTAAACATTATTAAA
Found at i:29069262 original size:20 final size:21
Alignment explanation
Indices: 29069237--29069279 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
29069227 TACTTACTAC
29069237 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
29069257 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
29069278 TA
1 TA
29069280 AAATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:29069659 original size:25 final size:23
Alignment explanation
Indices: 29069616--29069688 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 23
29069606 AAACACATTA
29069616 CCCTTTTTTCCTTTCTCTTTCTT
1 CCCTTTTTTCCTTTCTCTTTCTT
29069639 CCCTTTCTTCTCC-TTCTTCTTTCTTT
1 CCCTTT-TT-TCCTTTC-TCTTTC-TT
*
29069665 CTCTTTTTT-CTTTCT-TTT-TT
1 CCCTTTTTTCCTTTCTCTTTCTT
29069685 CCCT
1 CCCT
29069689 CAATTTTCGT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
20 5 0.12
22 3 0.07
23 8 0.19
24 9 0.21
25 11 0.26
26 7 0.16
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (23 bp):
CCCTTTTTTCCTTTCTCTTTCTT
Found at i:29084809 original size:114 final size:114
Alignment explanation
Indices: 29084608--29084813 Score: 333
Period size: 114 Copynumber: 1.8 Consensus size: 114
29084598 GGATCGGATT
* * *
29084608 AAAACAACGAAGTAGAACTCAACGTCTCTGAGGATACAGTGAAGTGGAGTGAAACTTTAAATCTC
1 AAAACAACGAAGCAGAACTCAACGTCTCTGAGGATACAATGAAGTGGAGTGAAACTTTAAATATC
29084673 ATCTTCCTGGTGAGGTACAGAGAAGTGGGTGCAAACAATATGTTGAATC
66 ATCTTCCTGGTGAGGTACAGAGAAGTGGGTGCAAACAATATGTTGAATC
* * *
29084722 AAAACAACGAAGCCGAGCTCAACGTC-CTTGAGGATACAATGGAGTGGAGTGAAACTTTAAATAT
1 AAAACAACGAAGCAGAACTCAACGTCTC-TGAGGATACAATGAAGTGGAGTGAAACTTTAAATAT
*
29084786 CATCTTCCTGGTGAGGTATAGAGAAGTG
65 CATCTTCCTGGTGAGGTACAGAGAAGTG
29084814 AGTTAAAACA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 1 0.01
114 83 0.99
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.23
Consensus pattern (114 bp):
AAAACAACGAAGCAGAACTCAACGTCTCTGAGGATACAATGAAGTGGAGTGAAACTTTAAATATC
ATCTTCCTGGTGAGGTACAGAGAAGTGGGTGCAAACAATATGTTGAATC
Found at i:29098322 original size:29 final size:30
Alignment explanation
Indices: 29098280--29098359 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
29098270 AAATTGGATC
*
29098280 AAATCAGAATTTCATGTATAAAAATACACA-
1 AAATCA-AAGTTCATGTATAAAAATACACAT
* * *
29098310 AAATCAAAGTTCATGTATACAATTGCACATT
1 AAATCAAAGTTCATGTATAAAAATACACA-T
*
29098341 AAATCATAGTTCATGTATA
1 AAATCAAAGTTCATGTATA
29098360 GTTTAGATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 19 0.44
30 6 0.14
31 18 0.42
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAAATACACAT
Found at i:29099197 original size:6 final size:6
Alignment explanation
Indices: 29099186--29099229 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
29099176 TTAGTGCCTA
*
29099186 GAGATG GAGATG GAGATG GAGACG GAGATG GAGATG GAGATG GA
1 GAGATG GAGATG GAGATG GAGATG GAGATG GAGATG GAGATG GA
29099230 TTTGAATGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.34, C:0.02, G:0.50, T:0.14
Consensus pattern (6 bp):
GAGATG
Found at i:29101181 original size:3 final size:3
Alignment explanation
Indices: 29101173--29101221 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
29101163 AAAAAGAATG
29101173 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29101221 T
1 T
29101222 TTGGATTTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:29104940 original size:37 final size:38
Alignment explanation
Indices: 29104859--29104948 Score: 128
Period size: 39 Copynumber: 2.4 Consensus size: 38
29104849 ATAGTGTTCC
* * **
29104859 AATTTCATCACATCTCAACATTAGGGTTTTTATAATTTT
1 AATTTCATTACATCCCAACATTAGGG-TTACATAATTTT
29104898 AATTTCATTACATCCCAACATTAGGG-TACATAATTTT
1 AATTTCATTACATCCCAACATTAGGGTTACATAATTTT
29104935 AATTTCATTACATC
1 AATTTCATTACATC
29104949 AATTCCTACT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
37 23 0.49
39 24 0.51
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (38 bp):
AATTTCATTACATCCCAACATTAGGGTTACATAATTTT
Found at i:29105441 original size:17 final size:17
Alignment explanation
Indices: 29105419--29105455 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
29105409 ATCTTATTAT
29105419 ATTCTTCTTACCCAAAA
1 ATTCTTCTTACCCAAAA
29105436 ATTCTTCTTACCCAAAA
1 ATTCTTCTTACCCAAAA
29105453 ATT
1 ATT
29105456 TTTCAACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTCTTCTTACCCAAAA
Found at i:29112023 original size:11 final size:12
Alignment explanation
Indices: 29111997--29112022 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29111987 AGTCTAACTC
29111997 AAATATAAAAAA
1 AAATATAAAAAA
29112009 AAATATAAAAAA
1 AAATATAAAAAA
29112021 AA
1 AA
29112023 TCTGATAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATATAAAAAA
Found at i:29126518 original size:25 final size:24
Alignment explanation
Indices: 29126467--29126522 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
29126457 ATTAACTCTT
29126467 TTATTTTCCTTTTTTTCTTTTACA
1 TTATTTTCCTTTTTTTCTTTTACA
29126491 TTATTTCTCTCTTTATTTT-TTTT-CA
1 TTATTT-TC-CTTT-TTTTCTTTTACA
29126516 TTATTTT
1 TTATTTT
29126523 TTTTCTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 7 0.24
25 10 0.34
26 8 0.28
27 4 0.14
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.73
Consensus pattern (24 bp):
TTATTTTCCTTTTTTTCTTTTACA
Found at i:29126521 original size:13 final size:13
Alignment explanation
Indices: 29126503--29126527 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29126493 ATTTCTCTCT
29126503 TTATTTTTTTTCA
1 TTATTTTTTTTCA
29126516 TTATTTTTTTTC
1 TTATTTTTTTTC
29126528 TTCTTCCTTT
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTTCA
Found at i:29127840 original size:19 final size:21
Alignment explanation
Indices: 29127813--29127863 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
29127803 ATATATAAAA
29127813 TTTGAAATTTTT-ATAAA-TAT
1 TTTGAAATTTTTGA-AAATTAT
29127833 TTTG-AATTTTTGAAAATTAT
1 TTTGAAATTTTTGAAAATTAT
*
29127853 TTTGTAATTTT
1 TTTGAAATTTT
29127864 GTTGAGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.36
20 12 0.43
21 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (21 bp):
TTTGAAATTTTTGAAAATTAT
Found at i:29129294 original size:21 final size:21
Alignment explanation
Indices: 29129269--29129309 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
29129259 CTTAATTAAG
*
29129269 TAAAATATGATTGATTAAAAC
1 TAAAATATGATTAATTAAAAC
29129290 TAAAATATGATTAATTAAAA
1 TAAAATATGATTAATTAAAA
29129310 TATAATTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.34
Consensus pattern (21 bp):
TAAAATATGATTAATTAAAAC
Found at i:29135390 original size:28 final size:30
Alignment explanation
Indices: 29135326--29135392 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
29135316 CCTTTAGGAG
*
29135326 TTAATAGGAGTATTTTAGGTAGCATAAAAAA
1 TTAATAAGAGTATTTTAGG-AGCATAAAAAA
* * *
29135357 TCAATAAGAGTATTTTA-G-GCATTAAAAC
1 TTAATAAGAGTATTTTAGGAGCATAAAAAA
29135385 TTAATAAG
1 TTAATAAG
29135393 GGCAATTAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 15 0.48
30 1 0.03
31 15 0.48
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (30 bp):
TTAATAAGAGTATTTTAGGAGCATAAAAAA
Found at i:29136421 original size:21 final size:22
Alignment explanation
Indices: 29136379--29136421 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
29136369 GAGTTTAGGG
*
29136379 TTTAGATTTGAGGTTTAAAATT
1 TTTAGATTTGAGGTTCAAAATT
* *
29136401 TTTAG-TTTGGGGTTCAGAATT
1 TTTAGATTTGAGGTTCAAAATT
29136422 CGGGATTGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (22 bp):
TTTAGATTTGAGGTTCAAAATT
Found at i:29142711 original size:6 final size:6
Alignment explanation
Indices: 29142700--29142736 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
29142690 TTTGTGATCA
*
29142700 AAAGTG AAAGTG AAAGTG AAAGTG AAATTG AAAGTG A
1 AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG A
29142737 TATGAATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.30, T:0.19
Consensus pattern (6 bp):
AAAGTG
Found at i:29144895 original size:52 final size:52
Alignment explanation
Indices: 29144807--29144996 Score: 281
Period size: 52 Copynumber: 3.7 Consensus size: 52
29144797 ATTCCGTTTA
* * * *
29144807 ATACTCACGATGACACATAGTTATCGGACCTCTTAATCCGTGAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGAATCAT
*
29144859 ATACTCACGATGACACATAGTCATCGAACCTTTTAATCCATAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGAATCAT
* * *
29144911 ATTCTCACGATAACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGAATCAT
* * *
29144963 ATACTCAGGATGACACATAGTCATCAGACTTTTT
1 ATACTCACGATGACACATAGTCATCGGACCTTTT
29144997 CTTTATTTAT
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 124 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGAATCAT
Found at i:29146851 original size:24 final size:24
Alignment explanation
Indices: 29146782--29146872 Score: 74
Period size: 24 Copynumber: 3.8 Consensus size: 24
29146772 TTTCAGAAAT
* * **
29146782 TTAGCTCATACGAGTCCAGACAAAA
1 TTAGCTCATACGAGCCCAGA-TAGG
**
29146807 TTAGCTCATACGAGCGTAGATAGG
1 TTAGCTCATACGAGCCCAGATAGG
* **
29146831 TTAGCTCTTACGAGCCCAGATAAA
1 TTAGCTCATACGAGCCCAGATAGG
* *
29146855 TTAGTTCATTCGAGCCCA
1 TTAGCTCATACGAGCCCA
29146873 AACAAAGTTT
Statistics
Matches: 52, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
24 35 0.67
25 17 0.33
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (24 bp):
TTAGCTCATACGAGCCCAGATAGG
Found at i:29149340 original size:21 final size:21
Alignment explanation
Indices: 29149316--29149358 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29149306 ACCAGTAAAA
*
29149316 AATACAGAGCAAGAGTATGTG
1 AATACAAAGCAAGAGTATGTG
* *
29149337 AATACAAAGTAGGAGTATGTG
1 AATACAAAGCAAGAGTATGTG
29149358 A
1 A
29149359 CTCAAGGTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.07, G:0.28, T:0.21
Consensus pattern (21 bp):
AATACAAAGCAAGAGTATGTG
Found at i:29151579 original size:32 final size:31
Alignment explanation
Indices: 29151534--29151623 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 31
29151524 ATCTAAATTT
*
29151534 TTTTTGTCC-AATTTGATACTTAAACTTGACA
1 TTTTT-TCCTAATTTGGTACTTAAACTTGACA
*
29151565 CTTTTTTCCTAATTTGGTA-TCGAAACTTGACA
1 -TTTTTTCCTAATTTGGTACT-TAAACTTGACA
* *
29151597 TTTTTTCTTAAATTGGTACTTAAACTT
1 TTTTTTCCTAATTTGGTACTTAAACTT
29151624 TTTGGGGGTC
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
31 26 0.52
32 24 0.48
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.48
Consensus pattern (31 bp):
TTTTTTCCTAATTTGGTACTTAAACTTGACA
Found at i:29152651 original size:22 final size:21
Alignment explanation
Indices: 29152626--29152666 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29152616 CTAATATATT
29152626 TTATAATTAAATTTAAATAAAA
1 TTATAATT-AATTTAAATAAAA
* *
29152648 TTATTATTATTTTAAATAA
1 TTATAATTAATTTAAATAA
29152667 CAAAATGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATAATTAATTTAAATAAAA
Found at i:29155063 original size:41 final size:42
Alignment explanation
Indices: 29155000--29155078 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 42
29154990 GCTTAGTTGG
* *
29155000 ACGAGCTTTCCTGAAAACTGTGCGAAAA-CTCACCCAACTGA
1 ACGAGCTTTCCTGAAAACTGTGCAAAAATCACACCCAACTGA
* * **
29155041 ACGAGCTTTCTTGCAAGTTGTGCAAAAATCACACCCAA
1 ACGAGCTTTCCTGAAAACTGTGCAAAAATCACACCCAA
29155079 TTGGACGCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
41 23 0.74
42 8 0.26
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (42 bp):
ACGAGCTTTCCTGAAAACTGTGCAAAAATCACACCCAACTGA
Found at i:29156928 original size:49 final size:49
Alignment explanation
Indices: 29156844--29156939 Score: 126
Period size: 49 Copynumber: 2.0 Consensus size: 49
29156834 ACAATCACAA
* *
29156844 GTTGAAGTATAACTAAGACTCCTATTTGATGGTGGTTATGTAGTCACGG
1 GTTGAAGTATAACTAAGACTCCTAATTGATGGTGGTTATGCAGTCACGG
29156893 GTTGAAGTATAACTCAAGAGC-CC-AATTGACT-GTGGTTATGCAGTCAC
1 GTTGAAGTATAACT-AAGA-CTCCTAATTGA-TGGTGGTTATGCAGTCAC
29156940 ATGTTCAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
49 34 0.81
50 7 0.17
51 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (49 bp):
GTTGAAGTATAACTAAGACTCCTAATTGATGGTGGTTATGCAGTCACGG
Found at i:29158023 original size:25 final size:26
Alignment explanation
Indices: 29157991--29158039 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
29157981 TTAAGGTTAG
29157991 GGTTACAATTATGAG-ATTTTTCATA
1 GGTTACAATTATGAGAATTTTTCATA
*
29158016 GGTTACAATTTTGAGAATTTTTCA
1 GGTTACAATTATGAGAATTTTTCA
29158040 CAAGTTAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (26 bp):
GGTTACAATTATGAGAATTTTTCATA
Found at i:29158046 original size:26 final size:25
Alignment explanation
Indices: 29157992--29158046 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
29157982 TAAGGTTAGG
* *
29157992 GTTACAATTATGAGATTTTTCATAG
1 GTTACAATTATGAGATTTTTCACAA
*
29158017 GTTACAATTTTGAGAATTTTTCACAA
1 GTTACAATTATGAG-ATTTTTCACAA
29158043 GTTA
1 GTTA
29158047 AGGTTAGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.44
Consensus pattern (25 bp):
GTTACAATTATGAGATTTTTCACAA
Found at i:29167780 original size:23 final size:23
Alignment explanation
Indices: 29167753--29167800 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
29167743 ATACTAATAA
*
29167753 AAGGTTTTACTAACTTTAAAAAT
1 AAGGTTTTACAAACTTTAAAAAT
*
29167776 AAGGTTTTCCAAACTTTAAAAAT
1 AAGGTTTTACAAACTTTAAAAAT
29167799 AA
1 AA
29167801 AGTATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.35
Consensus pattern (23 bp):
AAGGTTTTACAAACTTTAAAAAT
Found at i:29180620 original size:22 final size:22
Alignment explanation
Indices: 29180575--29180620 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
29180565 TTTACGGCTG
*
29180575 TTATGTTGTCATTTTGCTGCCA
1 TTATGTTGTCATTTTGCTACCA
** *
29180597 TTATGTTGTTGTTTTGCTATCA
1 TTATGTTGTCATTTTGCTACCA
29180619 TT
1 TT
29180621 TCTCTATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (22 bp):
TTATGTTGTCATTTTGCTACCA
Found at i:29185819 original size:6 final size:6
Alignment explanation
Indices: 29185808--29185836 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29185798 GTAGGTTCCA
29185808 AAAATG AAAATG AAAATG AAAATG AAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAAT
29185837 TTGCAATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:29193303 original size:12 final size:12
Alignment explanation
Indices: 29193286--29193332 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
29193276 TCACGAACAA
29193286 GCTCGTTTATTG
1 GCTCGTTTATTG
**
29193298 GCTCGTTTATAA
1 GCTCGTTTATTG
29193310 GCTCGTTTATTG
1 GCTCGTTTATTG
* *
29193322 ACTCATTTATT
1 GCTCGTTTATT
29193333 TAGTAATGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (12 bp):
GCTCGTTTATTG
Found at i:29193313 original size:24 final size:24
Alignment explanation
Indices: 29193284--29193331 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
29193274 TTTCACGAAC
* *
29193284 AAGCTCGTTTATTGGCTCGTTTAT
1 AAGCTCGTTTATTGACTCATTTAT
29193308 AAGCTCGTTTATTGACTCATTTAT
1 AAGCTCGTTTATTGACTCATTTAT
29193332 TTAGTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.46
Consensus pattern (24 bp):
AAGCTCGTTTATTGACTCATTTAT
Found at i:29193475 original size:23 final size:23
Alignment explanation
Indices: 29193430--29193551 Score: 167
Period size: 23 Copynumber: 5.3 Consensus size: 23
29193420 ATTGTTCGTA
*
29193430 AACATGTTCAATTATATGTTCATG
1 AACATGTTCGATTA-ATGTTCATG
29193454 AACATGTTCGATTAATGTTCATG
1 AACATGTTCGATTAATGTTCATG
29193477 AACATGTTCGATTAATGTTCATG
1 AACATGTTCGATTAATGTTCATG
**
29193500 AACATGTTCGATTATAT-TAAATG
1 AACATGTTCGATTA-ATGTTCATG
*
29193523 AACATGTTCGATT-ATGTTAAATG
1 AACATGTTCGATTAATGTT-CATG
29193546 AACATG
1 AACATG
29193552 GTCGTGAACA
Statistics
Matches: 91, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.02
22 1 0.01
23 73 0.80
24 15 0.16
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (23 bp):
AACATGTTCGATTAATGTTCATG
Found at i:29193565 original size:46 final size:46
Alignment explanation
Indices: 29193430--29193566 Score: 127
Period size: 46 Copynumber: 3.0 Consensus size: 46
29193420 ATTGTTCGTA
* * * * **
29193430 AACATGTTCAATTATATGTTCATGAACATGTTCGATTA-ATGTTCATG
1 AACATGTTCGATTA-ATGTTAATGAACATGGTCGATAACAT-TAAATG
* * * *
29193477 AACATGTTCGATTAATGTTCATGAACATGTTCGATTATATTAAATG
1 AACATGTTCGATTAATGTTAATGAACATGGTCGATAACATTAAATG
29193523 AACATGTTCGATT-ATGTTAAATGAACATGGTCG-TGAACATTAAA
1 AACATGTTCGATTAATGTT-AATGAACATGGTCGAT-AACATTAAA
29193567 CAAACGAATA
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
45 6 0.08
46 59 0.74
47 15 0.19
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (46 bp):
AACATGTTCGATTAATGTTAATGAACATGGTCGATAACATTAAATG
Found at i:29198067 original size:32 final size:32
Alignment explanation
Indices: 29198025--29198098 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
29198015 AACTATTTCA
* *
29198025 TTGACATTTCAATCATAAAAAAAATGAATTTT
1 TTGACATTTCAATAAAAAAAAAAATGAATTTT
*
29198057 TTGACCTTTCAATAAAAAAAAAAATGAATTTT
1 TTGACATTTCAATAAAAAAAAAAATGAATTTT
29198089 TTGATCATTT
1 TTGA-CATTT
29198099 AGTTTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 33 0.89
33 4 0.11
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (32 bp):
TTGACATTTCAATAAAAAAAAAAATGAATTTT
Found at i:29203140 original size:19 final size:19
Alignment explanation
Indices: 29203116--29203158 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
29203106 AAATATAAAT
29203116 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
29203135 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
29203154 TAAAT
1 TAAAT
29203159 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:29212061 original size:14 final size:14
Alignment explanation
Indices: 29212008--29212068 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
29211998 ATTTTAAATT
*
29212008 TTTTTTTGTTTGTA
1 TTTTTTTGTTTATA
** * *
29212022 TTCATTTATTTAAA
1 TTTTTTTGTTTATA
29212036 TTTATTTGTGTTTATA
1 TTT-TTT-TGTTTATA
29212052 TTTTTTTGTTTAATA
1 TTTTTTTGTTT-ATA
29212067 TT
1 TT
29212069 CACAAATAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
14 16 0.46
15 10 0.29
16 9 0.26
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.70
Consensus pattern (14 bp):
TTTTTTTGTTTATA
Found at i:29213088 original size:18 final size:18
Alignment explanation
Indices: 29213067--29213103 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
29213057 GTGGCAGTAG
*
29213067 GGTGATTGGTGGTGTTAT
1 GGTGATAGGTGGTGTTAT
29213085 GGTGATAGGTGGTGTTAT
1 GGTGATAGGTGGTGTTAT
29213103 G
1 G
29213104 ATAAATGATG
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:0.14, C:0.00, G:0.46, T:0.41
Consensus pattern (18 bp):
GGTGATAGGTGGTGTTAT
Found at i:29214015 original size:21 final size:21
Alignment explanation
Indices: 29213974--29214015 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
29213964 AAATTACATT
* *
29213974 CCTACCCCACTAACCCGTTTA
1 CCTACCACACTAACCCATTTA
29213995 CCTACCAC-CTAATCCCATTTA
1 CCTACCACACTAA-CCCATTTA
29214016 ATTAAACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.26, C:0.45, G:0.02, T:0.26
Consensus pattern (21 bp):
CCTACCACACTAACCCATTTA
Found at i:29215297 original size:24 final size:24
Alignment explanation
Indices: 29215235--29215298 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
29215225 CTAAACTAAT
* *
29215235 CAGAGTTTTACTCAAACAAATAAA
1 CAGAGTTTAACTGAAACAAATAAA
* *
29215259 TAGAGTTTAATTGAAACAAATAAA
1 CAGAGTTTAACTGAAACAAATAAA
29215283 CAGAGTTTAACTGAAA
1 CAGAGTTTAACTGAAA
29215299 GATTATTTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (24 bp):
CAGAGTTTAACTGAAACAAATAAA
Found at i:29216307 original size:25 final size:25
Alignment explanation
Indices: 29216279--29216346 Score: 127
Period size: 25 Copynumber: 2.7 Consensus size: 25
29216269 TTTCAGAAAT
*
29216279 TTAGCTCATACAAGCCTAGACAAAA
1 TTAGCTCATACGAGCCTAGACAAAA
29216304 TTAGCTCATACGAGCCTAGACAAAA
1 TTAGCTCATACGAGCCTAGACAAAA
29216329 TTAGCTCATACGAGCCTA
1 TTAGCTCATACGAGCCTA
29216347 AATAGGTTAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (25 bp):
TTAGCTCATACGAGCCTAGACAAAA
Found at i:29219510 original size:24 final size:24
Alignment explanation
Indices: 29219483--29219539 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
29219473 AACTAATCAG
*
29219483 AGTTTGACTCAAACAAATAAACAA
1 AGTTTAACTCAAACAAATAAACAA
* * *
29219507 AGTTTAATTGAAACAAATAAACAG
1 AGTTTAACTCAAACAAATAAACAA
29219531 AGTTTAACT
1 AGTTTAACT
29219540 AAAAGATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.26
Consensus pattern (24 bp):
AGTTTAACTCAAACAAATAAACAA
Found at i:29221020 original size:13 final size:13
Alignment explanation
Indices: 29221002--29221026 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29220992 CCTTAACCCA
29221002 AACCAAACCCAAC
1 AACCAAACCCAAC
29221015 AACCAAACCCAA
1 AACCAAACCCAA
29221027 ATCGATTTGA
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:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (13 bp):
AACCAAACCCAAC
Found at i:29221988 original size:18 final size:18
Alignment explanation
Indices: 29221945--29221978 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29221935 GCATTGCATT
29221945 ATGC-TTGTGATTGTATC
1 ATGCTTTGTGATTGTATC
*
29221962 ATGCTTTGTGGTTGTAT
1 ATGCTTTGTGATTGTAT
29221979 TATGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.15, C:0.09, G:0.26, T:0.50
Consensus pattern (18 bp):
ATGCTTTGTGATTGTATC
Found at i:29231697 original size:16 final size:17
Alignment explanation
Indices: 29231660--29231697 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
29231650 TGACTGAGCT
29231660 GATGACTTTGTTTGCCAG
1 GATGACTTTGTTTG-CAG
*
29231678 GATGAGTTTGTTTG-AG
1 GATGACTTTGTTTGCAG
29231694 GATG
1 GATG
29231698 GCAGTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.18, C:0.08, G:0.34, T:0.39
Consensus pattern (17 bp):
GATGACTTTGTTTGCAG
Found at i:29234869 original size:17 final size:18
Alignment explanation
Indices: 29234844--29234889 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
29234834 GTATGGGTGC
*
29234844 ATTGCATTATGC-TTGTG
1 ATTGTATTATGCTTTGTG
29234861 ATTGTATTATGCTTTGTG
1 ATTGTATTATGCTTTGTG
* *
29234879 GTTATATTATG
1 ATTGTATTATG
29234890 TGTTGTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.52
Consensus pattern (18 bp):
ATTGTATTATGCTTTGTG
Found at i:29235645 original size:34 final size:31
Alignment explanation
Indices: 29235574--29235640 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
29235564 CAATTTCATT
29235574 TTCTTC-C-CCATTTTTCCATCTAACAACTC
1 TTCTTCTCACCATTTTTCCATCTAACAACTC
*
29235603 TTCTTCTCACCATTTTTTCATCTAAC-ACTAC
1 TTCTTCTCACCATTTTTCCATCTAACAACT-C
29235634 TTCTTCT
1 TTCTTCT
29235641 TCTCATCATC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 6 0.18
30 4 0.12
31 24 0.71
ACGTcount: A:0.19, C:0.34, G:0.00, T:0.46
Consensus pattern (31 bp):
TTCTTCTCACCATTTTTCCATCTAACAACTC
Found at i:29236243 original size:40 final size:39
Alignment explanation
Indices: 29236188--29236278 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 39
29236178 AGAATACAGA
29236188 AAAATAATTTTAATAATTTTATATTTT-AAAAAATAATTTT
1 AAAATAATTTTAATAA-TTTATATTTTAAAAAAATAA-TTT
29236228 AAAATAATTTTAATAATTTATATTTTAAAAAAATAATTT
1 AAAATAATTTTAATAATTTATATTTTAAAAAAATAATTT
*
29236267 -CAATAATTTTAA
1 AAAATAATTTTAA
29236279 AATCATTTGC
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
38 11 0.22
39 13 0.27
40 25 0.51
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (39 bp):
AAAATAATTTTAATAATTTATATTTTAAAAAAATAATTT
Found at i:29236262 original size:20 final size:22
Alignment explanation
Indices: 29236239--29236280 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
29236229 AAATAATTTT
29236239 AATAATTT-AT-ATTTTAAAAA
1 AATAATTTAATAATTTTAAAAA
29236259 AATAATTTCAATAATTTTAAAA
1 AATAATTT-AATAATTTTAAAA
29236281 TCATTTGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
22 2 0.11
23 9 0.47
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAATTTAATAATTTTAAAAA
Found at i:29241503 original size:13 final size:13
Alignment explanation
Indices: 29241485--29241511 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29241475 AAGTTAACAG
29241485 CTTGCTCTATCTA
1 CTTGCTCTATCTA
29241498 CTTGCTCTATCTA
1 CTTGCTCTATCTA
29241511 C
1 C
29241512 AAATAATCCT
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:0.15, C:0.33, G:0.07, T:0.44
Consensus pattern (13 bp):
CTTGCTCTATCTA
Found at i:29245100 original size:24 final size:24
Alignment explanation
Indices: 29245045--29245127 Score: 125
Period size: 23 Copynumber: 3.5 Consensus size: 24
29245035 TATTTTAATT
*
29245045 ATTTATTTATTCTGCATGATTTT-
1 ATTTATTTATTTTGCATGATTTTA
29245068 ATTTATTTATTTTGCATGATTTTA
1 ATTTATTTATTTTGCATGATTTTA
* *
29245092 ATTTGTTTAATTTGCATGATTTTA
1 ATTTATTTATTTTGCATGATTTTA
29245116 A-TTATTTATTTT
1 ATTTATTTATTTT
29245128 ATTTATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
23 31 0.57
24 23 0.43
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.63
Consensus pattern (24 bp):
ATTTATTTATTTTGCATGATTTTA
Found at i:29245143 original size:47 final size:46
Alignment explanation
Indices: 29245043--29245145 Score: 120
Period size: 47 Copynumber: 2.2 Consensus size: 46
29245033 TATATTTTAA
* *
29245043 TTATTTATTTATTCTGCATGATTTTATTTATTTATTTTGCATGATTT
1 TTATTTGTTTATTCTGCATGATTTTAATTATTTATTTT-CATGATTT
* *
29245090 TAATTTGTTTAATT-TGCATGATTTTAATTATTTATTTT-ATTTATTAT
1 TTATTTGTTT-ATTCTGCATGATTTTAATTATTTATTTTCA-TGATT-T
29245137 TTATTTGTT
1 TTATTTGTT
29245146 ACCCATATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
45 1 0.02
46 4 0.08
47 40 0.83
48 3 0.06
ACGTcount: A:0.23, C:0.04, G:0.08, T:0.65
Consensus pattern (46 bp):
TTATTTGTTTATTCTGCATGATTTTAATTATTTATTTTCATGATTT
Found at i:29245358 original size:21 final size:21
Alignment explanation
Indices: 29245332--29245371 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29245322 ACGAGAACGA
29245332 TGATGTGGCAAGTTAACTTGC
1 TGATGTGGCAAGTTAACTTGC
*
29245353 TGATGTGGCCAGTTAACTT
1 TGATGTGGCAAGTTAACTT
29245372 ACCACGTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.35
Consensus pattern (21 bp):
TGATGTGGCAAGTTAACTTGC
Found at i:29245954 original size:15 final size:15
Alignment explanation
Indices: 29245934--29245969 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
29245924 CAATGGGATC
29245934 GTTGAAAAAATTATG
1 GTTGAAAAAATTATG
29245949 GTTGAAAAAATTATG
1 GTTGAAAAAATTATG
29245964 GTTGAA
1 GTTGAA
29245970 TCAAAGCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (15 bp):
GTTGAAAAAATTATG
Found at i:29247941 original size:21 final size:22
Alignment explanation
Indices: 29247903--29247953 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
29247893 ATATGTTGCT
*
29247903 TTGCATTTTTATTTTATATATG
1 TTGCATTTTTATTCTATATATG
*
29247925 TTGC-TTTTTGTTCTATATATG
1 TTGCATTTTTATTCTATATATG
29247946 TTGCATTT
1 TTGCATTT
29247954 AATTTGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.18, C:0.08, G:0.12, T:0.63
Consensus pattern (22 bp):
TTGCATTTTTATTCTATATATG
Found at i:29265315 original size:21 final size:21
Alignment explanation
Indices: 29265280--29265330 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
29265270 GGATTATGTA
*
29265280 ATTTCGATTTATAAAATTTAT
1 ATTTGGATTTATAAAATTTAT
* * *
29265301 GTTTGGATTTCTAAACTTTAT
1 ATTTGGATTTATAAAATTTAT
29265322 ATTTGGATT
1 ATTTGGATT
29265331 ATGTTATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (21 bp):
ATTTGGATTTATAAAATTTAT
Found at i:29270694 original size:26 final size:26
Alignment explanation
Indices: 29270663--29270715 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
29270653 TTAAATAAAC
* *
29270663 AGTTAATAGAATCAGTTGGTCAAATT
1 AGTTAACAGAATCAGTTGATCAAATT
*
29270689 AGTTAACAGATTCAGTTGATCAAATT
1 AGTTAACAGAATCAGTTGATCAAATT
29270715 A
1 A
29270716 ACCATTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (26 bp):
AGTTAACAGAATCAGTTGATCAAATT
Found at i:29279385 original size:18 final size:18
Alignment explanation
Indices: 29279364--29279417 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
29279354 AGTTCAAATA
* *
29279364 TTTTCATTTTTTAATTTT
1 TTTTAATTTTTCAATTTT
*
29279382 TTTTAATTTTTCAATTTC
1 TTTTAATTTTTCAATTTT
*
29279400 TTTAATATTTTTC-ATTTT
1 TTTTA-ATTTTTCAATTTT
29279418 CCAAAGAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 23 0.77
19 7 0.23
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTAATTTTTCAATTTT
Found at i:29279981 original size:15 final size:13
Alignment explanation
Indices: 29279950--29279977 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29279940 TTGTGTATGC
29279950 AATATATCAACTT
1 AATATATCAACTT
29279963 AATATATCAACTT
1 AATATATCAACTT
29279976 AA
1 AA
29279978 AATAATCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATATCAACTT
Found at i:29280379 original size:16 final size:17
Alignment explanation
Indices: 29280349--29280385 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
29280339 ATTTAAAATT
29280349 TTTAATTAATTAAATTTA
1 TTTAATTAA-TAAATTTA
29280367 TTTAATTAA-AAATTTA
1 TTTAATTAATAAATTTA
29280383 TTT
1 TTT
29280386 TCATTCTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATTAATAAATTTA
Found at i:29284754 original size:24 final size:24
Alignment explanation
Indices: 29284727--29284777 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
29284717 ATAAGAGTTG
*
29284727 TTGAAACAAATAAACATAGTTTAA
1 TTGAAACAAATAAACAAAGTTTAA
29284751 TTGAAACAAATAAACAAAGTTTAA
1 TTGAAACAAATAAACAAAGTTTAA
29284775 TTG
1 TTG
29284778 GAAGATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (24 bp):
TTGAAACAAATAAACAAAGTTTAA
Found at i:29286722 original size:24 final size:24
Alignment explanation
Indices: 29286694--29286740 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
29286684 GACTAATAAG
*
29286694 AGTTTGACTAAAACAAATAAACAA
1 AGTTTAACTAAAACAAATAAACAA
* *
29286718 AGTTTAATTGAAACAAATAAACA
1 AGTTTAACTAAAACAAATAAACA
29286741 GGATTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23
Consensus pattern (24 bp):
AGTTTAACTAAAACAAATAAACAA
Found at i:29286747 original size:24 final size:24
Alignment explanation
Indices: 29286704--29286754 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
29286694 AGTTTGACTA
29286704 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
*
29286728 AAACAAATAAAC-AGGATTTAATTG
1 AAACAAATAAACAAAG-TTTAATTG
29286752 AAA
1 AAA
29286755 GATTATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTG
Found at i:29294301 original size:57 final size:57
Alignment explanation
Indices: 29294212--29294344 Score: 189
Period size: 57 Copynumber: 2.4 Consensus size: 57
29294202 ATAGAAATTG
* * * *
29294212 TGAAAATGGATAAATGGGAAACATTTGGAAATGATTATGGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAAAAAT-GAAAACATTTGGAAATGAATATGATTTTCTCCAAAATGAAAA
* *
29294270 TGAAAATGGAGAAATGAAAACATTTGGAAATGAATGTGATTTTCTCCAAAATGAAAA
1 TGAAAATGGAAAAATGAAAACATTTGGAAATGAATATGATTTTCTCCAAAATGAAAA
29294327 T-AAAAT-GAAAAATGAAAA
1 TGAAAATGGAAAAATGAAAA
29294345 TGACCTAGAA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
55 11 0.16
56 5 0.07
57 39 0.57
58 14 0.20
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (57 bp):
TGAAAATGGAAAAATGAAAACATTTGGAAATGAATATGATTTTCTCCAAAATGAAAA
Found at i:29295983 original size:30 final size:30
Alignment explanation
Indices: 29295947--29296012 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
29295937 GTTTACATTT
*
29295947 CAGTCCCTCAACTTTGAAAATGTGACAAAA
1 CAGTCCCTCAACTTTGAAAATATGACAAAA
29295977 CAGTCCCTCAACTTTGAAAATATGACAAAA
1 CAGTCCCTCAACTTTGAAAATATGACAAAA
29296007 CAGTCC
1 CAGTCC
29296013 TTTTTCATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.23
Consensus pattern (30 bp):
CAGTCCCTCAACTTTGAAAATATGACAAAA
Found at i:29304151 original size:12 final size:12
Alignment explanation
Indices: 29304134--29304159 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29304124 AATTTGTTTG
29304134 TTGTTTTAATAT
1 TTGTTTTAATAT
29304146 TTGTTTTAATAT
1 TTGTTTTAATAT
29304158 TT
1 TT
29304160 TTAAGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:29304552 original size:25 final size:27
Alignment explanation
Indices: 29304524--29304577 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
29304514 TGAGATTGAC
29304524 ATTTAAA-T-TTTTTTATCAAAGTGAT
1 ATTTAAATTATTTTTTATCAAAGTGAT
* *
29304549 ATTTAAATTATTTTTTCTCAAATTGAT
1 ATTTAAATTATTTTTTATCAAAGTGAT
29304576 AT
1 AT
29304578 CTCTATTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.28
26 1 0.04
27 17 0.68
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (27 bp):
ATTTAAATTATTTTTTATCAAAGTGAT
Found at i:29305122 original size:22 final size:23
Alignment explanation
Indices: 29305097--29305143 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
29305087 TTCTTTCACA
29305097 TTATTTTTCTCTTTTTATT-TTT
1 TTATTTTTCTCTTTTTATTATTT
*
29305119 TTATTTTTCTCTTTTTCTTATTT
1 TTATTTTTCTCTTTTTATTATTT
29305142 TT
1 TT
29305144 TTTATAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.81
Consensus pattern (23 bp):
TTATTTTTCTCTTTTTATTATTT
Found at i:29305871 original size:98 final size:99
Alignment explanation
Indices: 29305756--29305956 Score: 271
Period size: 98 Copynumber: 2.0 Consensus size: 99
29305746 AGTGTAGAGA
* *
29305756 TGGAGAAGAAAAGAAAAAAAAT-AAAAAAATACCTTAATCCCTAAATCCCTTCCTCACGTATGAT
1 TGGAGAAGAAAAG-AAAAAAATCAAAAAAATACCTTAATCCCTAAATCCCTTACTAACGTATGAT
**
29305820 GAATTG-AAAAAAAGGCTCAAAATTAAATATGAGG
65 GAATTGAAAAAAAAAACTCAAAATTAAATATGAGG
* * * * * *
29305854 TGGAGAAGAAAAGAAAAAAATCGAGAAAATACCTTAATCTCTAAATCCCTTATTAACTTTTGATG
1 TGGAGAAGAAAAGAAAAAAATCAAAAAAATACCTTAATCCCTAAATCCCTTACTAACGTATGATG
* *
29305919 AATTGAAAAAAAAAACTCAAAATTTAATGTGAGG
66 AATTGAAAAAAAAAACTCAAAATTAAATATGAGG
29305953 TGGA
1 TGGA
29305957 AATTTTCTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
97 8 0.09
98 53 0.60
99 28 0.31
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (99 bp):
TGGAGAAGAAAAGAAAAAAATCAAAAAAATACCTTAATCCCTAAATCCCTTACTAACGTATGATG
AATTGAAAAAAAAAACTCAAAATTAAATATGAGG
Found at i:29308837 original size:273 final size:272
Alignment explanation
Indices: 29308328--29308875 Score: 841
Period size: 273 Copynumber: 2.0 Consensus size: 272
29308318 TAAGGTGTCC
* *
29308328 TTTCCAAATTTTTGTTTCAATAACATTTTTTAGATGTATGCATTGTTCAATTTGGTGGTCCCTGG
1 TTTCCAAATTTTTATTTCAATAACATTTTTTAGATGTACGCATTGTTCAATTTGGTGGTCCCTGG
29308393 CATTATGGTACATGTAGTGATGATTGTAGTTGTTGAGATGCTTATAGGATGGGAGGTATGGGGAC
66 CATTATGGTACATGTAGTGATGATTGTAGTTGTTGAGATGCTTATAGGA-GGGAGGTATGGGGAC
* *
29308458 ATTTCCAGGATTCCTTGATTTTCTACTCGATCGAACACTTGGGACGGGAAGTAGTTAAACTCATG
130 ACTTCCAGGATTCCTTGATTTTCTACTCGATCGAACACTTAGGACGGGAAGTAGTTAAACTCATG
* * * *
29308523 GTAGGTTTTGAAATAGTTGTGCAGTGCTTTAGGTCTATCACACCTGGTTTTCACTTATGCCCCAA
195 GTAGGTTTTGAAATAGTTGCGCAATGCTCTAGGTCTATCACACCTGGTTTTCACTTACGCCCCAA
29308588 AATTAAAGGAAAG
260 AATTAAAGGAAAG
*
29308601 TTTCCGAATTTTTATTTCAATAACATTTTTTAGATGTACGCATTGTTCAATTTGGTGGT-CCTCG
1 TTTCCAAATTTTTATTTCAATAACATTTTTTAGATGTACGCATTGTTCAATTTGGTGGTCCCT-G
** * *
29308665 GTGTTATGGTACATGTAGTGATGATTGTAGTTGTT-ATGGTGTTTATAAGGCA-GGAGGTATGGG
65 GCATTATGGTACATGTAGTGATGATTGTAGTTGTTGA-GATGCTTAT-AGG-AGGGAGGTATGGG
* * * * *
29308728 GCCACTTCCATGATTCCTTGGTTTTCTACTTGATCGAACACTTAGGATGGGAAGTAGTTAAACTC
127 GACACTTCCAGGATTCCTTGATTTTCTACTCGATCGAACACTTAGGACGGGAAGTAGTTAAACTC
* *
29308793 ATGGTAGGTTTTGACATAGTTGCGCAATGCTCTAGGTTTATCACACCTGGTTTTCACTTACGCCC
192 ATGGTAGGTTTTGAAATAGTTGCGCAATGCTCTAGGTCTATCACACCTGGTTTTCACTTACGCCC
*
29308858 CGAAATTAAAGGAAAG
257 CAAAATTAAAGGAAAG
29308874 TT
1 TT
29308876 AAGAGTTATT
Statistics
Matches: 250, Mismatches: 21, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
272 4 0.02
273 242 0.97
274 3 0.01
275 1 0.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.37
Consensus pattern (272 bp):
TTTCCAAATTTTTATTTCAATAACATTTTTTAGATGTACGCATTGTTCAATTTGGTGGTCCCTGG
CATTATGGTACATGTAGTGATGATTGTAGTTGTTGAGATGCTTATAGGAGGGAGGTATGGGGACA
CTTCCAGGATTCCTTGATTTTCTACTCGATCGAACACTTAGGACGGGAAGTAGTTAAACTCATGG
TAGGTTTTGAAATAGTTGCGCAATGCTCTAGGTCTATCACACCTGGTTTTCACTTACGCCCCAAA
ATTAAAGGAAAG
Found at i:29310084 original size:68 final size:68
Alignment explanation
Indices: 29309969--29310204 Score: 239
Period size: 68 Copynumber: 3.5 Consensus size: 68
29309959 ACCAGGGCAA
* *
29309969 TAAACATGGGATCATGTTGTGTAAGACCATAGTTGGGCTT-TGGCAACATATAAAGTCCGCTAGG
1 TAAACATGGAATCATGTTGTGTAAGACCATAGTTGGG-TTATGACAACATATAAAGTCCGCTAGG
29310033 ACAG
65 ACAG
* * ** *
29310037 TAAACATGGAATTATATTGTGTAAGACCATAACTGGGTTATGACAACATATAAAGTCCGTTAGGA
1 TAAACATGGAATCATGTTGTGTAAGACCATAGTTGGGTTATGACAACATATAAAGTCCGCTAGGA
29310102 CAG
66 CAG
* * * * **
29310105 TAAATAT-GAGATCATGTTGTGTAATACCATAGTTGAGTTAT-AGCAACATATGAAGT-CTATCA
1 TAAACATGGA-ATCATGTTGTGTAAGACCATAGTTGGGTTATGA-CAACATATAAAGTCCGCT-A
*
29310167 GGACAC
63 GGACAG
* * *
29310173 TAAACAT-GAGATCATATTATGTAACACCATAG
1 TAAACATGGA-ATCATGTTGTGTAAGACCATAG
29310205 CTACATATGA
Statistics
Matches: 142, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
67 7 0.05
68 135 0.95
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (68 bp):
TAAACATGGAATCATGTTGTGTAAGACCATAGTTGGGTTATGACAACATATAAAGTCCGCTAGGA
CAG
Found at i:29314856 original size:59 final size:59
Alignment explanation
Indices: 29314789--29314906 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
29314779 CACCTGAATC
29314789 CAAGTATCATAGCTCTAAACTTCCTGTCAGAAATCAGATACATTTGAATAGGATTTTTA
1 CAAGTATCATAGCTCTAAACTTCCTGTCAGAAATCAGATACATTTGAATAGGATTTTTA
29314848 CAAGTATCATAGCTCTAAACTTCCTGTCAGAAATCAGATACATTTGAATAGGATTTTTA
1 CAAGTATCATAGCTCTAAACTTCCTGTCAGAAATCAGATACATTTGAATAGGATTTTTA
29314907 TTACAAGTAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (59 bp):
CAAGTATCATAGCTCTAAACTTCCTGTCAGAAATCAGATACATTTGAATAGGATTTTTA
Found at i:29318397 original size:24 final size:23
Alignment explanation
Indices: 29318351--29318394 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
29318341 CCAAGAAAGA
29318351 AAGAAAAAAGAACAGGTTCTTGT
1 AAGAAAAAAGAACAGGTTCTTGT
29318374 AAGAAAAAA-AACAGGTT-TTGT
1 AAGAAAAAAGAACAGGTTCTTGT
29318395 TGTTGTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.19
22 8 0.38
23 9 0.43
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (23 bp):
AAGAAAAAAGAACAGGTTCTTGT
Found at i:29323586 original size:29 final size:29
Alignment explanation
Indices: 29323522--29323588 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
29323512 ACACATGAGG
* * **
29323522 GTTTAAGGTTTAGGGTTTCAAGATTTAAA
1 GTTTAAGGTCTAGAGTTTCAAGATACAAA
* * *
29323551 GTATAAGGTCTAGAGTTTCAAGGTACAAT
1 GTTTAAGGTCTAGAGTTTCAAGATACAAA
29323580 GTTTAAGGT
1 GTTTAAGGT
29323589 TTCAGGATTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.37
Consensus pattern (29 bp):
GTTTAAGGTCTAGAGTTTCAAGATACAAA
Found at i:29328625 original size:17 final size:17
Alignment explanation
Indices: 29328588--29328656 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
29328578 ATTCACATAA
*
29328588 AATAATAGTTCATATGA-
1 AATAATAGTTCAT-TCAT
*
29328605 AATAATAGTTCATGCAT
1 AATAATAGTTCATTCAT
*
29328622 AATAACAGTTCATTCA-
1 AATAATAGTTCATTCAT
*
29328638 ATATAATAATTCATTCAT
1 A-ATAATAGTTCATTCAT
29328656 A
1 A
29328657 TCACATCGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
16 2 0.05
17 40 0.93
18 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (17 bp):
AATAATAGTTCATTCAT
Found at i:29328632 original size:34 final size:34
Alignment explanation
Indices: 29328588--29328656 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
29328578 ATTCACATAA
* * *
29328588 AATAATAGTTCATATGAA-ATAATAGTTCATGCAT
1 AATAACAGTTCAT-TCAATATAATAATTCATGCAT
*
29328622 AATAACAGTTCATTCAATATAATAATTCATTCAT
1 AATAACAGTTCATTCAATATAATAATTCATGCAT
29328656 A
1 A
29328657 TCACATCGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 3 0.10
34 27 0.90
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (34 bp):
AATAACAGTTCATTCAATATAATAATTCATGCAT
Found at i:29331791 original size:18 final size:18
Alignment explanation
Indices: 29331744--29331791 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
29331734 CAATACATAT
* *
29331744 TTTGGCAAAGTAGTACAG
1 TTTGCCAAATTAGTACAG
29331762 TTTGCCAAATTAGTACAG
1 TTTGCCAAATTAGTACAG
*
29331780 TTTGCCATATTA
1 TTTGCCAAATTA
29331792 ATATAGATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (18 bp):
TTTGCCAAATTAGTACAG
Found at i:29334641 original size:3 final size:3
Alignment explanation
Indices: 29334635--29334664 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
29334625 TTATTTTGCT
29334635 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
29334665 ATACTGCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:29334755 original size:20 final size:20
Alignment explanation
Indices: 29334730--29334778 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
29334720 ATTAAATATA
29334730 AGAAAGAGGGGAAGAGGAAG
1 AGAAAGAGGGGAAGAGGAAG
29334750 AGAAAGAGGGGAAGAGGAAG
1 AGAAAGAGGGGAAGAGGAAG
*
29334770 GGAAAGAGG
1 AGAAAGAGG
29334779 AACAGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (20 bp):
AGAAAGAGGGGAAGAGGAAG
Found at i:29334852 original size:11 final size:11
Alignment explanation
Indices: 29334826--29334908 Score: 58
Period size: 11 Copynumber: 8.2 Consensus size: 11
29334816 TAATTTTATA
*
29334826 TTTAAAA-AAA
1 TTTAAAATAAT
*
29334836 TTTAAATTAAT
1 TTTAAAATAAT
29334847 TTTAAAATAAT
1 TTTAAAATAAT
29334858 TTTAAAA-AA-
1 TTTAAAATAAT
29334867 TTT---AT-AT
1 TTTAAAATAAT
29334874 TTTAAAAAATAAT
1 TTT--AAAATAAT
29334887 TTT--AATAAT
1 TTTAAAATAAT
*
29334896 TTTAAAATCAT
1 TTTAAAATAAT
29334907 TT
1 TT
29334909 ATTGACGTGG
Statistics
Matches: 58, Mismatches: 4, Indels: 21
0.70 0.05 0.25
Matches are distributed among these distances:
6 2 0.03
7 3 0.05
9 12 0.21
10 8 0.14
11 26 0.45
12 2 0.03
13 5 0.09
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (11 bp):
TTTAAAATAAT
Found at i:29334868 original size:21 final size:21
Alignment explanation
Indices: 29334826--29334869 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29334816 TAATTTTATA
*
29334826 TTTAAAAAAATTTAAATTAAT
1 TTTAAAAAAATTTAAATAAAT
*
29334847 TTTAAAATAATTTTAAA-AAAT
1 TTTAAAA-AAATTTAAATAAAT
29334868 TT
1 TT
29334870 ATATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAAAAAAATTTAAATAAAT
Found at i:29334890 original size:13 final size:13
Alignment explanation
Indices: 29334850--29334891 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 13
29334840 AATTAATTTT
29334850 AAAATAATTTTAA
1 AAAATAATTTTAA
29334863 AAAATTTATATTTTAA
1 AAAA--TA-ATTTTAA
29334879 AAAATAATTTTAA
1 AAAATAATTTTAA
29334892 TAATTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.42
14 2 0.08
15 2 0.08
16 11 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAATAATTTTAA
Found at i:29340131 original size:183 final size:183
Alignment explanation
Indices: 29339780--29340146 Score: 456
Period size: 183 Copynumber: 2.0 Consensus size: 183
29339770 ATCCGTCAAT
* * * *
29339780 TCATGGCACCCAGTGCCTAGCGGATAAACCGCAATATGTGAGCCCAGCTCTAGTTGGATTAACAA
1 TCATGGCACCCAGTGCCTAGCAGATAAACCGCAATAAGTGACCCCAACTCTAGTTGGATTAACAA
* * * * * *
29339845 TGATAATTTCCTCAATTCCTGATACCCAGTGCCTAGCGGATAAACTACAATAAATGAGCCCAGCT
66 -GAAAATATCCTCAAATCCTGACACCCAGTGCCTAGCGGATAAACCACAATAAATGAGCCCAACT
* * * *
29339910 CTAGTTGGATTAACCAACATTTTTGTGCCTAGCGCTAGTCGGGTAAACCGACGA
130 CTAGTTGGATTAACCAACATTTTTGCGCCCAACGCTAGTCAGGTAAACCGACGA
29339964 TCATGGCACCCAGTGCCTAGCAGATAAACCGCAA-AAGTGACCCCAACTCTAGTTGGATTAACCA
1 TCATGGCACCCAGTGCCTAGCAGATAAACCGCAATAAGTGACCCCAACTCTAGTTGGATTAA-CA
* * * *
29340028 A-AAAATAATCCGTCAAATCCT-AGCACCCAGTGTCTAGTGGATAAACCGCAA-AAGTGAGCCCA
65 AGAAAAT-ATCC-TCAAATCCTGA-CACCCAGTGCCTAGCGGATAAACCACAATAAATGAGCCCA
* * *
29340090 ACTCTAGTTGGATTAACCAATGA-TTTTGCGCCCAACGCTAGTCAGTTAAACTGACGA
127 ACTCTAGTTGGATTAACCAA-CATTTTTGCGCCCAACGCTAGTCAGGTAAACCGACGA
29340147 ACATTAAATA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
182 4 0.03
183 85 0.54
184 68 0.43
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.23
Consensus pattern (183 bp):
TCATGGCACCCAGTGCCTAGCAGATAAACCGCAATAAGTGACCCCAACTCTAGTTGGATTAACAA
GAAAATATCCTCAAATCCTGACACCCAGTGCCTAGCGGATAAACCACAATAAATGAGCCCAACTC
TAGTTGGATTAACCAACATTTTTGCGCCCAACGCTAGTCAGGTAAACCGACGA
Found at i:29348117 original size:29 final size:28
Alignment explanation
Indices: 29348024--29348139 Score: 133
Period size: 28 Copynumber: 4.1 Consensus size: 28
29348014 AGCAAAAAAA
* * *
29348024 TATCGCTCTTGCCGAGCCAAAATTAGAG
1 TATCGCTCTTGCCAAGCCAGAATCAGAG
* * * *
29348052 TATCACTCTTTCCAAGCTAGAATCAGAA
1 TATCGCTCTTGCCAAGCCAGAATCAGAG
*
29348080 TATCGCTCTTGCCAAGCTAGAATACAGAG
1 TATCGCTCTTGCCAAGCCAGAAT-CAGAG
*
29348109 TATCGCTCTTTCCAAGCCAGAATACAGAG
1 TATCGCTCTTGCCAAGCCAGAAT-CAGAG
29348138 TA
1 TA
29348140 ATTATTAAGC
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
28 42 0.56
29 33 0.44
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (28 bp):
TATCGCTCTTGCCAAGCCAGAATCAGAG
Found at i:29348120 original size:57 final size:57
Alignment explanation
Indices: 29348022--29348136 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 57
29348012 CCAGCAAAAA
* * *
29348022 AATATCGCTCTTGCCGAGCCAAAATTAGAGTATCACTCTTTCCAAGCTAGAAT-CAG
1 AATATCGCTCTTGCCAAGCCAAAATCAGAGTATCACTCTTTCCAAGCCAGAATACAG
* * *
29348078 AATATCGCTCTTGCCAAGCTAGAATACAGAGTATCGCTCTTTCCAAGCCAGAATACAG
1 AATATCGCTCTTGCCAAGCCAAAAT-CAGAGTATCACTCTTTCCAAGCCAGAATACAG
29348136 A
1 A
29348137 GTAATTATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
56 22 0.43
57 25 0.49
58 4 0.08
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (57 bp):
AATATCGCTCTTGCCAAGCCAAAATCAGAGTATCACTCTTTCCAAGCCAGAATACAG
Found at i:29350892 original size:17 final size:18
Alignment explanation
Indices: 29350866--29350907 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
29350856 TTGTTTTTAA
*
29350866 ATTT-TTTAAATCTA-AT
1 ATTTATTTAAAACTATAT
29350882 ATTTATTTAAAACTATAT
1 ATTTATTTAAAACTATAT
*
29350900 TTTTATTT
1 ATTTATTT
29350908 GAAGGGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 9 0.41
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTATTTAAAACTATAT
Found at i:29350899 original size:16 final size:16
Alignment explanation
Indices: 29350866--29350903 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
29350856 TTGTTTTTAA
*
29350866 ATTTTTTAAATCTAAT
1 ATTTTTTAAAACTAAT
29350882 ATTTATTTAAAACT-AT
1 ATTT-TTTAAAACTAAT
29350898 ATTTTT
1 ATTTTT
29350904 ATTTGAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 10 0.50
17 8 0.40
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTTTAAAACTAAT
Found at i:29354048 original size:18 final size:18
Alignment explanation
Indices: 29354025--29354059 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29354015 GGTTACAAGA
*
29354025 TATAAGAGGAGGGTAAAT
1 TATAAGAAGAGGGTAAAT
29354043 TATAAGAAGAGGGTAAA
1 TATAAGAAGAGGGTAAA
29354060 GCCCTAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.31, T:0.20
Consensus pattern (18 bp):
TATAAGAAGAGGGTAAAT
Found at i:29355822 original size:17 final size:18
Alignment explanation
Indices: 29355796--29355829 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29355786 AAAATATTGA
*
29355796 ATATATTCGTAT-TAAAC
1 ATATACTCGTATCTAAAC
29355813 ATATACTCGTATCTAAA
1 ATATACTCGTATCTAAA
29355830 GGACGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (18 bp):
ATATACTCGTATCTAAAC
Found at i:29365346 original size:22 final size:22
Alignment explanation
Indices: 29365318--29365366 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
29365308 TTATTATTGT
**
29365318 TTTTGCTATGT-TTTTGTTGTTG
1 TTTTGCTAT-TATTTTGTTACTG
29365340 TTTTGCTATTATTTTGTTACTG
1 TTTTGCTATTATTTTGTTACTG
29365362 TTTTG
1 TTTTG
29365367 GTTGTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.67
Consensus pattern (22 bp):
TTTTGCTATTATTTTGTTACTG
Found at i:29365917 original size:18 final size:19
Alignment explanation
Indices: 29365896--29365937 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
29365886 GGAAATATTT
29365896 TAAA-AATAAAGGGAGCCC
1 TAAATAATAAAGGGAGCCC
* **
29365914 TAAATTATTCAGGGAGCCC
1 TAAATAATAAAGGGAGCCC
29365933 TAAAT
1 TAAAT
29365938 TATTCAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (19 bp):
TAAATAATAAAGGGAGCCC
Found at i:29365929 original size:19 final size:19
Alignment explanation
Indices: 29365905--29365943 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
29365895 TTAAAAATAA
29365905 AGGGAGCCCTAAATTATTC
1 AGGGAGCCCTAAATTATTC
29365924 AGGGAGCCCTAAATTATTC
1 AGGGAGCCCTAAATTATTC
29365943 A
1 A
29365944 AAAAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (19 bp):
AGGGAGCCCTAAATTATTC
Found at i:29366854 original size:21 final size:21
Alignment explanation
Indices: 29366830--29366869 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29366820 TACTTTACTT
*
29366830 TAATTTAATTTTGTTAGTAAG
1 TAATTTAATTTTATTAGTAAG
*
29366851 TAATTTTATTTTATTAGTA
1 TAATTTAATTTTATTAGTA
29366870 GTAGTTAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
TAATTTAATTTTATTAGTAAG
Found at i:29367270 original size:14 final size:15
Alignment explanation
Indices: 29367251--29367296 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
29367241 AACCTAGCTA
29367251 ATTAATTACCAAAAT
1 ATTAATTACCAAAAT
*
29367266 A-TAATATA-AAAAAT
1 ATTAAT-TACCAAAAT
29367280 AATTAATTACCAAAAT
1 -ATTAATTACCAAAAT
29367296 A
1 A
29367297 ATATCATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 9 0.36
15 7 0.28
16 9 0.36
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAATTACCAAAAT
Found at i:29367294 original size:16 final size:16
Alignment explanation
Indices: 29367249--29367298 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
29367239 TAAACCTAGC
29367249 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
*
29367265 T-A-TAATATA-AAAAA
1 TAATTAAT-TACCAAAA
29367279 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
29367295 TAAT
1 TAAT
29367299 ATCATCATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:29367365 original size:30 final size:30
Alignment explanation
Indices: 29367331--29367425 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
29367321 AAATGGTACA
29367331 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTAGT
** * * *
29367361 AAAT-AAT-GGT-GTGTGAATACCATTTTGGT
1 AAATAAATATTTATTTTG--TACCATTTTAGT
*
29367390 ATATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTAGT
29367420 AAATAA
1 AAATAA
29367426 CTCATTTTAG
Statistics
Matches: 48, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
27 3 0.06
28 1 0.02
29 17 0.35
30 23 0.48
31 1 0.02
32 3 0.06
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (30 bp):
AAATAAATATTTATTTTGTACCATTTTAGT
Found at i:29369150 original size:2 final size:2
Alignment explanation
Indices: 29369137--29369216 Score: 151
Period size: 2 Copynumber: 40.0 Consensus size: 2
29369127 CACATGCTCA
*
29369137 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29369179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29369217 GTATGCATGA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29369810 original size:7 final size:7
Alignment explanation
Indices: 29369787--29369886 Score: 103
Period size: 7 Copynumber: 14.4 Consensus size: 7
29369777 TTTCGAAAAA
29369787 GTCAACG
1 GTCAACG
*
29369794 GTCAA-A
1 GTCAACG
29369800 GTCAACG
1 GTCAACG
29369807 GTCAACG
1 GTCAACG
* *
29369814 ATCAACT
1 GTCAACG
*
29369821 GTCAATG
1 GTCAACG
29369828 GTCAACG
1 GTCAACG
*
29369835 GTCAATG
1 GTCAACG
*
29369842 ATCAACG
1 GTCAACG
*
29369849 GTCAACT
1 GTCAACG
* *
29369856 ATCAATG
1 GTCAACG
29369863 GTCAACG
1 GTCAACG
29369870 GTCAACG
1 GTCAACG
*
29369877 ATCAACG
1 GTCAACG
29369884 GTC
1 GTC
29369887 GGTCAACGAC
Statistics
Matches: 72, Mismatches: 20, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
6 5 0.07
7 67 0.93
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (7 bp):
GTCAACG
Found at i:29369830 original size:21 final size:20
Alignment explanation
Indices: 29369787--29369881 Score: 118
Period size: 21 Copynumber: 4.6 Consensus size: 20
29369777 TTTCGAAAAA
* *
29369787 GTCAACGGTCAAAGTCAACG
1 GTCAACGATCAATGTCAACG
*
29369807 GTCAACGATCAACTGTCAATG
1 GTCAACGATCAA-TGTCAACG
*
29369828 GTCAACGGTCAATGATCAACG
1 GTCAACGATCAATG-TCAACG
*
29369849 GTCAACTATCAATGGTCAACG
1 GTCAACGATCAAT-GTCAACG
29369870 GTCAACGATCAA
1 GTCAACGATCAA
29369882 CGGTCGGTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
20 13 0.20
21 50 0.78
22 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (20 bp):
GTCAACGATCAATGTCAACG
Found at i:29369948 original size:15 final size:15
Alignment explanation
Indices: 29369930--29369963 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
29369920 GGGTTTGGAC
29369930 TTGGTTCAATTGGGT
1 TTGGTTCAATTGGGT
29369945 TTGGTTCAATTGGGT
1 TTGGTTCAATTGGGT
29369960 TTGG
1 TTGG
29369964 GCTTAATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.06, G:0.35, T:0.47
Consensus pattern (15 bp):
TTGGTTCAATTGGGT
Found at i:29371070 original size:43 final size:43
Alignment explanation
Indices: 29370988--29371072 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
29370978 ATTAACATGT
* *
29370988 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
29371031 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
29371073 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:29371699 original size:21 final size:22
Alignment explanation
Indices: 29371673--29371718 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
29371663 GAGCCACCGC
*
29371673 AATACTTTACTCCTCTCGGG-A
1 AATACTCTACTCCTCTCGGGCA
*
29371694 AATACTCTACTCCTCTGGGGCA
1 AATACTCTACTCCTCTCGGGCA
29371716 AAT
1 AAT
29371719 GAATCCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (22 bp):
AATACTCTACTCCTCTCGGGCA
Found at i:29371956 original size:7 final size:7
Alignment explanation
Indices: 29371944--29372039 Score: 56
Period size: 7 Copynumber: 13.7 Consensus size: 7
29371934 TTCATACTTA
*
29371944 TAAATCT
1 TAAACCT
29371951 TAAATCC-
1 TAAA-CCT
29371958 TAAA-CT
1 TAAACCT
29371964 ATAAACCT
1 -TAAACCT
*
29371972 TAAACCC
1 TAAACCT
* * *
29371979 TACATCA
1 TAAACCT
*
29371986 TAAACCC
1 TAAACCT
29371993 TAAACCT
1 TAAACCT
*
29372000 TAAA-TT
1 TAAACCT
29372006 TAAAACCT
1 T-AAACCT
29372014 TAAACCT
1 TAAACCT
*
29372021 TAAA-TT
1 TAAACCT
29372027 TAAAACCT
1 T-AAACCT
29372035 TAAAC
1 TAAAC
29372040 TCATGACTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
5 1 0.01
6 4 0.06
7 56 0.82
8 7 0.10
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (7 bp):
TAAACCT
Found at i:29372011 original size:21 final size:21
Alignment explanation
Indices: 29371987--29372039 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
29371977 CCTACATCAT
*
29371987 AAACCCTAAACCTTAAATTTA
1 AAACCTTAAACCTTAAATTTA
29372008 AAACCTTAAACCTTAAATTTA
1 AAACCTTAAACCTTAAATTTA
29372029 AAACCTTAAAC
1 AAACCTTAAAC
29372040 TCATGACTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (21 bp):
AAACCTTAAACCTTAAATTTA
Found at i:29374574 original size:24 final size:24
Alignment explanation
Indices: 29374547--29374593 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
29374537 CACCATACAC
*
29374547 GGAGTTGGATCTTCATTTTCTACT
1 GGAGTTGGATATTCATTTTCTACT
*
29374571 GGAGTTGTATATTCATTTTCTAC
1 GGAGTTGGATATTCATTTTCTAC
29374594 AAGTTCCACA
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:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (24 bp):
GGAGTTGGATATTCATTTTCTACT
Found at i:29375036 original size:26 final size:28
Alignment explanation
Indices: 29374980--29375036 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
29374970 TTTCAATAAA
* *
29374980 TAAAATATGAATTTAAAAATATATCATAC
1 TAAAATA-GAATTTAAAAATATAACACAC
29375009 TAAAATA-AATTTAAAAATA-AACACAC
1 TAAAATAGAATTTAAAAATATAACACAC
29375035 TA
1 TA
29375037 CATTTCTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 12 0.46
29 7 0.27
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (28 bp):
TAAAATAGAATTTAAAAATATAACACAC
Found at i:29375062 original size:4 final size:4
Alignment explanation
Indices: 29375055--29375098 Score: 70
Period size: 4 Copynumber: 10.5 Consensus size: 4
29375045 TCATTCTTCC
29375055 TTCT TTCT TTCT TTCTT TTCT TTCTT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTC-T TTCT TTC-T TTCT TTCT TTCT TTCT TT
29375099 TCTGCCCGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 30 0.79
5 8 0.21
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:29375076 original size:13 final size:13
Alignment explanation
Indices: 29375058--29375101 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
29375048 TTCTTCCTTC
29375058 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
29375071 TTTCTTTCTTT-T
1 TTTCTTTCTTTCT
29375083 CTTTCTTTCTTTCT
1 -TTTCTTTCTTTCT
29375097 TTTCT
1 TTTCT
29375102 GCCCGTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.03
13 27 0.93
14 1 0.03
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTTTCTTTCT
Found at i:29375077 original size:17 final size:18
Alignment explanation
Indices: 29375055--29375101 Score: 80
Period size: 17 Copynumber: 2.7 Consensus size: 18
29375045 TCATTCTTCC
29375055 TTCTTTC-TTTCTTTCTT
1 TTCTTTCTTTTCTTTCTT
29375072 TTCTTTCTTTTCTTTC-T
1 TTCTTTCTTTTCTTTCTT
29375089 TTCTTTCTTTTCT
1 TTCTTTCTTTTCT
29375102 GCCCGTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 21 0.72
18 8 0.28
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
TTCTTTCTTTTCTTTCTT
Found at i:29386148 original size:22 final size:23
Alignment explanation
Indices: 29386123--29386165 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
29386113 ATATAAAAAT
29386123 AATTATATTAA-AAATATTATTA
1 AATTATATTAATAAATATTATTA
*
29386145 AATTATATTAATAATTATTAT
1 AATTATATTAATAAATATTAT
29386166 ATTAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTATATTAATAAATATTATTA
Found at i:29386149 original size:17 final size:17
Alignment explanation
Indices: 29386103--29386183 Score: 55
Period size: 16 Copynumber: 4.8 Consensus size: 17
29386093 AAAATATTTG
29386103 AAATATT-TT-AATATAA
1 AAATATTATTAAAT-TAA
*
29386119 AAATA--ATTATATTAA
1 AAATATTATTAAATTAA
29386134 AAATATTATTAAATTATA
1 AAATATTATTAAATTA-A
* *
29386152 TTAATAATTATTATATT-A
1 -AAAT-ATTATTAAATTAA
*
29386170 AAATATGATTAAAT
1 AAATATTATTAAAT
29386184 CATTTATTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
15 10 0.20
16 15 0.29
17 11 0.22
18 2 0.04
19 3 0.06
20 10 0.20
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (17 bp):
AAATATTATTAAATTAA
Found at i:29386191 original size:23 final size:24
Alignment explanation
Indices: 29386126--29386192 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 24
29386116 TAAAAATAAT
* *
29386126 TATATTAAAAAT-A-TTATTAAAT
1 TATATTAATAATCATTTATTAAAA
*
29386148 TATATTAATAATTATTATATTAAAA
1 TATATTAATAATCATT-TATTAAAA
29386173 TATGATT-A-AATCATTTATTA
1 TAT-ATTAATAATCATTTATTA
29386193 TTTTTATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 11 0.29
23 6 0.16
24 7 0.18
25 11 0.29
26 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (24 bp):
TATATTAATAATCATTTATTAAAA
Found at i:29386236 original size:22 final size:24
Alignment explanation
Indices: 29386194--29386241 Score: 73
Period size: 22 Copynumber: 2.0 Consensus size: 24
29386184 CATTTATTAT
29386194 TTTTATTAAATTATTTTAATAACAA
1 TTTTATTAAA-TATTTTAATAACAA
29386219 TTTTATTAAA-A-TTTAATAACAA
1 TTTTATTAAATATTTTAATAACAA
29386241 T
1 T
29386242 AACAATAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 12 0.52
23 1 0.04
25 10 0.43
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTTATTAAATATTTTAATAACAA
Found at i:29386831 original size:13 final size:13
Alignment explanation
Indices: 29386815--29386867 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
29386805 AATTTAGTAT
*
29386815 TATTTTTTAAAAG
1 TATTTTTAAAAAG
*
29386828 TATTTTTAAAAAA
1 TATTTTTAAAAAG
* *
29386841 TAATTTTGAAAAG
1 TATTTTTAAAAAG
29386854 TATTTTTAAAAAG
1 TATTTTTAAAAAG
29386867 T
1 T
29386868 TTGATTTATG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (13 bp):
TATTTTTAAAAAG
Found at i:29386835 original size:12 final size:12
Alignment explanation
Indices: 29386818--29386864 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
29386808 TTAGTATTAT
29386818 TTTTTAAAAGTA
1 TTTTTAAAAGTA
*
29386830 TTTTTAAAAAATAA
1 TTTTT-AAAAGT-A
*
29386844 TTTTGAAAAGTA
1 TTTTTAAAAGTA
29386856 TTTTTAAAA
1 TTTTTAAAA
29386865 AGTTTGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 14 0.48
13 10 0.34
14 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (12 bp):
TTTTTAAAAGTA
Found at i:29387398 original size:30 final size:29
Alignment explanation
Indices: 29387307--29387399 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 29
29387297 ATAATAAATT
*
29387307 AAAATTTTGGA-TCCCTTAAAAGTTGGAAA
1 AAAATTTTTGAGTCCCTTAAAAGTT-GAAA
* * *
29387336 GAAATTTTTTAGACTCC-TAAAAGTTGATAA
1 AAAATTTTTGAGTC-CCTTAAAAGTTGA-AA
*
29387366 AAAATTTGTTGAGTCCCTTAAAAATTGAAA
1 AAAATTT-TTGAGTCCCTTAAAAGTTGAAA
29387396 AAAA
1 AAAA
29387400 AAATTTAAGC
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
29 10 0.20
30 25 0.49
31 16 0.31
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (29 bp):
AAAATTTTTGAGTCCCTTAAAAGTTGAAA
Found at i:29387399 original size:31 final size:30
Alignment explanation
Indices: 29387307--29387400 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 30
29387297 ATAATAAATT
* *
29387307 AAAATTTTGGA-TCCCTTAAAAGTTGGAAA
1 AAAATTTTTGAGTCCCTTAAAAGTTGAAAA
* * * *
29387336 GAAATTTTTTAGACTCC-TAAAAGTTGATAA
1 AAAATTTTTGAGTC-CCTTAAAAGTTGAAAA
*
29387366 AAAATTTGTTGAGTCCCTTAAAAATTGAAAA
1 AAAATTT-TTGAGTCCCTTAAAAGTTGAAAA
29387397 AAAA
1 AAAA
29387401 AATTTAAGCT
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
29 8 0.16
30 20 0.40
31 22 0.44
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.32
Consensus pattern (30 bp):
AAAATTTTTGAGTCCCTTAAAAGTTGAAAA
Found at i:29390366 original size:79 final size:79
Alignment explanation
Indices: 29390235--29390544 Score: 458
Period size: 79 Copynumber: 3.9 Consensus size: 79
29390225 CGATTATGGT
* * *
29390235 ACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAAATCTAGTTGGATTAACCAACAATATC
1 ACCCAGTGCCTAGCAGATAAACCGCAATTGTGAGCCCAACTCTAGTTGGATTAACCAACAATATC
29390300 CGTCAAATCCTGGC
66 CGTCAAATCCTGGC
* *
29390314 ACCCAGTGCTTAGCAGATAAACCGCAATTGTGAGCCCAGCTCTAGTTGGATTAACCAACAATATC
1 ACCCAGTGCCTAGCAGATAAACCGCAATTGTGAGCCCAACTCTAGTTGGATTAACCAACAATATC
* *
29390379 CGTCAAATCGTAGC
66 CGTCAAATCCTGGC
* *
29390393 ACCCAGTGCCTAGCAGATAAACCGCAATTGTGAGCCCAACTCTAGTTGAATTAACCAACAACATC
1 ACCCAGTGCCTAGCAGATAAACCGCAATTGTGAGCCCAACTCTAGTTGGATTAACCAACAATATC
*
29390458 CGTCAAATCTTGGC
66 CGTCAAATCCTGGC
* * * * * * *
29390472 ACCTAATGCCTAGCGGATAAATCTCAATTGTGAGCCCAGCTCTAGTTGGATTAACCAACAATGTC
1 ACCCAGTGCCTAGCAGATAAACCGCAATTGTGAGCCCAACTCTAGTTGGATTAACCAACAATATC
*
29390537 CATCAAAT
66 CGTCAAAT
29390545 AACCAATTTC
Statistics
Matches: 208, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 208 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.23
Consensus pattern (79 bp):
ACCCAGTGCCTAGCAGATAAACCGCAATTGTGAGCCCAACTCTAGTTGGATTAACCAACAATATC
CGTCAAATCCTGGC
Found at i:29395186 original size:10 final size:10
Alignment explanation
Indices: 29395171--29395195 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29395161 ATGATTGCAA
29395171 AATCCAATCT
1 AATCCAATCT
29395181 AATCCAATCT
1 AATCCAATCT
29395191 AATCC
1 AATCC
29395196 TAAAGATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (10 bp):
AATCCAATCT
Done.