Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 140 of 185
Found at i:42683428 original size:23 final size:23
Alignment explanation
Indices: 42683400--42683443 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
42683390 CAAGCAAGAA
* *
42683400 AATTAATAATAATAAACAAAAGC
1 AATTAAAAAAAATAAACAAAAGC
*
42683423 AATTAAAAAAAATACACAAAA
1 AATTAAAAAAAATAAACAAAA
42683444 AAAACTTATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.18
Consensus pattern (23 bp):
AATTAAAAAAAATAAACAAAAGC
Found at i:42688533 original size:65 final size:66
Alignment explanation
Indices: 42688452--42688583 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
42688442 CTTCTTTCAA
* *
42688452 AAATTTTATATGCCTTCAAGATATAACAAAG-CCTCAATATTTTAAACAGAACAATAAAAATGAC
1 AAATTTTATATGCCTTCAAAATATAACAAAGCCCTCAACATTTTAAACAGAACAATAAAAATGAC
42688516 T
66 T
*
42688517 AAATTTTATATGCCTTCAAAATATAACAAAGCCCTCAACATTTTAAATAGAACAATAAAAATGAC
1 AAATTTTATATGCCTTCAAAATATAACAAAGCCCTCAACATTTTAAACAGAACAATAAAAATGAC
42688582 T
66 T
42688583 A
1 A
42688584 CGGACATTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 30 0.48
66 33 0.52
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (66 bp):
AAATTTTATATGCCTTCAAAATATAACAAAGCCCTCAACATTTTAAACAGAACAATAAAAATGAC
T
Found at i:42690452 original size:8 final size:8
Alignment explanation
Indices: 42690439--42690474 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
42690429 TAATAAATAA
42690439 AAATTATT
1 AAATTATT
42690447 AAATTATT
1 AAATTATT
42690455 AAA-TATT
1 AAATTATT
42690462 -AATTATT
1 AAATTATT
42690469 AAATTA
1 AAATTA
42690475 AAAATATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 2 0.08
7 8 0.31
8 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
AAATTATT
Found at i:42690573 original size:18 final size:19
Alignment explanation
Indices: 42690527--42690574 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
42690517 AATAGACTTA
42690527 AAATATTCTATA-AAATTG
1 AAATATTCTATATAAATTG
* *
42690545 AGAGATT-TATATAAATT-
1 AAATATTCTATATAAATTG
42690562 AAATATTCTATAT
1 AAATATTCTATAT
42690575 TTTTCGTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (19 bp):
AAATATTCTATATAAATTG
Found at i:42701366 original size:29 final size:29
Alignment explanation
Indices: 42701266--42701369 Score: 77
Period size: 29 Copynumber: 3.5 Consensus size: 29
42701256 TTTTCTTTTT
*
42701266 TGGTCACTCAATTATGAAAAGTTACAAAA
1 TGGTCACTCAACTATGAAAAGTTACAAAA
* * * ****
42701295 TGGTCACCCAACTATAAGTAAACTT-CTTTTT
1 TGGTCACTCAACTAT--GAAAAGTTAC-AAAA
*
42701326 TGGTTAAC-CAACTATGAAAAGTTACAAAA
1 TGG-TCACTCAACTATGAAAAGTTACAAAA
42701355 TGGTCACTCAACTAT
1 TGGTCACTCAACTAT
42701370 TCAATTTTGT
Statistics
Matches: 53, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
28 3 0.06
29 29 0.55
30 2 0.04
31 16 0.30
32 3 0.06
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (29 bp):
TGGTCACTCAACTATGAAAAGTTACAAAA
Found at i:42701383 original size:60 final size:58
Alignment explanation
Indices: 42701255--42701387 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 58
42701245 TCCAATTATT
* *
42701255 TTTTTCTTTTTTGGTCACTCAATTATGAAAAGTTACAAAATGGTCACCCAACTATAAG
1 TTTTTCTTTTTTGGTAACTCAACTATGAAAAGTTACAAAATGGTCACCCAACTATAAG
** *
42701313 TAAACTTCTTTTTTGGTTAAC-CAACTATGAAAAGTTACAAAATGGTCACTCAACTATTCAA-
1 T--TTTTCTTTTTTGG-TAACTCAACTATGAAAAGTTACAAAATGGTCACCCAACTA-T-AAG
42701374 TTTTGTCTTTTTTG
1 TTTT-TCTTTTTTG
42701388 TAATGTCTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
58 1 0.02
59 1 0.02
60 53 0.85
61 5 0.08
62 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41
Consensus pattern (58 bp):
TTTTTCTTTTTTGGTAACTCAACTATGAAAAGTTACAAAATGGTCACCCAACTATAAG
Found at i:42706026 original size:18 final size:18
Alignment explanation
Indices: 42705999--42706033 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42705989 ATAAATAAAC
42705999 ATAATAACTTACAATATT
1 ATAATAACTTACAATATT
* *
42706017 ATAATCACTTATAATAT
1 ATAATAACTTACAATAT
42706034 ATCATCTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATAACTTACAATATT
Found at i:42706944 original size:433 final size:433
Alignment explanation
Indices: 42706138--42707005 Score: 1736
Period size: 433 Copynumber: 2.0 Consensus size: 433
42706128 AATATTACAT
42706138 TGGCAAGAACTTTCTAAACACATGTTTTGAACAAATTCACCGGCACATAGCCTGCTAGGCTTGAA
1 TGGCAAGAACTTTCTAAACACATGTTTTGAACAAATTCACCGGCACATAGCCTGCTAGGCTTGAA
42706203 GCCTGATCCAGTACACCGGCATTAAGCCTGCTAGACGTATAGTCTGAAATATTTCACCAGTATTA
66 GCCTGATCCAGTACACCGGCATTAAGCCTGCTAGACGTATAGTCTGAAATATTTCACCAGTATTA
42706268 AGCCTACTAGGTACTAGCCTGAAAATCTCAGATACAAAGATGATTCTTTCGTATAGTTCTTTATA
131 AGCCTACTAGGTACTAGCCTGAAAATCTCAGATACAAAGATGATTCTTTCGTATAGTTCTTTATA
42706333 TTTACATAAGTTTTACTCAATAACCGTATATCCACAACATTAAATTATATTCGATTCTTCATAGT
196 TTTACATAAGTTTTACTCAATAACCGTATATCCACAACATTAAATTATATTCGATTCTTCATAGT
42706398 AAACATGCATTCGAACCATATAGATATAACTCAAAAACATTAAATCCAGCTCAAAGTCTTTTGTA
261 AAACATGCATTCGAACCATATAGATATAACTCAAAAACATTAAATCCAGCTCAAAGTCTTTTGTA
42706463 ACCTATGTTCGAACCCCTTATGTATATAAAATACATACATCAATTCTCCAACTCAAGAACTTGAA
326 ACCTATGTTCGAACCCCTTATGTATATAAAATACATACATCAATTCTCCAACTCAAGAACTTGAA
42706528 TATATGTATATATGTATGTTCGAGCCACATGCATATAAATATA
391 TATATGTATATATGTATGTTCGAGCCACATGCATATAAATATA
42706571 TGGCAAGAACTTTCTAAACACATGTTTTGAACAAATTCACCGGCACATAGCCTGCTAGGCTTGAA
1 TGGCAAGAACTTTCTAAACACATGTTTTGAACAAATTCACCGGCACATAGCCTGCTAGGCTTGAA
42706636 GCCTGATCCAGTACACCGGCATTAAGCCTGCTAGACGTATAGTCTGAAATATTTCACCAGTATTA
66 GCCTGATCCAGTACACCGGCATTAAGCCTGCTAGACGTATAGTCTGAAATATTTCACCAGTATTA
42706701 AGCCTACTAGGTACTAGCCTGAAAATCTCAGATACAAAGATGATTCTTTCGTATAGTTCTTTATA
131 AGCCTACTAGGTACTAGCCTGAAAATCTCAGATACAAAGATGATTCTTTCGTATAGTTCTTTATA
42706766 TTTACATAAGTTTTACTCAATAACCGTATATCCACAACATTAAATTATATTCGATTCTTCATAGT
196 TTTACATAAGTTTTACTCAATAACCGTATATCCACAACATTAAATTATATTCGATTCTTCATAGT
42706831 AAACATGCATTCGAACCATATAGATATAACTCAAAAACATTAAATCCAGCTCAAAGTCTTTTGTA
261 AAACATGCATTCGAACCATATAGATATAACTCAAAAACATTAAATCCAGCTCAAAGTCTTTTGTA
42706896 ACCTATGTTCGAACCCCTTATGTATATAAAATACATACATCAATTCTCCAACTCAAGAACTTGAA
326 ACCTATGTTCGAACCCCTTATGTATATAAAATACATACATCAATTCTCCAACTCAAGAACTTGAA
42706961 TATATGTATATATGTATGTTCGAGCCACATGCATATAAATATA
391 TATATGTATATATGTATGTTCGAGCCACATGCATATAAATATA
42707004 TG
1 TG
42707006 TAATTCATAA
Statistics
Matches: 435, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
433 435 1.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (433 bp):
TGGCAAGAACTTTCTAAACACATGTTTTGAACAAATTCACCGGCACATAGCCTGCTAGGCTTGAA
GCCTGATCCAGTACACCGGCATTAAGCCTGCTAGACGTATAGTCTGAAATATTTCACCAGTATTA
AGCCTACTAGGTACTAGCCTGAAAATCTCAGATACAAAGATGATTCTTTCGTATAGTTCTTTATA
TTTACATAAGTTTTACTCAATAACCGTATATCCACAACATTAAATTATATTCGATTCTTCATAGT
AAACATGCATTCGAACCATATAGATATAACTCAAAAACATTAAATCCAGCTCAAAGTCTTTTGTA
ACCTATGTTCGAACCCCTTATGTATATAAAATACATACATCAATTCTCCAACTCAAGAACTTGAA
TATATGTATATATGTATGTTCGAGCCACATGCATATAAATATA
Found at i:42708574 original size:25 final size:25
Alignment explanation
Indices: 42708546--42708601 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
42708536 CTGTTATTTA
*
42708546 GCTCTTATGGGCATCCCGA-TATATG
1 GCTCTTATGAGCATCCCGATTA-ATG
** *
42708571 GCTCACATGAGCTTCCCGATTAATG
1 GCTCTTATGAGCATCCCGATTAATG
42708596 GCTCTT
1 GCTCTT
42708602 CGAAGCTTCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (25 bp):
GCTCTTATGAGCATCCCGATTAATG
Found at i:42708704 original size:25 final size:24
Alignment explanation
Indices: 42708676--42708758 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 24
42708666 TGGCTCGTAT
*
42708676 GAGCTTCTCGATAATTGGCTCACAA
1 GAGCTTC-CCATAATTGGCTCACAA
*
42708701 GAGCTTCCCATTACA-TGGCTCACAT
1 GAGCTTCCCA-TA-ATTGGCTCACAA
*
42708726 GAGCTTCCCATTATATGGCTCGA-AA
1 GAGCTTCCCATAAT-TGGCTC-ACAA
42708751 GAGCTTCC
1 GAGCTTCC
42708759 TGATTACATG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
23 1 0.02
24 3 0.06
25 43 0.88
26 2 0.04
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (24 bp):
GAGCTTCCCATAATTGGCTCACAA
Found at i:42708753 original size:50 final size:51
Alignment explanation
Indices: 42708665--42708768 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 51
42708655 CTGCCCGTTT
** *
42708665 ATGGCTCGTATGAGCTTCTCGATAATTGGCTCACAAGAGCTTCC-CATTAC
1 ATGGCTCACATGAGCTTCTCCATAATTGGCTCACAAGAGCTTCCTCATTAC
* *
42708715 ATGGCTCACATGAGCTTC-CCATTATATGGCTCGA-AAGAGCTTCCTGATTAC
1 ATGGCTCACATGAGCTTCTCCATAAT-TGGCTC-ACAAGAGCTTCCTCATTAC
42708766 ATG
1 ATG
42708769 CTTGCACGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
49 5 0.11
50 32 0.70
51 9 0.20
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (51 bp):
ATGGCTCACATGAGCTTCTCCATAATTGGCTCACAAGAGCTTCCTCATTAC
Found at i:42710209 original size:105 final size:101
Alignment explanation
Indices: 42710063--42710292 Score: 241
Period size: 105 Copynumber: 2.2 Consensus size: 101
42710053 ACACATACAT
** * ** * *
42710063 TGCCATGGCCCTGCCATGGTCTTACATTTGTAGTGCCATAACCTAGTTATGGTCTTATT-ATCAG
1 TGCCATGGCCCAACCATGGTCTTACAGTTCAAGTGCCATAACCCAGTTATGGTCTT-TTCATCAA
* * *
42710127 AATGT-CATAGCCCAGATATGGTCTTACACATGTATATATAC
65 AAT-TCCATAGCCCAGATATAGTCTT--ACAT-T-TAAACAC
* *
42710168 TGCCATGGCCCAACCATGGTCTTAC-GTTCAAGATGTCATAACCCAGTTATGGTCTTTTCATTAA
1 TGCCATGGCCCAACCATGGTCTTACAGTTCAAG-TGCCATAACCCAGTTATGGTCTTTTCATCAA
* *
42710232 AATTCCATAGCTCAGCTATAGTCTTACATTTAAACAC
65 AATTCCATAGCCCAGATATAGTCTTACATTTAAACAC
*
42710269 TGCCATGGTCCAACCATGGTCTTA
1 TGCCATGGCCCAACCATGGTCTTA
42710293 TCCGTCAATT
Statistics
Matches: 107, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
101 28 0.26
102 1 0.01
103 4 0.04
104 7 0.07
105 67 0.63
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (101 bp):
TGCCATGGCCCAACCATGGTCTTACAGTTCAAGTGCCATAACCCAGTTATGGTCTTTTCATCAAA
ATTCCATAGCCCAGATATAGTCTTACATTTAAACAC
Found at i:42715998 original size:17 final size:17
Alignment explanation
Indices: 42715964--42716001 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
42715954 AAAACTAATT
**
42715964 TTTTTTAGTTTATTCAG
1 TTTTTTAGTTTAACCAG
42715981 TTTTTTAGTTTAACCAG
1 TTTTTTAGTTTAACCAG
42715998 TTTT
1 TTTT
42716002 CATGTTCGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.08, G:0.11, T:0.63
Consensus pattern (17 bp):
TTTTTTAGTTTAACCAG
Found at i:42722355 original size:20 final size:20
Alignment explanation
Indices: 42722330--42722379 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
42722320 TGGCTTAAAA
42722330 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
42722350 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
42722367 GTGGTAGTGGATT
1 TTGGTAGTGGATT
42722380 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:42730187 original size:31 final size:29
Alignment explanation
Indices: 42730144--42730205 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
42730134 TTTTATAAAT
*
42730144 AATTAATATTTAT-TAATTAAAAATATTTAC
1 AATTAATATTTATAT-ATT-AAAATATTAAC
*
42730174 AATTTATATTTTATATATTAAAATATTAAC
1 AATTAATA-TTTATATATTAAAATATTAAC
42730204 AA
1 AA
42730206 CAAGTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 8 0.29
32 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
AATTAATATTTATATATTAAAATATTAAC
Found at i:42730391 original size:13 final size:13
Alignment explanation
Indices: 42730375--42730425 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
42730365 TTTAAACCAA
42730375 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
42730388 ACTTCTCAAAATC
1 ACTTTTCAAAAGC
*
42730401 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
42730414 ACTTTTCAAAAG
1 ACTTTTCAAAAG
42730426 TAATTAAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 4 0.13
13 23 0.74
14 4 0.13
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.31
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:42732403 original size:7 final size:7
Alignment explanation
Indices: 42732391--42732416 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
42732381 ATTGAGTAAA
42732391 AATATTC
1 AATATTC
42732398 AATATTC
1 AATATTC
42732405 AATATTC
1 AATATTC
42732412 AATAT
1 AATAT
42732417 GAAATTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATTC
Found at i:42736245 original size:85 final size:85
Alignment explanation
Indices: 42736102--42736271 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
42736092 AAAAAATGTT
*
42736102 GAAGAGATTGATTAATTTAATAAGTATGTATGAGCAGTAGTTAGCAAATTATCGAGTTGCCGTGA
1 GAAGAGATTGATTAATTTAATAAATATGTATGAGCAGTAGTTAGCAAATTATCGAGTTGCCGTGA
42736167 ATTTGTTCGTAGCAATATAA
66 ATTTGTTCGTAGCAATATAA
42736187 GAAGAGATTGATTAATTTAATAAATATGTATGAGCAGTAGTTAGCAAATTATCGAGTTGCCGTGA
1 GAAGAGATTGATTAATTTAATAAATATGTATGAGCAGTAGTTAGCAAATTATCGAGTTGCCGTGA
42736252 ATTTGTTCGTAGCAATATAA
66 ATTTGTTCGTAGCAATATAA
42736272 ACATAAGTTT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (85 bp):
GAAGAGATTGATTAATTTAATAAATATGTATGAGCAGTAGTTAGCAAATTATCGAGTTGCCGTGA
ATTTGTTCGTAGCAATATAA
Found at i:42736417 original size:14 final size:14
Alignment explanation
Indices: 42736398--42736425 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42736388 TATATTTTTA
42736398 CTTAGTTTTTAATC
1 CTTAGTTTTTAATC
42736412 CTTAGTTTTTAATC
1 CTTAGTTTTTAATC
42736426 ATTTTTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
CTTAGTTTTTAATC
Found at i:42738383 original size:20 final size:21
Alignment explanation
Indices: 42738346--42738387 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
42738336 AGAGTTGATT
42738346 TAATGAAAATGTAAAATTAAC
1 TAATGAAAATGTAAAATTAAC
* *
42738367 TAAT-AAAATTTACAATTAAC
1 TAATGAAAATGTAAAATTAAC
42738387 T
1 T
42738388 TTCATCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (21 bp):
TAATGAAAATGTAAAATTAAC
Found at i:42745920 original size:3 final size:3
Alignment explanation
Indices: 42745912--42745946 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
42745902 AGAAGGATGA
42745912 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
42745947 GCTTTTGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:42746118 original size:3 final size:3
Alignment explanation
Indices: 42746110--42746167 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
42746100 TTTGTTTGTG
42746110 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
42746158 TTC TTC TTC T
1 TTC TTC TTC T
42746168 CGTGTACTGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:42751357 original size:25 final size:25
Alignment explanation
Indices: 42751224--42751357 Score: 105
Period size: 25 Copynumber: 5.4 Consensus size: 25
42751214 AGCTCTTGCC
* *
42751224 AGCCAATTATCGGGAAGCTCAT-ACG
1 AGCCAAATAACGGGAAGCTCATGA-G
* * * *
42751249 AGCCATA-AACGAGAAGCTCAAGAA
1 AGCCAAATAACGGGAAGCTCATGAG
*
42751273 AGCCATTAATTA--GGAAGCTCATGAG
1 AGCCA--AATAACGGGAAGCTCATGAG
*
42751298 AGCCAAATATCGGGAAGCTCATGAG
1 AGCCAAATAACGGGAAGCTCATGAG
* * *
42751323 AGCCATATAACGGGATGCTCATAAG
1 AGCCAAATAACGGGAAGCTCATGAG
*
42751348 AGCTAAATAA
1 AGCCAAATAA
42751358 TGGAACGCTT
Statistics
Matches: 84, Mismatches: 19, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
23 3 0.04
24 16 0.19
25 63 0.75
26 1 0.01
27 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (25 bp):
AGCCAAATAACGGGAAGCTCATGAG
Found at i:42754570 original size:30 final size:29
Alignment explanation
Indices: 42754529--42754684 Score: 136
Period size: 30 Copynumber: 5.2 Consensus size: 29
42754519 AGTTTTTTTG
* *
42754529 CATTTTAACCCCTATACTTTTCAAAATTTA
1 CATTTTGACCCCTAAACTTTTCAAAA-TTA
*
42754559 CATTTTGACCCC-AAAATTTTCTAAAATTTA
1 CATTTTGACCCCTAAACTTTTC-AAAA-TTA
* *
42754589 CATTTTGACCGCAAAAC-TTTCTAAAATTA
1 CATTTTGACCCCTAAACTTTTC-AAAATTA
* **
42754618 CATTTTGACCCTTAGGCTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTT-TCAAAATTA
* * * *
42754648 CACTTTAACCCCTAAACTCTTAAGAAATTA
1 CATTTTGACCCCTAAACTTTTCA-AAATTA
42754678 CATTTTG
1 CATTTTG
42754685 GCCCATATTT
Statistics
Matches: 102, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
29 24 0.24
30 73 0.72
31 5 0.05
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.38
Consensus pattern (29 bp):
CATTTTGACCCCTAAACTTTTCAAAATTA
Found at i:42754637 original size:29 final size:28
Alignment explanation
Indices: 42754547--42754718 Score: 116
Period size: 30 Copynumber: 5.9 Consensus size: 28
42754537 CCCCTATACT
*
42754547 TTTC-AAAATTTACATTTTGACCCCAAAAT
1 TTTCTAAAA-TTACATTTTGA-CCCAAAAC
42754576 TTTCTAAAATTTACATTTTGACCGCAAAAC
1 TTTCTAAAA-TTACATTTTGACC-CAAAAC
* **
42754606 TTTCTAAAATTACATTTTGACCCTTAGGC
1 TTTCTAAAATTACATTTTGACCC-AAAAC
* * *
42754635 TTTCTCAAAATTACACTTTAACCCCTAAAC
1 TTTCT-AAAATTACATTTTGA-CCCAAAAC
* * * *
42754665 TCTT-AAGAAATTACATTTTGGCCC-ATAT
1 T-TTCTA-AAATTACATTTTGACCCAAAAC
*
42754693 TTTGCTAAAATTACACTTTTGCCCCA
1 TTT-CTAAAATTACA-TTTTGACCCA
42754719 GAAGCTTTAC
Statistics
Matches: 116, Mismatches: 16, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.02
28 12 0.10
29 39 0.34
30 58 0.50
31 5 0.04
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (28 bp):
TTTCTAAAATTACATTTTGACCCAAAAC
Found at i:42755244 original size:11 final size:11
Alignment explanation
Indices: 42755228--42755286 Score: 82
Period size: 11 Copynumber: 5.3 Consensus size: 11
42755218 GAGCGACCCG
42755228 AAAAAGAAGGA
1 AAAAAGAAGGA
*
42755239 AAAAAGAAAGA
1 AAAAAGAAGGA
*
42755250 AAAAAGAAGTA
1 AAAAAGAAGGA
42755261 GAAAAAGAAGGA
1 -AAAAAGAAGGA
*
42755273 AAAAAGAAAGA
1 AAAAAGAAGGA
42755284 AAA
1 AAA
42755287 GAAAAGAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
11 32 0.76
12 10 0.24
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (11 bp):
AAAAAGAAGGA
Found at i:42755253 original size:12 final size:11
Alignment explanation
Indices: 42755228--42755297 Score: 63
Period size: 11 Copynumber: 6.3 Consensus size: 11
42755218 GAGCGACCCG
*
42755228 AAAAAGAAGGA
1 AAAAAGAAGAA
42755239 AAAAAGAA-AGA
1 AAAAAGAAGA-A
*
42755250 AAAAAGAAGTAG
1 AAAAAGAAG-AA
*
42755262 AAAAAGAAGGA
1 AAAAAGAAGAA
42755273 AAAAAGAAAGAA
1 AAAAAG-AAGAA
*
42755285 AAGAA-AAGAA
1 AAAAAGAAGAA
42755295 AAA
1 AAA
42755298 GAAAAATCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
10 7 0.15
11 23 0.48
12 17 0.35
13 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.01
Consensus pattern (11 bp):
AAAAAGAAGAA
Found at i:42755255 original size:22 final size:22
Alignment explanation
Indices: 42755228--42755297 Score: 88
Period size: 23 Copynumber: 3.2 Consensus size: 22
42755218 GAGCGACCCG
42755228 AAAAAGAAGGAAAAAAGAAAGA
1 AAAAAGAAGGAAAAAAGAAAGA
* *
42755250 AAAAAGAAGTAGAAAAAGAAGGA
1 AAAAAGAAGGA-AAAAAGAAAGA
* *
42755273 AAAAAGAAAGAAAAGA-AAAGA
1 AAAAAGAAGGAAAAAAGAAAGA
42755294 AAAA
1 AAAA
42755298 GAAAAATCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
21 8 0.20
22 14 0.34
23 19 0.46
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.01
Consensus pattern (22 bp):
AAAAAGAAGGAAAAAAGAAAGA
Found at i:42755432 original size:11 final size:11
Alignment explanation
Indices: 42755401--42755454 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
42755391 AGCAGCTCAA
42755401 AAAAAAAACA-
1 AAAAAAAACAG
*
42755411 AACAAAAACAG
1 AAAAAAAACAG
42755422 AAAAAAAACAG
1 AAAAAAAACAG
*
42755433 CAGAAAAAAAAAG
1 -A-AAAAAAACAG
42755446 AGAAAAAAA
1 A-AAAAAAA
42755455 ACAAAGCAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 9 0.24
11 10 0.26
12 10 0.26
13 9 0.24
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAG
Found at i:42755436 original size:14 final size:14
Alignment explanation
Indices: 42755419--42755457 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
42755409 CAAACAAAAA
42755419 CAGAAAAAAAACAG
1 CAGAAAAAAAACAG
42755433 CAGAAAAAAAA-AG
1 CAGAAAAAAAACAG
42755446 -AGAAAAAAAACA
1 CAGAAAAAAAACA
42755458 AAGCAGGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.42
13 3 0.12
14 11 0.46
ACGTcount: A:0.77, C:0.10, G:0.13, T:0.00
Consensus pattern (14 bp):
CAGAAAAAAAACAG
Found at i:42755455 original size:11 final size:12
Alignment explanation
Indices: 42755399--42755455 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
42755389 AAAGCAGCTC
*
42755399 AAAAAAAAA-AC
1 AAAAAAAAAGAG
* *
42755410 AAACAAAAACAG
1 AAAAAAAAAGAG
42755422 AAAAAAAACAGCAG
1 AAAAAAAA-AG-AG
42755436 AAAAAAAAAGAG
1 AAAAAAAAAGAG
42755448 AAAAAAAA
1 AAAAAAAA
42755456 CAAAGCAGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
11 8 0.21
12 18 0.46
13 3 0.08
14 10 0.26
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAG
Found at i:42756174 original size:18 final size:17
Alignment explanation
Indices: 42756140--42756502 Score: 170
Period size: 17 Copynumber: 20.2 Consensus size: 17
42756130 AAAAAGAAGA
42756140 AAAAATTCTCGTG-TTTC
1 AAAAATT-TCGTGTTTTC
42756157 AAAGAATTTCGTGTTTTC
1 AAA-AATTTCGTGTTTTC
42756175 AAAAAATTCTCGTGTTTT-
1 -AAAAATT-TCGTGTTTTC
42756193 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
* *
42756211 AAAAATTT-TTTTGTTTC
1 AAAAATTTCGTGT-TTTC
*
42756228 AAAAATCCTCGTGTTTTC
1 AAAAAT-TTCGTGTTTTC
** *
42756246 AAAAATCCCG-GTGCTTC
1 AAAAATTTCGTGT-TTTC
* *
42756263 AAAAAAATTTTGTGTTCTC
1 --AAAAATTTCGTGTTTTC
* * *
42756282 AAAAATTCCAATG--ATC
1 AAAAATTTC-GTGTTTTC
42756298 AAAAATTTTTTTTCGTGTTTTC
1 AAAAA-----TTTCGTGTTTTC
*
42756320 TAAAAAAATTCCGTG-TTTC
1 ---AAAAATTTCGTGTTTTC
42756339 AAAAATTTTCGTGTTTTTC
1 AAAAA-TTTCGTG-TTTTC
* *
42756358 AACAATTCTCGT-ATTTC
1 AAAAATT-TCGTGTTTTC
*
42756375 AAAAATTTTCGCG-TTTC
1 AAAAA-TTTCGTGTTTTC
** **
42756392 AAAAAAAATATTGTTTTC
1 -AAAAATTTCGTGTTTTC
*
42756410 AAAAATTGTCGTGTTCTC
1 AAAAATT-TCGTGTTTTC
*
42756428 AAAAATATTCGTGTTTTT
1 AAAAAT-TTCGTGTTTTC
* *
42756446 AAGAATTTTCGTG-TCTC
1 AA-AAATTTCGTGTTTTC
* *
42756463 TAAAATTCTCGTGTTTTAA
1 AAAAATT-TCGTGTTTT-C
42756482 AAAAATTTCGTGTTTTC
1 AAAAATTTCGTGTTTTC
42756499 AAAA
1 AAAA
42756503 TAAAATTTGT
Statistics
Matches: 262, Mismatches: 46, Indels: 76
0.68 0.12 0.20
Matches are distributed among these distances:
16 20 0.08
17 88 0.34
18 85 0.32
19 49 0.19
20 10 0.04
21 3 0.01
22 2 0.01
25 5 0.02
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:42756179 original size:35 final size:35
Alignment explanation
Indices: 42756140--42756538 Score: 262
Period size: 35 Copynumber: 11.1 Consensus size: 35
42756130 AAAAAGAAGA
42756140 AAAAATTCTCGTGTTTCAAAGAA-TTTCGTGTTTTC
1 AAAAATTCTCGTGTTTCAAA-AATTTTCGTGTTTTC
*
42756175 AAAAAATTCTCGTGTTTTAAAAATTTTCGTGTTTTC
1 -AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
* ** **
42756211 AAAAATTTTTTTGTTTCAAAAATCCTCGTGTTTTC
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
* * *
42756246 AAAAA-TCCCGGTGCTTCAAAAAAATTTT-GTGTTCTC
1 AAAAATTCTC-GTGTTTC--AAAAATTTTCGTGTTTTC
* *
42756282 AAAAATTC-CAATG-ATCAAAAATTTTTTTTCGTGTTTTC
1 AAAAATTCTC-GTGTTTCAAAAA----TTTTCGTGTTTTC
42756320 TAAAAAAATTC-CGTGTTTCAAAAATTTTCGTGTTTTTC
1 ---AAAAATTCTCGTGTTTCAAAAATTTTCGTG-TTTTC
* * *
42756358 AACAATTCTCGTATTTCAAAAATTTTCGCG-TTTC
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
* * * * *
42756392 AAAAAAAATATTGT-TTTCAAAAATTGTCGTGTTCTC
1 --AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
* * *
42756428 AAAAATAT-TCGTGTTTTTAAGAATTTTCGTG-TCTC
1 AAAAAT-TCTCGTG-TTTCAAAAATTTTCGTGTTTTC
* * *
42756463 TAAAATTCTCGTGTTTTAAAAAAATTTCGTGTTTTC
1 AAAAATTCTCGTG-TTTCAAAAATTTTCGTGTTTTC
*** * * *
42756499 AAAATAAAAT-TTGTTTCAAAAATCTTCGTGTTTTA
1 AAAA-ATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
42756534 AAAAA
1 AAAAA
42756539 ATTGTATTTT
Statistics
Matches: 288, Mismatches: 50, Indels: 52
0.74 0.13 0.13
Matches are distributed among these distances:
33 5 0.02
34 15 0.05
35 117 0.41
36 98 0.34
37 23 0.08
38 12 0.04
40 2 0.01
41 16 0.06
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (35 bp):
AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
Found at i:42756521 original size:53 final size:53
Alignment explanation
Indices: 42756354--42756541 Score: 151
Period size: 53 Copynumber: 3.6 Consensus size: 53
42756344 TTTTCGTGTT
* * * * *
42756354 TTTCAACAATTCTCGT-ATTTCAAAAATTTTCGCG-TTTCAAAA-AAAATATTG
1 TTTCAAAAATTCTCGTGTTTTAAAAAAATTTCGTGTTTTCAAAATAAAAT-TTG
* * * *
42756405 TTTTCAAAAATTGTCGTGTTCT-CAAAAATATTCGTGTTTTTAAGAAT----TTTCG
1 -TTTCAAAAATTCTCGTGTTTTAAAAAAAT-TTCGTGTTTTCAA-AATAAAATTT-G
*
42756457 TGTCTCTAAAATTCTCGTGTTTTAAAAAAATTTCGTGTTTTCAAAATAAAATTTG
1 T-T-TCAAAAATTCTCGTGTTTTAAAAAAATTTCGTGTTTTCAAAATAAAATTTG
42756512 TTTCAAAAA-TCTTCGTGTTTTAAAAAAATT
1 TTTCAAAAATTC-TCGTGTTTTAAAAAAATT
42756542 GTATTTTGAT
Statistics
Matches: 108, Mismatches: 14, Indels: 27
0.72 0.09 0.18
Matches are distributed among these distances:
51 3 0.03
52 27 0.25
53 59 0.55
54 12 0.11
55 4 0.04
56 3 0.03
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (53 bp):
TTTCAAAAATTCTCGTGTTTTAAAAAAATTTCGTGTTTTCAAAATAAAATTTG
Found at i:42756530 original size:17 final size:16
Alignment explanation
Indices: 42756140--42756537 Score: 149
Period size: 18 Copynumber: 22.3 Consensus size: 16
42756130 AAAAAGAAGA
42756140 AAAAATTCTCGTGTTTC
1 AAAAATT-TCGTGTTTC
42756157 AAAGAATTTCGTGTTTTC
1 AAA-AATTTCGTG-TTTC
*
42756175 AAAAAATTCTCGTGTTTT
1 -AAAAATT-TCGTGTTTC
42756193 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTG-TTTC
**
42756211 AAAAATTTTTTTGTTTC
1 AAAAA-TTTCGTGTTTC
*
42756228 AAAAATCCTCGTGTTTTC
1 AAAAAT-TTCGTG-TTTC
** *
42756246 AAAAATCCCGGTGCTTC
1 AAAAATTTC-GTGTTTC
*
42756263 AAAAAAATTTTGTGTTCTC
1 --AAAAATTTCGTGTT-TC
* * *
42756282 AAAAATTCCAATG-ATC
1 AAAAATTTC-GTGTTTC
42756298 AAAAATTTTTTTTCGTGTTTTC
1 AAAAA-----TTTCGTG-TTTC
*
42756320 TAAAAAAATTCCGTGTTTC
1 ---AAAAATTTCGTGTTTC
42756339 AAAAATTTTCGTGTTTTTC
1 AAAAA-TTTCGTG--TTTC
* *
42756358 AACAATTCTCGTATTTC
1 AAAAATT-TCGTGTTTC
*
42756375 AAAAATTTTCGCGTTTC
1 AAAAA-TTTCGTGTTTC
42756392 AAAAAAAATATT-GT-TTTC
1 ---AAAAAT-TTCGTGTTTC
42756410 AAAAATTGTCGTGTTCTC
1 AAAAATT-TCGTGTT-TC
*
42756428 AAAAATATTCGTGTTTTT
1 AAAAAT-TTCGTG-TTTC
* *
42756446 AAGAATTTTCGTGTCTC
1 AA-AAATTTCGTGTTTC
* *
42756463 TAAAATTCTCGTGTTTTAA
1 AAAAATT-TCGTG-TTT-C
42756482 AAAAATTTCGTGTTTTC
1 AAAAATTTCGTG-TTTC
*
42756499 AAAATAAAATT--TGTTTC
1 --AA-AAATTTCGTGTTTC
*
42756516 AAAAATCTTCGTGTTTT
1 AAAAAT-TTCGTGTTTC
42756533 AAAAA
1 AAAAA
42756538 AATTGTATTT
Statistics
Matches: 292, Mismatches: 41, Indels: 96
0.68 0.10 0.22
Matches are distributed among these distances:
14 4 0.01
15 11 0.04
16 19 0.07
17 87 0.30
18 93 0.32
19 48 0.16
20 20 0.07
21 3 0.01
22 2 0.01
25 5 0.02
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (16 bp):
AAAAATTTCGTGTTTC
Found at i:42758389 original size:47 final size:48
Alignment explanation
Indices: 42758336--42758434 Score: 173
Period size: 47 Copynumber: 2.1 Consensus size: 48
42758326 AAAAGCTAAC
* *
42758336 GAAGTTGACGGGGATGACTGATACATGGGCTGAAAAACAGATAAAG-A
1 GAAGTTGACAGGGATGACTGATACATGGGATGAAAAACAGATAAAGAA
42758383 GAAGTTGACAGGGATGACTGATACATGGGATGAAAAACAGATAAAGAA
1 GAAGTTGACAGGGATGACTGATACATGGGATGAAAAACAGATAAAGAA
42758431 GAAG
1 GAAG
42758435 AATGAAGTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 44 0.90
48 5 0.10
ACGTcount: A:0.43, C:0.09, G:0.31, T:0.16
Consensus pattern (48 bp):
GAAGTTGACAGGGATGACTGATACATGGGATGAAAAACAGATAAAGAA
Found at i:42758607 original size:43 final size:43
Alignment explanation
Indices: 42758552--42758636 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
42758542 CGTCTTCCCG
*
42758552 AAGGTTCTTGGGCATATTGAAGTTGCGGTTGTGGATTTCTTCA
1 AAGGTTCATGGGCATATTGAAGTTGCGGTTGTGGATTTCTTCA
42758595 AAGGTTCATGGGCATATTGAAGTTGCGGTTGTGGATTTCTTC
1 AAGGTTCATGGGCATATTGAAGTTGCGGTTGTGGATTTCTTC
42758637 GAAAAGTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.19, C:0.12, G:0.31, T:0.39
Consensus pattern (43 bp):
AAGGTTCATGGGCATATTGAAGTTGCGGTTGTGGATTTCTTCA
Found at i:42763987 original size:10 final size:10
Alignment explanation
Indices: 42763966--42763994 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
42763956 TCCTTTTCCA
42763966 TCATAT-ATC
1 TCATATCATC
42763975 TCATATCATC
1 TCATATCATC
42763985 TCATATCATC
1 TCATATCATC
42763995 ATGTGTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (10 bp):
TCATATCATC
Found at i:42767502 original size:11 final size:11
Alignment explanation
Indices: 42767480--42767527 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
42767470 TTATGCCTGA
42767480 AAAAAAACAAC
1 AAAAAAACAAC
42767491 AACAAAAA-AAC
1 AA-AAAAACAAC
42767502 AAAAAAACAAC
1 AAAAAAACAAC
42767513 AAAAAAACAA-
1 AAAAAAACAAC
42767523 AAAAA
1 AAAAA
42767528 GAAAAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.29
11 20 0.57
12 5 0.14
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAC
Found at i:42767504 original size:8 final size:8
Alignment explanation
Indices: 42767491--42767534 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
42767481 AAAAAACAAC
42767491 AACAAAAA
1 AACAAAAA
42767499 AACAAAAAAA
1 AAC--AAAAA
42767509 CAACAAAAA
1 -AACAAAAA
42767518 AACAAAAA
1 AACAAAAA
*
42767526 AAGAAAAA
1 AACAAAAA
42767534 A
1 A
42767535 GAAAAATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 19 0.59
9 5 0.16
10 5 0.16
11 3 0.09
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (8 bp):
AACAAAAA
Found at i:42767510 original size:19 final size:19
Alignment explanation
Indices: 42767482--42767527 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
42767472 ATGCCTGAAA
42767482 AAAAACAACAACAAAAAAAC
1 AAAAA-AACAACAAAAAAAC
42767502 AAAAAAACAACAAAAAAAC
1 AAAAAAACAACAAAAAAAC
42767521 AAAAAAA
1 AAAAAAA
42767528 GAAAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAAACAACAAAAAAAC
Found at i:42768694 original size:76 final size:76
Alignment explanation
Indices: 42768411--42769468 Score: 1299
Period size: 76 Copynumber: 13.7 Consensus size: 76
42768401 TTAATCTGTG
*
42768411 TTTT-TTTTTCAAAAATTAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT
1 TTTTGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT
42768475 TTCTTTTAAAT
66 TTCTTTTAAAT
* * * *
42768486 TTCTGTTTTTCAAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGA
1 TTTTGTTTTTC----AAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCATGCCGA
42768551 GGTATTT-TTTTAAATT
61 GGTATTTCTTTTAAA-T
*
42768567 TCTGTTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGG
1 T-T-TTGTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGG
42768632 TATTTCTTTTAAAT
63 TATTTCTTTTAAAT
*
42768646 TTTTGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGATAT
1 TTTTGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT
42768711 TTCTTTTAAAT
66 TTCTTTTAAAT
* * * * *
42768722 TTTTGTTTTTAAAAAAAAAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCGGGTCACGCTGA
1 TTTTGTTTTT----CAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCATGCCGA
* *
42768787 GGTATTTTTTTTAATT
61 GGTATTTCTTTTAAAT
* * **
42768803 TCTGTTTTTTTTCAAAAATTCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTAAGG
1 T-T-TTGTTTTTCAAAAA-TCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGG
42768868 TATTT-TTTTAAAT
63 TATTTCTTTTAAAT
* * * *
42768881 TTCTGTTTTTTTCAAAAAATTAACTCATAATACAGAGGTGAGTTGAGTCACGGGTCATGCCGAGG
1 TT-T-TGTTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGG
42768946 TATTTCTTTTAAAT
63 TATTTCTTTTAAAT
** *
42768960 TTCCGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAACCTCGGGTCATGCCGAGGTAT
1 TTTTGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT
42769025 TTCTTTTAAAT
66 TTCTTTTAAAT
* * *
42769036 TTTCGTTTTTCAAAAATCAACTCATAATACGGAGGTGAGTTGAGCCTCGGGTCATGCCGAGTTAT
1 TTTTGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT
42769101 TTCTTTTAAAT
66 TTCTTTTAAAT
* *
42769112 TTCTGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCTGAGGTAT
1 TTTTGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT
42769177 TTCTTTTAAAT
66 TTCTTTTAAAT
* * * * ** *
42769188 TTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATACCGAGGTA
1 TTTTGTTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTA
42769253 TTTCTTTTAAAT
65 TTTCTTTTAAAT
* * * *
42769265 TTCTGTTTTTCAAAAATCAACTCATAATGCGAGAGATGAGTTGAGCCTCGGGTCACGCCGAGGTA
1 TTTTGTTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTA
*
42769330 --T-TTTTCAAT
65 TTTCTTTTAAAT
** * * ** * *
42769339 TCATGTTTTTCAAAAATTAACTCATATTGTTAGAGGTGAGTTGAGCCTCGGGGCACATGTCGAGG
1 TTTTGTTTTTCAAAAATCAACTCATAAT-ACAGAGGTGAGTTGAGCCTC-GGG-TCATGCCGAGG
**
42769404 TA----TTTTCGAT
63 TATTTCTTTTAAAT
* * * * *
42769414 TTTTGTTTTGCGAAGATCAACTCATAATCCAAGAGGTGAGTTGAGTCTCGGGTCA
1 TTTTGTTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCA
42769469 CACGCCGAGC
Statistics
Matches: 871, Mismatches: 86, Indels: 54
0.86 0.09 0.05
Matches are distributed among these distances:
73 2 0.00
74 51 0.06
75 52 0.06
76 322 0.37
77 115 0.13
78 62 0.07
79 92 0.11
80 81 0.09
81 78 0.09
82 2 0.00
83 14 0.02
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (76 bp):
TTTTGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT
TTCTTTTAAAT
Found at i:42768828 original size:236 final size:230
Alignment explanation
Indices: 42768411--42769469 Score: 1356
Period size: 236 Copynumber: 4.6 Consensus size: 230
42768401 TTAATCTGTG
42768411 TTTT-TTTTTCAAAAATTAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT
1 TTTTGTTTTTCAAAAATTAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT
42768475 TTCTTTTAAATTTCTGTTTTTCAAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
66 TTCTTTTAAATTTCTGTTTTT----AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
*
42768540 GGTCACGCTGAGGTATTTTTTTAAATTTCTGTTTTTTTTCAAAAAATCAACTCATAATACAGAGG
127 GGTCACGCCGAGGTATTTTTTTAAATTTCTGTTTTTTTTC-AAAAATCAACTCATAATACAGAGG
*
42768605 TGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTTTTAAAT
191 TGAGTTGAGCCTCGGGTCACGCCGAGGTATTT-TTTTAAAT
* *
42768646 TTTTGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGATAT
1 TTTTGTTTTTCAAAAATTAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT
* *
42768711 TTCTTTTAAATTTTTGTTTTTAAAAAAAAAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCG
66 TTCTTTTAAATTTCTGTTTTT----AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
* *
42768776 GGTCACGCTGAGGTATTTTTTTTAATTTCTGTTTTTTTTCAAAAATTCAACTCATAATACAGAGG
127 GGTCACGCCGAGGTATTTTTTTAAATTTCTGTTTTTTTTCAAAAA-TCAACTCATAATACAGAGG
**
42768841 TGAGTTGAGCCTCGGGTCACGCTAAGGTATTTTTTTAAAT
191 TGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTTTTAAAT
* * *
42768881 TTCTGTTTTTTTCAAAAAATTAACTCATAATACAGAGGTGAGTTGAGTCACGGGTCATGCCGAGG
1 TT-T-TGTTTTTC-AAAAATTAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGG
* * * *
42768946 TATTTCTTTTAAATTTCCGTTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAACCTCGG
63 TATTTCTTTTAAATTTCTGTTTTTAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
* *
42769010 GTCATGCCGAGGTATTTCTTTTAAATTT-TCG---TTTTTCAAAAATCAACTCATAATACGGAGG
128 GTCACGCCGAGGTATTT-TTTTAAATTTCT-GTTTTTTTTCAAAAATCAACTCATAATACAGAGG
* *
42769071 TGAGTTGAGCCTCGGGTCATGCCGAGTTATTTCTTTTAAAT
191 TGAGTTGAGCCTCGGGTCACGCCGAGGTATTT-TTTTAAAT
* * *
42769112 TTCTGTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCTGAGGTAT
1 TTTTGTTTTTCAAAAATTAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT
* * * **
42769177 TTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACC
66 TTCTTTTAAATTTCTGTTTTTAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC
** * *
42769242 ATACCGAGGTATTTCTTTTAAATTTCTG---TTTTTCAAAAATCAACTCATAATGCGAGAGATGA
131 ACGCCGAGGTATTT-TTTTAAATTTCTGTTTTTTTTCAAAAATCAACTCATAATAC-AGAGGTGA
*
42769304 GTTGAGCCTCGGGTCACGCCGAGGTA--TTTTTCAAT
194 GTTGAGCCTCGGGTCACGCCGAGGTATTTTTTTAAAT
** * ** * *
42769339 TCATGTTTTTCAAAAATTAACTCATATTGTTAGAGGTGAGTTGAGCCTCGGGGCACATGTCGAGG
1 TTTTGTTTTTCAAAAATTAACTCATAAT-ACAGAGGTGAGTTGAGCCTC-GGG-TCATGCCGAGG
** * *** * * * *
42769404 TA----TTTTCGATTTTTGTTTTGCGAAGATCAACTCATAATCCAAGAGGTGAGTTGAGTCTCGG
63 TATTTCTTTTAAATTTCTGTTTTTAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
42769465 GTCAC
128 GTCAC
42769470 ACGCCGAGCT
Statistics
Matches: 739, Mismatches: 71, Indels: 37
0.87 0.08 0.04
Matches are distributed among these distances:
226 50 0.07
227 31 0.04
228 107 0.14
229 78 0.11
230 87 0.12
231 21 0.03
233 34 0.05
234 28 0.04
235 19 0.03
236 208 0.28
237 7 0.01
238 69 0.09
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (230 bp):
TTTTGTTTTTCAAAAATTAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTAT
TTCTTTTAAATTTCTGTTTTTAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC
ACGCCGAGGTATTTTTTTAAATTTCTGTTTTTTTTCAAAAATCAACTCATAATACAGAGGTGAGT
TGAGCCTCGGGTCACGCCGAGGTATTTTTTTAAAT
Found at i:42769706 original size:30 final size:31
Alignment explanation
Indices: 42769665--42769801 Score: 142
Period size: 30 Copynumber: 4.6 Consensus size: 31
42769655 GTTTTTTTTG
* *
42769665 CATTTTAACCCCTATACTTTTC-AAAATTTA
1 CATTTTGACCCCTAAACTTTTCTAAAATTTA
42769695 CATTTTGACCCC-AAACTTTTCTAAAATTTA
1 CATTTTGACCCCTAAACTTTTCTAAAATTTA
*
42769725 CATTTTGACCCCAAAAC-TTTCTAAAA-TTA
1 CATTTTGACCCCTAAACTTTTCTAAAATTTA
* * * *
42769754 CATTTCGACCCTTAGACTTTT-TCAAAA-TTG
1 CATTTTGACCCCTAAACTTTTCT-AAAATTTA
* *
42769784 CACTTTGACCCTTAAACT
1 CATTTTGACCCCTAAACT
42769802 CTTAAGAAAT
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
29 25 0.27
30 64 0.69
31 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (31 bp):
CATTTTGACCCCTAAACTTTTCTAAAATTTA
Found at i:42769772 original size:29 final size:28
Alignment explanation
Indices: 42769683--42769818 Score: 98
Period size: 30 Copynumber: 4.6 Consensus size: 28
42769673 CCCCTATACT
*
42769683 TTTC-AAAATTTACATTTTGACCC-CAAAC
1 TTTCTAAAA-TTACA-TTTGACCCTTAAAC
**
42769711 TTTTCTAAAATTTACATTTTGACCCCAAAAC
1 -TTTCTAAAA-TTACA-TTTGACCCTTAAAC
*
42769742 TTTCTAAAATTACATTTCGACCCTTAGAC
1 TTTCTAAAATTACATTT-GACCCTTAAAC
* *
42769771 TTTTTCAAAATTGCACTTTGACCCTTAAAC
1 TTTCT-AAAATTACA-TTTGACCCTTAAAC
*
42769801 TCTT-AAGAAATTACATTT
1 T-TTCTA-AAATTACATTT
42769819 TGGCCCATAT
Statistics
Matches: 91, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
28 3 0.03
29 25 0.27
30 54 0.59
31 9 0.10
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (28 bp):
TTTCTAAAATTACATTTGACCCTTAAAC
Found at i:42770193 original size:20 final size:20
Alignment explanation
Indices: 42770163--42770202 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
42770153 CTACACTTAG
42770163 CAAAGCAAGCAAGAATCCAAA
1 CAAAGCAAGCAA-AATCCAAA
42770184 CAAA-CAAGCAAAATCCAAA
1 CAAAGCAAGCAAAATCCAAA
42770203 AGAAAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 7 0.37
21 4 0.21
ACGTcount: A:0.60, C:0.25, G:0.10, T:0.05
Consensus pattern (20 bp):
CAAAGCAAGCAAAATCCAAA
Found at i:42770230 original size:20 final size:21
Alignment explanation
Indices: 42770193--42770232 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42770183 ACAAACAAGC
*
42770193 AAAATCCAAAAGAAAAGAGAG
1 AAAACCCAAAAGAAAAGAGAG
42770214 AAAACCCAAAA-AAAAGAGA
1 AAAACCCAAAAGAAAAGAGA
42770233 CAAAGAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.70, C:0.12, G:0.15, T:0.03
Consensus pattern (21 bp):
AAAACCCAAAAGAAAAGAGAG
Found at i:42770379 original size:11 final size:11
Alignment explanation
Indices: 42770363--42770465 Score: 87
Period size: 11 Copynumber: 9.7 Consensus size: 11
42770353 GAGCGACCCG
42770363 AAAAAGAAGGA
1 AAAAAGAAGGA
*
42770374 AAAAAGAAAGA
1 AAAAAGAAGGA
*
42770385 AAAAAGAAGTA
1 AAAAAGAAGGA
42770396 GAAAAAGAAGGA
1 -AAAAAGAAGGA
*
42770408 AAAAAGAAAGA
1 AAAAAGAAGGA
42770419 AAAGAA-AA-G-
1 AAA-AAGAAGGA
42770428 AAAAAGAA--A
1 AAAAAGAAGGA
42770437 AAAGAAGAA-G-
1 AAA-AAGAAGGA
42770447 AAAAAG-AGAGA
1 AAAAAGAAG-GA
42770458 AAAAAGAA
1 AAAAAGAA
42770466 AAGAAAAAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
8 3 0.04
9 11 0.14
10 10 0.13
11 40 0.52
12 13 0.17
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (11 bp):
AAAAAGAAGGA
Found at i:42770405 original size:34 final size:33
Alignment explanation
Indices: 42770362--42770476 Score: 140
Period size: 34 Copynumber: 3.3 Consensus size: 33
42770352 GGAGCGACCC
*
42770362 GAAAAAGAAGGAAAAAAGAAAGAAAAAAGAAGTA
1 GAAAAAGAAGGAAAAAAGAAAGAAAAAAGAA-AA
42770396 GAAAAAGAAGGAAAAAAGAAAGAAAAGAAAAGAAAAA
1 GAAAAAGAAGGAAAAAAGAAAG--AA-AAAAG-AAAA
* *
42770433 GAAAAAAGAAGAAGAAAAAGAGAGAAAAAAGAAAA
1 G-AAAAAGAAGGA-AAAAAGAAAGAAAAAAGAAAA
42770468 GAAAAAGAA
1 GAAAAAGAA
42770477 AAATCAACAG
Statistics
Matches: 72, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
34 30 0.42
35 5 0.07
36 7 0.10
37 9 0.12
38 12 0.17
39 9 0.12
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.01
Consensus pattern (33 bp):
GAAAAAGAAGGAAAAAAGAAAGAAAAAAGAAAA
Found at i:42770440 original size:50 final size:52
Alignment explanation
Indices: 42770372--42770479 Score: 161
Period size: 50 Copynumber: 2.1 Consensus size: 52
42770362 GAAAAAGAAG
*
42770372 GAAAAAAGAAAGAAAAAAGAAGTAGAAAAAGA-AGGAAAAAAG-AAAG-AAAA
1 GAAAAAAGAAAGAAAAAAGAAGAAGAAAAAGAGA-GAAAAAAGAAAAGAAAAA
42770422 GAAAAGAA-AAAGAAAAAAGAAGAAGAAAAAGAGAGAAAAAAGAAAAGAAAAA
1 GAAAA-AAGAAAGAAAAAAGAAGAAGAAAAAGAGAGAAAAAAGAAAAGAAAAA
42770474 GAAAAA
1 GAAAAA
42770480 TCAACAGTCG
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
50 36 0.68
51 8 0.15
52 9 0.17
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (52 bp):
GAAAAAAGAAAGAAAAAAGAAGAAGAAAAAGAGAGAAAAAAGAAAAGAAAAA
Found at i:42770472 original size:11 final size:11
Alignment explanation
Indices: 42770374--42770478 Score: 82
Period size: 11 Copynumber: 9.9 Consensus size: 11
42770364 AAAAGAAGGA
42770374 AAAAAG-AAAG
1 AAAAAGAAAAG
*
42770384 AAAAAAGAAGTAG
1 -AAAAAGAA-AAG
*
42770397 AAAAAG-AAGG
1 AAAAAGAAAAG
42770407 AAAAA-AGAAAG
1 AAAAAGA-AAAG
42770418 -AAAAGAAAAG
1 AAAAAGAAAAG
42770428 AAAAAGAAAA-
1 AAAAAGAAAAG
*
42770438 AAGAAG--AAG
1 AAAAAGAAAAG
*
42770447 AAAAAG-AGAG
1 AAAAAGAAAAG
42770457 AAAAAAGAAAAG
1 -AAAAAGAAAAG
42770469 AAAAAGAAAA
1 AAAAAGAAAA
42770479 ATCAACAGTC
Statistics
Matches: 76, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
8 2 0.03
9 5 0.07
10 21 0.28
11 36 0.47
12 10 0.13
13 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:42770599 original size:14 final size:13
Alignment explanation
Indices: 42770575--42770629 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
42770565 AAAGCAGCTC
42770575 AAAAAAA-A-AAA
1 AAAAAAACAGAAA
*
42770586 ACAAAAACAGAAA
1 AAAAAAACAGAAA
*
42770599 AAAAATAGCAG-AA
1 AAAAA-AACAGAAA
*
42770612 AAAAAAAGAGAAA
1 AAAAAAACAGAAA
42770625 AAAAA
1 AAAAA
42770630 CAAAGCAGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 6 0.17
12 4 0.11
13 21 0.60
14 4 0.11
ACGTcount: A:0.84, C:0.05, G:0.09, T:0.02
Consensus pattern (13 bp):
AAAAAAACAGAAA
Found at i:42771291 original size:21 final size:21
Alignment explanation
Indices: 42771266--42771312 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
42771256 TCCCGTGGTC
*
42771266 AAAAATTTCGAGTTTT-A-AAA
1 AAAAAATT-GAGTTTTCACAAA
42771286 AAAAAATTGAGTTTTCACAAA
1 AAAAAATTGAGTTTTCACAAA
42771307 AAAAAA
1 AAAAAA
42771313 GAAGAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 7 0.29
20 8 0.33
21 9 0.38
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (21 bp):
AAAAAATTGAGTTTTCACAAA
Found at i:42771352 original size:18 final size:17
Alignment explanation
Indices: 42771318--42771679 Score: 143
Period size: 17 Copynumber: 20.2 Consensus size: 17
42771308 AAAAAGAAGA
42771318 AAAAATTCTCGTG-TTTC
1 AAAAATT-TCGTGTTTTC
42771335 AAAGAATTTCGTGTTTTC
1 AAA-AATTTCGTGTTTTC
*
42771353 AAAAAATTC-TCGTTTT-
1 AAAAATTTCGT-GTTTTC
*
42771369 AAAAATTTTCTTGTTTTC
1 AAAAA-TTTCGTGTTTTC
42771387 AAAAATTTTCGTG-TTTC
1 AAAAA-TTTCGTGTTTTC
*
42771404 AAAAATCCTCGTGTTTTC
1 AAAAAT-TTCGTGTTTTC
** *
42771422 AAAAATCCCG-GTGCTTC
1 AAAAATTTCGTGT-TTTC
* *
42771439 AAAAAAATTTTGTGTTCTC
1 --AAAAATTTCGTGTTTTC
* *
42771458 AAAAATTCCGATG--ATC
1 AAAAATTTCG-TGTTTTC
*
42771474 AAAATTTTTTTTTCGTGTTTTC
1 AAAA-----ATTTCGTGTTTTC
*
42771496 TAAAAAAATTCCGTG-TTTC
1 ---AAAAATTTCGTGTTTTC
42771515 AAAAATTTTCGTGTTTTTC
1 AAAAA-TTTCGTG-TTTTC
* *
42771534 AACAATTCTCGT-ATTTC
1 AAAAATT-TCGTGTTTTC
*
42771551 AAAAATTTTCGCG-TTTC
1 AAAAA-TTTCGTGTTTTC
** **
42771568 AAAAAAAAATATTGTTTTC
1 --AAAAATTTCGTGTTTTC
* *
42771587 AAAAATTGTCGTGTTCTA
1 AAAAATT-TCGTGTTTTC
*
42771605 AAAAATATTCGTGTTTTT
1 AAAAAT-TTCGTGTTTTC
* *
42771623 AAGAATTTTCGTG-TCTC
1 AA-AAATTTCGTGTTTTC
* * *
42771640 TAAAATTCTAGTGTTTTAA
1 AAAAATT-TCGTGTTTT-C
42771659 AAAAATTTCGTGTTTTC
1 AAAAATTTCGTGTTTTC
42771676 AAAA
1 AAAA
42771680 TAAAATTTGT
Statistics
Matches: 259, Mismatches: 48, Indels: 76
0.68 0.13 0.20
Matches are distributed among these distances:
16 24 0.09
17 91 0.35
18 80 0.31
19 44 0.17
20 10 0.04
21 4 0.02
22 2 0.01
25 4 0.02
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:42771357 original size:36 final size:35
Alignment explanation
Indices: 42771317--42771679 Score: 191
Period size: 36 Copynumber: 10.1 Consensus size: 35
42771307 AAAAAAGAAG
42771317 AAAAAATTCTCGTGTTTCAAAGAATTTCGTGTTTTC
1 AAAAAATTCTCGTGTTTCAAA-AATTTCGTGTTTTC
*
42771353 AAAAAATTCTCGT-TTT-AAAAATTTTCTTGTTTTC
1 AAAAAATTCTCGTGTTTCAAAAA-TTTCGTGTTTTC
* *
42771387 -AAAAATTTTCGTGTTTCAAAAATCCTCGTGTTTTC
1 AAAAAATTCTCGTGTTTCAAAAAT-TTCGTGTTTTC
* * * *
42771422 -AAAAA-TCCCGGTGCTTCAAAAAAATTTTGTGTTCTC
1 AAAAAATTCTC-GTGTTTC--AAAAATTTCGTGTTTTC
* *
42771458 -AAAAATTC-CGATG-ATCAAAATTTTTTTTTCGTGTTTTC
1 AAAAAATTCTCG-TGTTTCAAAA-----ATTTCGTGTTTTC
42771496 TAAAAAAATTC-CGTGTTTCAAAAATTTTCGTGTTTTTC
1 --AAAAAATTCTCGTGTTTCAAAAA-TTTCGTG-TTTTC
* * *
42771534 -AACAATTCTCGTATTTCAAAAATTTTCGCG-TTTC
1 AAAAAATTCTCGTGTTTCAAAAA-TTTCGTGTTTTC
* * * *
42771568 AAAAAAAAATATTGT-TTTCAAAAATTGTCGTGTTCT-
1 --AAAAAATTCTCGTGTTTCAAAAATT-TCGTGTTTTC
* * *
42771604 AAAAAATAT-TCGTGTTTTTAAGAATTTTCGTG-TCTC
1 AAAAAAT-TCTCGTG-TTTCAA-AAATTTCGTGTTTTC
* * *
42771640 -TAAAATTCTAGTGTTTTAAAAAAATTTCGTGTTTTC
1 AAAAAATTCTCGTG-TTT-CAAAAATTTCGTGTTTTC
42771676 AAAA
1 AAAA
42771680 TAAAATTTGT
Statistics
Matches: 257, Mismatches: 35, Indels: 69
0.71 0.10 0.19
Matches are distributed among these distances:
33 17 0.07
34 34 0.13
35 66 0.26
36 76 0.30
37 31 0.12
38 15 0.06
40 2 0.01
41 16 0.06
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (35 bp):
AAAAAATTCTCGTGTTTCAAAAATTTCGTGTTTTC
Found at i:42772344 original size:25 final size:25
Alignment explanation
Indices: 42772293--42772372 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
42772283 CCTCTCTCAT
* * * **
42772293 GCCATATAACAGGAAGCTCATGTGA
1 GCCATGTAACGGGAAGCTTATAAGA
* **
42772318 GCCATGTATCGGGAAGCTTATTCGA
1 GCCATGTAACGGGAAGCTTATAAGA
** *
42772343 GCTGTTTAACGGGAAGCTTATAAGA
1 GCCATGTAACGGGAAGCTTATAAGA
42772368 GCCAT
1 GCCAT
42772373 AATCAGAAAG
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (25 bp):
GCCATGTAACGGGAAGCTTATAAGA
Found at i:42772441 original size:25 final size:25
Alignment explanation
Indices: 42772413--42772529 Score: 93
Period size: 25 Copynumber: 4.7 Consensus size: 25
42772403 GTAGCTCCGA
42772413 AGAGCCATTAATCAGGAAGCTTCAG
1 AGAGCCATTAATCAGGAAGCTTCAG
* *
42772438 AGAGCTA-TATATCGGGAAG-TTCA-
1 AGAGCCATTA-ATCAGGAAGCTTCAG
*
42772461 AGCAAGCCA-T-ATCGGGAAGCTTC-G
1 AG--AGCCATTAATCAGGAAGCTTCAG
* *
42772485 AAGAGCCATTAATCAGGAAGCTCACAA
1 -AGAGCCATTAATCAGGAAGCT-TCAG
*
42772512 AGAGCCTTTAATCAGGAA
1 AGAGCCATTAATCAGGAA
42772530 AATCACGAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
23 16 0.21
24 10 0.13
25 31 0.41
26 18 0.24
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (25 bp):
AGAGCCATTAATCAGGAAGCTTCAG
Found at i:42772491 original size:23 final size:22
Alignment explanation
Indices: 42772412--42772493 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 22
42772402 GGTAGCTCCG
*
42772412 AAGAGCCATTAATCAGGAAGCTTC
1 AAGAGCCA-T-ATCGGGAAGCTTC
*
42772436 AGAGAGCTATATATCGGGAAG-TTC
1 A-AGAGC--CATATCGGGAAGCTTC
42772460 AAGCAAGCCATATCGGGAAGCTTC
1 AAG--AGCCATATCGGGAAGCTTC
42772484 GAAGAGCCAT
1 -AAGAGCCAT
42772494 TAATCAGGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
23 19 0.40
24 8 0.17
25 19 0.40
26 1 0.02
27 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (22 bp):
AAGAGCCATATCGGGAAGCTTC
Found at i:42772517 original size:26 final size:26
Alignment explanation
Indices: 42772485--42772545 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
42772475 GGAAGCTTCG
**
42772485 AAGAGCCATTAATCAGGAAGCTCACA
1 AAGAGCCATTAATCAGGAAAATCACA
* *
42772511 AAGAGCCTTTAATCAGGAAAATCACG
1 AAGAGCCATTAATCAGGAAAATCACA
42772537 AAGAGCCAT
1 AAGAGCCAT
42772546 ATATCGAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.16
Consensus pattern (26 bp):
AAGAGCCATTAATCAGGAAAATCACA
Found at i:42775191 original size:13 final size:13
Alignment explanation
Indices: 42775173--42775197 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42775163 GAGCCCCCAA
42775173 CTAAGTTGGTGTC
1 CTAAGTTGGTGTC
42775186 CTAAGTTGGTGT
1 CTAAGTTGGTGT
42775198 AATGAGTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.32, T:0.40
Consensus pattern (13 bp):
CTAAGTTGGTGTC
Found at i:42783321 original size:23 final size:23
Alignment explanation
Indices: 42783286--42783394 Score: 148
Period size: 23 Copynumber: 4.7 Consensus size: 23
42783276 ACACTAATAT
* *
42783286 TAGCCGAAGCTACCACTGATATG
1 TAGCTGAAGCTACCACTGAAATG
42783309 TAGCTGTAA-CTACCACTGAAATG
1 TAGCTG-AAGCTACCACTGAAATG
* *
42783332 TAGCCGAAGCTACCACTGATATG
1 TAGCTGAAGCTACCACTGAAATG
* *
42783355 TAGCTGTAGCTACCATTGAAATG
1 TAGCTGAAGCTACCACTGAAATG
42783378 TAGCTGAAGCTACCACT
1 TAGCTGAAGCTACCACT
42783395 AATCAATAAC
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
22 2 0.03
23 70 0.95
24 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (23 bp):
TAGCTGAAGCTACCACTGAAATG
Found at i:42783353 original size:46 final size:46
Alignment explanation
Indices: 42783286--42783394 Score: 191
Period size: 46 Copynumber: 2.4 Consensus size: 46
42783276 ACACTAATAT
42783286 TAGCCGAAGCTACCACTGATATGTAGCTGTAACTACCACTGAAATG
1 TAGCCGAAGCTACCACTGATATGTAGCTGTAACTACCACTGAAATG
* *
42783332 TAGCCGAAGCTACCACTGATATGTAGCTGTAGCTACCATTGAAATG
1 TAGCCGAAGCTACCACTGATATGTAGCTGTAACTACCACTGAAATG
*
42783378 TAGCTGAAGCTACCACT
1 TAGCCGAAGCTACCACT
42783395 AATCAATAAC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (46 bp):
TAGCCGAAGCTACCACTGATATGTAGCTGTAACTACCACTGAAATG
Found at i:42787212 original size:38 final size:38
Alignment explanation
Indices: 42787154--42787226 Score: 87
Period size: 36 Copynumber: 1.9 Consensus size: 38
42787144 ATTTAATCCA
*
42787154 TTTTTTAAAAAAACTTTTATTTTATT-TA-ATTATTAT
1 TTTTTTAAAAAAACTTTTATTATATTATATATTATTAT
* *
42787190 TTTTTTTAAAAAGCATTATTATTATATTATATATTAT
1 TTTTTTAAAAAAAC-TT-TTATTATATTATATATTAT
42787227 CATTATTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 12 0.40
37 2 0.07
38 9 0.30
39 2 0.07
40 5 0.17
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (38 bp):
TTTTTTAAAAAAACTTTTATTATATTATATATTATTAT
Found at i:42787239 original size:12 final size:12
Alignment explanation
Indices: 42787203--42787244 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
42787193 TTTTAAAAAG
42787203 CATTATTATTAT
1 CATTATTATTAT
42787215 -ATTATATATTAT
1 CATTAT-TATTAT
*
42787227 CATTATTACTAT
1 CATTATTATTAT
42787239 CATTAT
1 CATTAT
42787245 CTTTGTATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (12 bp):
CATTATTATTAT
Found at i:42787578 original size:16 final size:17
Alignment explanation
Indices: 42787546--42787580 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
42787536 CCACTCTCAT
42787546 ATTTTATAATGCATATAC
1 ATTTTATAA-GCATATAC
42787564 ATTTTATAA-CATATAC
1 ATTTTATAAGCATATAC
42787580 A
1 A
42787581 CCTTCCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (17 bp):
ATTTTATAAGCATATAC
Found at i:42789438 original size:8 final size:8
Alignment explanation
Indices: 42789425--42789465 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
42789415 TAAAAGTTAC
42789425 AAAAAATA
1 AAAAAATA
42789433 AAAAAATA
1 AAAAAATA
* *
42789441 TAAATATA
1 AAAAAATA
42789449 AATAAAATA
1 AA-AAAATA
42789458 AAAAAATA
1 AAAAAATA
42789466 TTAATTACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAAAATA
Found at i:42791025 original size:8 final size:8
Alignment explanation
Indices: 42791012--42791052 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
42791002 TAAAAGTTAC
42791012 AAAAAATA
1 AAAAAATA
42791020 AAAAAATA
1 AAAAAATA
* *
42791028 TAAATATA
1 AAAAAATA
42791036 AATAAAATA
1 AA-AAAATA
42791045 AAAAAATA
1 AAAAAATA
42791053 TTAATTACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAAAATA
Found at i:42793575 original size:19 final size:19
Alignment explanation
Indices: 42793551--42793597 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
42793541 AACGTCTCTT
*
42793551 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
42793570 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
42793589 TATGCATTA
1 TTTGCATTA
42793598 AACACCGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:42796448 original size:7 final size:7
Alignment explanation
Indices: 42796423--42796464 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
42796413 GTGATGTGAA
42796423 AAAAATG
1 AAAAATG
42796430 AAAAGATG
1 AAAA-ATG
42796438 -AAAATG
1 AAAAATG
42796444 AAAAATG
1 AAAAATG
42796451 AAAAA-G
1 AAAAATG
42796457 TAAAAATG
1 -AAAAATG
42796465 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.13
7 23 0.74
8 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:42796462 original size:21 final size:21
Alignment explanation
Indices: 42796423--42796464 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42796413 GTGATGTGAA
*
42796423 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAGATAAAAATG
42796444 AAAAATGAAAA-AGTAAAAATG
1 AAAAATGAAAAGA-TAAAAATG
42796465 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAATG
Found at i:42797937 original size:44 final size:44
Alignment explanation
Indices: 42797740--42798639 Score: 876
Period size: 44 Copynumber: 20.4 Consensus size: 44
42797730 GCTAAAAAGC
* * *
42797740 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
*** * ***
42797784 AGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCGAAGAT
*** * *
42797829 AATTGATCTTGTCTTCATGTATTGACACGGAGTAGATC-AGAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGAT
42797873 A-CAGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGAT
* *
42797916 AGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGGT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
** * *
42797960 AGTGGATCTTATCTTTATGTATTGACATGAAGTAGATC-AGAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGAT
*
42798004 AGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
** * *
42798048 AATAGATATTGTCTTCATGTATTGACATGAAGTAGGTC-AGAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGAT
* * * *
42798092 AGAAGATCTTATCTTCATGTATTAACATGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
***
42798136 AATGGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGAT
* *** *
42798180 AGCAGATCTTGTCTTCATGTACTGGTGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
* * * * *
42798224 AGCATATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
* * * *
42798268 AGTAGATCTTGTCTTCCTGTACT-AGCAATGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCATGTATTGA-C-ATGAAGTAGATCGAAGAT
* * ** * *
42798313 AACAGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTT--CAT-GTATTGACATGAAGTAGATCGAAGAT
* *
42798358 AGCAGATCTTGTCTTCATGT-TTTAGCGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTATTGA-CATGAAGTAGATCGAAGAT
*
42798402 AGCAGATCTTGTCTTCATGCATTGGA-ATGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTATT-GACATGAAGTAGATCGAAGAT
* ** *
42798446 AGCAGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTT--CAT-GTATTGACATGAAGTAGATCGAAGAT
* * * *
42798491 AGTAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
* ** *
42798535 AGCAGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTT--CAT-GTATTGACATGAAGTAGATCGAAGAT
* * * *
42798580 AGTAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
42798624 AGCAGATCTTGTCTTC
1 AGCAGATCTTGTCTTC
42798640 CCATACTGGT
Statistics
Matches: 720, Mismatches: 104, Indels: 64
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.00
42 12 0.02
43 52 0.07
44 481 0.67
45 155 0.22
46 8 0.01
47 8 0.01
48 3 0.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (44 bp):
AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
Found at i:42807556 original size:106 final size:104
Alignment explanation
Indices: 42807446--42807769 Score: 410
Period size: 106 Copynumber: 3.1 Consensus size: 104
42807436 TTTTATTGTG
42807446 ATTTTTTATGAATGTAAATTTTTAAAAATTATTTT-TTAGTATTTATGATTAGGTTATAAATTGT
1 ATTTTTT-TGAATGT--ATTTTTAAAAATTATTTTGTTAGTATTTATGATTAGGTTATAAATTGT
* * * *
42807510 TTGTGTTTAGTTTAGTGTTTTATTGTGATTTTTTAAGAATG-C
63 TTGTGTTTAGTTTAGTG-TTTATTTTTATTTTTTATGAATGTA
* *
42807552 ATTTTTTTAAAT-TA-TTTT-AAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTT
1 ATTTTTTTGAATGTATTTTTAAAAATTATTTTGTTAGT-ATTTATGATTAGGTTATAAATTGTTT
* * *
42807614 GTGTTTAATTTAGTGTTTATTTTTAATTTTTATGAAGGTA
65 GTGTTTAGTTTAGTGTTTATTTTTATTTTTTATGAATGTA
* *
42807654 AGTTTTTTTG-GT-TTTTTTTAAAAAAATTATTTTGTTAGTAGTTTATGATTAGGTTATAAATTG
1 A-TTTTTTTGAATGTATTTTT--AAAAATTATTTTGTTAGTA-TTTATGATTAGGTTATAAATTG
42807717 TTTGTGTTTAGTTTAGTGTTTATTTTTATTTTTTATGAATGTA
62 TTTGTGTTTAGTTTAGTGTTTATTTTTATTTTTTATGAATGTA
42807760 ATTTTATTTG
1 ATTTT-TTTG
42807770 TTTTTGATTT
Statistics
Matches: 192, Mismatches: 16, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
100 10 0.05
101 27 0.14
102 44 0.23
103 11 0.06
104 1 0.01
105 9 0.05
106 90 0.47
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (104 bp):
ATTTTTTTGAATGTATTTTTAAAAATTATTTTGTTAGTATTTATGATTAGGTTATAAATTGTTTG
TGTTTAGTTTAGTGTTTATTTTTATTTTTTATGAATGTA
Found at i:42807648 original size:53 final size:53
Alignment explanation
Indices: 42807589--42807754 Score: 135
Period size: 53 Copynumber: 3.1 Consensus size: 53
42807579 TTGTTAGTAA
42807589 TTTATGATTAGGTTATAAATTGTTTGTGTTTAATTTAGTGTTTATTTTTAATT
1 TTTATGATTAGGTTATAAATTGTTTGTGTTTAATTTAGTGTTTATTTTTAATT
** * ** **** * *
42807642 TTTATGA--AGG-TA-AGTTTTTTTG-GTTTTTTTTAAAAAAATTATTTTGTTAGTAG
1 TTTATGATTAGGTTATAAATTGTTTGTGTTTAATTT--AGTGTTTA-TTT-TTAAT-T
* *
42807695 TTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTTAGTGTTTATTTTTATTT
1 TTTATGATTAGGTTATAAATTGTTTGTGTTTAATTTAGTGTTTATTTTTAATT
42807748 TTTATGA
1 TTTATGA
42807755 ATGTAATTTT
Statistics
Matches: 81, Mismatches: 22, Indels: 20
0.66 0.18 0.16
Matches are distributed among these distances:
48 7 0.09
49 7 0.09
50 6 0.07
51 6 0.07
52 4 0.05
53 21 0.26
54 4 0.05
55 6 0.07
56 6 0.07
57 7 0.09
58 7 0.09
ACGTcount: A:0.25, C:0.00, G:0.16, T:0.59
Consensus pattern (53 bp):
TTTATGATTAGGTTATAAATTGTTTGTGTTTAATTTAGTGTTTATTTTTAATT
Found at i:42808066 original size:21 final size:22
Alignment explanation
Indices: 42808015--42808067 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
42808005 TTGTTGTAAT
* *
42808015 TATATTATTATTGTACTATATT
1 TATAATATTATTGTACTATATG
** *
42808037 TATCGTATTATT-TACTGTATG
1 TATAATATTATTGTACTATATG
42808058 TATAATATTA
1 TATAATATTA
42808068 ATGGGTTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.55
Consensus pattern (22 bp):
TATAATATTATTGTACTATATG
Found at i:42810329 original size:48 final size:47
Alignment explanation
Indices: 42810231--42810334 Score: 145
Period size: 48 Copynumber: 2.2 Consensus size: 47
42810221 GTATTTATTT
* * * *
42810231 AATTGAGATTCATTGCAACATTAAAAATAGAACAAACTTTGTAATTTA
1 AATT-AGATTAATTGCAACATTAAAAAGAGAACAAAATTTGTAATATA
*
42810279 AATTAGATTAATTGCAACATTAAAACGAGGAACAAAATTTGTAATATA
1 AATTAGATTAATTGCAACATTAAAAAGA-GAACAAAATTTGTAATATA
42810327 AATTAGAT
1 AATTAGAT
42810335 ACATTGGAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
47 21 0.42
48 29 0.58
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.32
Consensus pattern (47 bp):
AATTAGATTAATTGCAACATTAAAAAGAGAACAAAATTTGTAATATA
Found at i:42811019 original size:26 final size:26
Alignment explanation
Indices: 42810989--42811040 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
42810979 GTAGCCGAGA
*
42810989 ACATAGATAAAATTAGAAGATGTCGT
1 ACATAGATAAAATCAGAAGATGTCGT
42811015 ACATAGATAAAATCAGAAGATGTCGT
1 ACATAGATAAAATCAGAAGATGTCGT
42811041 TTTTTCATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (26 bp):
ACATAGATAAAATCAGAAGATGTCGT
Found at i:42815466 original size:42 final size:42
Alignment explanation
Indices: 42815384--42815513 Score: 136
Period size: 42 Copynumber: 3.1 Consensus size: 42
42815374 CAGAGAAACA
* * * *
42815384 CATAAGTGCTAAACAGAAACCTATAAAGGTTGAACGGAAGCT
1 CATAAGAGCTAAACAGAAACCCATAAGGGTTAAACGGAAGCT
* *
42815426 CATAAGAGCTGAAC-GAAAGCCCATAAGGGTTAAACTGAAGCT
1 CATAAGAGCTAAACAGAAA-CCCATAAGGGTTAAACGGAAGCT
* * * * * *
42815468 CAAAATAACTAAACAGAAACCCATTAGGGTTAAACGAAAACT
1 CATAAGAGCTAAACAGAAACCCATAAGGGTTAAACGGAAGCT
42815510 CATA
1 CATA
42815514 TGAGTTAACT
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
41 4 0.06
42 63 0.89
43 4 0.06
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (42 bp):
CATAAGAGCTAAACAGAAACCCATAAGGGTTAAACGGAAGCT
Found at i:42816913 original size:11 final size:11
Alignment explanation
Indices: 42816877--42816912 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
42816867 GCTGTTACAC
42816877 AAAATTAATTA
1 AAAATTAATTA
42816888 AAAATTAATTA
1 AAAATTAATTA
*
42816899 AAAACTAA-TA
1 AAAATTAATTA
42816909 AAAA
1 AAAA
42816913 AATTACATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (11 bp):
AAAATTAATTA
Found at i:42816973 original size:17 final size:18
Alignment explanation
Indices: 42816947--42816985 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
42816937 CACAATAAAC
42816947 ATTAAACTAAACA-AAAA
1 ATTAAACTAAACACAAAA
* *
42816964 ATTAACCTAATCACAAAA
1 ATTAAACTAAACACAAAA
42816982 ATTA
1 ATTA
42816986 CAAACAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (18 bp):
ATTAAACTAAACACAAAA
Found at i:42816979 original size:19 final size:20
Alignment explanation
Indices: 42816934--42816982 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
42816924 TAACCTAACA
42816934 AATCACAATAAACATTAAACT
1 AATCACAA-AAACATTAAACT
*
42816955 AA--ACAAAAA-ATTAACCT
1 AATCACAAAAACATTAAACT
42816972 AATCACAAAAA
1 AATCACAAAAA
42816983 TTACAAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 9 0.36
18 3 0.12
19 11 0.44
21 2 0.08
ACGTcount: A:0.63, C:0.18, G:0.00, T:0.18
Consensus pattern (20 bp):
AATCACAAAAACATTAAACT
Found at i:42817067 original size:113 final size:114
Alignment explanation
Indices: 42816875--42817079 Score: 315
Period size: 113 Copynumber: 1.8 Consensus size: 114
42816865 AGGCTGTTAC
* *
42816875 ACAAAATTAATTAAAAATTAATTAAAAACTAATAAAAAAATTACATTCATAACCTAACAAATCAC
1 ACAAAATTAATTAAAAATAAATTAAAAACTAATAAAAAAATTACATTCATAACCGAACAAATCAC
42816940 AATAAACATTAAACTAAACAAAAAATTAACCTAATCACAAAAATTACAA
66 AATAAACATTAAACTAAACAAAAAATTAACCTAATCACAAAAATTACAA
* * * * *
42816989 ACAAAA-TAAGTTTAAAATAAATTAAAAATTAAT-AAAAATTTATATTTATAACCGAACAAATCA
1 ACAAAATTAA-TTAAAAATAAATTAAAAACTAATAAAAAAATTACATTCATAACCGAACAAATCA
*
42817052 CAATAAACATTAAACTAAACAAATAATT
65 CAATAAACATTAAACTAAACAAAAAATT
42817080 TATAATAGTT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
113 56 0.68
114 26 0.32
ACGTcount: A:0.60, C:0.13, G:0.01, T:0.26
Consensus pattern (114 bp):
ACAAAATTAATTAAAAATAAATTAAAAACTAATAAAAAAATTACATTCATAACCGAACAAATCAC
AATAAACATTAAACTAAACAAAAAATTAACCTAATCACAAAAATTACAA
Found at i:42817108 original size:105 final size:108
Alignment explanation
Indices: 42816875--42817132 Score: 299
Period size: 113 Copynumber: 2.3 Consensus size: 108
42816865 AGGCTGTTAC
* * *
42816875 ACAAAATTAATTAAAAATTAATTAAAAACTAATAAAAAAATTACATTCATAACCTAACAAATCAC
1 ACAAAA-TAATTTAAAATAAATTAAAAACTAATAAAAAAATTACATTCATAACCGAACAAATCAC
42816940 AATAAACATTAAACTAAACAAAAAATTAACCTAATCACAAAAATTACAA
65 AATAAACATTAAACTAAACAAAAAATT-A--TAAT--CAAAAATTACAA
* * * *
42816989 ACAAAATAAGTTTAAAATAAATTAAAAATTAAT-AAAAATTTATATTTATAACCGAACAAATCAC
1 ACAAAATAA-TTTAAAATAAATTAAAAACTAATAAAAAAATTACATTCATAACCGAACAAATCAC
* * * *
42817053 AATAAACATTAAACTAAACAAATAATT-T-AT-AATAGTTACTA
65 AATAAACATTAAACTAAACAAAAAATTATAATCAAAAATTACAA
*
42817094 ACAAAATAACTTTAAAATAAATTAAAAACAACATAAAAA
1 ACAAAATAA-TTTAAAATAAATTAAAAACTA-ATAAAAA
42817133 CAACAATAAA
Statistics
Matches: 127, Mismatches: 14, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
105 36 0.28
106 2 0.02
107 4 0.03
108 2 0.02
109 1 0.01
113 56 0.44
114 26 0.20
ACGTcount: A:0.61, C:0.12, G:0.01, T:0.26
Consensus pattern (108 bp):
ACAAAATAATTTAAAATAAATTAAAAACTAATAAAAAAATTACATTCATAACCGAACAAATCACA
ATAAACATTAAACTAAACAAAAAATTATAATCAAAAATTACAA
Found at i:42823758 original size:27 final size:27
Alignment explanation
Indices: 42823720--42824052 Score: 307
Period size: 27 Copynumber: 12.4 Consensus size: 27
42823710 GTGATAACAG
* **
42823720 TCATTTGACCCTATGGTTGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
42823747 TCATTCTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
42823774 TTATTTTACCCTATGGGGATATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
42823801 TCATTTTACCCTATGGGGGTATTTC-A
1 TCATTTTACCCTATGGGGGTATTTCGA
* * ** *
42823827 GTCATTCTACCATACAGAGGTATTTC-A
1 -TCATTTTACCCTATGGGGGTATTTCGA
* * * * *
42823854 GCCACTCTACCATATGGGGGTATTTCGG
1 -TCATTTTACCCTATGGGGGTATTTCGA
* *
42823882 TTATTTTACCCTATGGGGGTATTTCAA
1 TCATTTTACCCTATGGGGGTATTTCGA
*
42823909 TCATTTTACCCTAT-GGGCTATTTC-A
1 TCATTTTACCCTATGGGGGTATTTCGA
* * *
42823934 GTAATTTTACCCTATGAGGGTATTTCGG
1 -TCATTTTACCCTATGGGGGTATTTCGA
*
42823962 TCATTCTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* ** * *
42823989 TCATTTCACCCTATAAGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGA
* * *
42824016 TTATTTTACTCTATGTGGGTATTTC-A
1 TCATTTTACCCTATGGGGGTATTTCGA
42824042 GTCATTTTACC
1 -TCATTTTACC
42824053 TATTTTGGGG
Statistics
Matches: 246, Mismatches: 54, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
25 1 0.00
26 23 0.09
27 222 0.90
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGA
Found at i:42827573 original size:19 final size:19
Alignment explanation
Indices: 42827549--42827605 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
42827539 TACCCAATGC
42827549 ATAAAAGACATTCGTTCAA
1 ATAAAAGACATTCGTTCAA
*
42827568 AT-AAA-ACA-T-GTGC--
1 ATAAAAGACATTCGTTCAA
42827581 ATAAAAGACATTCGTTCAA
1 ATAAAAGACATTCGTTCAA
42827600 ATAAAA
1 ATAAAA
42827606 CATGTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
13 2 0.07
14 3 0.10
15 6 0.20
16 2 0.07
17 6 0.20
18 3 0.10
19 8 0.27
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.25
Consensus pattern (19 bp):
ATAAAAGACATTCGTTCAA
Found at i:42827587 original size:32 final size:32
Alignment explanation
Indices: 42827546--42827610 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
42827536 TTGTACCCAA
42827546 TGCATAAAAGACATTCGTTCAAATAAAACATG
1 TGCATAAAAGACATTCGTTCAAATAAAACATG
42827578 TGCATAAAAGACATTCGTTCAAATAAAACATG
1 TGCATAAAAGACATTCGTTCAAATAAAACATG
42827610 T
1 T
42827611 TTATAGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.26
Consensus pattern (32 bp):
TGCATAAAAGACATTCGTTCAAATAAAACATG
Found at i:42828013 original size:72 final size:72
Alignment explanation
Indices: 42827915--42828053 Score: 242
Period size: 72 Copynumber: 1.9 Consensus size: 72
42827905 TTTATATATC
* *
42827915 TATATATATAATGTGGCTTGGCCACTAATTCAGAGCAAATCACTTCCTCCTTCACAAATATCCTA
1 TATATATATAACGTGGCTTAGCCACTAATTCAGAGCAAATCACTTCCTCCTTCACAAATATCCTA
42827980 AACCCAT
66 AACCCAT
* *
42827987 TATATATATAACGTGGCTTAGCCACTAATTCAGAGCAGATCACTTCCTCTTTCACAAATATCCTA
1 TATATATATAACGTGGCTTAGCCACTAATTCAGAGCAAATCACTTCCTCCTTCACAAATATCCTA
42828052 AA
66 AA
42828054 TTCATGCAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (72 bp):
TATATATATAACGTGGCTTAGCCACTAATTCAGAGCAAATCACTTCCTCCTTCACAAATATCCTA
AACCCAT
Found at i:42829220 original size:36 final size:38
Alignment explanation
Indices: 42829180--42829272 Score: 93
Period size: 38 Copynumber: 2.5 Consensus size: 38
42829170 TCAAGTATTG
* *
42829180 AAACAAGCAAAAAT-ATAA-AAGAAGAAGAAAAGAAAA
1 AAACAAGAAAAAATAAGAATAAGAAGAAGAAAAGAAAA
* *
42829216 AAACAAAGAAAAAATAAGAATAAGAATAAGAAAGGAAACA
1 AAAC-AAGAAAAAATAAGAATAAGAAGAAGAAAAGAAA-A
* *
42829256 AAA-AGGAAAAAAAAAGA
1 AAACAAGAAAAAATAAGA
42829273 TCATAGAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
36 4 0.09
37 9 0.19
38 15 0.32
39 15 0.32
40 4 0.09
ACGTcount: A:0.75, C:0.04, G:0.15, T:0.05
Consensus pattern (38 bp):
AAACAAGAAAAAATAAGAATAAGAAGAAGAAAAGAAAA
Found at i:42829281 original size:39 final size:39
Alignment explanation
Indices: 42829198--42829272 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
42829188 AAAAATATAA
* *
42829198 AAGAAGAAGAAAAGAAAAAAACAAAGAAAAAATAAGAAT
1 AAGAATAAGAAAAGAAAAAAACAAAGAAAAAAAAAGAAT
* * *
42829237 AAGAATAAGAAAGGAAACAAA-AAGGAAAAAAAAAGA
1 AAGAATAAGAAAAGAAAAAAACAAAGAAAAAAAAAGA
42829273 TCATAGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 13 0.42
39 18 0.58
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.04
Consensus pattern (39 bp):
AAGAATAAGAAAAGAAAAAAACAAAGAAAAAAAAAGAAT
Found at i:42836936 original size:12 final size:12
Alignment explanation
Indices: 42836844--42836936 Score: 65
Period size: 12 Copynumber: 7.8 Consensus size: 12
42836834 TAAAATAAAT
42836844 GAAAGAAAAAGA
1 GAAAGAAAAAGA
*
42836856 -ATAG-AAAA-A
1 GAAAGAAAAAGA
42836865 G-AAGAACAAAGTA
1 GAAAGAA-AAAG-A
*
42836878 GAACA-AAATAGA
1 GAA-AGAAAAAGA
42836890 G-AAGAAAACGAGA
1 GAAAGAAAA--AGA
42836903 GAAAGAAAAAGA
1 GAAAGAAAAAGA
42836915 GAAAGAAAAATGA
1 GAAAGAAAAA-GA
42836928 GAAA-AAAAA
1 GAAAGAAAAA
42836937 ATTAGGGTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 24
0.70 0.04 0.26
Matches are distributed among these distances:
9 3 0.05
10 6 0.09
11 10 0.15
12 20 0.31
13 15 0.23
14 10 0.15
15 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.22, T:0.04
Consensus pattern (12 bp):
GAAAGAAAAAGA
Found at i:42845418 original size:22 final size:25
Alignment explanation
Indices: 42845392--42845445 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
42845382 TTAAAAATTC
42845392 AATTTAAAAG-ATA-TAAT-ACAAT
1 AATTTAAAAGCATATTAATAACAAT
*
42845414 AATTT-CAAGCATATTTAATAACAAT
1 AATTTAAAAGCATA-TTAATAACAAT
42845439 AATTTAA
1 AATTTAA
42845446 TCAGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
24 4 0.16
25 10 0.40
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTTAAAAGCATATTAATAACAAT
Found at i:42850496 original size:18 final size:18
Alignment explanation
Indices: 42850465--42850499 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42850455 ACCATACATT
*
42850465 ATTGTGGACGAACCACTC
1 ATTGTGGACAAACCACTC
*
42850483 ATTGTGGATAAACCACT
1 ATTGTGGACAAACCACT
42850500 AGTGATAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (18 bp):
ATTGTGGACAAACCACTC
Found at i:42850863 original size:34 final size:34
Alignment explanation
Indices: 42850802--42850866 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
42850792 CATTACGGTA
* *
42850802 GCAATCATTATGCTTATAATAGTTTGATTCAGTG
1 GCAATCATTATGCCTATAACAGTTTGATTCAGTG
*
42850836 GCAATTATTATGCCTATAACA-TATTGATTCA
1 GCAATCATTATGCCTATAACAGT-TTGATTCA
42850867 ATAGCAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 1 0.04
34 26 0.96
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (34 bp):
GCAATCATTATGCCTATAACAGTTTGATTCAGTG
Found at i:42851409 original size:8 final size:8
Alignment explanation
Indices: 42851396--42851423 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
42851386 GATTTTTAAA
42851396 TATTATTT
1 TATTATTT
42851404 TATTATTT
1 TATTATTT
42851412 TATTATTT
1 TATTATTT
42851420 TATT
1 TATT
42851424 GTTTAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTATTT
Found at i:42857970 original size:19 final size:19
Alignment explanation
Indices: 42857946--42857983 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
42857936 CTCCATGACA
42857946 TTTTTAAGCAGGTTCTATT
1 TTTTTAAGCAGGTTCTATT
*
42857965 TTTTTAAGTAGGTTCTATT
1 TTTTTAAGCAGGTTCTATT
42857984 GTTGGTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.08, G:0.16, T:0.55
Consensus pattern (19 bp):
TTTTTAAGCAGGTTCTATT
Found at i:42860477 original size:17 final size:18
Alignment explanation
Indices: 42860446--42860479 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42860436 GAATTTTGTG
*
42860446 TTTATGTTTTGAGGGTTC
1 TTTATGTTTTCAGGGTTC
42860464 TTTAT-TTTTCAGGGTT
1 TTTATGTTTTCAGGGTT
42860480 TAGTTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.12, C:0.06, G:0.24, T:0.59
Consensus pattern (18 bp):
TTTATGTTTTCAGGGTTC
Found at i:42869907 original size:21 final size:21
Alignment explanation
Indices: 42869889--42869926 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
42869879 ATTTTAAACC
42869889 TTTTGTTA-ATT-TAAATAAA
1 TTTTGTTATATTATAAATAAA
42869908 TTTTGTTATATTATAAATA
1 TTTTGTTATATTATAAATA
42869927 TTTTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTTGTTATATTATAAATAAA
Found at i:42869929 original size:19 final size:19
Alignment explanation
Indices: 42869889--42869934 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
42869879 ATTTTAAACC
42869889 TTTTGTTA-ATTTAAATAAA
1 TTTTGTTATATTTAAAT-AA
42869908 TTTTGTTATATTATAAAT-A
1 TTTTGTTATATT-TAAATAA
42869927 TTTT-TTAT
1 TTTTGTTAT
42869935 TTAAAAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.16
19 13 0.52
20 3 0.12
21 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTGTTATATTTAAATAA
Found at i:42870032 original size:21 final size:21
Alignment explanation
Indices: 42870008--42870052 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
42869998 TATATAAAAA
42870008 AAATTTTGA-ATTATAGA-ATTT
1 AAATTTT-ATATTATA-ATATTT
42870029 AAATTTTATATTATAATATTT
1 AAATTTTATATTATAATATTT
42870050 AAA
1 AAA
42870053 AAATGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
AAATTTTATATTATAATATTT
Found at i:42871064 original size:47 final size:47
Alignment explanation
Indices: 42870982--42871087 Score: 167
Period size: 47 Copynumber: 2.3 Consensus size: 47
42870972 TTGCGGGAAA
* *
42870982 CTCAATTATGCATGATTGAAACTTATTAATGGATTCCACCTCCCTTT
1 CTCAATTATGCAAGATTGAAACTTATCAATGGATTCCACCTCCCTTT
* * *
42871029 CTCGATTTTGCAAGATTGAAACTTATCAATGGATTCCACTTCCCTTT
1 CTCAATTATGCAAGATTGAAACTTATCAATGGATTCCACCTCCCTTT
42871076 CTCAATTATGCA
1 CTCAATTATGCA
42871088 TGGAAACTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (47 bp):
CTCAATTATGCAAGATTGAAACTTATCAATGGATTCCACCTCCCTTT
Found at i:42885555 original size:43 final size:43
Alignment explanation
Indices: 42885506--42885619 Score: 192
Period size: 43 Copynumber: 2.7 Consensus size: 43
42885496 AATCACCACA
* * *
42885506 AAAGATCATGTTCTTTAGCGGCATTTGTAGTAAAAGCGCCGCT
1 AAAGATCATGTTCTTTAGCGGCGTTTGTAGTAAAAGCACAGCT
42885549 AAAGATCATGTTCTTTAGCGGCGTTTGTAGTAAAAGCACAGCT
1 AAAGATCATGTTCTTTAGCGGCGTTTGTAGTAAAAGCACAGCT
*
42885592 AAAGATAATGTTCTTTAGCGGCGTTTGT
1 AAAGATCATGTTCTTTAGCGGCGTTTGT
42885620 GGGACCACTA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (43 bp):
AAAGATCATGTTCTTTAGCGGCGTTTGTAGTAAAAGCACAGCT
Found at i:42887481 original size:29 final size:31
Alignment explanation
Indices: 42887442--42887510 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
42887432 CCACAATTAG
42887442 AGTTTCATGTATATAATTGC-ATTAAATCAA
1 AGTTTCATGTATATAATTGCAATTAAATCAA
42887472 AGTTT-ATGTATATAATTGCAGATTAAATCAA
1 AGTTTCATGTATATAATTGCA-ATTAAATCAA
42887503 AG-TTCATG
1 AGTTTCATG
42887511 CATAATTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
29 14 0.39
30 7 0.19
31 15 0.42
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (31 bp):
AGTTTCATGTATATAATTGCAATTAAATCAA
Found at i:42887515 original size:29 final size:28
Alignment explanation
Indices: 42887445--42887517 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
42887435 CAATTAGAGT
*
42887445 TTCATGTATATAATTGCATTAAATCAAAG
1 TTCATG-ACATAATTGCATTAAATCAAAG
* *
42887474 TTTATGTATATAATTGCAGATTAAATCAAAG
1 TTCATG-ACATAATTGC--ATTAAATCAAAG
42887505 TTCATG-CATAATT
1 TTCATGACATAATT
42887518 TGTTAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 22 0.56
31 17 0.44
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (28 bp):
TTCATGACATAATTGCATTAAATCAAAG
Found at i:42890483 original size:12 final size:12
Alignment explanation
Indices: 42890466--42890492 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42890456 TATATTTTAT
42890466 AAAGTTATATAA
1 AAAGTTATATAA
42890478 AAAGTTATATAA
1 AAAGTTATATAA
42890490 AAA
1 AAA
42890493 TTAGTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (12 bp):
AAAGTTATATAA
Found at i:42890554 original size:29 final size:29
Alignment explanation
Indices: 42890513--42890584 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
42890503 TCAATAATTT
* *
42890513 TTTTATATTTTTTT-CTATATTTATACATA
1 TTTTATATTTTTTTACAATATTTATA-AAA
*
42890542 TTTTATATTTTTTTACAATTTTTATAAAA
1 TTTTATATTTTTTTACAATATTTATAAAA
42890571 TTTTACTATTTTTT
1 TTTTA-TATTTTTT
42890585 ATAAAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.55
30 17 0.45
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (29 bp):
TTTTATATTTTTTTACAATATTTATAAAA
Found at i:42890574 original size:19 final size:19
Alignment explanation
Indices: 42890552--42890645 Score: 73
Period size: 19 Copynumber: 4.8 Consensus size: 19
42890542 TTTTATATTT
42890552 TTTTACAATTTTTATAAAA
1 TTTTACAATTTTTATAAAA
*
42890571 TTTTACTATTTTTTATAAAAAA
1 TTTTAC-AATTTTTAT--AAAA
* * * **
42890593 ATTTATAATTTTTTTCTAA
1 TTTTACAATTTTTATAAAA
*
42890612 TTTTA-AATTTTTATTTAAA
1 TTTTACAATTTTTA-TAAAA
*
42890631 TTTAACAATTTTTAT
1 TTTTACAATTTTTAT
42890646 TGATTTTTAT
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
18 7 0.12
19 20 0.34
20 16 0.28
21 7 0.12
22 8 0.14
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTACAATTTTTATAAAA
Found at i:42890597 original size:22 final size:20
Alignment explanation
Indices: 42890560--42890606 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
42890550 TTTTTTACAA
*
42890560 TTTTTATAAAATTTTACT-AT
1 TTTTTATAAAAATTTA-TAAT
42890580 TTTTTATAAAAAAATTTATAAT
1 TTTTTAT--AAAAATTTATAAT
42890602 TTTTT
1 TTTTT
42890607 TCTAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 7 0.30
21 1 0.04
22 15 0.65
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTATAAAAATTTATAAT
Found at i:42890634 original size:18 final size:20
Alignment explanation
Indices: 42890591--42890646 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 20
42890581 TTTTATAAAA
*
42890591 AAATTTATAATTTTT-TTCT
1 AAATTTACAATTTTTATTCT
*
42890610 AATTTTA-AATTTTTATT-T
1 AAATTTACAATTTTTATTCT
42890628 AAATTTAACAATTTTTATT
1 AAATTT-ACAATTTTTATT
42890647 GATTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 13 0.41
19 9 0.28
20 10 0.31
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTTACAATTTTTATTCT
Found at i:42891686 original size:28 final size:28
Alignment explanation
Indices: 42891649--42891706 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
42891639 AATAAAAATC
42891649 ATGTATACACAAACTAATTATGACGAAA
1 ATGTATACACAAACTAATTATGACGAAA
*
42891677 ATGTATACACAAACTCATTATGACGAAA
1 ATGTATACACAAACTAATTATGACGAAA
42891705 AT
1 AT
42891707 AGGGATCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (28 bp):
ATGTATACACAAACTAATTATGACGAAA
Found at i:42893580 original size:11 final size:11
Alignment explanation
Indices: 42893560--42893590 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
42893550 TATTATCAAA
42893560 TTTTAACTTTT
1 TTTTAACTTTT
*
42893571 TTTTACCTTTT
1 TTTTAACTTTT
42893582 TTTTAACTT
1 TTTTAACTT
42893591 AAATTAGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTAACTTTT
Found at i:42894701 original size:30 final size:30
Alignment explanation
Indices: 42894667--42894724 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
42894657 ACAAATCCTA
*
42894667 TCTCAATTTCCTTCCAAAATTCTCTCAAAC
1 TCTCAATTTCCTTCCAAAATCCTCTCAAAC
42894697 TCTCAATTTCCTTCCAAAATCCTCTCAA
1 TCTCAATTTCCTTCCAAAATCCTCTCAA
42894725 TTTCCTTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.36
Consensus pattern (30 bp):
TCTCAATTTCCTTCCAAAATCCTCTCAAAC
Found at i:42894721 original size:22 final size:22
Alignment explanation
Indices: 42894696--42894746 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
42894686 TTCTCTCAAA
42894696 CTCTCAATTTCCTTCC-AAAAT
1 CTCTCAATTTCCTTCCAAAAAT
42894717 CCTCTCAATTTCCTTCCAAAAAT
1 -CTCTCAATTTCCTTCCAAAAAT
42894740 CTCTCAA
1 CTCTCAA
42894747 ATCCATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAAAT
Found at i:42894822 original size:32 final size:31
Alignment explanation
Indices: 42894781--42894846 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 31
42894771 TTCAATTTCA
42894781 TTTTTTAAAAATAATTTTAATTTTTTTTATAT
1 TTTTTTAAAAATAATTTTAA-TTTTTTTATAT
42894813 TTTTTTAAAAATAATTTTAATTTTTTTATAT
1 TTTTTTAAAAATAATTTTAATTTTTTTATAT
42894844 TTT
1 TTT
42894847 CATCAATGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 14 0.41
32 20 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
TTTTTTAAAAATAATTTTAATTTTTTTATAT
Found at i:42895978 original size:25 final size:25
Alignment explanation
Indices: 42895950--42896024 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
42895940 ATTTATACCT
42895950 GAATACATAGCTAATACATACATTC
1 GAATACATAGCTAATACATACATTC
*
42895975 GAATATATA--T-ATACAT--ATTC
1 GAATACATAGCTAATACATACATTC
42895995 GAATACATAGCTAATACATACATTC
1 GAATACATAGCTAATACATACATTC
42896020 GAATA
1 GAATA
42896025 TATATATACA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
20 12 0.28
22 7 0.16
23 7 0.16
25 17 0.40
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (25 bp):
GAATACATAGCTAATACATACATTC
Found at i:42895990 original size:18 final size:18
Alignment explanation
Indices: 42895967--42896035 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
42895957 TAGCTAATAC
42895967 ATACATTCGAATATATAT
1 ATACATTCGAATATATAT
42895985 ATACATATTCGAATACATAGCTAAT
1 ATAC--ATTCGAAT--ATA--T-AT
42896010 ACATACATTCGAATATATAT
1 --ATACATTCGAATATATAT
42896030 ATACAT
1 ATACAT
42896036 ATTCATCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 18
0.70 0.00 0.30
Matches are distributed among these distances:
18 10 0.24
20 10 0.24
21 1 0.02
22 3 0.07
23 3 0.07
24 1 0.02
25 10 0.24
27 4 0.10
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (18 bp):
ATACATTCGAATATATAT
Found at i:42895996 original size:20 final size:20
Alignment explanation
Indices: 42895971--42896039 Score: 84
Period size: 20 Copynumber: 3.2 Consensus size: 20
42895961 TAATACATAC
42895971 ATTCGAATATATATATACAT
1 ATTCGAATATATATATACAT
*
42895991 ATTCGAATACATAGCTAATACAT
1 ATTCGAATATATA--T-ATACAT
42896014 ACATTCGAATATATATATACAT
1 --ATTCGAATATATATATACAT
42896036 ATTC
1 ATTC
42896040 ATCATATACA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
20 16 0.38
22 7 0.17
23 7 0.17
25 12 0.29
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.36
Consensus pattern (20 bp):
ATTCGAATATATATATACAT
Found at i:42896003 original size:45 final size:45
Alignment explanation
Indices: 42895950--42896039 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
42895940 ATTTATACCT
42895950 GAATACATAGCTAATACATACATTCGAATATATATATACATATTC
1 GAATACATAGCTAATACATACATTCGAATATATATATACATATTC
42895995 GAATACATAGCTAATACATACATTCGAATATATATATACATATTC
1 GAATACATAGCTAATACATACATTCGAATATATATATACATATTC
42896040 ATCATATACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (45 bp):
GAATACATAGCTAATACATACATTCGAATATATATATACATATTC
Found at i:42896450 original size:41 final size:41
Alignment explanation
Indices: 42896389--42896492 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
42896379 ACCAGCTTTT
* * * *
42896389 AGCCTGCTAGACCTATAGTCTGAAATGTATCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGAAATATATCACCGGCATCA
* *
42896430 AGCCTGCTAGACGTAAAGTCTGAATTATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAATATATCACCGGCATCA
42896471 AGCCTGCTAGACGTAAAGTCTG
1 AGCCTGCTAGACGTAAAGTCTG
42896493 TATTACATTC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAATATATCACCGGCATCA
Found at i:42897760 original size:13 final size:13
Alignment explanation
Indices: 42897742--42897766 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42897732 CAATCAAATG
42897742 CACACAAAATAAA
1 CACACAAAATAAA
42897755 CACACAAAATAA
1 CACACAAAATAA
42897767 TATTAATAAT
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:42898294 original size:7 final size:7
Alignment explanation
Indices: 42898282--42898314 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
42898272 AGTGGATTGA
42898282 TATTTAG
1 TATTTAG
42898289 TATTTAG
1 TATTTAG
42898296 TATTTAG
1 TATTTAG
42898303 TATTTAG
1 TATTTAG
42898310 TATTT
1 TATTT
42898315 TGTCTTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (7 bp):
TATTTAG
Found at i:42899561 original size:30 final size:30
Alignment explanation
Indices: 42899525--42899822 Score: 370
Period size: 30 Copynumber: 9.7 Consensus size: 30
42899515 TAATTAAAAT
*
42899525 CCTAATTTAATTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
42899555 CCTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
42899584 TCTAATTTAATT-AAAACCCTAAATCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCT--A----AACCCTAA
** * **
42899619 CCCTAACCTAATTTAATTAAAAACCCTAAACCCTAA
1 -CCTAATTTAA-TT-A--AAAACCCTAAA-CCCTAA
*
42899655 CTTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
42899684 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
42899714 CTTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
42899743 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
42899773 CCTAATTTAATTAAAAACCATAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
42899803 CCTAATTTAATTAAAAACCC
1 CCTAATTTAATTAAAAACCC
42899823 CCAAACTTGT
Statistics
Matches: 234, Mismatches: 18, Indels: 32
0.82 0.06 0.11
Matches are distributed among these distances:
28 8 0.03
29 72 0.31
30 107 0.46
31 6 0.03
33 1 0.00
34 2 0.01
35 17 0.07
36 13 0.06
37 2 0.01
41 6 0.03
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (30 bp):
CCTAATTTAATTAAAAACCCTAAACCCTAA
Done.