Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 22 of 144
Found at i:5422604 original size:18 final size:19
Alignment explanation
Indices: 5422563--5422608 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
5422553 ATCTCACTTG
*
5422563 TTTCTTTTTCTCTCTTTTT
1 TTTCTTTTTCTCTCTTTCT
5422582 TTTCTTCTTTCT-T-TTTCT
1 TTTCTT-TTTCTCTCTTTCT
5422600 TTTCTTTTT
1 TTTCTTTTT
5422609 TTGGGGTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 10 0.40
19 7 0.28
20 5 0.20
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTCTTTTTCTCTCTTTCT
Found at i:5422605 original size:11 final size:12
Alignment explanation
Indices: 5422563--5422608 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
5422553 ATCTCACTTG
5422563 TTTCTTTTTCTC
1 TTTCTTTTTCTC
*
5422575 TCTTTTTTTTCTTC
1 T-TTCTTTTTC-TC
5422589 TTTCTTTTTCT-
1 TTTCTTTTTCTC
5422600 TTTCTTTTT
1 TTTCTTTTT
5422609 TTGGGGTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 9 0.30
12 2 0.07
13 16 0.53
14 3 0.10
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTCTTTTTCTC
Found at i:5423291 original size:3 final size:3
Alignment explanation
Indices: 5423268--5423305 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
5423258 TTGACCCTTT
*
5423268 TTC TTT TTC TT- TTC TTTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TT
5423306 TTGACCTCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (3 bp):
TTC
Found at i:5424228 original size:9 final size:9
Alignment explanation
Indices: 5424213--5424251 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
5424203 TTAATTTTCG
5424213 AATTCGAAT
1 AATTCGAAT
*
5424222 TATTCGAAT
1 AATTCGAAT
5424231 AATTCGAAT
1 AATTCGAAT
**
5424240 AAACCGAAT
1 AATTCGAAT
5424249 AAT
1 AAT
5424252 ACTATATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5424463 original size:58 final size:58
Alignment explanation
Indices: 5424392--5424507 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
5424382 ATTAACAAAG
* *
5424392 TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAA-AACACTCATAAAC
1 TAAACCAAAATATTTTTAAACCCAAATATAATTTCATTCCT-AAATAACACTCATAAAC
** *
5424450 TAAACCAAAATATTTTTAAATTCAAATATAATTTTATTCCTAAATAACACTCATAAAC
1 TAAACCAAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAC
5424508 AACTCCTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
57 3 0.06
58 49 0.94
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (58 bp):
TAAACCAAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAC
Found at i:5430485 original size:21 final size:21
Alignment explanation
Indices: 5430461--5430513 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
5430451 TACTTTAGCC
*
5430461 ATTTTTTATTTTTGT-TTTAAT
1 ATTTTCTATTTTT-TATTTAAT
*
5430482 ATTTTCAATTTTTTATTTAAT
1 ATTTTCTATTTTTTATTTAAT
5430503 -TTTTCTATTTT
1 ATTTTCTATTTT
5430514 AATTTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (21 bp):
ATTTTCTATTTTTTATTTAAT
Found at i:5430493 original size:20 final size:20
Alignment explanation
Indices: 5430470--5430513 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5430460 CATTTTTTAT
5430470 TTTTGT-TTTAATATTTTCAA
1 TTTTGTATTTAAT-TTTTCAA
* *
5430490 TTTTTTATTTAATTTTTCTA
1 TTTTGTATTTAATTTTTCAA
5430510 TTTT
1 TTTT
5430514 AATTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTGTATTTAATTTTTCAA
Found at i:5430506 original size:28 final size:26
Alignment explanation
Indices: 5430461--5430521 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
5430451 TACTTTAGCC
*
5430461 ATTTTTTATTTTTGTTTTAATATTTTCA
1 ATTTTTTATTTATGTTTT-ATATTTT-A
*
5430489 ATTTTTTATTTAAT-TTTTCTATTTTA
1 ATTTTTTATTT-ATGTTTTATATTTTA
5430515 ATTTTTT
1 ATTTTTT
5430522 TTGTTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 8 0.27
27 6 0.20
28 15 0.50
29 1 0.03
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (26 bp):
ATTTTTTATTTATGTTTTATATTTTA
Found at i:5430511 original size:13 final size:13
Alignment explanation
Indices: 5430461--5430521 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
5430451 TACTTTAGCC
*
5430461 ATTTTTTATTTTT
1 ATTTTTTATTTTA
* *
5430474 GTTTTAATATTTTCA
1 ATTTT-TTATTTT-A
5430489 ATTTTTTA-TTTA
1 ATTTTTTATTTTA
5430501 ATTTTTCTATTTTA
1 ATTTTT-TATTTTA
5430515 ATTTTTT
1 ATTTTTT
5430522 TTGTTTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
12 7 0.18
13 10 0.26
14 18 0.46
15 4 0.10
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (13 bp):
ATTTTTTATTTTA
Found at i:5450686 original size:23 final size:23
Alignment explanation
Indices: 5450660--5450712 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
5450650 GCTTTAATCT
* *
5450660 TTTTTTTAACTCTTCAGCCATTA
1 TTTTTGTAACTCTTCAACCATTA
5450683 TTTTTGTAACTCTTCAACCATTA
1 TTTTTGTAACTCTTCAACCATTA
*
5450706 TATTTGT
1 TTTTTGT
5450713 TTTATATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.53
Consensus pattern (23 bp):
TTTTTGTAACTCTTCAACCATTA
Found at i:5454630 original size:13 final size:13
Alignment explanation
Indices: 5454612--5454644 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
5454602 ATGGGCCGAA
5454612 TTATTTTAATTTT
1 TTATTTTAATTTT
5454625 TTA-TTTAATTTT
1 TTATTTTAATTTT
5454637 TTACTTTT
1 TTA-TTTT
5454645 TTTAATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.67
13 3 0.17
14 3 0.17
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTAATTTT
Found at i:5454869 original size:18 final size:18
Alignment explanation
Indices: 5454842--5454884 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5454832 ATTATTTAAC
*
5454842 AATA-TTTTTATTTCAAA
1 AATATTTTTTATCTCAAA
*
5454859 ACTATTTTTTATCTCAAA
1 AATATTTTTTATCTCAAA
5454877 AATATTTT
1 AATATTTT
5454885 CCCAACAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATTTTTTATCTCAAA
Found at i:5460012 original size:51 final size:51
Alignment explanation
Indices: 5459939--5460175 Score: 350
Period size: 51 Copynumber: 4.6 Consensus size: 51
5459929 TTTCATTTAA
* * * *
5459939 TACTCACGATGACA-TATTGTCATCGGACCTTTAATTCGTCATGGATTCATT
1 TACTCACGATGACACT-TAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
5459990 TACTCACGATGACACTTAGTCATCGGACATTTAATCCGTAAAGGATTCAAT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
5460041 TACTCACAATGACACTTAGTCACCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
5460092 TTCTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
5460143 TACTCACAATGACACTTAGTCATCGGACTCTTT
1 TACTCACGATGACACTTAGTCATCGGAC-CTTT
5460176 TGTTTATAAC
Statistics
Matches: 168, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
51 163 0.97
52 5 0.03
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:5467975 original size:18 final size:19
Alignment explanation
Indices: 5467941--5467978 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5467931 AATAATTTTC
5467941 AAAAATTCAGAATATTTAT
1 AAAAATTCAGAATATTTAT
5467960 AAAAATTTCA-AA-ATTTAT
1 AAAAA-TTCAGAATATTTAT
5467978 A
1 A
5467979 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 7 0.39
20 4 0.22
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (19 bp):
AAAAATTCAGAATATTTAT
Found at i:5469881 original size:48 final size:48
Alignment explanation
Indices: 5469842--5470098 Score: 415
Period size: 48 Copynumber: 5.4 Consensus size: 48
5469832 CTCATAAACA
* *
5469842 TTTACACTCGTCAGCTTGCACACGTTTACGCTCGTCAACTTATATACG
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
5469890 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
* * *
5469938 TTTACGCTCGTCAGCTTGCACATGTTTACACTCATCAGCTTATATACG
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
*
5469986 TTTACTCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
* * * *
5470034 TTTACGCTTGTCAGCTTGCACACATTTATGATCGTCAGCTTATATACG
1 TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
*
5470082 TTTACGCTCATCAGCTT
1 TTTACGCTCGTCAGCTT
5470099 TTATATGTTT
Statistics
Matches: 193, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 193 1.00
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (48 bp):
TTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAGCTTATATACG
Found at i:5470103 original size:24 final size:24
Alignment explanation
Indices: 5469842--5470111 Score: 288
Period size: 24 Copynumber: 11.2 Consensus size: 24
5469832 CTCATAAACA
* ** *
5469842 TTTACACTCGTCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTATATACG
*
5469866 TTTACGCTCGTCAACTTATATACG
1 TTTACGCTCGTCAGCTTATATACG
** *
5469890 TTTACGCTCGTCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTATATACG
5469914 TTTACGCTCGTCAGCTTATATACG
1 TTTACGCTCGTCAGCTTATATACG
** * *
5469938 TTTACGCTCGTCAGCTTGCACATG
1 TTTACGCTCGTCAGCTTATATACG
* *
5469962 TTTACACTCATCAGCTTATATACG
1 TTTACGCTCGTCAGCTTATATACG
* ** *
5469986 TTTACTCTCGTCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTATATACG
5470010 TTTACGCTCGTCAGCTTATATACG
1 TTTACGCTCGTCAGCTTATATACG
* ** * *
5470034 TTTACGCTTGTCAGCTTGCACACA
1 TTTACGCTCGTCAGCTTATATACG
* *
5470058 TTTATGATCGTCAGCTTATATACG
1 TTTACGCTCGTCAGCTTATATACG
* * *
5470082 TTTACGCTCATCAGCTTTTATATG
1 TTTACGCTCGTCAGCTTATATACG
5470106 TTTACG
1 TTTACG
5470112 TTATTTCATA
Statistics
Matches: 198, Mismatches: 48, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 198 1.00
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (24 bp):
TTTACGCTCGTCAGCTTATATACG
Found at i:5473305 original size:25 final size:23
Alignment explanation
Indices: 5473264--5473310 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
5473254 CCAATTAGGG
5473264 AATTATTGTTTAGATTTAATTTT
1 AATTATTGTTTAGATTTAATTTT
*
5473287 AATTATCTTTTTAGAATTTAATTT
1 AATTAT-TGTTTAG-ATTTAATTT
5473311 GGATCAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTTT
Found at i:5476617 original size:28 final size:28
Alignment explanation
Indices: 5476586--5476639 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5476576 ACTCCCAAGA
*
5476586 CCCAAAG-CTCAAACCCACACTATTTCTC
1 CCCAAAGTC-CAAACCAACACTATTTCTC
*
5476614 CCCAAAGTCCAAACCAACCCTATTTC
1 CCCAAAGTCCAAACCAACACTATTTC
5476640 CCAAAACCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.33, C:0.43, G:0.04, T:0.20
Consensus pattern (28 bp):
CCCAAAGTCCAAACCAACACTATTTCTC
Found at i:5484620 original size:17 final size:16
Alignment explanation
Indices: 5484598--5484651 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
5484588 TAAATTCATT
5484598 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTT-AA
5484615 TTTAAATTTA-CTT-A
1 TTTAAATTTATCTTAA
*
5484629 TTTAAATTTAAACTTAA
1 TTTAAATTT-ATCTTAA
5484646 TTTAAA
1 TTTAAA
5484652 ATAATATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 6 0.18
17 17 0.50
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAATTTATCTTAA
Found at i:5484636 original size:31 final size:30
Alignment explanation
Indices: 5484564--5484651 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
5484554 TGGGCTTTTG
* *
5484564 ATTTGTTAAAGTTTGAA-TTAATTTTAAATTC
1 ATTT-TTAAA-TTTAAACTTAAATTTAAATTC
* *
5484595 ATTTTTAAATTT-ATCTTAAATTTAAATTT
1 ATTTTTAAATTTAAACTTAAATTTAAATTC
5484624 ACTTATTTAAATTTAAACTT-AATTTAAA
1 A-TT-TTTAAATTTAAACTTAAATTTAAA
5484652 ATAATATTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
28 1 0.02
29 16 0.33
30 7 0.14
31 21 0.43
32 4 0.08
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (30 bp):
ATTTTTAAATTTAAACTTAAATTTAAATTC
Found at i:5485402 original size:19 final size:19
Alignment explanation
Indices: 5485366--5485464 Score: 76
Period size: 19 Copynumber: 5.1 Consensus size: 19
5485356 TAATGACACT
* * *
5485366 AATAATGTTAACAGTAATA
1 AATAATATTAATAATAATA
*
5485385 AATAATATTAATAATAATT
1 AATAATATTAATAATAATA
*
5485404 AATAA-AGGGTTTTATAATAA-A
1 AATAATA----TTAATAATAATA
*
5485425 TATAATATTAATAATAATA
1 AATAATATTAATAATAATA
* *
5485444 AATATTAATAATAATAATA
1 AATAATATTAATAATAATA
5485463 AA
1 AA
5485465 AGAAGATAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
18 10 0.16
19 39 0.62
21 4 0.06
22 10 0.16
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (19 bp):
AATAATATTAATAATAATA
Found at i:5485439 original size:3 final size:3
Alignment explanation
Indices: 5485417--5485463 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
5485407 AAAGGGTTTT
* *
5485417 ATA ATA A-A TATA ATA TTA ATA ATA ATAA ATA TTA ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
5485463 A
1 A
5485464 AAGAAGATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 1 0.03
3 32 0.86
4 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:5485473 original size:19 final size:19
Alignment explanation
Indices: 5485417--5485473 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
5485407 AAAGGGTTTT
*
5485417 ATAATAAATATAATATTAATA
1 ATAATAAATAGAA-A-TAATA
**
5485438 ATAATAAATATTAATAATA
1 ATAATAAATAGAAATAATA
5485457 ATAATAAA-AGAAGATAA
1 ATAATAAATAGAA-ATAA
5485474 AAGGCTAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 2 0.06
19 17 0.53
20 1 0.03
21 12 0.38
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (19 bp):
ATAATAAATAGAAATAATA
Found at i:5485732 original size:7 final size:7
Alignment explanation
Indices: 5485720--5485760 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
5485710 AACAATAAAG
5485720 AAAGAAA
1 AAAGAAA
5485727 AAAGAAA
1 AAAGAAA
5485734 ACAA-AAA
1 A-AAGAAA
5485741 AGAAGAAA
1 A-AAGAAA
5485749 AAAGAAA
1 AAAGAAA
5485756 AAAGA
1 AAAGA
5485761 GAAGAAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:5485732 original size:11 final size:11
Alignment explanation
Indices: 5485716--5485755 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
5485706 TTTTAACAAT
5485716 AAAGAAAGAAA
1 AAAGAAAGAAA
*
5485727 AAAGAAAACAAA
1 AAAG-AAAGAAA
5485739 AAAG-AAGAAA
1 AAAGAAAGAAA
5485749 AAAGAAA
1 AAAGAAA
5485756 AAAGAGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 9 0.36
11 6 0.24
12 10 0.40
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:5485757 original size:23 final size:23
Alignment explanation
Indices: 5485710--5485756 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
5485700 ATTTTGTTTT
*
5485710 AACAATAAAGAAAGAAAAAAGAA
1 AACAAAAAAGAAAGAAAAAAGAA
5485733 AACAAAAAAG-AAGAAAAAAGAA
1 AACAAAAAAGAAAGAAAAAAGAA
5485755 AA
1 AA
5485757 AAGAGAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (23 bp):
AACAAAAAAGAAAGAAAAAAGAA
Found at i:5486400 original size:162 final size:163
Alignment explanation
Indices: 5486201--5486523 Score: 459
Period size: 162 Copynumber: 2.0 Consensus size: 163
5486191 CTTTCAATTT
* *
5486201 AGTCCTATCACTGTTTGACTGTACCAGAGGTTGCCACGTGTCATTTTTTGGCCTATTTATGCATA
1 AGTCCTATCACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATTTTTTGGCCTATTTATGCATA
* *
5486266 TAGTCCCTGACATTATTAATTTGTTTTAA-TTTAATCCTTAAATCAACTTTTATTTAATTACGAA
66 TAGTCCCTGACATTATTAATTTATTTTAATTTTAATCCTTAAATCAACTTTTATTTAATTACAAA
* * *
5486330 ATTGGTCCAACAATTTTTCAAGGTTTATAAAGA
131 ATTGGTCCAAAAATTTTCCAAGATTTATAAAGA
* * * * *
5486363 AGTCCTTTGACTGTTTGACTGCACTAGAGGCTGCCACGTGTCGTTTTTTGGCCTATTTATGCATT
1 AGTCCTATCACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATTTTTTGGCCTATTTATGCATA
* *** * * *
5486428 TAGTCCTTTTTATTTTTAATTTATTTTAATTTTAGTCCTTAAATTAACTTTTATTTAATTACAAA
66 TAGTCCCTGACATTATTAATTTATTTTAATTTTAATCCTTAAATCAACTTTTATTTAATTACAAA
*
5486493 ATTGGTCCAAAAATTTTCCAAGATTTTTAAA
131 ATTGGTCCAAAAATTTTCCAAGATTTATAAA
5486524 TTAGTCCCTT
Statistics
Matches: 140, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
162 81 0.58
163 59 0.42
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (163 bp):
AGTCCTATCACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATTTTTTGGCCTATTTATGCATA
TAGTCCCTGACATTATTAATTTATTTTAATTTTAATCCTTAAATCAACTTTTATTTAATTACAAA
ATTGGTCCAAAAATTTTCCAAGATTTATAAAGA
Found at i:5486695 original size:30 final size:30
Alignment explanation
Indices: 5486610--5486976 Score: 381
Period size: 30 Copynumber: 12.3 Consensus size: 30
5486600 TAAATTATCC
* *
5486610 AAAAATTACATTTCGACCCTAAAACTTTTT
1 AAAAATTACATTTTGACCCTAAAACTTTCT
* * *
5486640 GAAACTTATATTTTGACCC-AAAACTTTCT
1 AAAAATTACATTTTGACCCTAAAACTTTCT
*
5486669 AAAAATTACATTTTAACCCTAAAACTTTTCT
1 AAAAATTACATTTTGACCCTAAAAC-TTTCT
* *
5486700 -AAAATTACATTTCGACCCTAAAACTATCT
1 AAAAATTACATTTTGACCCTAAAACTTTCT
* * *
5486729 AAAAATTATATTTTGACCCCAAAACTTTCC
1 AAAAATTACATTTTGACCCTAAAACTTTCT
*
5486759 AAAAATTACATTTTAACCCTAAAACTTT-T
1 AAAAATTACATTTTGACCCTAAAACTTTCT
* ** *
5486788 CCAAAATTACATTTCAACCCCAAAACTTTCT
1 -AAAAATTACATTTTGACCCTAAAACTTTCT
* * *
5486819 AAAAATTATATTTTAACCCTAAAACTTTCC
1 AAAAATTACATTTTGACCCTAAAACTTTCT
5486849 AAAAATTACATTTTGACCCCT-AAACTTT-T
1 AAAAATTACATTTTGA-CCCTAAAACTTTCT
* * **
5486878 CCAAAATTATATTTTGACCCCGAAACTTT-T
1 -AAAAATTACATTTTGACCCTAAAACTTTCT
* *
5486908 CCAAAATTACATTTTGACCCTAAAACTTTTT
1 -AAAAATTACATTTTGACCCTAAAACTTTCT
* *
5486939 AAAAATTATACTTTGA-CCTCAAAACTTTC-
1 AAAAATTACATTTTGACCCT-AAAACTTTCT
5486968 AAAAATTAC
1 AAAAATTAC
5486977 CATATTACCC
Statistics
Matches: 284, Mismatches: 43, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
29 42 0.15
30 231 0.81
31 11 0.04
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCTAAAACTTTCT
Found at i:5486785 original size:90 final size:90
Alignment explanation
Indices: 5486611--5486976 Score: 454
Period size: 90 Copynumber: 4.1 Consensus size: 90
5486601 AAATTATCCA
* * * * *
5486611 AAAATTACATTTCGACCCTAAAACTTTTTGAAACTTATATTTTGA-CCCAAAACTTTCTAAAAAT
1 AAAATTACATTTCGACCCCAAAACTTTCTAAAAATTATATTTTGACCCCAAAACTTTCCAAAAAT
*
5486675 TACATTTTAACCCTAAAACTTTTCT
66 TACATTTTAACCCTAAAACTTTTCC
* *
5486700 AAAATTACATTTCGACCCTAAAACTATCTAAAAATTATATTTTGACCCCAAAACTTTCCAAAAAT
1 AAAATTACATTTCGACCCCAAAACTTTCTAAAAATTATATTTTGACCCCAAAACTTTCCAAAAAT
5486765 TACATTTTAACCCTAAAACTTTTCC
66 TACATTTTAACCCTAAAACTTTTCC
* * *
5486790 AAAATTACATTTCAACCCCAAAACTTTCTAAAAATTATATTTTAACCCTAAAACTTTCCAAAAAT
1 AAAATTACATTTCGACCCCAAAACTTTCTAAAAATTATATTTTGACCCCAAAACTTTCCAAAAAT
*
5486855 TACATTTTGACCCCT-AAACTTTTCC
66 TACATTTT-AACCCTAAAACTTTTCC
* * * * * * **
5486880 AAAATTATATTTTGACCCCGAAACTTT-TCCAAAATTACATTTTGACCCTAAAACTTTTTAAAAA
1 AAAATTACATTTCGACCCCAAAACTTTCT-AAAAATTATATTTTGACCCCAAAACTTTCCAAAAA
* * * *
5486944 TTATACTTTGA-CCTCAAAAC-TTTCA
65 TTACATTTTAACCCT-AAAACTTTTCC
5486969 AAAATTAC
1 AAAATTAC
5486977 CATATTACCC
Statistics
Matches: 245, Mismatches: 27, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
88 3 0.01
89 53 0.22
90 184 0.75
91 5 0.02
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.36
Consensus pattern (90 bp):
AAAATTACATTTCGACCCCAAAACTTTCTAAAAATTATATTTTGACCCCAAAACTTTCCAAAAAT
TACATTTTAACCCTAAAACTTTTCC
Found at i:5487030 original size:59 final size:57
Alignment explanation
Indices: 5486967--5487162 Score: 189
Period size: 59 Copynumber: 3.4 Consensus size: 57
5486957 TCAAAACTTT
* *
5486967 CAAAAATTACCATATTACCCCCAAACTTCCCTAAATCTCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCC-AAAT-TCATTTTTAACCCCGATTTCAC
* * * ** * ** **
5487026 CAAAACTTACCATTTTGCCTCTGAACTTTCCAAAATTTCATTTTTGACCTTG-TTTTGC
1 CAAAAATTACCATTTTACCCCCAAACTTTCC-AAA-TTCATTTTTAACCCCGATTTCAC
* * *
5487084 CAAAATTTACCATTTTATTCCCCAAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA-
1 CAAAAATTACCATTTTA-CCCCCAAACTTTCCAAATT-CATTTTTAACCCCGATTTCAC
5487142 CAAAAATTACCATTTTACCCC
1 CAAAAATTACCATTTTACCCC
5487163 TAAAAACCCA
Statistics
Matches: 106, Mismatches: 27, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
57 5 0.05
58 48 0.45
59 52 0.49
60 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.04, T:0.36
Consensus pattern (57 bp):
CAAAAATTACCATTTTACCCCCAAACTTTCCAAATTCATTTTTAACCCCGATTTCAC
Found at i:5499203 original size:69 final size:68
Alignment explanation
Indices: 5498865--5499480 Score: 869
Period size: 68 Copynumber: 8.9 Consensus size: 68
5498855 ATTATTTCCT
* *
5498865 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
5498930 CGTC
65 CGTC
* *
5498934 ATCCCCTTAAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATT-AAGTAAGAGCAAT
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
5498998 GTC
66 GTC
*
5499001 ATCCCCTTGAAATTGAAGTAGAGTGGATAACGAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
5499066 GTC
66 GTC
*
5499069 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
5499134 GTC
66 GTC
* *
5499137 ATCCCCTTGAAATTGAAGTAGAGTTGGATAACATGTCTTTATCTCTGAAATT-AAGGTAAGAACA
1 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAA-GTAAGAGCA
5499201 ACGTC
64 ACGTC
*
5499206 ATCCCCTTGAAATTGAAGTAGAGTTGGATAACATGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
*
5499271 TGTC
65 CGTC
* * * * *
5499275 GTCCTCTTGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAATTAAAGTAAGAGCAAT
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
5499340 GTC
66 GTC
* * * * * *
5499343 ATCCTCTTGAAATTGAAGAAGAGTGGATAAGACGCCTTTATCTCTGAATTTGAAGTAAGAGCAA-
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
5499407 GATC
66 G-TC
* * *
5499411 ATTTCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGT
1 A--TC---CC-CTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTAT--CTCTGAAATTGAAGT
5499476 AAGAG
57 AAGAG
5499481 TAAGATGAAG
Statistics
Matches: 502, Mismatches: 31, Indels: 20
0.91 0.06 0.04
Matches are distributed among these distances:
67 65 0.13
68 238 0.47
69 144 0.29
70 4 0.01
73 1 0.00
74 17 0.03
75 14 0.03
77 19 0.04
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (68 bp):
ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
GTC
Found at i:5499286 original size:31 final size:31
Alignment explanation
Indices: 5499251--5499365 Score: 106
Period size: 31 Copynumber: 3.5 Consensus size: 31
5499241 TCTTTATCTC
*
5499251 TGAAATTGAAGTAAGAGCAATGTCGTCCTCT
1 TGAAATTGAAGTAAGAGCAATGTCATCCTCT
** * **
5499282 TGAAATTGAAGTAGAGTGGATAACATGTCTTTATCT
1 TGAAATTGAAGTA-A---GAGCA-ATGTCATCCTCT
*
5499318 CTGAAATTAAAGTAAGAGCAATGTCATCCTCT
1 -TGAAATTGAAGTAAGAGCAATGTCATCCTCT
5499350 TGAAATTGAAG-AAGAG
1 TGAAATTGAAGTAAGAG
5499366 TGGATAAGAC
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
30 5 0.08
31 23 0.35
32 10 0.15
33 3 0.05
35 3 0.05
36 10 0.15
37 12 0.18
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.30
Consensus pattern (31 bp):
TGAAATTGAAGTAAGAGCAATGTCATCCTCT
Found at i:5499357 original size:274 final size:272
Alignment explanation
Indices: 5498865--5499479 Score: 903
Period size: 274 Copynumber: 2.2 Consensus size: 272
5498855 ATTATTTCCT
* * *
5498865 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCCCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAACAA
5498930 CGTCATCCCCTTAAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTAAGTAAGAGC
66 CGTCATCCCCTTAAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTAAGTAAGAGC
*
5498995 AATGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACGAGTCTTTATCTCTGAAATTGAAGTAAG
131 AATGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACGAGTCTTTATCTCTGAAATTAAAGTAAG
* *
5499060 AGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGT
196 AGCAACGTCATCCCCTTGAAATTGAAGAAGAGTGGATAACAAGCCTTCATCTCTGAAATTGAAGT
5499125 AAGAGCAACG-TC
261 AAGAGCAA-GATC
* *
5499137 ATCCCCTTGAAATTGAAGTAGAGTTGGATAACATGTCTTTATCTCTGAAATT-AAGGTAAGAACA
1 ATCCCCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA-GTAAGAACA
* *
5499201 ACGTCATCCCCTTGAAATTGAAGTAGAGTTGGATAACATGTCTTTATCTCTGAAATTGAAGTAAG
65 ACGTCATCCCCTTAAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATT-AAGTAAG
* *
5499266 AGCAATGTCGTCCTCTTGAAATTGAAGTAGAGTGGATAAC-ATGTCTTTATCTCTGAAATTAAAG
128 AGCAATGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACGA-GTCTTTATCTCTGAAATTAAAG
* * * * * *
5499330 TAAGAGCAATGTCATCCTCTTGAAATTGAAGAAGAGTGGATAAGACGCCTTTATCTCTGAATTTG
192 TAAGAGCAACGTCATCCCCTTGAAATTGAAGAAGAGTGGATAACAAGCCTTCATCTCTGAAATTG
5499395 AAGTAAGAGCAAGATC
257 AAGTAAGAGCAAGATC
* * *
5499411 ATTTCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGT
1 A--TC---CC-CTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTAT--CTCTGAAATTGAAGT
5499476 AAGA
58 AAGA
5499480 GTAAGATGAA
Statistics
Matches: 306, Mismatches: 23, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
271 2 0.01
272 83 0.27
273 29 0.09
274 138 0.45
276 2 0.01
279 2 0.01
280 32 0.10
282 16 0.05
283 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (272 bp):
ATCCCCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAACAA
CGTCATCCCCTTAAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTAAGTAAGAGC
AATGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACGAGTCTTTATCTCTGAAATTAAAGTAAG
AGCAACGTCATCCCCTTGAAATTGAAGAAGAGTGGATAACAAGCCTTCATCTCTGAAATTGAAGT
AAGAGCAAGATC
Found at i:5499850 original size:17 final size:16
Alignment explanation
Indices: 5499828--5499881 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
5499818 TAAATTCATT
5499828 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTT-AA
5499845 TTTAAATTTA-CTT-A
1 TTTAAATTTATCTTAA
*
5499859 TTTAAATTTAAACTTAA
1 TTTAAATTT-ATCTTAA
5499876 TTTAAA
1 TTTAAA
5499882 ATAATATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 6 0.18
17 17 0.50
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAATTTATCTTAA
Found at i:5499866 original size:31 final size:30
Alignment explanation
Indices: 5499794--5499881 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
5499784 TGGGCTTTTG
* *
5499794 ATTTGTTAAAGTTTGAA-TTAATTTTAAATTC
1 ATTT-TTAAA-TTTAAACTTAAATTTAAATTC
* *
5499825 ATTTTTAAATTT-ATCTTAAATTTAAATTT
1 ATTTTTAAATTTAAACTTAAATTTAAATTC
5499854 ACTTATTTAAATTTAAACTT-AATTTAAA
1 A-TT-TTTAAATTTAAACTTAAATTTAAA
5499882 ATAATATTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
28 1 0.02
29 16 0.33
30 7 0.14
31 21 0.43
32 4 0.08
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (30 bp):
ATTTTTAAATTTAAACTTAAATTTAAATTC
Found at i:5500665 original size:3 final size:3
Alignment explanation
Indices: 5500643--5500689 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
5500633 TAAAGGTTTT
*
5500643 ATA ATA A-A TATA ATA TTA ATA ATA ATA ATAA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
5500689 A
1 A
5500690 AAGAAGACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 1 0.03
3 34 0.87
4 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5500689 original size:16 final size:16
Alignment explanation
Indices: 5500659--5500690 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5500649 AATATAATAT
5500659 TAATAATAATAATAAA
1 TAATAATAATAATAAA
5500675 TAATAATAATAATAAA
1 TAATAATAATAATAAA
5500691 AGAAGACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATAATAATAATAAA
Found at i:5500962 original size:12 final size:12
Alignment explanation
Indices: 5500945--5500990 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
5500935 TTTTAACAAT
5500945 AAAGAAAGAAAA
1 AAAGAAAGAAAA
5500957 AAAGAAA-ACAAA
1 AAAGAAAGA-AAA
5500969 AAAG-AAG-AAA
1 AAAGAAAGAAAA
5500979 AAAGAGAAGAAA
1 AAAGA-AAGAAA
5500991 TACTACCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
10 7 0.24
11 3 0.10
12 17 0.59
13 2 0.07
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:5500980 original size:23 final size:25
Alignment explanation
Indices: 5500939--5500986 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
5500929 ATTTTGTTTT
*
5500939 AACAATAAAGAAAGAAAAAA-AGAA
1 AACAAAAAAGAAAGAAAAAAGAGAA
5500963 AACAAAAAAG-AAGAAAAAAGAGAA
1 AACAAAAAAGAAAGAAAAAAGAGAA
5500987 GAAATACTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (25 bp):
AACAAAAAAGAAAGAAAAAAGAGAA
Found at i:5501621 original size:162 final size:163
Alignment explanation
Indices: 5501435--5501729 Score: 443
Period size: 162 Copynumber: 1.8 Consensus size: 163
5501425 CCTATGATTG
* *
5501435 TTTGACTGTACCAGAGGTTGCCACGTGTCATTTTTTGGCCTATTTATGCATATAGTCCCTGAC-A
1 TTTGACTGCACCAGAGGCTGCCACGTGTCATTTTTTGGCCTATTTATGCATATAGT-CCTGACTA
* *
5501499 TTATTAATTTGTTTTAA-TTTAATCCTTAAATCAACTTTTATTTAATTACGAAATTGGTCC-AAC
65 TTATTAATTTATTTTAATTTTAATCCTTAAATCAACTTTTATTTAATTACAAAATTGGTCCGAA-
5501562 AATTTTTCAAGGTTTATAAAGAAGTCTTTTGACTA
129 AATTTTTCAAGGTTTATAAAGAAGTCTTTTGACTA
* * **
5501597 TTTGACTGCACTAGAGGCTGCCACGTGTCATTTTTTGGCCTATTTATGCATTTAGTCCTTTCTAT
1 TTTGACTGCACCAGAGGCTGCCACGTGTCATTTTTTGGCCTATTTATGCATATAGTCCTGACTAT
* * * *
5501662 TTTTAATTTATTTTAATTTTAGTCCTTAAATTAACTTTTATTTAATTGCAAAATTGGTCCGAAAA
66 TATTAATTTATTTTAATTTTAATCCTTAAATCAACTTTTATTTAATTACAAAATTGGTCCGAAAA
5501727 TTT
131 TTT
5501730 CCAAGATTTT
Statistics
Matches: 118, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
161 4 0.03
162 68 0.58
163 44 0.37
164 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (163 bp):
TTTGACTGCACCAGAGGCTGCCACGTGTCATTTTTTGGCCTATTTATGCATATAGTCCTGACTAT
TATTAATTTATTTTAATTTTAATCCTTAAATCAACTTTTATTTAATTACAAAATTGGTCCGAAAA
TTTTTCAAGGTTTATAAAGAAGTCTTTTGACTA
Found at i:5501887 original size:30 final size:30
Alignment explanation
Indices: 5501830--5502206 Score: 380
Period size: 30 Copynumber: 12.7 Consensus size: 30
5501820 TAAATTATCC
*
5501830 AAAAATTACATTTCGACCCCAAAAACTTTCT
1 AAAAATTACATTTTGACCCC-AAAACTTTCT
* *
5501861 AAAAATTATATTTTAACCCCAAAACTTTCT
1 AAAAATTACATTTTGACCCCAAAACTTTCT
*
5501891 AAAAATTACATTTTGACACCAAAACTTTTCT
1 AAAAATTACATTTTGACCCCAAAAC-TTTCT
* *
5501922 -AAAATTACATTTCGA-CCCTAAACTTT-T
1 AAAAATTACATTTTGACCCCAAAACTTTCT
* *
5501949 CCAAAATTATATTTTGACCCCAAAACTTT-T
1 -AAAAATTACATTTTGACCCCAAAACTTTCT
* **
5501979 CCAAAATTACATTTCAACCCCAAAACTTT-T
1 -AAAAATTACATTTTGACCCCAAAACTTTCT
* * *
5502009 CCAAAATTACATTTCGACCCTAAAACTTTCT
1 -AAAAATTACATTTTGACCCCAAAACTTTCT
* * *
5502040 AAAAATTATATTTTAACCCTAAAACTTTCT
1 AAAAATTACATTTTGACCCCAAAACTTTCT
*
5502070 AAAAATTACATTTTGACCCCTAAACTTT-T
1 AAAAATTACATTTTGACCCCAAAACTTTCT
* * *
5502099 CCAAAA-TATA-TTTGACCCCGAAACTTT-T
1 -AAAAATTACATTTTGACCCCAAAACTTTCT
* *
5502127 CCAAAATTACATTTCGACCCCAAAACTTTCT
1 -AAAAATTACATTTTGACCCCAAAACTTTCT
* *
5502158 AAAAATTATACTTTGACCCCAAAACTTTC-
1 AAAAATTACATTTTGACCCCAAAACTTTCT
5502187 AAAAATTACCATTTT-ACCCC
1 AAAAATTA-CATTTTGACCCC
5502207 CAACTTCCCT
Statistics
Matches: 299, Mismatches: 37, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.00
28 26 0.09
29 39 0.13
30 209 0.70
31 24 0.08
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCCAAAACTTTCT
Found at i:5501985 original size:89 final size:90
Alignment explanation
Indices: 5501831--5502200 Score: 459
Period size: 89 Copynumber: 4.1 Consensus size: 90
5501821 AAATTATCCA
*
5501831 AAAATTACATTTCGACCCCAAAAACTTTCTAAAAATTATATTTTAACCCCAAAACTTTCTAAAAA
1 AAAATTACATTTCGACCCC-TAAACTTTCTAAAAATTATATTTTAACCCCAAAACTTTCTAAAAA
* *
5501896 TTACATTTTGACACCAAAACTTTTCT
65 TTACATTTTGACCCCAAAACTTTTCC
* * *
5501922 AAAATTACATTTCGA-CCCTAAACTTT-TCCAAAATTATATTTTGACCCCAAAACTTT-TCCAAA
1 AAAATTACATTTCGACCCCTAAACTTTCT-AAAAATTATATTTTAACCCCAAAACTTTCT-AAAA
**
5501984 ATTACATTTCAACCCCAAAACTTTTCC
64 ATTACATTTTGACCCCAAAACTTTTCC
*
5502011 AAAATTACATTTCGA-CCCTAAAACTTTCTAAAAATTATATTTTAACCCTAAAACTTTCTAAAAA
1 AAAATTACATTTCGACCCCT-AAACTTTCTAAAAATTATATTTTAACCCCAAAACTTTCTAAAAA
*
5502075 TTACATTTTGACCCCTAAACTTTTCC
65 TTACATTTTGACCCCAAAACTTTTCC
* * * * **
5502101 AAAA-TATATTT-GACCCCGAAACTTT-TCCAAAATTACATTTCGACCCCAAAACTTTCTAAAAA
1 AAAATTACATTTCGACCCCTAAACTTTCT-AAAAATTATATTTTAACCCCAAAACTTTCTAAAAA
* * *
5502163 TTATACTTTGACCCCAAAAC-TTTCA
65 TTACATTTTGACCCCAAAACTTTTCC
5502188 AAAATTACCATTT
1 AAAATTA-CATTT
5502201 TACCCCCAAC
Statistics
Matches: 243, Mismatches: 27, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
87 9 0.04
88 60 0.25
89 91 0.37
90 66 0.27
91 17 0.07
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (90 bp):
AAAATTACATTTCGACCCCTAAACTTTCTAAAAATTATATTTTAACCCCAAAACTTTCTAAAAAT
TACATTTTGACCCCAAAACTTTTCC
Found at i:5502258 original size:118 final size:116
Alignment explanation
Indices: 5501830--5502206 Score: 370
Period size: 118 Copynumber: 3.2 Consensus size: 116
5501820 TAAATTATCC
* * ** * *
5501830 AAAAATTACATTTCGACCCCAAAAACTTTCTAAAAATTATATTTTAACCCCAAAACTTTCTAAAA
1 AAAAATTACATTTTGACCCC-TAAACTTTCCCAAAA-TATA-TTTAACCCC-GAACTTTC-CAAA
* * * * *
5501895 ATTACATTTTGACACCAAAACTTTTCT-AAAATTACA-TTTCGA-CCCTAAACTTT-T
61 ATTACATTTCGACCCCAAAAC-TTTCTAAAAATTATACTTT-AACCCCAAAACTTTCT
* * * * * *
5501949 CCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTACATTTCAACCCCAAAACTTTTCCAAA
1 -AAAAATTACATTTTGACCCCTAAACTTTCCCAAAA-TATATTT-AACCCC-GAAC-TTTCCAAA
* * *
5502014 ATTACATTTCGACCCTAAAACTTTCTAAAAATTATATTTTAACCCTAAAACTTTCT
61 ATTACATTTCGACCCCAAAACTTTCTAAAAATTATACTTTAACCCCAAAACTTTCT
* *
5502070 AAAAATTACATTTTGACCCCTAAACTTTTCCAAAATATATTTGACCCCGAAACTTTTCCAAAATT
1 AAAAATTACATTTTGACCCCTAAACTTTCCCAAAATATATTTAACCCCG-AAC-TTTCCAAAATT
*
5502135 ACATTTCGACCCCAAAACTTTCTAAAAATTATACTTTGACCCCAAAACTTTC-
64 ACATTTCGACCCCAAAACTTTCTAAAAATTATACTTTAACCCCAAAACTTTCT
5502187 AAAAATTACCATTTT-ACCCC
1 AAAAATTA-CATTTTGACCCC
5502207 CAACTTCCCT
Statistics
Matches: 224, Mismatches: 25, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
117 13 0.06
118 82 0.37
119 63 0.28
120 65 0.29
121 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (116 bp):
AAAAATTACATTTTGACCCCTAAACTTTCCCAAAATATATTTAACCCCGAACTTTCCAAAATTAC
ATTTCGACCCCAAAACTTTCTAAAAATTATACTTTAACCCCAAAACTTTCT
Found at i:5511900 original size:20 final size:20
Alignment explanation
Indices: 5511877--5511947 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
5511867 CGCAAATGAT
5511877 TTTAAAATTATTAAAATTAA
1 TTTAAAATTATTAAAATTAA
**
5511897 TTTAAAATTATT--TTTTAAAA
1 TTTAAAATTATTAAAATT--AA
* *
5511917 TATAAAATTATTAAAATTAT
1 TTTAAAATTATTAAAATTAA
5511937 TTTAAAATTAT
1 TTTAAAATTAT
5511948 AATCATCATC
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
18 2 0.05
20 36 0.90
22 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAAATTATTAAAATTAA
Found at i:5511947 original size:11 final size:11
Alignment explanation
Indices: 5511870--5511947 Score: 64
Period size: 11 Copynumber: 7.6 Consensus size: 11
5511860 CCACGTCCGC
*
5511870 AAATGATTTTA
1 AAATTATTTTA
5511881 AAATTA--TTA
1 AAATTATTTTA
*
5511890 AAATTAATTTA
1 AAATTATTTTA
5511901 AAATTATTTTTTA
1 AAATTA--TTTTA
5511914 AAA-TA---TA
1 AAATTATTTTA
5511921 AAATTA--TTA
1 AAATTATTTTA
5511930 AAATTATTTTA
1 AAATTATTTTA
5511941 AAATTAT
1 AAATTAT
5511948 AATCATCATC
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
7 5 0.09
8 2 0.04
9 17 0.30
11 24 0.42
12 2 0.04
13 7 0.12
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:5512388 original size:34 final size:34
Alignment explanation
Indices: 5512345--5512450 Score: 180
Period size: 34 Copynumber: 3.2 Consensus size: 34
5512335 TTGGATGATG
5512345 AGAAGAAGTGGTGCTAGATGGAAAATTGGTGAGA
1 AGAAGAAGTGGTGCTAGATGGAAAATTGGTGAGA
5512379 AGAAGAAGTGGTGCTAGATGGAAAATTGGTGAGA
1 AGAAGAAGTGGTGCTAGATGGAAAATTGGTGAGA
* *
5512413 AGAAGAAGTGGTGTTAGATGGAAAAATGG-G-GA
1 AGAAGAAGTGGTGCTAGATGGAAAATTGGTGAGA
5512445 AGAAGA
1 AGAAGA
5512451 TGAAATCGGG
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.11
33 1 0.01
34 61 0.87
ACGTcount: A:0.41, C:0.02, G:0.39, T:0.19
Consensus pattern (34 bp):
AGAAGAAGTGGTGCTAGATGGAAAATTGGTGAGA
Found at i:5512461 original size:17 final size:16
Alignment explanation
Indices: 5512436--5512486 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
5512426 TTAGATGGAA
5512436 AAATGGGGAAGAAGATG
1 AAAT-GGGAAGAAGATG
5512453 AAATCGGGAAGAA-AT-
1 AAAT-GGGAAGAAGATG
*
5512468 AAA-GGGGAGAAGATG
1 AAATGGGAAGAAGATG
5512483 AAAT
1 AAAT
5512487 TGAAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 7 0.24
14 2 0.07
15 6 0.21
16 2 0.07
17 12 0.41
ACGTcount: A:0.51, C:0.02, G:0.35, T:0.12
Consensus pattern (16 bp):
AAATGGGAAGAAGATG
Found at i:5512516 original size:9 final size:9
Alignment explanation
Indices: 5512502--5512553 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 9
5512492 ATTAAAATTA
5512502 TTTAATAAT
1 TTTAATAAT
5512511 TTTAATAAT
1 TTTAATAAT
5512520 TTT-AT-AT
1 TTTAATAAT
5512527 TTTAA-AA-
1 TTTAATAAT
5512534 ---AATAAT
1 TTTAATAAT
5512540 TTTAATAAT
1 TTTAATAAT
5512549 TTTAA
1 TTTAA
5512554 AATCATTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
4 2 0.06
5 2 0.06
7 5 0.14
8 4 0.11
9 23 0.64
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TTTAATAAT
Found at i:5512537 original size:20 final size:22
Alignment explanation
Indices: 5512514--5512555 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
5512504 TAATAATTTT
5512514 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
5512534 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
5512556 TCATTTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:5512556 original size:20 final size:20
Alignment explanation
Indices: 5512493--5512561 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
5512483 AAATTGAAAA
*
5512493 TTAAAATTA-TTTAATAATT
1 TTAAAATAATTTTAATAATT
5512512 TT--AATAATTTT-AT-ATT
1 TTAAAATAATTTTAATAATT
5512528 TTAAAAAATAATTTTAATAATT
1 TT--AAAATAATTTTAATAATT
*
5512550 TTAAAATCATTT
1 TTAAAATAATTT
5512562 ATTGACGTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
16 5 0.12
17 6 0.15
18 3 0.07
19 2 0.05
20 18 0.44
21 2 0.05
22 5 0.12
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAAAATAATTTTAATAATT
Found at i:5513876 original size:16 final size:16
Alignment explanation
Indices: 5513855--5513886 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5513845 TTGATATTTG
*
5513855 ATAATTTTACTAATAT
1 ATAATTTTAATAATAT
5513871 ATAATTTTAATAATAT
1 ATAATTTTAATAATAT
5513887 TTACATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAATTTTAATAATAT
Found at i:5514753 original size:19 final size:19
Alignment explanation
Indices: 5514731--5514770 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5514721 TATATATAAA
*
5514731 ATTAAAATGTAAATAT-TAT
1 ATTAAAAT-AAAATATGTAT
5514750 ATTAAAATAAAATATGTAT
1 ATTAAAATAAAATATGTAT
5514769 AT
1 AT
5514771 ATAATACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
ATTAAAATAAAATATGTAT
Found at i:5514760 original size:24 final size:23
Alignment explanation
Indices: 5514718--5514785 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 23
5514708 ATAATATATG
5514718 AAATATATATAAAATTAAAATGT
1 AAATATATATAAAATTAAAATGT
*
5514741 AAATATTATATTAAAATAAAATATGT
1 AAATA-TATA-TAAAATTAAA-ATGT
* *
5514767 ATATATA-ATACAATTAAAA
1 AAATATATATAAAATTAAAA
5514786 ATAAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 1 0.03
23 13 0.34
24 5 0.13
25 11 0.29
26 8 0.21
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (23 bp):
AAATATATATAAAATTAAAATGT
Found at i:5514766 original size:26 final size:25
Alignment explanation
Indices: 5514707--5514772 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 25
5514697 TTAACCTAAT
*
5514707 AATAATATATG-AAATA-TATATAA
1 AATAAAATATGTAAATATTATATAA
*
5514730 AATTAAA-ATGTAAATATTATATTAA
1 AATAAAATATGTAAATATTATA-TAA
*
5514755 AATAAAATATGTATATAT
1 AATAAAATATGTAAATAT
5514773 AATACAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 3 0.09
23 10 0.29
24 4 0.11
25 9 0.26
26 9 0.26
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.38
Consensus pattern (25 bp):
AATAAAATATGTAAATATTATATAA
Found at i:5530178 original size:16 final size:16
Alignment explanation
Indices: 5530157--5530191 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5530147 GCAATATATG
5530157 CTGTGACTTTTGCCAA
1 CTGTGACTTTTGCCAA
5530173 CTGTGACTTTTGCCAA
1 CTGTGACTTTTGCCAA
5530189 CTG
1 CTG
5530192 AAACCCCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (16 bp):
CTGTGACTTTTGCCAA
Found at i:5534500 original size:83 final size:83
Alignment explanation
Indices: 5534356--5534606 Score: 430
Period size: 83 Copynumber: 3.0 Consensus size: 83
5534346 AAATACTGAC
5534356 AGTCTTTATGTTCTACAAGGTTCAACGTGATTGGTAAAGCAACAATTTCCTCATCTGTTAAGGAG
1 AGTCTTTATGTTCTACAAGGTTCAACGTGATTGGTAAAGCAACAATTTCCTCATCTGTTAAGGAG
*
5534421 TCGAAGTCAACTTATTTG
66 TCGAAGTCGACTTATTTG
* *
5534439 AGTTTTTATGTTCTACAAGGTTCAACGTGATTGGTAAAGCAACAATTTCCTCATCTATTAAGGAG
1 AGTCTTTATGTTCTACAAGGTTCAACGTGATTGGTAAAGCAACAATTTCCTCATCTGTTAAGGAG
*
5534504 TTGAAGTCGACTTATTTG
66 TCGAAGTCGACTTATTTG
* * *
5534522 AGTCTTTATGTTCTACAAGGTTTAATGTGATTGGTAAAGGAACAATTTCCTCATCTGTTAAGGAG
1 AGTCTTTATGTTCTACAAGGTTCAACGTGATTGGTAAAGCAACAATTTCCTCATCTGTTAAGGAG
*
5534587 TCGAAGTTGACTTATTTG
66 TCGAAGTCGACTTATTTG
5534605 AG
1 AG
5534607 GCATAGGTAA
Statistics
Matches: 157, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 157 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (83 bp):
AGTCTTTATGTTCTACAAGGTTCAACGTGATTGGTAAAGCAACAATTTCCTCATCTGTTAAGGAG
TCGAAGTCGACTTATTTG
Found at i:5539272 original size:18 final size:19
Alignment explanation
Indices: 5539249--5539293 Score: 76
Period size: 18 Copynumber: 2.5 Consensus size: 19
5539239 AATTTATATG
5539249 AAAATCCCT-GAAGGATTT
1 AAAATCCCTAGAAGGATTT
5539267 AAAAT-CCTAGAAGGATTT
1 AAAATCCCTAGAAGGATTT
5539285 AAAATCCCT
1 AAAATCCCT
5539294 TAATGATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.12
18 19 0.76
19 3 0.12
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (19 bp):
AAAATCCCTAGAAGGATTT
Found at i:5542250 original size:22 final size:22
Alignment explanation
Indices: 5542223--5542268 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5542213 ATATATATAT
*
5542223 AATATTT-TTTATTATATAATTA
1 AATATTTATTAATTAT-TAATTA
5542245 AATATTTATTAATTATTAATTA
1 AATATTTATTAATTATTAATTA
5542267 AA
1 AA
5542269 AATTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATTTATTAATTATTAATTA
Found at i:5544124 original size:30 final size:30
Alignment explanation
Indices: 5544090--5544428 Score: 299
Period size: 30 Copynumber: 11.5 Consensus size: 30
5544080 ATTTTATTTG
* * * * *
5544090 AAAATCACATTTTGACCCCCAAAATTTTCT
1 AAAATTACATTTTAACCCCTAAACTTTTCC
*
5544120 AAAATTACATTTTAACCCTTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* *
5544150 AAAATTACATTTTTACCTCTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
*
5544180 AAAATTACATTTTAAACCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* * *
5544210 AAAATCACATTTTGACCTC-AAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
*
5544239 AAAATTACATTTTAACCCCTAAACTTCTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* * *
5544269 AAGATTACATTTTAACCTCC-AAACTTCTCT
1 AAAATTACATTTTAACC-CCTAAACTTTTCC
** *
5544299 AAAATCCCATTTTAACCCC-AAACTTCTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* * *
5544328 AAAATTATAATTTT-ACCCCTGAA--TATCC
1 AAAATTA-CATTTTAACCCCTAAACTTTTCC
*
5544356 AAAAATTACCATTTT-A-CCCTCAAAC--ATCC
1 -AAAATTA-CATTTTAACCCCT-AAACTTTTCC
*
5544385 AAAAATTACCATTTT-ACCCCTAAA--TATCC
1 -AAAATTA-CATTTTAACCCCTAAACTTTTCC
5544414 AAAATTACCATTTTA
1 AAAATTA-CATTTTA
5544429 CCCTCGAACA
Statistics
Matches: 265, Mismatches: 34, Indels: 21
0.83 0.11 0.07
Matches are distributed among these distances:
28 22 0.08
29 89 0.34
30 152 0.57
31 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.01, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTTCC
Found at i:5544262 original size:89 final size:87
Alignment explanation
Indices: 5544090--5544380 Score: 309
Period size: 89 Copynumber: 3.3 Consensus size: 87
5544080 ATTTTATTTG
* * * * *
5544090 AAAATCACATTTTGACCCCCAAAATTTTCTAAAATTACATTTTAACCCTTAAACTTTTCCAAAAT
1 AAAATTACATTTT-AACCCCAAACTTTTCTAAAATCACATTTTAA-CCTCAAACTTTTCCAAAAT
* *
5544155 TACATTTTTACCTCTAAACTTTTCC
64 TACA-TTTTACCCCTAAACTTCTCC
* * *
5544180 AAAATTACATTTTAAACCCTAAACTTTTCCAAAATCACATTTTGACCTCAAACTTTTCCAAAATT
1 AAAATTACATTTT-AACCCCAAACTTTTCTAAAATCACATTTTAACCTCAAACTTTTCCAAAATT
5544245 ACATTTTAACCCCTAAACTTCTCC
65 ACATTTT-ACCCCTAAACTTCTCC
* * * * *
5544269 AAGATTACATTTTAACCTCCAAACTTCTCTAAAATCCCATTTTAACCCCAAACTTCTCCAAAATT
1 AAAATTACATTTTAACC-CCAAACTTTTCTAAAATCACATTTTAACCTCAAACTTTTCCAAAATT
* * *
5544334 ATAATTTTACCCCTGAA-TATC-CA
65 A-CATTTTACCCCTAAACT-TCTCC
5544357 AAAATTACCATTTT-ACCCTCAAAC
1 AAAATTA-CATTTTAACCC-CAAAC
5544381 ATCCAAAAAT
Statistics
Matches: 172, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
87 1 0.01
88 24 0.14
89 105 0.61
90 42 0.24
ACGTcount: A:0.37, C:0.27, G:0.01, T:0.35
Consensus pattern (87 bp):
AAAATTACATTTTAACCCCAAACTTTTCTAAAATCACATTTTAACCTCAAACTTTTCCAAAATTA
CATTTTACCCCTAAACTTCTCC
Found at i:5544345 original size:29 final size:30
Alignment explanation
Indices: 5544097--5544479 Score: 244
Period size: 30 Copynumber: 13.0 Consensus size: 30
5544087 TTGAAAATCA
* * * *
5544097 CATTTTGACCCCCAAAATTTTCTAAAATTA-
1 CATTTT-AACCCCAAACTTCTCCAAAATTAC
* *
5544127 CATTTTAACCCTTAAACTTTTCCAAAATTA-
1 CATTTTAACCC-CAAACTTCTCCAAAATTAC
* * *
5544157 CATTTTTACCTCTAAACTTTTCCAAAATTA-
1 CATTTTAACC-CCAAACTTCTCCAAAATTAC
* * *
5544187 CATTTTAAACCCTAAACTTTTCCAAAATCA-
1 CATTTT-AACCCCAAACTTCTCCAAAATTAC
* * *
5544217 CATTTTGACCTCAAACTTTTCCAAAATTA-
1 CATTTTAACCCCAAACTTCTCCAAAATTAC
*
5544246 CATTTTAACCCCTAAACTTCTCCAAGATTA-
1 CATTTTAACCCC-AAACTTCTCCAAAATTAC
* *
5544276 CATTTTAACCTCCAAACTTCTCTAAAA-TCC
1 CATTTTAACC-CCAAACTTCTCCAAAATTAC
*
5544306 CATTTTAACCCCAAACTTCTCCAAAATTAT
1 CATTTTAACCCCAAACTTCTCCAAAATTAC
* * *
5544336 AATTTT-ACCCCTGAA-TATC-CAAAAATTAC
1 CATTTTAACCCC-AAACT-TCTCCAAAATTAC
* *
5544365 CATTTT-ACCCTCAAACATC-CAAAAATTAC
1 CATTTTAACCC-CAAACTTCTCCAAAATTAC
*
5544394 CATTTT-ACCCCTAAA--TATCCAAAATTAC
1 CATTTTAACCCC-AAACTTCTCCAAAATTAC
* * * *
5544422 CATTTT-ACCCTCGAACATC-CAAAAATTTC
1 CATTTTAACCC-CAAACTTCTCCAAAATTAC
* * *
5544451 AATTTTGACCCCAAA-TTCCTCAAAAATTA
1 CATTTTAACCCCAAACTT-CTCCAAAATTA
5544480 TATTTTCATC
Statistics
Matches: 296, Mismatches: 38, Indels: 38
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.00
28 23 0.08
29 117 0.40
30 149 0.50
31 6 0.02
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (30 bp):
CATTTTAACCCCAAACTTCTCCAAAATTAC
Found at i:5544375 original size:28 final size:30
Alignment explanation
Indices: 5544305--5544462 Score: 157
Period size: 29 Copynumber: 5.4 Consensus size: 30
5544295 CTCTAAAATC
* * *
5544305 CCATTTTAACCC-CAAACTTCTCCAAAATTA
1 CCATTTTACCCCTCAAACATC-CAAAAATTA
** * *
5544335 TAATTTTACCCCT-GAATATCCAAAAATTA
1 CCATTTTACCCCTCAAACATCCAAAAATTA
5544364 CCATTTTA-CCCTCAAACATCCAAAAATTA
1 CCATTTTACCCCTCAAACATCCAAAAATTA
*
5544393 CCATTTTACCCCT-AAATATCC-AAAATTA
1 CCATTTTACCCCTCAAACATCCAAAAATTA
* *
5544421 CCATTTTA-CCCTCGAACATCCAAAAATTT
1 CCATTTTACCCCTCAAACATCCAAAAATTA
*
5544450 CAATTTTGACCCC
1 CCATTTT-ACCCC
5544463 AAATTCCTCA
Statistics
Matches: 105, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
27 4 0.04
28 25 0.24
29 55 0.52
30 18 0.17
31 3 0.03
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.31
Consensus pattern (30 bp):
CCATTTTACCCCTCAAACATCCAAAAATTA
Found at i:5544424 original size:57 final size:58
Alignment explanation
Indices: 5544305--5544479 Score: 214
Period size: 57 Copynumber: 3.0 Consensus size: 58
5544295 CTCTAAAATC
* * * *
5544305 CCATTTTAACCC-CAAACTTCTCCAAAATTATAATTTTACCCCTGAATATCCAAAAATTA
1 CCATTTT-ACCCTCAAACATC-CAAAAATTACAATTTTACCCCTAAATATCCAAAAATTA
*
5544364 CCATTTTACCCTCAAACATCCAAAAATTACCATTTTACCCCTAAATATCC-AAAATTA
1 CCATTTTACCCTCAAACATCCAAAAATTACAATTTTACCCCTAAATATCCAAAAATTA
* *
5544421 CCATTTTACCCTCGAACATCCAAAAATTTCAATTTTGACCCC-AAAT-TCCTCAAAAATTA
1 CCATTTTACCCTCAAACATCCAAAAATTACAATTTT-ACCCCTAAATAT-C-CAAAAATTA
5544480 TATTTTCATC
Statistics
Matches: 103, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
56 1 0.01
57 45 0.44
58 36 0.35
59 21 0.20
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.31
Consensus pattern (58 bp):
CCATTTTACCCTCAAACATCCAAAAATTACAATTTTACCCCTAAATATCCAAAAATTA
Found at i:5546188 original size:12 final size:13
Alignment explanation
Indices: 5546157--5546191 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
5546147 ACTTTTTATT
5546157 TTTCTTAGTTAAA
1 TTTCTTAGTTAAA
*
5546170 TTACTTAGTT-AA
1 TTTCTTAGTTAAA
5546182 TTTCTTAGTT
1 TTTCTTAGTT
5546192 TTTATAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (13 bp):
TTTCTTAGTTAAA
Found at i:5548968 original size:24 final size:24
Alignment explanation
Indices: 5548941--5549078 Score: 132
Period size: 24 Copynumber: 5.8 Consensus size: 24
5548931 GTCATGATCA
*
5548941 TTGTCTTCATCTTCACCTCCACCC
1 TTGTCTTCATCTTCATCTCCACCC
* *
5548965 TTGTGTTCATCTTCATCTCGACCC
1 TTGTCTTCATCTTCATCTCCACCC
** *
5548989 ACGTCTTCATCTTCACCTCCACCC
1 TTGTCTTCATCTTCATCTCCACCC
* *
5549013 TTGTGTTCATCTTCATCTCAACCC
1 TTGTCTTCATCTTCATCTCCACCC
** * *
5549037 TCATTTTCATCTTCATCTCTACCC
1 TTGTCTTCATCTTCATCTCCACCC
** * *
5549061 CCGTCTTTATCTCCATCT
1 TTGTCTTCATCTTCATCT
5549079 TCTTCTTTCG
Statistics
Matches: 92, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 92 1.00
ACGTcount: A:0.14, C:0.40, G:0.06, T:0.40
Consensus pattern (24 bp):
TTGTCTTCATCTTCATCTCCACCC
Found at i:5549014 original size:48 final size:48
Alignment explanation
Indices: 5548943--5549060 Score: 182
Period size: 48 Copynumber: 2.5 Consensus size: 48
5548933 CATGATCATT
*
5548943 GTCTTCATCTTCACCTCCACCCTTGTGTTCATCTTCATCTCGACCCAC
1 GTCTTCATCTTCACCTCCACCCTTGTGTTCATCTTCATCTCAACCCAC
*
5548991 GTCTTCATCTTCACCTCCACCCTTGTGTTCATCTTCATCTCAACCCTC
1 GTCTTCATCTTCACCTCCACCCTTGTGTTCATCTTCATCTCAACCCAC
* * * *
5549039 ATTTTCATCTTCATCTCTACCC
1 GTCTTCATCTTCACCTCCACCC
5549061 CCGTCTTTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 64 1.00
ACGTcount: A:0.15, C:0.41, G:0.06, T:0.38
Consensus pattern (48 bp):
GTCTTCATCTTCACCTCCACCCTTGTGTTCATCTTCATCTCAACCCAC
Found at i:5561136 original size:25 final size:25
Alignment explanation
Indices: 5561102--5561154 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
5561092 TTAGTGTAAA
5561102 AAAAGAGATAAAATAACAAGAATTC
1 AAAAGAGATAAAATAACAAGAATTC
5561127 AAAAGAGATAAAATAACAAGAATTC
1 AAAAGAGATAAAATAACAAGAATTC
5561152 AAA
1 AAA
5561155 CCAAGCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.66, C:0.08, G:0.11, T:0.15
Consensus pattern (25 bp):
AAAAGAGATAAAATAACAAGAATTC
Found at i:5562523 original size:3 final size:3
Alignment explanation
Indices: 5562515--5562558 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
5562505 TAAATACATT
* * *
5562515 TAA TAA TAA TAA TAA TAA TAA TTAA TAA CAC TAA TAA TAT TAA T
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA T
5562559 TGATATTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5563285 original size:32 final size:33
Alignment explanation
Indices: 5563248--5563311 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
5563238 TGCGTGTTTG
*
5563248 GTCC-TTCCATATTTTTTAATTA-TTTTAATTTA
1 GTCCTTTCCATA-CTTTTAATTATTTTTAATTTA
*
5563280 GTCCTTTTCATACTTTTAATTATTTTTAATTT
1 GTCCTTTCCATACTTTTAATTATTTTTAATTT
5563312 GGCCCGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.23, C:0.12, G:0.03, T:0.61
Consensus pattern (33 bp):
GTCCTTTCCATACTTTTAATTATTTTTAATTTA
Found at i:5563623 original size:29 final size:29
Alignment explanation
Indices: 5563577--5564110 Score: 220
Period size: 29 Copynumber: 18.2 Consensus size: 29
5563567 TTTTATAGAT
*
5563577 CCCT-GAACTGTTCAAAAATTACCATTTTA
1 CCCTCGAACT-TTCCAAAATTACCATTTTA
**
5563606 CCCTCGAACTTTCCAAAATT-TTATTTTTA
1 CCCTCGAACTTTCCAAAATTACCA-TTTTA
5563635 CCC-CG-A-TTTCACCAAAAATTACCATTTTA
1 CCCTCGAACTTT--CC-AAAATTACCATTTTA
*
5563664 CCC-CTGAACTTCCCAAAATT-CCATTTTTA
1 CCCTC-GAACTTTCCAAAATTACCA-TTTTA
* *
5563693 ACCTCG-ATTTTACCAAAAATTACCATTTTA
1 CCCTCGAACTTT-CC-AAAATTACCATTTTA
* *
5563723 CCC-CTAAAC-TTCTTAAAATT-CCATTTTTAA
1 CCCTC-GAACTTTC-CAAAATTACCA-TTTT-A
*
5563753 CCC-CG-A-TTTCACTGAAATTACCATTTTA
1 CCCTCGAACTTTC-C-AAAATTACCATTTTA
* *
5563781 CCC-CGAAACTTCCCAAAATT-CTATTTTTA
1 CCCTCG-AACTTTCCAAAATTACCA-TTTTA
* *
5563810 ACCTC-TA-TTTCACCAAAAATTACCATTTTA
1 CCCTCGAACTTT--CC-AAAATTACCATTTTA
* *
5563840 CCCCCGAGCTTTCCAAAATT-CCATTTTTAA
1 CCCTCGAACTTTCCAAAATTACCA-TTTT-A
*
5563870 CCCT--AATTTTACCATAAATTACCATTTTA
1 CCCTCGAACTTT-CCA-AAATTACCATTTTA
5563899 CCCTCGAACTTTCCAAAATT-CCATTTTTA
1 CCCTCGAACTTTCCAAAATTACCA-TTTTA
*
5563928 ACCTCG-A-TTTCACCAAAAATTACCATTTTA
1 CCCTCGAACTTT--CC-AAAATTACCATTTTA
* **
5563958 CCCCTCGAACCTTCCAAAA-CCCCATTTTA
1 -CCCTCGAACTTTCCAAAATTACCATTTTA
* * *
5563987 GGCCC-CGATCTCATCAAAAATTACCATTTTA
1 --CCCTCGAACT-TTCCAAAATTACCATTTTA
5564018 -CC-CGTAAGCTTTCCAAAATT-CCATTTTTGA
1 CCCTCG-AA-CTTTCCAAAATTACCA-TTTT-A
*
5564048 CCCT--AA-TTTCACCAAAAAT-CACATTTTTA
1 CCCTCGAACTTT--CCAAAATTAC-CA-TTTTA
** *
5564077 CCCTCGAA-AGT-CAAAATTACCATTTCA
1 CCCTCGAACTTTCCAAAATTACCATTTTA
5564104 CCCTCGA
1 CCCTCGA
5564111 GCATCCAAAG
Statistics
Matches: 390, Mismatches: 52, Indels: 128
0.68 0.09 0.22
Matches are distributed among these distances:
26 3 0.01
27 20 0.05
28 53 0.14
29 163 0.42
30 102 0.26
31 41 0.11
32 6 0.02
33 2 0.01
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
CCCTCGAACTTTCCAAAATTACCATTTTA
Found at i:5563724 original size:59 final size:59
Alignment explanation
Indices: 5563589--5564079 Score: 568
Period size: 59 Copynumber: 8.3 Consensus size: 59
5563579 CTGAACTGTT
**
5563589 CAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTTTATTTTT-ACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCT-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * *
5563647 CAAAAATTACCATTTTACCCCTGAACTTCCCAAAATTCCATTTTTAACCTCGATTTTAC
1 CAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* *
5563706 CAAAAATTACCATTTTACCCCTAAAC-TTCTTAAAATTCCATTTTTAACCCCGATTTCA-
1 CAAAAATTACCATTTTACCCCTGAACTTTC-CAAAATTCCATTTTTAACCCCGATTTCAC
** * * * *
5563764 CTGAAATTACCATTTTACCCC-GAAACTTCCCAAAATTCTATTTTTAACCTCTATTTCAC
1 CAAAAATTACCATTTTACCCCTG-AACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * ** *
5563823 CAAAAATTACCATTTTACCCCCGAGCTTTCCAAAATTCCATTTTTAACCCTAATTTTAC
1 CAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* *
5563882 CATAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCT-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* ** * * *
5563941 CAAAAATTACCATTTTACCCCTCGAACCTTCCAAAACCCCA-TTTTAGGCCCCGATCTCAT
1 CAAAAATTACCATTTTACCCCT-GAACTTTCCAAAATTCCATTTTTA-ACCCCGATTTCAC
* * **
5564001 CAAAAATTACCATTTTACCCGT-AAGCTTTCCAAAATTCCATTTTTGACCCTAATTTCAC
1 CAAAAATTACCATTTTACCCCTGAA-CTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
*
5564060 CAAAAATCA-CATTTTTACCC
1 CAAAAATTACCA-TTTTACCC
5564080 TCGAAAGTCA
Statistics
Matches: 367, Mismatches: 53, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
58 92 0.25
59 220 0.60
60 55 0.15
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:5563795 original size:117 final size:118
Alignment explanation
Indices: 5563589--5564079 Score: 588
Period size: 117 Copynumber: 4.2 Consensus size: 118
5563579 CTGAACTGTT
* **
5563589 CAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTTTATTTTT-ACCCCGATTTCACCAAAA
1 CAAAAATTACCATTTTACCCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
*
5563652 ATTACCATTTTACCCCTGAACTTCCCAAAATTCCATTTTTAACCTCGATTTTAC
66 ATTACCATTTTACCCC-GAACTTCCCAAAATTCCATTTTTAACCTCGATTTCAC
* **
5563706 CAAAAATTACCATTTTACCCCT-AAAC-TTCTTAAAATTCCATTTTTAACCCCGATTTCA-CTGA
1 CAAAAATTACCATTTTACCCCTCAAACTTTC-CAAAATTCCATTTTTAACCCCGATTTCACCAAA
* *
5563768 AATTACCATTTTACCCCGAAACTTCCCAAAATTCTATTTTTAACCTCTATTTCAC
65 AATTACCATTTTACCCCG-AACTTCCCAAAATTCCATTTTTAACCTCGATTTCAC
* * ** * *
5563823 CAAAAATTACCATTTTACCCC-CGAGCTTTCCAAAATTCCATTTTTAACCCTAATTTTACCATAA
1 CAAAAATTACCATTTTACCCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
*
5563887 ATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
66 ATTACCATTTTACCC-CGAACTTCCCAAAATTCCATTTTTAACCTCGATTTCAC
* * ** * * *
5563941 CAAAAATTACCATTTTACCCCTCGAACCTTCCAAAACCCCA-TTTTAGGCCCCGATCTCATCAAA
1 CAAAAATTACCATTTTACCCCTCAAACTTTCCAAAATTCCATTTTTA-ACCCCGATTTCACCAAA
* * *
5564005 AATTACCATTTTA-CCCGTAAGCTTTCCAAAATTCCATTTTTGACC-CTAATTTCAC
65 AATTACCATTTTACCCCG-AA-CTTCCCAAAATTCCATTTTTAACCTC-GATTTCAC
*
5564060 CAAAAATCA-CATTTTTACCC
1 CAAAAATTACCA-TTTTACCC
5564080 TCGAAAGTCA
Statistics
Matches: 326, Mismatches: 34, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
116 4 0.01
117 133 0.41
118 103 0.32
119 86 0.26
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (118 bp):
CAAAAATTACCATTTTACCCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
ATTACCATTTTACCCCGAACTTCCCAAAATTCCATTTTTAACCTCGATTTCAC
Found at i:5565625 original size:41 final size:41
Alignment explanation
Indices: 5565568--5565835 Score: 276
Period size: 41 Copynumber: 6.6 Consensus size: 41
5565558 ATTAGACTTT
** * **
5565568 TATTGCTTTGACCTTTAGCGGCGCTTTCCCATAAGCGTTGC
1 TATTGCTCCGACCTTTAGCGGCGCTTTGCCATAAGCGCCGC
* * *
5565609 TATTGCTCCGACCTTTAGCAGCGCTTGGCCATAAGCGCCTC
1 TATTGCTCCGACCTTTAGCGGCGCTTTGCCATAAGCGCCGC
** **
5565650 TATTGCTTTGACCTTTAGCGGCGCTTATGAGA-AAGCGCCGC
1 TATTGCTCCGACCTTTAGCGGCGCTT-TGCCATAAGCGCCGC
* *
5565691 TATTGCTCCGACCTTTAGCGGGGCTTGGCCATAAGCGCCGC
1 TATTGCTCCGACCTTTAGCGGCGCTTTGCCATAAGCGCCGC
* *
5565732 TATTGCTCCGACCTTTAGCGGCACTTGTGGGC--AAGCGCCGC
1 TATTGCTCCGACCTTTAGCGGCGCTT-T-GCCATAAGCGCCGC
* **
5565773 TATTGCTCTGACCTTTAGCGGCGCTCTT-ATATAAGCGCCGC
1 TATTGCTCCGACCTTTAGCGGCGCT-TTGCCATAAGCGCCGC
* *
5565814 TATTGCT-CTACCTTTTGCGGCG
1 TATTGCTCCGACCTTTAGCGGCG
5565836 TTTTCTTTCC
Statistics
Matches: 188, Mismatches: 32, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
40 14 0.07
41 169 0.90
42 3 0.02
43 2 0.01
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.30
Consensus pattern (41 bp):
TATTGCTCCGACCTTTAGCGGCGCTTTGCCATAAGCGCCGC
Found at i:5565705 original size:82 final size:81
Alignment explanation
Indices: 5565568--5565835 Score: 315
Period size: 82 Copynumber: 3.3 Consensus size: 81
5565558 ATTAGACTTT
*** ** *
5565568 TATTGCTTTGACCTTTAGCGGCGCTTTCCCATAAGCGTTGCTATTGCTCCGACCTTTAGCAGCGC
1 TATTGCTTTGACCTTTAGCGGCGCTTTGAGA-AAGCGCCGCTATTGCTCCGACCTTTAGCGGCGC
*
5565633 TTGGCCATAAGCGCCTC
65 TTGGCCATAAGCGCCGC
*
5565650 TATTGCTTTGACCTTTAGCGGCGCTTATGAGAAAGCGCCGCTATTGCTCCGACCTTTAGCGGGGC
1 TATTGCTTTGACCTTTAGCGGCGCTT-TGAGAAAGCGCCGCTATTGCTCCGACCTTTAGCGGCGC
5565715 TTGGCCATAAGCGCCGC
65 TTGGCCATAAGCGCCGC
** * * * *
5565732 TATTGCTCCGACCTTTAGCGGCACTTGTGGGCAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
1 TATTGCTTTGACCTTTAGCGGCGCTT-TGAGAAAGCGCCGCTATTGCTCCGACCTTTAGCGGCGC
***
5565797 TCT-TATATAAGCGCCGC
65 T-TGGCCATAAGCGCCGC
* *
5565814 TATTGCTCT-ACCTTTTGCGGCG
1 TATTGCTTTGACCTTTAGCGGCG
5565836 TTTTCTTTCC
Statistics
Matches: 162, Mismatches: 22, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
81 11 0.07
82 148 0.91
83 3 0.02
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.30
Consensus pattern (81 bp):
TATTGCTTTGACCTTTAGCGGCGCTTTGAGAAAGCGCCGCTATTGCTCCGACCTTTAGCGGCGCT
TGGCCATAAGCGCCGC
Found at i:5565787 original size:123 final size:121
Alignment explanation
Indices: 5565568--5565835 Score: 326
Period size: 123 Copynumber: 2.2 Consensus size: 121
5565558 ATTAGACTTT
** * ** *
5565568 TATTGCTTTGACCTTTAGCGGCGCTTTCCCATAAGCGTTGCTATTGCTCCGACCTTTAGCAGCGC
1 TATTGCTCCGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCCGACCTTTAGCAGCAC
* *
5565633 TTGGCCATAAGCGCCTCTATTGCTTTGACCTTTAGCGGCG-CTTATGAGAAAGCGCCGC
66 TTGGCCA-AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCCTTAT-A-AAAGCGCCGC
* * *
5565691 TATTGCTCCGACCTTTAGCGGGGCTTGGCCATAAGCGCCGCTATTGCTCCGACCTTTAGCGGCAC
1 TATTGCTCCGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCCGACCTTTAGCAGCAC
* *
5565756 TTGTGGGC-AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTCTTATATAAGCGCCGC
66 -T-TGGCCAAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC-CTTATAAAAGCGCCGC
* *
5565814 TATTGCT-CTACCTTTTGCGGCG
1 TATTGCTCCGACCTTTAGCGGCG
5565836 TTTTCTTTCC
Statistics
Matches: 125, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
122 12 0.10
123 102 0.82
124 2 0.02
125 9 0.07
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.30
Consensus pattern (121 bp):
TATTGCTCCGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCCGACCTTTAGCAGCAC
TTGGCCAAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCCTTATAAAAGCGCCGC
Found at i:5569906 original size:20 final size:20
Alignment explanation
Indices: 5569881--5569919 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5569871 GCAATGGTTG
5569881 CAATTACCTGTATCATTATT
1 CAATTACCTGTATCATTATT
*
5569901 CAATTACCTGTATCGTTAT
1 CAATTACCTGTATCATTAT
5569920 ATTACTGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.44
Consensus pattern (20 bp):
CAATTACCTGTATCATTATT
Found at i:5570698 original size:43 final size:42
Alignment explanation
Indices: 5570622--5570842 Score: 194
Period size: 43 Copynumber: 5.1 Consensus size: 42
5570612 TTTGTTAATA
* * ** * *
5570622 TTAGTGGCGTTTGTGGGAAAAGCATAACAAAAGATCATGGTTT
1 TTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGACCAT-GTTT
* *
5570665 TTAGCGACGTTTGT-GGAATAAGCGTCGCTAAAGACCATGTCAT
1 TTAGCGGCGTTTGTGGGAA-AAGCGTCGCTAAAGACCATGT-TT
* * * * *
5570708 TTAGCGGTGTTTGTGGGAAAAG-TTCCGTTAAAGATCATGGTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGT-CGCTAAAGACCAT-GTTT
5570751 TTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGACCATGTT-T
* ** * * *
5570794 TTAGCGGCGTTTATGATATAAGTGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGACCATGTT-T
5570837 TTAGCG
1 TTAGCG
5570843 ATGTTTTTGA
Statistics
Matches: 146, Mismatches: 25, Indels: 14
0.79 0.14 0.08
Matches are distributed among these distances:
42 9 0.06
43 130 0.89
44 7 0.05
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (42 bp):
TTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGACCATGTTT
Found at i:5570775 original size:86 final size:86
Alignment explanation
Indices: 5570651--5570848 Score: 256
Period size: 86 Copynumber: 2.3 Consensus size: 86
5570641 AAGCATAACA
*
5570651 AAAGATCATGGTTTTTAGCGACGTTTGTGGAATAAGCGTCGCTAAAGACCATG-TCATTTAGCGG
1 AAAGATCATGGTCTTTAGCGACGTTTGTGGAATAAGCGTCGCTAAAGACCATGTTC-TTTAGCGG
* * * * *
5570715 TGTTTGTGGGAAAAGTTCCGTT
65 CGTTTATGAGAAAAGTGCCGCT
*
5570737 AAAGATCATGGTCTTTAGCGGCGTTTGTGGGAA-AAGCGTCGCTAAAGACCATGTTCTTTAGCGG
1 AAAGATCATGGTCTTTAGCGACGTTTGT-GGAATAAGCGTCGCTAAAGACCATGTTCTTTAGCGG
* *
5570801 CGTTTATGATATAAGTGCCGCT
65 CGTTTATGAGAAAAGTGCCGCT
* * *
5570823 AAAGACCATGTTCTTTAGCGATGTTT
1 AAAGATCATGGTCTTTAGCGACGTTT
5570849 TTGAGAAAGT
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
86 91 0.94
87 6 0.06
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (86 bp):
AAAGATCATGGTCTTTAGCGACGTTTGTGGAATAAGCGTCGCTAAAGACCATGTTCTTTAGCGGC
GTTTATGAGAAAAGTGCCGCT
Found at i:5573038 original size:17 final size:17
Alignment explanation
Indices: 5573016--5573056 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
5573006 CGTCGACATT
5573016 GCTGGTCGCAATTCCAA
1 GCTGGTCGCAATTCCAA
5573033 GCTGGTCGCAATTCCAA
1 GCTGGTCGCAATTCCAA
5573050 GCTGGTC
1 GCTGGTC
5573057 TTGTGGCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.24
Consensus pattern (17 bp):
GCTGGTCGCAATTCCAA
Found at i:5575295 original size:11 final size:11
Alignment explanation
Indices: 5575279--5575308 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
5575269 GAGGTATATG
5575279 ATGAATAAATT
1 ATGAATAAATT
5575290 ATGAATAAATT
1 ATGAATAAATT
5575301 ATGAATAA
1 ATGAATAA
5575309 TGATGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (11 bp):
ATGAATAAATT
Found at i:5575449 original size:22 final size:22
Alignment explanation
Indices: 5575390--5575511 Score: 129
Period size: 22 Copynumber: 5.4 Consensus size: 22
5575380 ACACTTGCGC
*
5575390 GCCTACTGTTTAGCAC-GTTTCGT
1 GCCT-CTGTTTAGCACTGTGT-GT
*
5575413 GCCATCTGTTCAGCACTGTGTGT
1 GCC-TCTGTTTAGCACTGTGTGT
5575436 GCCTCTGTTTAGCACTGTGTGT
1 GCCTCTGTTTAGCACTGTGTGT
* * * *
5575458 GCTTCTGTTCAGCATTATGTGT
1 GCCTCTGTTTAGCACTGTGTGT
* *
5575480 GCTTCTGTTTAGCACTTTGTGT
1 GCCTCTGTTTAGCACTGTGTGT
5575502 GCCTACTGTT
1 GCCT-CTGTT
5575512 GCCAGCATTT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
22 58 0.68
23 23 0.27
24 4 0.05
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42
Consensus pattern (22 bp):
GCCTCTGTTTAGCACTGTGTGT
Found at i:5582652 original size:22 final size:22
Alignment explanation
Indices: 5582624--5582687 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 22
5582614 TTTTGTGCCC
5582624 TCTGTTCAGCTTTGTGTGTGCT
1 TCTGTTCAGCTTTGTGTGTGCT
*
5582646 TCTGTTCAGCATTT-TGTATGCT
1 TCTGTTCAGC-TTTGTGTGTGCT
*
5582668 TCTGTTTAGCACTTTGTGTG
1 TCTGTTCAG--CTTTGTGTG
5582688 CCTACTGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 25 0.71
23 6 0.17
24 4 0.11
ACGTcount: A:0.09, C:0.17, G:0.23, T:0.50
Consensus pattern (22 bp):
TCTGTTCAGCTTTGTGTGTGCT
Found at i:5594361 original size:18 final size:19
Alignment explanation
Indices: 5594328--5594364 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5594318 ATCAACAAAA
*
5594328 TAAAATAATTTTAAAATTT
1 TAAAATAATTTGAAAATTT
5594347 TAAAA-AATTTGAAAATTT
1 TAAAATAATTTGAAAATTT
5594365 AAACTTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
TAAAATAATTTGAAAATTT
Found at i:5599773 original size:14 final size:13
Alignment explanation
Indices: 5599740--5599785 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
5599730 GTAAAAAATT
*
5599740 TTAAAAATAGTAA
1 TTAAAAATAATAA
*
5599753 GTGAAAAATAATATA
1 -TTAAAAATAATA-A
5599768 TTAAAAATAATAA
1 TTAAAAATAATAA
5599781 TTAAA
1 TTAAA
5599786 TTAACTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 6 0.21
14 21 0.75
15 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (13 bp):
TTAAAAATAATAA
Found at i:5606530 original size:20 final size:19
Alignment explanation
Indices: 5606505--5606544 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5606495 CTTCATGTAC
5606505 ATATATA-TTGGAATTTAT
1 ATATATATTTGGAATTTAT
* *
5606523 ATATATATTTTGAATTTTT
1 ATATATATTTGGAATTTAT
5606542 ATA
1 ATA
5606545 ATTTATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (19 bp):
ATATATATTTGGAATTTAT
Found at i:5606561 original size:28 final size:28
Alignment explanation
Indices: 5606516--5606582 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
5606506 TATATATTGG
*
5606516 AATTTATATATATATTTT-GAATTTTTAT
1 AATTTATATA-ATATTTTACAATTTTTAT
*
5606544 AATTTATATAACTTTTTTACAATTTTTAT
1 AATTTATATAA-TATTTTACAATTTTTAT
5606573 --TTTATATAAT
1 AATTTATATAAT
5606583 TTATATGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 1 0.03
27 10 0.29
28 15 0.43
29 9 0.26
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (28 bp):
AATTTATATAATATTTTACAATTTTTAT
Found at i:5607780 original size:37 final size:37
Alignment explanation
Indices: 5607731--5607859 Score: 165
Period size: 37 Copynumber: 3.5 Consensus size: 37
5607721 TAAACATATA
* *
5607731 AATAATCTATTCAAAAGAAGAAGAAATATTCCATCAT
1 AATAATCGATTCAAAAGAAGAAGAAATATTCCAACAT
*
5607768 AATAATCGATTCAAAAGAAGCAG---TATTCCAACAT
1 AATAATCGATTCAAAAGAAGAAGAAATATTCCAACAT
* * * *
5607802 TACAATTCGATTCAAAAGAAAAAGAAATATTCCACCAT
1 AATAA-TCGATTCAAAAGAAGAAGAAATATTCCAACAT
5607840 AATAATCGATTCAAAAGAAG
1 AATAATCGATTCAAAAGAAG
5607860 CAGTATTCCA
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
34 13 0.17
35 16 0.21
37 35 0.45
38 13 0.17
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.24
Consensus pattern (37 bp):
AATAATCGATTCAAAAGAAGAAGAAATATTCCAACAT
Found at i:5607786 original size:34 final size:34
Alignment explanation
Indices: 5607748--5607873 Score: 144
Period size: 34 Copynumber: 3.6 Consensus size: 34
5607738 TATTCAAAAG
*
5607748 AAGAAGAAATATTCCATCATAATAATCGATTCAA
1 AAGAAGAAATATTCCAACATAATAATCGATTCAA
* * * *
5607782 AAGAAGCAGTATTCCAACATTACAATTCGATTCAA
1 AAGAAGAAATATTCCAACATAATAA-TCGATTCAA
*
5607817 AAGAAAAAGAAATATTCCACCATAATAATCGATTCAA
1 AAG---AAGAAATATTCCAACATAATAATCGATTCAA
* *
5607854 AAGAAGCAGTATTCCAACAT
1 AAGAAGAAATATTCCAACAT
5607874 TACAATTGAT
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
34 34 0.45
35 12 0.16
37 12 0.16
38 17 0.23
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.24
Consensus pattern (34 bp):
AAGAAGAAATATTCCAACATAATAATCGATTCAA
Found at i:5607856 original size:72 final size:71
Alignment explanation
Indices: 5607739--5607884 Score: 265
Period size: 72 Copynumber: 2.0 Consensus size: 71
5607729 TAAATAATCT
* *
5607739 ATTCAAAAGAAGAAGAAATATTCCATCATAATAATCGATTCAAAAGAAGCAGTATTCCAACATTA
1 ATTCAAAAGAAAAAGAAATATTCCACCATAATAATCGATTCAAAAGAAGCAGTATTCCAACATTA
5607804 CAATTCG
66 CAATT-G
5607811 ATTCAAAAGAAAAAGAAATATTCCACCATAATAATCGATTCAAAAGAAGCAGTATTCCAACATTA
1 ATTCAAAAGAAAAAGAAATATTCCACCATAATAATCGATTCAAAAGAAGCAGTATTCCAACATTA
5607876 CAATTG
66 CAATTG
5607882 ATT
1 ATT
5607885 TAAACATATA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 4 0.06
72 68 0.94
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.25
Consensus pattern (71 bp):
ATTCAAAAGAAAAAGAAATATTCCACCATAATAATCGATTCAAAAGAAGCAGTATTCCAACATTA
CAATTG
Found at i:5607926 original size:54 final size:55
Alignment explanation
Indices: 5607843--5607970 Score: 188
Period size: 54 Copynumber: 2.3 Consensus size: 55
5607833 CCACCATAAT
* * * *
5607843 AATCGATTCAAAAGAAGCAGTATTCCAACATTACAATTGATTTAAACATATAAAC
1 AATCGATTCAAAAAAAACAGTATTCCAACATGACAATTGATTTAAACATAAAAAC
5607898 AATCGATT-AAAAAAAACAGTATTCCAACATGACAATTGATTTAAACATAAAAAC
1 AATCGATTCAAAAAAAACAGTATTCCAACATGACAATTGATTTAAACATAAAAAC
*
5607952 AATTC-ATTCAAAAGAAACA
1 AA-TCGATTCAAAAAAAACA
5607971 ACATTTTTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
54 47 0.71
55 19 0.29
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.25
Consensus pattern (55 bp):
AATCGATTCAAAAAAAACAGTATTCCAACATGACAATTGATTTAAACATAAAAAC
Found at i:5609632 original size:19 final size:19
Alignment explanation
Indices: 5609604--5609644 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5609594 AGTTTATTTA
5609604 AAAATAAATAAATAATAAG
1 AAAATAAATAAATAATAAG
* * *
5609623 AAAATTAATAATTATTAAG
1 AAAATAAATAAATAATAAG
5609642 AAA
1 AAA
5609645 TTTCCCTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAATAAATAAATAATAAG
Found at i:5612871 original size:31 final size:31
Alignment explanation
Indices: 5612835--5612923 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
5612825 TGAAAAACCC
** * *
5612835 TTATTTGAACACTTTTTAAAATATTTGATAT
1 TTATTTGAACACTTTCGAAAAGATTTGACAT
* *
5612866 TTATTTGATCACTTTCGAAAAGATTTGACCT
1 TTATTTGAACACTTTCGAAAAGATTTGACAT
* *
5612897 TTATTTGACCAATTT-G-AAAGATTTGAC
1 TTATTTGAACACTTTCGAAAAGATTTGAC
5612924 CTTATGTGAG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
29 11 0.22
30 1 0.02
31 38 0.76
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (31 bp):
TTATTTGAACACTTTCGAAAAGATTTGACAT
Found at i:5612924 original size:29 final size:31
Alignment explanation
Indices: 5612865--5612926 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 31
5612855 ATATTTGATA
* *
5612865 TTTATTTGATCACTTTCGAAAAGATTTGACC
1 TTTATTTGACCAATTTCGAAAAGATTTGACC
5612896 TTTATTTGACCAATTT-G-AAAGATTTGACC
1 TTTATTTGACCAATTTCGAAAAGATTTGACC
5612925 TT
1 TT
5612927 ATGTGAGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 14 0.48
30 1 0.03
31 14 0.48
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.44
Consensus pattern (31 bp):
TTTATTTGACCAATTTCGAAAAGATTTGACC
Found at i:5617350 original size:30 final size:30
Alignment explanation
Indices: 5617316--5617375 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
5617306 ATATATGTTT
* * *
5617316 GTTTTGGGGCCTAATTAAAATTTTTAAAAA
1 GTTTTGGAGACTAATTAAAAGTTTTAAAAA
*
5617346 GTTTTGGAGATTAATTAAAAGTTTTAAAAA
1 GTTTTGGAGACTAATTAAAAGTTTTAAAAA
5617376 ATTTGAAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (30 bp):
GTTTTGGAGACTAATTAAAAGTTTTAAAAA
Found at i:5619065 original size:39 final size:40
Alignment explanation
Indices: 5619020--5619109 Score: 146
Period size: 39 Copynumber: 2.2 Consensus size: 40
5619010 AAAAATTATA
* *
5619020 TTTAATATAATAAAATATTTCTTATATTTAT-TTGTGTTT
1 TTTAATATAATAAAATATTTATTATATTTATATAGTGTTT
5619059 TTTAATATAATAAAATATTTATTATATTTATGATAGTGTTT
1 TTTAATATAATAAAATATTTATTATATTTAT-ATAGTGTTT
5619100 TTTAATATAA
1 TTTAATATAA
5619110 ATACTTTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 30 0.64
41 17 0.36
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.56
Consensus pattern (40 bp):
TTTAATATAATAAAATATTTATTATATTTATATAGTGTTT
Found at i:5619569 original size:43 final size:43
Alignment explanation
Indices: 5619475--5619700 Score: 260
Period size: 43 Copynumber: 5.3 Consensus size: 43
5619465 TTATTAGGAA
* * * * * *
5619475 AAACACCGCTATAGAACATGATCTTTAACGGTGCTTT-TCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
* * * *
5619517 AAAGGCCGCTAAAGAACATGGTCTTCAGCGGCACTTACCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
* * *
5619560 AAACGCCGCTGAAGACCATGGTCTTTAGCGGCGC-TTCCCTAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
* * *
5619602 AAGCCCCGCTGAAA-ACCATGGTCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCT-AAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
*
5619645 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
*
5619688 AAACGCTGCTAAA
1 AAACGCCGCTAAA
5619701 ATTCACAGAT
Statistics
Matches: 154, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
42 65 0.42
43 89 0.58
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
Found at i:5620035 original size:21 final size:21
Alignment explanation
Indices: 5619984--5620035 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 21
5619974 ATTTTCTTGT
* * *
5619984 TGCCTCTGCTTCCCTCGCTGC
1 TGCCTCCGCTCCCCTCGCTAC
* * *
5620005 TACTTTCGCTCCCCTCGCTAC
1 TGCCTCCGCTCCCCTCGCTAC
5620026 TGCCTCCGCT
1 TGCCTCCGCT
5620036 TTAAGTTGTA
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.48, G:0.15, T:0.33
Consensus pattern (21 bp):
TGCCTCCGCTCCCCTCGCTAC
Found at i:5621589 original size:39 final size:40
Alignment explanation
Indices: 5621546--5621635 Score: 155
Period size: 39 Copynumber: 2.2 Consensus size: 40
5621536 AAAAATTATA
*
5621546 TTTAATATAATAAAATATTTATTATTTTTAT-TTTTATTT
1 TTTAATATAATAAAATATTTATTATTTTTATGTATTATTT
5621585 TTTAATATAATAAAATATTTATTATTTTTATGGTATTATTT
1 TTTAATATAATAAAATATTTATTATTTTTAT-GTATTATTT
5621626 TTTAATATAA
1 TTTAATATAA
5621636 ATATTTTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 31 0.65
41 17 0.35
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (40 bp):
TTTAATATAATAAAATATTTATTATTTTTATGTATTATTT
Found at i:5621714 original size:17 final size:18
Alignment explanation
Indices: 5621694--5621728 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5621684 TAGTATATTA
*
5621694 TATTTTTTAA-AAAAACT
1 TATTTTTAAATAAAAACT
5621711 TATTTTTAAATAAAAACT
1 TATTTTTAAATAAAAACT
5621729 AACAATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTTTTAAATAAAAACT
Found at i:5625641 original size:36 final size:35
Alignment explanation
Indices: 5625515--5625681 Score: 154
Period size: 36 Copynumber: 4.7 Consensus size: 35
5625505 TCAAAGGAAA
* *
5625515 GCATATGTCTCGGTTAGATCATATTGGTAAGATGTT
1 GCATATGTCTCGGTTAGAGCATATTGCTAA-ATGTT
** * *
5625551 GCATATGTCTCGGTTAGAGTGTATTGTTATGATGTT
1 GCATATGTCTCGGTTAGAGCATATTGCTA-AATGTT
* *
5625587 GCATATGTCTCGATTAGAGCATACTGCTACAATGTT
1 GCATATGTCTCGGTTAGAGCATATTGCTA-AATGTT
* * * * * *
5625623 GCATACGTCTCGGTTAGAGCGTAATGCTAAGTAATC
1 GCATATGTCTCGGTTAGAGCATATTGCTAAAT-GTT
* *
5625659 GCTTATGTCTCAGTTAGAGCATA
1 GCATATGTCTCGGTTAGAGCATA
5625682 AGGCCATTTT
Statistics
Matches: 106, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
35 2 0.02
36 104 0.98
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (35 bp):
GCATATGTCTCGGTTAGAGCATATTGCTAAATGTT
Found at i:5625666 original size:72 final size:72
Alignment explanation
Indices: 5625515--5625681 Score: 178
Period size: 72 Copynumber: 2.3 Consensus size: 72
5625505 TCAAAGGAAA
* * * * * * * *
5625515 GCATATGTCTCGGTTAGATCATATTGGTAAGATGTTGCATATGTCTCGGTTAGAGTGTATTGTTA
1 GCATATGTCTCGATTAGAGCATACTGCTAAGATGTTGCATACGTCTCGGTTAGAGCGTAATGCTA
* * *
5625580 TGATGTT
66 AGATATC
5625587 GCATATGTCTCGATTAGAGCATACTGCTACA-ATGTTGCATACGTCTCGGTTAGAGCGTAATGCT
1 GCATATGTCTCGATTAGAGCATACTGCTA-AGATGTTGCATACGTCTCGGTTAGAGCGTAATGCT
5625651 AAG-TAATC
65 AAGAT-ATC
*
5625659 GCTTATGTCTC-AGTTAGAGCATA
1 GCATATGTCTCGA-TTAGAGCATA
5625682 AGGCCATTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
71 2 0.03
72 77 0.96
73 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (72 bp):
GCATATGTCTCGATTAGAGCATACTGCTAAGATGTTGCATACGTCTCGGTTAGAGCGTAATGCTA
AGATATC
Found at i:5627008 original size:81 final size:80
Alignment explanation
Indices: 5626869--5627079 Score: 273
Period size: 80 Copynumber: 2.6 Consensus size: 80
5626859 TTAACCAGTA
* * * * *
5626869 CATGATGCTGCTAACACAAGCTATCAGGAAATTGCAATATATAG-AGAATCCCAACCATCGGT-G
1 CATGATGCTGCTCACACAAGCTGTCAAGAAACTGCAACATAT-GCAGAATCCCAACCATC-GTAG
5626932 CGGTCCATATTACCCACT
64 -GGTCCATATTACCCACT
*
5626950 CATGATGCTGCTCACACAAGCTGTCAAGAAACTGCAACATATGCAGAATCCCAGCCATCGTAGGG
1 CATGATGCTGCTCACACAAGCTGTCAAGAAACTGCAACATATGCAGAATCCCAACCATCGTAGGG
*
5627015 TCCATGTTACCCACT
66 TCCATATTACCCACT
* * * * *
5627030 CACGATGATGCTCACAGAAGTTGTCAAGAAACTACAACATATGCAGAATC
1 CATGATGCTGCTCACACAAGCTGTCAAGAAACTGCAACATATGCAGAATC
5627080 TTAGTCATCG
Statistics
Matches: 116, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
80 64 0.55
81 52 0.45
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (80 bp):
CATGATGCTGCTCACACAAGCTGTCAAGAAACTGCAACATATGCAGAATCCCAACCATCGTAGGG
TCCATATTACCCACT
Found at i:5630952 original size:22 final size:22
Alignment explanation
Indices: 5630924--5630965 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5630914 ACTTACCAAG
* *
5630924 CAAGTCTTGAGACATAATGATC
1 CAAGTCTTAAGACACAATGATC
5630946 CAAGTCTTAAGACACAATGA
1 CAAGTCTTAAGACACAATGA
5630966 CTTATATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (22 bp):
CAAGTCTTAAGACACAATGATC
Found at i:5632851 original size:20 final size:20
Alignment explanation
Indices: 5632809--5632900 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
5632799 ACAGGATTAT
* * * *
5632809 ACTTCAGTGCCTTTGTTTGC
1 ACTTCAGTGTCTCTATTTAC
*
5632829 ACTTCGGTGTCTCTATTTAC
1 ACTTCAGTGTCTCTATTTAC
* * * *
5632849 ACTTCAGTGCCTTTGTTTGC
1 ACTTCAGTGTCTCTATTTAC
*
5632869 ACTTCGGTGTCTCTATTTAC
1 ACTTCAGTGTCTCTATTTAC
5632889 ACTTCAGTGTCT
1 ACTTCAGTGTCT
5632901 TTGTTTGAAC
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (20 bp):
ACTTCAGTGTCTCTATTTAC
Found at i:5632864 original size:40 final size:40
Alignment explanation
Indices: 5632809--5632922 Score: 192
Period size: 40 Copynumber: 2.9 Consensus size: 40
5632799 ACAGGATTAT
5632809 ACTTCAGTGCCTTTGTTTGCACTTCGGTGTCTCTATTTAC
1 ACTTCAGTGCCTTTGTTTGCACTTCGGTGTCTCTATTTAC
5632849 ACTTCAGTGCCTTTGTTTGCACTTCGGTGTCTCTATTTAC
1 ACTTCAGTGCCTTTGTTTGCACTTCGGTGTCTCTATTTAC
* * * *
5632889 ACTTCAGTGTCTTTGTTTGAACTACGGTGCCTCT
1 ACTTCAGTGCCTTTGTTTGCACTTCGGTGTCTCT
5632923 GATCGCACAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 70 1.00
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.44
Consensus pattern (40 bp):
ACTTCAGTGCCTTTGTTTGCACTTCGGTGTCTCTATTTAC
Found at i:5632982 original size:20 final size:21
Alignment explanation
Indices: 5632936--5632985 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5632926 CGCACAATCG
* *
5632936 TGCCTTTG-TTAGCACTACGA
1 TGCCTCTGTTTAGCACTACAA
*
5632956 TGCCTCTGTTTAGCATTACAA
1 TGCCTCTGTTTAGCACTACAA
5632977 TGCTCTCTG
1 TGC-CTCTG
5632986 GTGTGGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.28
21 13 0.52
22 5 0.20
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (21 bp):
TGCCTCTGTTTAGCACTACAA
Found at i:5634451 original size:29 final size:29
Alignment explanation
Indices: 5634419--5634477 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
5634409 TCCACCTGGA
* * *
5634419 CACGAATTATCTACGAACAAGTTCTTCAC
1 CACGAACTATCAACGAACAAGTTCTCCAC
*
5634448 CACGAACTCTCAACGAACAAGTTCTCCAC
1 CACGAACTATCAACGAACAAGTTCTCCAC
5634477 C
1 C
5634478 TCTTCCACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.10, T:0.22
Consensus pattern (29 bp):
CACGAACTATCAACGAACAAGTTCTCCAC
Found at i:5651537 original size:45 final size:45
Alignment explanation
Indices: 5651487--5651576 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
5651477 TTAATTTGTC
5651487 GATAATGAATGCAAGGTTGCGAAATGACATCACTACATATCATTA
1 GATAATGAATGCAAGGTTGCGAAATGACATCACTACATATCATTA
5651532 GATAATGAATGCAAGGTTGCGAAATGACATCACTACATATCATTA
1 GATAATGAATGCAAGGTTGCGAAATGACATCACTACATATCATTA
5651577 ACTCGATGAT
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:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (45 bp):
GATAATGAATGCAAGGTTGCGAAATGACATCACTACATATCATTA
Found at i:5657024 original size:11 final size:11
Alignment explanation
Indices: 5656997--5657026 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
5656987 AACTCGTGCA
5656997 TCCAAAAACAC
1 TCCAAAAACAC
5657008 TCCCAAAAACAC
1 T-CCAAAAACAC
5657020 TCCAAAA
1 TCCAAAA
5657027 CCTTCATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.37, G:0.00, T:0.10
Consensus pattern (11 bp):
TCCAAAAACAC
Found at i:5657738 original size:17 final size:18
Alignment explanation
Indices: 5657718--5657757 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5657708 TTAGTTTTAA
5657718 TGCATTTT-TATTGTCAT
1 TGCATTTTATATTGTCAT
*
5657735 TGCATTTTATTTTGTCAT
1 TGCATTTTATATTGTCAT
*
5657753 CGCAT
1 TGCAT
5657758 CATTTTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.55
Consensus pattern (18 bp):
TGCATTTTATATTGTCAT
Found at i:5660053 original size:20 final size:20
Alignment explanation
Indices: 5660028--5660065 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5660018 TATCAACTAT
5660028 ACTTGCATCAA-CGTGTGTAC
1 ACTTGCA-CAATCGTGTGTAC
5660048 ACTTGCACAATCGTGTGT
1 ACTTGCACAATCGTGTGT
5660066 CGTAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
ACTTGCACAATCGTGTGTAC
Found at i:5660962 original size:24 final size:23
Alignment explanation
Indices: 5660930--5660977 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
5660920 AATAAAAATT
5660930 TTAAATATTTGTAAACAATTAATA
1 TTAAATATTTGTAAA-AATTAATA
* *
5660954 TTAAGTATTTGTAAAATTTAATA
1 TTAAATATTTGTAAAAATTAATA
5660977 T
1 T
5660978 CTATATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (23 bp):
TTAAATATTTGTAAAAATTAATA
Found at i:5664993 original size:58 final size:59
Alignment explanation
Indices: 5664889--5665032 Score: 175
Period size: 58 Copynumber: 2.5 Consensus size: 59
5664879 TTAATATAAC
* * * * * *
5664889 ATTTGGTACTTGAATTTGATATTTTTTTTAAATTTGGCACTTAAACTTTTTTTGG-TCTA
1 ATTTGGTACTTGAACTTGACACTTTTTTTAAAGTTGGCACTTAAAC-TTTTTGGGATCCA
*
5664948 ATTTGGTACTTAAACTTGACACTTTTTTT-AAGTTGGCACTTAAACTTTTTGGGATCCA
1 ATTTGGTACTTGAACTTGACACTTTTTTTAAAGTTGGCACTTAAACTTTTTGGGATCCA
* * *
5665006 AATTGGTACCTGAACTTGACTCTTTTT
1 ATTTGGTACTTGAACTTGACACTTTTT
5665033 CCTAATTGGT
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
57 7 0.10
58 41 0.56
59 25 0.34
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (59 bp):
ATTTGGTACTTGAACTTGACACTTTTTTTAAAGTTGGCACTTAAACTTTTTGGGATCCA
Found at i:5665294 original size:28 final size:28
Alignment explanation
Indices: 5665216--5665307 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 28
5665206 AATTGAATCT
*
5665216 TAAAAAAAGCTTAGGTACCAAATTAGGA
1 TAAAAAAAGTTTAGGTACCAAATTAGGA
* * * * *
5665244 AAAAAATGTCAAGTTCAAGTACCAAATTGGGC
1 TAAAAA----AAGTTTAGGTACCAAATTAGGA
5665276 TAAAAAAAGTTTAGGTACCAAATTAGGA
1 TAAAAAAAGTTTAGGTACCAAATTAGGA
5665304 -AAAA
1 TAAAA
5665308 GTGTCAAGTT
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
27 4 0.08
28 23 0.47
32 22 0.45
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (28 bp):
TAAAAAAAGTTTAGGTACCAAATTAGGA
Found at i:5665316 original size:59 final size:60
Alignment explanation
Indices: 5665199--5665389 Score: 231
Period size: 60 Copynumber: 3.2 Consensus size: 60
5665189 TAATAAATTT
* * * *
5665199 AGTACCAAATTGAATCTTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAAATGTCAAGTTCA
1 AGTACCAAATTGGAGC-TAAAAAAAGTTTAGGTACCAAATTAGG-AAAAAGTGTCAAGTTCA
5665261 AGTACCAAATTGG-GCTAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCA
1 AGTACCAAATTGGAGCTAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCA
* * * * * * * * *
5665320 AATACCAAAATGGATCAAAAAAAAGTTAAGGTATCAACTTAAGAAAAAGTGTTAAGTTCA
1 AGTACCAAATTGGAGCTAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCA
*
5665380 AGTACTAAAT
1 AGTACCAAAT
5665390 GTTATATTAA
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
59 27 0.24
60 72 0.64
61 1 0.01
62 12 0.11
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (60 bp):
AGTACCAAATTGGAGCTAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCA
Found at i:5671374 original size:2 final size:2
Alignment explanation
Indices: 5671367--5671393 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5671357 TTTGCTCCTT
5671367 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
5671394 GCAATTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5681477 original size:32 final size:32
Alignment explanation
Indices: 5681383--5681477 Score: 84
Period size: 32 Copynumber: 3.0 Consensus size: 32
5681373 TGGTTTGAGG
* * * * *
5681383 GGTTTTAAAAATGTGGGGGTTTTCGGGTTTTA
1 GGTTTTAAAAATTTAGGGATTTTCAGGATTTA
* * * *
5681415 GATTTTAAAATTTTTGGGAATTT-AGGGATTTA
1 GGTTTTAAAAATTTAGGGATTTTCA-GGATTTA
*
5681447 GGTTTTAAAAATTTAGGGATTTTCATGATTT
1 GGTTTTAAAAATTTAGGGATTTTCAGGATTT
5681478 TTAAGGTTGT
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
32 47 0.98
33 1 0.02
ACGTcount: A:0.26, C:0.02, G:0.25, T:0.46
Consensus pattern (32 bp):
GGTTTTAAAAATTTAGGGATTTTCAGGATTTA
Found at i:5681537 original size:44 final size:43
Alignment explanation
Indices: 5681487--5681575 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 43
5681477 TTTAAGGTTG
* *
5681487 TTGGGTTTGGGGAATTTGGTTTAGGTTTAAGAAATTTGGGGATT
1 TTGGGTTTGGAGAATTTGGTTTAAGTTTAA-AAATTTGGGGATT
*
5681531 TTGGGTTTGGAGATTTTGGTTTAAGTTTAAAAATTTGGGGATT
1 TTGGGTTTGGAGAATTTGGTTTAAGTTTAAAAATTTGGGGATT
5681574 TT
1 TT
5681576 CGAGACTTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 15 0.36
44 27 0.64
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (43 bp):
TTGGGTTTGGAGAATTTGGTTTAAGTTTAAAAATTTGGGGATT
Found at i:5683352 original size:18 final size:18
Alignment explanation
Indices: 5683325--5683360 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5683315 CTGTTAGTGA
* *
5683325 AGGTGTTGAGGGTGAGGG
1 AGGTGGTGAGGATGAGGG
5683343 AGGTGGTGAGGATGAGGG
1 AGGTGGTGAGGATGAGGG
5683361 TGAGGGAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.61, T:0.19
Consensus pattern (18 bp):
AGGTGGTGAGGATGAGGG
Found at i:5683541 original size:63 final size:59
Alignment explanation
Indices: 5683480--5683647 Score: 170
Period size: 54 Copynumber: 2.8 Consensus size: 59
5683470 AGTAAGGGTA
*
5683480 GTGAGGGTTTGAAAGGTGGTGAGGGTTCGAGTAAGGGTGATGTTAGTGAAGGTGTTGAGG-
1 GTGAGGG--TGAAAGGTGGTGAGGGTTCGAGTAAGGGTGCTGTTAGTGAAGGTGTTGAGGT
*
5683540 GTGA-GG-G--AGGTGGTGAGGG-T-GAGGGAAGGGGTGCTGTTAGTGAAGGTGTTGAAGGT
1 GTGAGGGTGAAAGGTGGTGAGGGTTCGA-GTAA-GGGTGCTGTTAGTGAAGGTGTTG-AGGT
* * *
5683596 GTTGAGGGTGAAGGAGGTGGTGAGGGTTCGGGTAAAGGTGCTATTAGTGAAG
1 G-TGAGGGTGAA--AGGTGGTGAGGGTTCGAGTAAGGGTGCTGTTAGTGAAG
5683648 ATGATATTTA
Statistics
Matches: 89, Mismatches: 6, Indels: 23
0.75 0.05 0.19
Matches are distributed among these distances:
52 2 0.02
53 4 0.04
54 34 0.38
55 3 0.03
56 2 0.02
57 3 0.03
58 2 0.02
59 3 0.03
60 4 0.04
63 27 0.30
64 4 0.04
65 1 0.01
ACGTcount: A:0.21, C:0.02, G:0.51, T:0.26
Consensus pattern (59 bp):
GTGAGGGTGAAAGGTGGTGAGGGTTCGAGTAAGGGTGCTGTTAGTGAAGGTGTTGAGGT
Done.