Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 88 of 163
Found at i:28492690 original size:24 final size:24
Alignment explanation
Indices: 28492638--28492696 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
28492628 TCTGTGGTTA
*
28492638 AATGACTAATTTGTCTGTGTTTGG
1 AATGACTGATTTGTCTGTGTTTGG
*
28492662 TATGACTGATTTGTCTGTGATTT-G
1 AATGACTGATTTGTCTGTG-TTTGG
28492686 AATGACTGATT
1 AATGACTGATT
28492697 CTGAGCATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.46
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGTTTGG
Found at i:28492802 original size:27 final size:27
Alignment explanation
Indices: 28492760--28492824 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
28492750 ATGGAGGAAG
*
28492760 TACTGTT-CTAGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTGGCT-TGGCCACATA
28492785 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
*
28492813 TACTATTACTGG
1 TACTGTTACTGG
28492825 CAGCTTTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 7 0.21
27 24 0.71
28 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:28492830 original size:27 final size:27
Alignment explanation
Indices: 28492778--28492830 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
28492768 TAGTGGCTCT
* **
28492778 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAATCACTATTACTGGCAGCTTG
28492805 GCCACATAT-ACTATTACTGGCAGCTT
1 GCCACA-ATCACTATTACTGGCAGCTT
28492831 TGCTGCGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTATTACTGGCAGCTTG
Found at i:28492877 original size:26 final size:26
Alignment explanation
Indices: 28492822--28492877 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
28492812 ATACTATTAC
* *
28492822 TGGCAGCTTTGCTGCGATACTGCTGC
1 TGGCAGCTTTGCTGCGATACTACTGA
* *
28492848 TGGCAGCTTTGCTGTGATGCTACTGA
1 TGGCAGCTTTGCTGCGATACTACTGA
28492874 TGGC
1 TGGC
28492878 TTTGTGCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.12, C:0.23, G:0.32, T:0.32
Consensus pattern (26 bp):
TGGCAGCTTTGCTGCGATACTACTGA
Found at i:28492988 original size:32 final size:32
Alignment explanation
Indices: 28492868--28492989 Score: 156
Period size: 32 Copynumber: 3.8 Consensus size: 32
28492858 GCTGTGATGC
*
28492868 TACTGATGGCTTTGTGCCAATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
28492900 TACTAATAGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
**
28492932 TACTGATGAATTTGTG-CGAATCATATTACCGT
1 TACTGATGGCTTTGTGCCG-ATCATATTACCGT
* * *
28492964 TACTGATGGCTGTGTACCGGTCATAT
1 TACTGATGGCTTTGTGCCGATCATAT
28492990 CACTACTACT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
31 2 0.03
32 72 0.95
33 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:28492988 original size:64 final size:64
Alignment explanation
Indices: 28492868--28492989 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
28492858 GCTGTGATGC
** * *
28492868 TACTGATGGCTTTGTGCCAATCATATTACCGTTACTAATAGCTTTGTGCCGATCATATTACCGT
1 TACTGATGAATTTGTGCCAATCATATTACCGTTACTAATAGCTGTGTACCGATCATATTACCGT
* * * *
28492932 TACTGATGAATTTGTGCGAATCATATTACCGTTACTGATGGCTGTGTACCGGTCATAT
1 TACTGATGAATTTGTGCCAATCATATTACCGTTACTAATAGCTGTGTACCGATCATAT
28492990 CACTACTACT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (64 bp):
TACTGATGAATTTGTGCCAATCATATTACCGTTACTAATAGCTGTGTACCGATCATATTACCGT
Found at i:28493010 original size:64 final size:64
Alignment explanation
Indices: 28492875--28493023 Score: 163
Period size: 64 Copynumber: 2.3 Consensus size: 64
28492865 TGCTACTGAT
* * * ** * *
28492875 GGCTTTGTGCCAATCATATTACCGTTACTAATAGCTTTGTGCCGATCATATTACCGTTACTGAT
1 GGCTTTGTGCCAATCATATTACCGTTACTAATAGCTGTGTACCGATCATATCACCACTACTAAA
** * * * * *
28492939 GAATTTGTGCGAATCATATTACCGTTACTGATGGCTGTGTACCGGTCATATCACTACTACTAAA
1 GGCTTTGTGCCAATCATATTACCGTTACTAATAGCTGTGTACCGATCATATCACCACTACTAAA
*
28493003 GGCTTTGTGCCAATGATATTA
1 GGCTTTGTGCCAATCATATTA
28493024 TTGTACTTAT
Statistics
Matches: 67, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (64 bp):
GGCTTTGTGCCAATCATATTACCGTTACTAATAGCTGTGTACCGATCATATCACCACTACTAAA
Found at i:28507116 original size:53 final size:53
Alignment explanation
Indices: 28507058--28507160 Score: 188
Period size: 53 Copynumber: 1.9 Consensus size: 53
28507048 GTAAACAAAG
* *
28507058 TAAGCTTTTATAGCTTAGTAATTTTATAGCATAACCACAAATATATATATTTA
1 TAAGCTTTTATAGCTTAGTAAGTCTATAGCATAACCACAAATATATATATTTA
28507111 TAAGCTTTTATAGCTTAGTAAGTCTATAGCATAACCACAAATATATATAT
1 TAAGCTTTTATAGCTTAGTAAGTCTATAGCATAACCACAAATATATATAT
28507161 AAATATATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.39
Consensus pattern (53 bp):
TAAGCTTTTATAGCTTAGTAAGTCTATAGCATAACCACAAATATATATATTTA
Found at i:28511081 original size:25 final size:27
Alignment explanation
Indices: 28511044--28511103 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
28511034 ATAGTATAGT
*
28511044 TATTTTGAATTAATTTAATATAATTTATAA
1 TATTTT-AATTAA-ATAATAT-ATTTATAA
*
28511074 TATTTTAATTAAATAATATTTTTATAA
1 TATTTTAATTAAATAATATATTTATAA
28511101 TAT
1 TAT
28511104 AAATCAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 10 0.36
28 6 0.21
29 6 0.21
30 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
TATTTTAATTAAATAATATATTTATAA
Found at i:28511105 original size:16 final size:17
Alignment explanation
Indices: 28511069--28511105 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
28511059 TAATATAATT
28511069 TATAATATTTTAATTAA
1 TATAATATTTTAATTAA
*
28511086 -ATAATATTTTTA-TAA
1 TATAATATTTTAATTAA
28511101 TATAA
1 TATAA
28511106 ATCAAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAATATTTTAATTAA
Found at i:28518088 original size:21 final size:23
Alignment explanation
Indices: 28518063--28518137 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
28518053 GACATACGAG
*
28518063 GTGTCT-A-ATAATACACATAAA
1 GTGTCTGAGATAAGACACATAAA
*
28518084 GTGTCTGAGATACGACACATAAA
1 GTGTCTGAGATAAGACACATAAA
*
28518107 GTGTCTGATG-TACGACACATAAA
1 GTGTCTGA-GATAAGACACATAAA
*
28518130 GTGCCTGA
1 GTGTCTGA
28518138 TCGGCAAACC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
21 6 0.12
22 1 0.02
23 40 0.83
24 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (23 bp):
GTGTCTGAGATAAGACACATAAA
Found at i:28518101 original size:23 final size:23
Alignment explanation
Indices: 28518075--28518138 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
28518065 GTCTAATAAT
28518075 ACACATAAAGTGTCTGA-GATACG
1 ACACATAAAGTGTCTGATG-TACG
28518098 ACACATAAAGTGTCTGATGTACG
1 ACACATAAAGTGTCTGATGTACG
*
28518121 ACACATAAAGTGCCTGAT
1 ACACATAAAGTGTCTGAT
28518139 CGGCAAACCG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (23 bp):
ACACATAAAGTGTCTGATGTACG
Found at i:28518464 original size:16 final size:17
Alignment explanation
Indices: 28518443--28518474 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28518433 TAATAATAAT
28518443 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
28518459 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
28518475 GCTTACCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:28519213 original size:30 final size:27
Alignment explanation
Indices: 28519177--28519241 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
28519167 TTTCCTATAA
*
28519177 TATAATATCTTAACTTTAATTAATATAATT
1 TATAATATCTTAA--TTAAATAATAT-ATT
* *
28519207 TATAATATTTTAATTAAATAATATTTT
1 TATAATATCTTAATTAAATAATATATT
28519234 TATAATAT
1 TATAATAT
28519242 AAATCAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.31
28 10 0.31
30 12 0.38
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
TATAATATCTTAATTAAATAATATATT
Found at i:28519243 original size:16 final size:17
Alignment explanation
Indices: 28519207--28519243 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
28519197 TAATATAATT
28519207 TATAATATTTTAATTAA
1 TATAATATTTTAATTAA
*
28519224 -ATAATATTTTTA-TAA
1 TATAATATTTTAATTAA
28519239 TATAA
1 TATAA
28519244 ATCAAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAATATTTTAATTAA
Found at i:28522557 original size:36 final size:37
Alignment explanation
Indices: 28522510--28522600 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 37
28522500 GTCTCCAAAT
* *
28522510 TCACATTTCAATTCAATTTCACTTTTTCACTTTCAA-
1 TCACAATTCAATTCAATTTCACTTTTCCACTTTCAAG
* *
28522546 TCACAATTCAATTCAAAATTCACTTTTCCATTTTCAAG
1 TCACAATTCAATTC-AATTTCACTTTTCCACTTTCAAG
*
28522584 TCA-ATATTCATTTCAAT
1 TCACA-ATTCAATTCAAT
28522601 CCCACACATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
36 13 0.28
37 22 0.48
38 11 0.24
ACGTcount: A:0.32, C:0.23, G:0.01, T:0.44
Consensus pattern (37 bp):
TCACAATTCAATTCAATTTCACTTTTCCACTTTCAAG
Found at i:28523308 original size:9 final size:9
Alignment explanation
Indices: 28523296--28523327 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
28523286 TTTTCCATTC
28523296 TTTCTTTCT
1 TTTCTTTCT
28523305 TTTCTTTCT
1 TTTCTTTCT
*
28523314 TTCCTTTCT
1 TTTCTTTCT
28523323 TTTCT
1 TTTCT
28523328 CCATGTGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:28523309 original size:13 final size:13
Alignment explanation
Indices: 28523287--28523324 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
28523277 AACTCTAGTT
*
28523287 TTTCCATTCTTTC
1 TTTCCTTTCTTTC
*
28523300 TTTCTTTTCTTTC
1 TTTCCTTTCTTTC
28523313 TTTCCTTTCTTT
1 TTTCCTTTCTTT
28523325 TCTCCATGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCCTTTCTTTC
Found at i:28523537 original size:11 final size:11
Alignment explanation
Indices: 28523499--28523537 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
28523489 TTAATTATAA
28523499 TATAATTAATT
1 TATAATTAATT
*
28523510 TAATAATATACTT
1 T-ATAAT-TAATT
28523523 TATAATTAATT
1 TATAATTAATT
28523534 TATA
1 TATA
28523538 TATTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATTAATT
Found at i:28534335 original size:11 final size:11
Alignment explanation
Indices: 28534319--28534343 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28534309 GAACAGTGCT
28534319 GACGTGGCCGC
1 GACGTGGCCGC
28534330 GACGTGGCCGC
1 GACGTGGCCGC
28534341 GAC
1 GAC
28534344 TTGCCCCGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.36, G:0.44, T:0.08
Consensus pattern (11 bp):
GACGTGGCCGC
Found at i:28534478 original size:11 final size:11
Alignment explanation
Indices: 28534456--28534528 Score: 105
Period size: 11 Copynumber: 6.6 Consensus size: 11
28534446 AACTAATCCT
28534456 CTCTCAAATTTC
1 CTCTC-AATTTC
28534468 CTCTCAATTTC
1 CTCTCAATTTC
*
28534479 CTCTCAACTTC
1 CTCTCAATTTC
28534490 CTCTCAATTTC
1 CTCTCAATTTC
28534501 CT-TCAAATTTC
1 CTCTC-AATTTC
28534512 CTCTCAATTTC
1 CTCTCAATTTC
28534523 CT-TCAA
1 CTCTCAA
28534529 AAAATCTCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
10 6 0.11
11 44 0.77
12 7 0.12
ACGTcount: A:0.22, C:0.36, G:0.00, T:0.42
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:28534493 original size:22 final size:22
Alignment explanation
Indices: 28534459--28534529 Score: 117
Period size: 22 Copynumber: 3.2 Consensus size: 22
28534449 TAATCCTCTC
28534459 TCAAATTTCCTCTCAATTTCCT
1 TCAAATTTCCTCTCAATTTCCT
*
28534481 CTC-AACTTCCTCTCAATTTCCT
1 -TCAAATTTCCTCTCAATTTCCT
28534503 TCAAATTTCCTCTCAATTTCCT
1 TCAAATTTCCTCTCAATTTCCT
28534525 TCAAA
1 TCAAA
28534530 AAATCTCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
21 2 0.04
22 41 0.91
23 2 0.04
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.42
Consensus pattern (22 bp):
TCAAATTTCCTCTCAATTTCCT
Found at i:28534625 original size:12 final size:12
Alignment explanation
Indices: 28534610--28534640 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28534600 TTTTAAATAA
28534610 TTTTAAAATTTT
1 TTTTAAAATTTT
*
28534622 TTTTTAAATTTT
1 TTTTAAAATTTT
28534634 TTTTAAA
1 TTTTAAA
28534641 CCGTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTAAAATTTT
Found at i:28534637 original size:11 final size:11
Alignment explanation
Indices: 28534597--28534640 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
28534587 CTTAACTCCC
28534597 TTTTTTTAAAT
1 TTTTTTTAAAT
** *
28534608 AATTTTAAAATT
1 TTTTTTTAAA-T
28534620 TTTTTTTAAAT
1 TTTTTTTAAAT
28534631 TTTTTTTAAA
1 TTTTTTTAAA
28534641 CCGTAAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTTTTAAAT
Found at i:28535757 original size:7 final size:7
Alignment explanation
Indices: 28535745--28535769 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28535735 AGTCGATTGA
28535745 TATTTAG
1 TATTTAG
28535752 TATTTAG
1 TATTTAG
28535759 TATTTAG
1 TATTTAG
28535766 TATT
1 TATT
28535770 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:28536438 original size:18 final size:18
Alignment explanation
Indices: 28536411--28536450 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
28536401 CAGGTGCGTT
* *
28536411 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATATA
28536429 TCCTAACCCTTATATATA
1 TCCTAACCCTTATATATA
28536447 TCCT
1 TCCT
28536451 TTTCCGAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATATA
Found at i:28537922 original size:111 final size:111
Alignment explanation
Indices: 28537725--28537929 Score: 374
Period size: 111 Copynumber: 1.8 Consensus size: 111
28537715 NNNNNNNNNN
**
28537725 TTCACATAATGTTAGATTTGGAAAAATGTTTTGATTGGTACTAACAATTAATAATTTTATATAAT
1 TTCACATAATGTTAGATTTGGAAAAATGTTTTGACCGGTACTAACAATTAATAATTTTATATAAT
* *
28537790 TTGATAATTTTACTAATCATTAATACAATCAATTAATAATTTTACA
66 TTGAAAATTTTACTAACCATTAATACAATCAATTAATAATTTTACA
28537836 TTCACATAATGTTAGATTTGGAAAAATGTTTTGACCGGTACTAACAATTAATAATTTTATATAAT
1 TTCACATAATGTTAGATTTGGAAAAATGTTTTGACCGGTACTAACAATTAATAATTTTATATAAT
28537901 TTGAAAATTTTACTAACCATTAATACAAT
66 TTGAAAATTTTACTAACCATTAATACAAT
28537930 TTATCAATTA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 90 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.41
Consensus pattern (111 bp):
TTCACATAATGTTAGATTTGGAAAAATGTTTTGACCGGTACTAACAATTAATAATTTTATATAAT
TTGAAAATTTTACTAACCATTAATACAATCAATTAATAATTTTACA
Found at i:28541214 original size:124 final size:125
Alignment explanation
Indices: 28540918--28541263 Score: 599
Period size: 124 Copynumber: 2.8 Consensus size: 125
28540908 AACATGCTAT
* *
28540918 TGTAGGAAAAACGTGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
1 TGTAGCAAAAACGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
28540983 AAGCGA-TTTATACTATTTGCTCAGAAACGTC-AAAAAAATTATTACTTCCATGACCTAC
66 AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTACTTCCATGACCTAC
*
28541041 TGTAGCAAAAACGCGTCCATGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
1 TGTAGCAAAAACGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
*
28541106 AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCTAC
66 AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTACTTCCATGACCTAC
* * *
28541166 TGTAGCAAAAGCGCGTTCACGAGGGCACGA-TTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
1 TGTAGCAAAAACGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
*
28541230 AAGCGATTTTATACTATTTGATCAGAAACGTCAA
66 AAGCGATTTTATACTATTTGCTCAGAAACGTCAA
28541264 CTCGAAATTA
Statistics
Matches: 212, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
123 68 0.32
124 92 0.43
125 52 0.25
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (125 bp):
TGTAGCAAAAACGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
AAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTACTTCCATGACCTAC
Found at i:28547851 original size:21 final size:21
Alignment explanation
Indices: 28547827--28547868 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
28547817 AACACAATAG
28547827 ATAAAGATAGAAACATAAACA
1 ATAAAGATAGAAACATAAACA
28547848 ATAAAGATAGAAACATAAACA
1 ATAAAGATAGAAACATAAACA
28547869 TTCATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.14
Consensus pattern (21 bp):
ATAAAGATAGAAACATAAACA
Found at i:28549521 original size:15 final size:15
Alignment explanation
Indices: 28549501--28549531 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28549491 TTCAGCAGAT
28549501 AATTTGCATAGCATC
1 AATTTGCATAGCATC
28549516 AATTTGCATAGCATC
1 AATTTGCATAGCATC
28549531 A
1 A
28549532 TTCATGGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (15 bp):
AATTTGCATAGCATC
Found at i:28552800 original size:21 final size:22
Alignment explanation
Indices: 28552775--28552819 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
28552765 TTTGGGTCGT
*
28552775 TTTAGATTGTATTAGTG-TTGG
1 TTTAGATTGTATTAGGGTTTGG
* *
28552796 TTTAGGTTGTTTTAGGGTTTGG
1 TTTAGATTGTATTAGGGTTTGG
28552818 TT
1 TT
28552820 CATGGTGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.13, C:0.00, G:0.31, T:0.56
Consensus pattern (22 bp):
TTTAGATTGTATTAGGGTTTGG
Found at i:28553046 original size:21 final size:20
Alignment explanation
Indices: 28553022--28553063 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
28553012 TTATGGGTTC
28553022 GGTTTGGGATTATAGTGTTTA
1 GGTTTGGGATTAT-GTGTTTA
* *
28553043 GGTTTGGGGTTATGTTTTTA
1 GGTTTGGGATTATGTGTTTA
28553063 G
1 G
28553064 TGTGGTGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (20 bp):
GGTTTGGGATTATGTGTTTA
Found at i:28553310 original size:32 final size:32
Alignment explanation
Indices: 28553264--28553372 Score: 148
Period size: 32 Copynumber: 3.4 Consensus size: 32
28553254 GTTAGTTCGG
* * *
28553264 GTTTAGTACAGTTTGGGTGTAGGTCTGTTTGA
1 GTTTAGTACGGTTTGTGTGTAAGTCTGTTTGA
*
28553296 GTTTAATACGGTTTGTGTGTAAGTCTGTTTGA
1 GTTTAGTACGGTTTGTGTGTAAGTCTGTTTGA
*
28553328 GTTTAGTACGATTTGTGTGTAAGT-TAGTTTGA
1 GTTTAGTACGGTTTGTGTGTAAGTCT-GTTTGA
*
28553360 GTTTAGTATGGTT
1 GTTTAGTACGGTT
28553373 CAAGTTTTAG
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 1 0.01
32 67 0.99
ACGTcount: A:0.18, C:0.05, G:0.30, T:0.47
Consensus pattern (32 bp):
GTTTAGTACGGTTTGTGTGTAAGTCTGTTTGA
Found at i:28555693 original size:23 final size:23
Alignment explanation
Indices: 28555628--28555726 Score: 85
Period size: 23 Copynumber: 4.3 Consensus size: 23
28555618 CATATTGTAG
** *
28555628 GTTGTTTCACTGTTGTTTTTAGT
1 GTTGTTTCACTACTGTTTTTAAT
* * *
28555651 ATTGTTTCACTGCCGTTTTTAAT
1 GTTGTTTCACTACTGTTTTTAAT
* *
28555674 GTTGTTTCACTACTGCTTTTAAA
1 GTTGTTTCACTACTGTTTTTAAT
28555697 GTT-TTTC-CGTTACTGTTTTTAAT
1 GTTGTTTCAC--TACTGTTTTTAAT
*
28555720 ATTGTTT
1 GTTGTTT
28555727 GGATATTGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
21 1 0.02
22 4 0.07
23 53 0.87
24 3 0.05
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.57
Consensus pattern (23 bp):
GTTGTTTCACTACTGTTTTTAAT
Found at i:28555945 original size:14 final size:14
Alignment explanation
Indices: 28555926--28555960 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
28555916 AAGTATAAAT
28555926 TACCTTAAAATGAC
1 TACCTTAAAATGAC
*
28555940 TACCTTAAAATGAT
1 TACCTTAAAATGAC
28555954 TACCTTA
1 TACCTTA
28555961 TCATGCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (14 bp):
TACCTTAAAATGAC
Found at i:28556906 original size:187 final size:187
Alignment explanation
Indices: 28556570--28556940 Score: 432
Period size: 187 Copynumber: 2.0 Consensus size: 187
28556560 AAAAACCGAG
* * * * * * *
28556570 CAACAAAATTTATTCACACATGCAGAGGTAGCAAGTGTACACCCCAACCTATTGCATGCTCGTAC
1 CAACAAAACTCATTCACACATGCAGAAGTAACAAATGTACACCACAACCTATTGCATGCTCATAC
* * * **
28556635 AAAAATAAACTCAAAAATATATAGGAAGGAATTTGCTGCAGTAGTGTGGGATAACTCTGGTCAAG
66 AAAAATAAACTCAAAAATATATA-GAAGAAATTTGCTGCAATAGTGTGAGATAACAATGGTCAAG
* *
28556700 ACTCATTTAAAACTCATAGAAAGCTTGATAAATAAGAA-CTATTAGGAAAACAACCATAGAGC
130 ACTCATTTAAAAATCATAGAAAACTT-A-AAA-AAGAATC-ATT-GGAAAACAACCATAGAGC
* * *
28556762 CAACAAAACTCATTCACACATGTAGAAGTAACAAATGTACA-TACAA-CTATATGCCTGCTCATA
1 CAACAAAACTCATTCACACATGCAGAAGTAACAAATGTACACCACAACCTAT-TGCATGCTCATA
* * *
28556825 CAAAAATAAAC-CCAAAA-ATAT-GAAGAAATTTGTTGCAATAGTGTGAGATAACAATGGTTAA-
65 CAAAAATAAACTCAAAAATATATAGAAGAAATTTGCTGCAATAGTGTGAGATAACAATGGTCAAG
*
28556886 ATCTCATTTAAAAATCATAGAAAACTTAATAAAGAATCATTGGAAAACAACCATA
130 A-CTCATTTAAAAATCATAGAAAACTTAAAAAAGAATCATTGGAAAACAACCATA
28556941 AAGCTTCAGA
Statistics
Matches: 155, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
183 14 0.09
184 8 0.05
185 3 0.02
186 2 0.01
187 56 0.36
189 4 0.03
190 9 0.06
191 24 0.15
192 35 0.23
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.24
Consensus pattern (187 bp):
CAACAAAACTCATTCACACATGCAGAAGTAACAAATGTACACCACAACCTATTGCATGCTCATAC
AAAAATAAACTCAAAAATATATAGAAGAAATTTGCTGCAATAGTGTGAGATAACAATGGTCAAGA
CTCATTTAAAAATCATAGAAAACTTAAAAAAGAATCATTGGAAAACAACCATAGAGC
Found at i:28558674 original size:30 final size:27
Alignment explanation
Indices: 28558640--28558701 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 27
28558630 TATTTTAAAA
28558640 ATAAAATGTGAAATTGATAATATAAATAAT
1 ATAAAATGTGAAATT--TAAT-TAAATAAT
*
28558670 ATAAAATGTGAAATTTAATTTAATAAT
1 ATAAAATGTGAAATTTAATTAAATAAT
28558697 ATAAA
1 ATAAA
28558702 TAGTAGATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 12 0.39
28 4 0.13
30 15 0.48
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (27 bp):
ATAAAATGTGAAATTTAATTAAATAAT
Found at i:28562265 original size:13 final size:13
Alignment explanation
Indices: 28562247--28562307 Score: 86
Period size: 13 Copynumber: 4.7 Consensus size: 13
28562237 AGTTTTTCAT
28562247 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
28562260 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
*
28562273 TGTTTTTGAGAAG
1 TGCTTTTGAGAAG
* *
28562286 TGCTTTTCAAAAG
1 TGCTTTTGAGAAG
28562299 TGCTTTTGA
1 TGCTTTTGA
28562308 AACATTTGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.43
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:28562281 original size:26 final size:26
Alignment explanation
Indices: 28562247--28562307 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
28562237 AGTTTTTCAT
*
28562247 TGCTTTTGAGAAGTGCTTTTCAGAAG
1 TGCTTTTGAGAAGTGCTTTTCAAAAG
*
28562273 TGTTTTTGAGAAGTGCTTTTCAAAAG
1 TGCTTTTGAGAAGTGCTTTTCAAAAG
28562299 TGCTTTTGA
1 TGCTTTTGA
28562308 AACATTTGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.43
Consensus pattern (26 bp):
TGCTTTTGAGAAGTGCTTTTCAAAAG
Found at i:28563196 original size:21 final size:21
Alignment explanation
Indices: 28563172--28563216 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
28563162 TAAGCTGACA
28563172 ACAAATTGAACAGCATTGCCT
1 ACAAATTGAACAGCATTGCCT
28563193 ACAAATTGAACAGCATTGCCT
1 ACAAATTGAACAGCATTGCCT
28563214 ACA
1 ACA
28563217 TACCAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.22
Consensus pattern (21 bp):
ACAAATTGAACAGCATTGCCT
Found at i:28574395 original size:30 final size:30
Alignment explanation
Indices: 28574350--28574410 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
28574340 GGGGGTGGGA
* *
28574350 TGGGAGGGAAGTAAAAGTTTTAGGGGGAAAG
1 TGGGAGGGAAGTAAAAATTTT-GGGAGAAAG
28574381 TGGGAGGG-AGTAAAAATTTTGGGAGAAAG
1 TGGGAGGGAAGTAAAAATTTTGGGAGAAAG
28574410 T
1 T
28574411 AAAGAGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.32
30 11 0.39
31 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (30 bp):
TGGGAGGGAAGTAAAAATTTTGGGAGAAAG
Found at i:28575520 original size:25 final size:25
Alignment explanation
Indices: 28575449--28575546 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 25
28575439 AGATACACCA
28575449 CAGCTCTCACGAGCTTCCC-ATTATT
1 CAGCTCTCACGAGCTTCCCGA-TATT
* * ** *
28575474 TAGCTCTTATAAGCATCCCGATATT
1 CAGCTCTCACGAGCTTCCCGATATT
*
28575499 CAGCTCTCACGAGCTTCTCGATATT
1 CAGCTCTCACGAGCTTCCCGATATT
** **
28575524 TGGCTCTCTTGAGCTTCCCGATA
1 CAGCTCTCACGAGCTTCCCGATA
28575547 AATGGCTCGC
Statistics
Matches: 56, Mismatches: 16, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
25 55 0.98
26 1 0.02
ACGTcount: A:0.20, C:0.31, G:0.15, T:0.34
Consensus pattern (25 bp):
CAGCTCTCACGAGCTTCCCGATATT
Found at i:28575630 original size:50 final size:50
Alignment explanation
Indices: 28575534--28575630 Score: 126
Period size: 50 Copynumber: 1.9 Consensus size: 50
28575524 TGGCTCTCTT
* *
28575534 GAGCTTCCCGATAAATGGCTCGCAAGAGCTTCCCGTTATATAGCTCGGAA
1 GAGCTTCCCGATAAATAGCTCGCAAGAGCTTCCCGTTACATAGCTCGGAA
* *
28575584 GAGCTTCCC-ATTATATAGCTCGGAAGAGCTTCCCGTTTACAT-GCTCG
1 GAGCTTCCCGA-TAAATAGCTCGCAAGAGCTTCCCG-TTACATAGCTCG
28575631 TATGAGCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 1 0.02
50 35 0.85
51 5 0.12
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (50 bp):
GAGCTTCCCGATAAATAGCTCGCAAGAGCTTCCCGTTACATAGCTCGGAA
Found at i:28575637 original size:25 final size:25
Alignment explanation
Indices: 28575534--28575620 Score: 129
Period size: 25 Copynumber: 3.5 Consensus size: 25
28575524 TGGCTCTCTT
* * * *
28575534 GAGCTTCCCGATAAATGGCTCGCAA
1 GAGCTTCCCGTTATATAGCTCGGAA
28575559 GAGCTTCCCGTTATATAGCTCGGAA
1 GAGCTTCCCGTTATATAGCTCGGAA
*
28575584 GAGCTTCCCATTATATAGCTCGGAA
1 GAGCTTCCCGTTATATAGCTCGGAA
28575609 GAGCTTCCCGTT
1 GAGCTTCCCGTT
28575621 TACATGCTCG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.26
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCGGAA
Found at i:28581400 original size:16 final size:16
Alignment explanation
Indices: 28581379--28581410 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28581369 AATTATCTTC
*
28581379 ATGCATATCCACAAGT
1 ATGCATAACCACAAGT
28581395 ATGCATAACCACAAGT
1 ATGCATAACCACAAGT
28581411 TAGATGAGCG
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:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (16 bp):
ATGCATAACCACAAGT
Found at i:28581834 original size:21 final size:22
Alignment explanation
Indices: 28581793--28581835 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28581783 TAATACTCCC
28581793 AAAGAATAATTAGACATAAAAT
1 AAAGAATAATTAGACATAAAAT
* *
28581815 AAAGAATAGTTAG-TATAAAAT
1 AAAGAATAATTAGACATAAAAT
28581836 TAGAAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.60, C:0.02, G:0.12, T:0.26
Consensus pattern (22 bp):
AAAGAATAATTAGACATAAAAT
Found at i:28585819 original size:25 final size:25
Alignment explanation
Indices: 28585741--28585908 Score: 107
Period size: 25 Copynumber: 6.8 Consensus size: 25
28585731 TAAGCTCATA
*
28585741 AGAGCC-TTAATCAGGAAGCT-CATG
1 AGAGCCATTAATCGGGAAGCTCCA-G
* * * *
28585765 TGAGCCAATAA-CGGGTAA-CTCTAA
1 AGAGCCATTAATCGGG-AAGCTCCAG
*
28585789 AGAGCCATTAATCGGGAAGCTCCGG
1 AGAGCCATTAATCGGGAAGCTCCAG
* * * *
28585814 ATAGCCA-TATATTGGAAAGCTCAAG
1 AGAGCCATTA-ATCGGGAAGCTCCAG
* **
28585839 TGAGCCA-T-ATCGGGAAGCTTTAG
1 AGAGCCATTAATCGGGAAGCTCCAG
* *
28585862 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATCGGGAAGCTC-CAG
*
28585888 AGAGCCTTTAATCGGGAAGCT
1 AGAGCCATTAATCGGGAAGCT
28585909 TACGAAGAGC
Statistics
Matches: 107, Mismatches: 28, Indels: 16
0.71 0.19 0.11
Matches are distributed among these distances:
23 17 0.16
24 24 0.22
25 46 0.43
26 20 0.19
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (25 bp):
AGAGCCATTAATCGGGAAGCTCCAG
Found at i:28585856 original size:23 final size:25
Alignment explanation
Indices: 28585830--28585908 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 25
28585820 ATATATTGGA
* *
28585830 AAGCTCAAGTGAGCCA-T-ATCGGG
1 AAGCTCAAGAGAGCCATTAATCAGG
**
28585853 AAGCTTTAGAGAGCCATTAATCAGG
1 AAGCTCAAGAGAGCCATTAATCAGG
* * *
28585878 AAGCTCACAAAGAGCCTTTAATCGGG
1 AAGCTCA-AGAGAGCCATTAATCAGG
28585904 AAGCT
1 AAGCT
28585909 TACGAAGAGC
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 13 0.30
24 1 0.02
25 10 0.23
26 20 0.45
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.20
Consensus pattern (25 bp):
AAGCTCAAGAGAGCCATTAATCAGG
Found at i:28585927 original size:26 final size:27
Alignment explanation
Indices: 28585847--28585930 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 27
28585837 AGTGAGCCAT
28585847 ATCGGGAAGCTTTA-G-AGAGCCAT-TA
1 ATCGGGAAGC-TTACGAAGAGCCATATA
* * * *
28585872 ATCAGGAAGCTCACAAAGAGCC-TTTA
1 ATCGGGAAGCTTACGAAGAGCCATATA
28585898 ATCGGGAAGCTTACGAAGAGCCATAT-
1 ATCGGGAAGCTTACGAAGAGCCATATA
28585924 ATCGGGA
1 ATCGGGA
28585931 TGCTCATAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
24 2 0.04
25 10 0.21
26 34 0.71
27 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (27 bp):
ATCGGGAAGCTTACGAAGAGCCATATA
Found at i:28586368 original size:5 final size:5
Alignment explanation
Indices: 28586339--28586377 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
28586329 GAATTTAATA
* *
28586339 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
28586378 CATCTTAGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:28587849 original size:45 final size:44
Alignment explanation
Indices: 28587794--28587880 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
28587784 TTAAAACTGT
* *
28587794 AATTTAAAATGTTCAAATTTATTAATAAACAATATCATGTTTTA
1 AATTTAAAATGTTAAAAATTATTAATAAACAATATCATGTTTTA
28587838 AATTATAAAATGTTAAAAATTATTAATAAACAATATCATGTTT
1 AATT-TAAAATGTTAAAAATTATTAATAAACAATATCATGTTT
28587881 AGGAGCATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 4 0.10
45 36 0.90
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (44 bp):
AATTTAAAATGTTAAAAATTATTAATAAACAATATCATGTTTTA
Found at i:28598713 original size:17 final size:17
Alignment explanation
Indices: 28598691--28598724 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28598681 AGTAACTCTC
28598691 TTATATACACAATCTAG
1 TTATATACACAATCTAG
28598708 TTATATACACAATCTAG
1 TTATATACACAATCTAG
28598725 ACAGACTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (17 bp):
TTATATACACAATCTAG
Found at i:28605422 original size:39 final size:41
Alignment explanation
Indices: 28605351--28605428 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 41
28605341 AAAAATAAAA
***
28605351 ATAAAAGTATCAAAAATTATTTTTTTTCAAATT-AAAAATC
1 ATAAAAGTATCAAAAATTATTTTTTAAAAAATTGAAAAATC
28605391 ATAAAAGT-TCAAAAA-TATATTTTTAAAAAATTGAAAAA
1 ATAAAAGTATCAAAAATTAT-TTTTTAAAAAATTGAAAAA
28605429 AATAAGAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 3 0.09
39 17 0.52
40 13 0.39
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (41 bp):
ATAAAAGTATCAAAAATTATTTTTTAAAAAATTGAAAAATC
Found at i:28610024 original size:29 final size:28
Alignment explanation
Indices: 28609945--28610049 Score: 96
Period size: 25 Copynumber: 3.9 Consensus size: 28
28609935 TTTAGGTATC
28609945 AAATTAGATAAAAAAATTTAAA-A-ACT
1 AAATTAGATAAAAAAATTTAAATATACT
**
28609971 AAATTA-ATAAAAAAAAGTACCAATATACT
1 AAATTAGATAAAAAAATTTA--AATATACT
*
28610000 AAATTAGACTAAAAATATTTAAATAT-C-
1 AAATTAGA-TAAAAAAATTTAAATATACT
* *
28610027 AAATTA-AGAAAAAAATTGAAATA
1 AAATTAGATAAAAAAATTTAAATA
28610050 CCAAAAATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
25 24 0.37
26 7 0.11
27 8 0.12
28 2 0.03
29 14 0.22
30 1 0.02
31 9 0.14
ACGTcount: A:0.63, C:0.06, G:0.05, T:0.27
Consensus pattern (28 bp):
AAATTAGATAAAAAAATTTAAATATACT
Found at i:28611889 original size:15 final size:15
Alignment explanation
Indices: 28611869--28611899 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28611859 TCATTGATAA
28611869 TTTCTTCTTCTTCTT
1 TTTCTTCTTCTTCTT
28611884 TTTCTTCTTCTTCTT
1 TTTCTTCTTCTTCTT
28611899 T
1 T
28611900 AGCATACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCTTCTTCTTCTT
Found at i:28617050 original size:12 final size:11
Alignment explanation
Indices: 28617031--28617064 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
28617021 TCAATTATTT
28617031 TCTCAATTTCC
1 TCTCAATTTCC
* *
28617042 TCTCAAATTGC
1 TCTCAATTTCC
28617053 TCTCAATTTCC
1 TCTCAATTTCC
28617064 T
1 T
28617065 TCCAAATTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.21, C:0.32, G:0.03, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:28617080 original size:22 final size:22
Alignment explanation
Indices: 28617031--28617072 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
28617021 TCAATTATTT
28617031 TCTCAATTTCCTCTCAAATTGC
1 TCTCAATTTCCTCTCAAATTGC
28617053 TCTCAATTTCCT-TCCAAATT
1 TCTCAATTTCCTCT-CAAATT
28617073 TCTTTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.43
Consensus pattern (22 bp):
TCTCAATTTCCTCTCAAATTGC
Found at i:28617999 original size:7 final size:7
Alignment explanation
Indices: 28617989--28618013 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28617979 TTGGTATTTA
28617989 GTATTAT
1 GTATTAT
28617996 GTATTAT
1 GTATTAT
28618003 GTATTAT
1 GTATTAT
28618010 GTAT
1 GTAT
28618014 ATAACTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTAT
Found at i:28618662 original size:18 final size:18
Alignment explanation
Indices: 28618639--28618676 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28618629 TGTGAGGTGC
* *
28618639 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
28618657 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
28618675 GT
1 GT
28618677 GTCTTTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:28619196 original size:7 final size:7
Alignment explanation
Indices: 28619176--28619215 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
28619166 ATTTATTAAA
28619176 AATTTAT
1 AATTTAT
28619183 AAATTTAT
1 -AATTTAT
28619191 AATTTAT
1 AATTTAT
28619198 AA-TTA-
1 AATTTAT
28619203 AATTTAT
1 AATTTAT
28619210 AATTTA
1 AATTTA
28619216 ATTGACAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.07
6 6 0.20
7 15 0.50
8 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTTAT
Found at i:28619270 original size:20 final size:21
Alignment explanation
Indices: 28619232--28619270 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28619222 AAACCCTAAC
*
28619232 AAAAACCCTAACCCTTAACTT
1 AAAAACCCTAACCCATAACTT
*
28619253 AAAAATCCTAA-CCATAAC
1 AAAAACCCTAACCCATAAC
28619271 CCTAACCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAAACCCTAACCCATAACTT
Found at i:28619272 original size:33 final size:33
Alignment explanation
Indices: 28619222--28619306 Score: 134
Period size: 33 Copynumber: 2.6 Consensus size: 33
28619212 TTTAATTGAC
* *
28619222 AAACCCTAACAAAAACCCTAACCCTTAACTTAA
1 AAACCCTAACCATAACCCTAACCCTTAACTTAA
*
28619255 AAATCCTAACCATAACCCTAACCCTTAACTTAA
1 AAACCCTAACCATAACCCTAACCCTTAACTTAA
*
28619288 AAACCCTAACCTTAACCCT
1 AAACCCTAACCATAACCCT
28619307 TAACTTAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (33 bp):
AAACCCTAACCATAACCCTAACCCTTAACTTAA
Found at i:28619273 original size:27 final size:27
Alignment explanation
Indices: 28619262--28619423 Score: 103
Period size: 27 Copynumber: 6.4 Consensus size: 27
28619252 TAAAAATCCT
* *
28619262 AACCATAACCCTAACCCTTAACTTAAA
1 AACCCTAACCATAACCCTTAACTTAAA
*
28619289 AACCCTAACCTTAACCCTTAACTTAAA
1 AACCCTAACCATAACCCTTAACTTAAA
* *
28619316 AA--C--ACCAAAATCC-TAAC--AAA
1 AACCCTAACCATAACCCTTAACTTAAA
* * * **
28619336 AATCCTAACAAAAACCC-TAAC--CCA
1 AACCCTAACCATAACCCTTAACTTAAA
* * *
28619360 AACCCTAACCCTAAACATTAACTTAAA
1 AACCCTAACCATAACCCTTAACTTAAA
* *
28619387 AACCCTAATCATAACCC-TAACCCTAAA
1 AACCCTAACCATAACCCTTAA-CTTAAA
28619414 AACCCTAACC
1 AACCCTAACC
28619424 CTTAACTAAA
Statistics
Matches: 104, Mismatches: 23, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
20 5 0.05
22 5 0.05
23 7 0.07
24 24 0.23
25 5 0.05
26 3 0.03
27 55 0.53
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.19
Consensus pattern (27 bp):
AACCCTAACCATAACCCTTAACTTAAA
Found at i:28619294 original size:15 final size:15
Alignment explanation
Indices: 28619274--28619318 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
28619264 CCATAACCCT
28619274 AACCCTTAACTTAAA
1 AACCCTTAACTTAAA
28619289 AACCC-TAACCTT---
1 AACCCTTAA-CTTAAA
28619301 AACCCTTAACTTAAA
1 AACCCTTAACTTAAA
28619316 AAC
1 AAC
28619319 ACCAAAATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
12 8 0.32
13 3 0.12
14 3 0.12
15 11 0.44
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.24
Consensus pattern (15 bp):
AACCCTTAACTTAAA
Found at i:28619339 original size:12 final size:12
Alignment explanation
Indices: 28619322--28619356 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
28619312 TAAAAACACC
28619322 AAAATCCTAACA
1 AAAATCCTAACA
28619334 AAAATCCTAACA
1 AAAATCCTAACA
*
28619346 AAAACCCTAAC
1 AAAATCCTAAC
28619357 CCAAACCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAATCCTAACA
Found at i:28619362 original size:12 final size:13
Alignment explanation
Indices: 28619347--28619425 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 13
28619337 ATCCTAACAA
28619347 AAACCCTAACCC-
1 AAACCCTAACCCT
28619359 AAACCCTAACCCT
1 AAACCCTAACCCT
** *
28619372 AAACATTAA-CTT
1 AAACCCTAACCCT
* *
28619384 AAAAACCCTAATCAT
1 --AAACCCTAACCCT
28619399 -AACCCTAACCCT
1 AAACCCTAACCCT
28619411 AAAAACCCTAACCCT
1 --AAACCCTAACCCT
28619426 TAACTAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
12 24 0.46
13 7 0.13
14 7 0.13
15 14 0.27
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (13 bp):
AAACCCTAACCCT
Found at i:28619436 original size:22 final size:21
Alignment explanation
Indices: 28619410--28619573 Score: 188
Period size: 22 Copynumber: 7.8 Consensus size: 21
28619400 ACCCTAACCC
28619410 TAAAAACCCTAACCCTTAACT
1 TAAAAACCCTAACCCTTAACT
* *
28619431 AAAAAACCCTAACCCTTAAAT
1 TAAAAACCCTAACCCTTAACT
*
28619452 TAAAAA-CCTAAACCTTAACT
1 TAAAAACCCTAACCCTTAACT
* *
28619472 TAAAAACCCTAAACCATTAAAT
1 TAAAAACCCT-AACCCTTAACT
* *
28619494 TAAAAACCCTCA-CCTTAAAT
1 TAAAAACCCTAACCCTTAACT
* *
28619514 TAATAAGCCTAAACCCTTAACT
1 TAAAAACCCT-AACCCTTAACT
* *
28619536 TAAAAACCATAAACCTTTAACT
1 TAAAAACCCT-AACCCTTAACT
28619558 TAAAAACCCTAACCCT
1 TAAAAACCCTAACCCT
28619574 AACCATTAAC
Statistics
Matches: 119, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
20 33 0.28
21 34 0.29
22 52 0.44
ACGTcount: A:0.48, C:0.28, G:0.01, T:0.24
Consensus pattern (21 bp):
TAAAAACCCTAACCCTTAACT
Found at i:28619456 original size:42 final size:43
Alignment explanation
Indices: 28619410--28619573 Score: 201
Period size: 42 Copynumber: 3.9 Consensus size: 43
28619400 ACCCTAACCC
*
28619410 TAAAAACCCTAACCCTTAACTAAAAAACCCT-AACCCTTAAAT
1 TAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAAAT
* *
28619452 TAAAAA-CCTAAACCTTAACTTAAAAACCCTAAACCATTAAAT
1 TAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAAAT
* * * * *
28619494 TAAAAACCCTCA-CCTTAAATTAATAAGCCTAAACCCTTAACT
1 TAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAAAT
* *
28619536 TAAAAACCATAAACCTTTAACTTAAAAACCCT-AACCCT
1 TAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCT
28619574 AACCATTAAC
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
41 22 0.21
42 56 0.54
43 11 0.11
44 14 0.14
ACGTcount: A:0.48, C:0.28, G:0.01, T:0.24
Consensus pattern (43 bp):
TAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAAAT
Found at i:28619582 original size:22 final size:20
Alignment explanation
Indices: 28619398--28619576 Score: 144
Period size: 21 Copynumber: 8.5 Consensus size: 20
28619388 ACCCTAATCA
*
28619398 TAACCCTAACCCTAAAAACCC
1 TAACCCTAA-CTTAAAAACCC
*
28619419 TAACCCTTAACTAAAAAACCC
1 TAACCC-TAACTTAAAAACCC
*
28619440 TAACCCTTAAATTAAAAA-CC
1 TAACCC-TAACTTAAAAACCC
*
28619460 TAAACCTTAACTTAAAAACCC
1 T-AACCCTAACTTAAAAACCC
* *
28619481 TAAACCATTAAATTAAAAACCC
1 T-AACC-CTAACTTAAAAACCC
* * * * *
28619503 TCACCTTAAATTAATAAGCC
1 TAACCCTAACTTAAAAACCC
*
28619523 TAAACCCTTAACTTAAAAACCA
1 T-AACCC-TAACTTAAAAACCC
*
28619545 TAAACCTTTAACTTAAAAACCC
1 T-AACC-CTAACTTAAAAACCC
28619567 TAACCCTAAC
1 TAACCCTAAC
28619577 CATTAACTTA
Statistics
Matches: 132, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
20 31 0.23
21 53 0.40
22 48 0.36
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.23
Consensus pattern (20 bp):
TAACCCTAACTTAAAAACCC
Found at i:28619594 original size:64 final size:61
Alignment explanation
Indices: 28619410--28619575 Score: 174
Period size: 64 Copynumber: 2.7 Consensus size: 61
28619400 ACCCTAACCC
* * * * *
28619410 TAAAAACCCT-AACCCTTAACTAAAAAACCCTAACCCTTAAATTAAAAACCTAAA-CCTTAACT
1 TAAAAACCATAAACCATTAAATTAAAAACCCTAACCC-TAAATTAATAA-C-AAACCCTTAACT
* * *
28619472 TAAAAACCCTAAACCATTAAATTAAAAACCCTCACCTTAAATTAATAAGCCTAAACCCTTAACT
1 TAAAAACCATAAACCATTAAATTAAAAACCCTAACCCTAAATTAATAA--C-AAACCCTTAACT
* *
28619536 TAAAAACCATAAACCTTTAACTTAAAAACCCTAACCCTAA
1 TAAAAACCATAAACCATTAAATTAAAAACCCTAACCCTAA
28619576 CCATTAACTT
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
62 20 0.22
63 27 0.30
64 43 0.48
ACGTcount: A:0.48, C:0.28, G:0.01, T:0.23
Consensus pattern (61 bp):
TAAAAACCATAAACCATTAAATTAAAAACCCTAACCCTAAATTAATAACAAACCCTTAACT
Found at i:28619624 original size:15 final size:15
Alignment explanation
Indices: 28619604--28619632 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28619594 TAACCTTAAC
28619604 CCTTAACTTAAAAAT
1 CCTTAACTTAAAAAT
28619619 CCTTAACTTAAAAA
1 CCTTAACTTAAAAA
28619633 CATCAAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (15 bp):
CCTTAACTTAAAAAT
Found at i:28619629 original size:27 final size:27
Alignment explanation
Indices: 28619525--28619617 Score: 115
Period size: 27 Copynumber: 3.6 Consensus size: 27
28619515 AATAAGCCTA
*
28619525 AACCCTTAACTTAAAAA-CC--A--TA
1 AACCCTTAACTTAAAAACCCTAACCTT
* *
28619547 AACCTTTAACTTAAAAACCCTAACCCT
1 AACCCTTAACTTAAAAACCCTAACCTT
*
28619574 AACCATTAACTTAAAAACCCTAACCTT
1 AACCCTTAACTTAAAAACCCTAACCTT
28619601 AACCCTTAACTTAAAAA
1 AACCCTTAACTTAAAAA
28619618 TCCTTAACTT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
22 16 0.27
23 2 0.03
25 1 0.02
27 41 0.68
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (27 bp):
AACCCTTAACTTAAAAACCCTAACCTT
Found at i:28619668 original size:6 final size:6
Alignment explanation
Indices: 28619651--28619713 Score: 65
Period size: 6 Copynumber: 10.0 Consensus size: 6
28619641 CCTTAACAAA
* *
28619651 AACCCT AGCCCT AACCCT AACCCTT AA-CTT AAAAACCCT AACCCT AACCCT
1 AACCCT AACCCT AACCCT AACCC-T AACCCT ---AACCCT AACCCT AACCCT
28619702 AACCCT AACCCT
1 AACCCT AACCCT
28619714 TAACTTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
5 1 0.02
6 40 0.83
7 3 0.06
8 2 0.04
9 2 0.04
ACGTcount: A:0.35, C:0.44, G:0.02, T:0.19
Consensus pattern (6 bp):
AACCCT
Found at i:28619689 original size:21 final size:21
Alignment explanation
Indices: 28619663--28619751 Score: 105
Period size: 21 Copynumber: 4.4 Consensus size: 21
28619653 CCCTAGCCCT
28619663 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
28619684 AACCCTAACCC-TAACCCT---
1 AACCCTAACCCTTAA-CTTAAA
28619702 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* *
28619723 AACCTTAATCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
28619744 AACACTAA
1 AACCCTAA
28619752 AACCCTAATG
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
18 13 0.23
19 3 0.05
20 3 0.05
21 38 0.67
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.24
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:28619694 original size:39 final size:39
Alignment explanation
Indices: 28619651--28619726 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
28619641 CCTTAACAAA
*
28619651 AACCCTAGCCCTAACCCTAACCCTTAACTTAAAAACCCT
1 AACCCTAACCCTAACCCTAACCCTTAACTTAAAAACCCT
28619690 AACCCTAACCCTAACCCTAACCCTTAACTTAAAAACC
1 AACCCTAACCCTAACCCTAACCCTTAACTTAAAAACC
28619727 TTAATCCTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.41, G:0.01, T:0.20
Consensus pattern (39 bp):
AACCCTAACCCTAACCCTAACCCTTAACTTAAAAACCCT
Found at i:28619766 original size:95 final size:95
Alignment explanation
Indices: 28619560--28619759 Score: 239
Period size: 95 Copynumber: 2.1 Consensus size: 95
28619550 CTTTAACTTA
* * *
28619560 AAAACCCTAACCCTAACCATTAACTTAAAAACCCTAACCTTAACCCTTAACTTAAAAATCCTTAA
1 AAAACCCTAACCCTAACCATTAACTTAAAAACCCTAACCCTAACCCTTAACCT--AAACCCTTAA
*
28619625 CTTAAAAACATCAAAACCTTAACAAAAACCCT
64 CTTAAAAACATCAAAACCTTAACAAAAACACT
* *
28619657 --AGCCCTAACCCTAACCCTTAACTTAAAAACCCTAACCCTAACCC-TAACCCT-AACCCTTAAC
1 AAAACCCTAACCCTAACCATTAACTTAAAAACCCTAACCCTAACCCTTAA-CCTAAACCCTTAAC
* * *
28619718 TTAAAAACCT-TAATCCTTAACTTAAAAACACT
65 TTAAAAACATCAAAACCTTAAC--AAAAACACT
28619750 AAAACCCTAA
1 AAAACCCTAA
28619760 TGCTAACAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
91 9 0.10
92 18 0.20
93 8 0.09
94 3 0.03
95 50 0.57
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.23
Consensus pattern (95 bp):
AAAACCCTAACCCTAACCATTAACTTAAAAACCCTAACCCTAACCCTTAACCTAAACCCTTAACT
TAAAAACATCAAAACCTTAACAAAAACACT
Found at i:28619783 original size:18 final size:18
Alignment explanation
Indices: 28619750--28619784 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28619740 TAAAAACACT
**
28619750 AAAACCCTAATGCTAACA
1 AAAACCCTAACCCTAACA
28619768 AAAACCCTAACCCTAAC
1 AAAACCCTAACCCTAAC
28619785 CCTAATCTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.34, G:0.03, T:0.14
Consensus pattern (18 bp):
AAAACCCTAACCCTAACA
Found at i:28619843 original size:35 final size:36
Alignment explanation
Indices: 28619804--28619966 Score: 98
Period size: 35 Copynumber: 4.4 Consensus size: 36
28619794 ATATAATTTC
28619804 ATAATTTTACTAACAATTAATACAATTA-ACAATGA
1 ATAATTTTACTAACAATTAATACAATTACACAATGA
* * ** * * * *
28619839 ATAATTTGACTAACAAAATGTTAGATTTTACAAAATGTT
1 ATAATTTTACTAAC-AATTAATACA-ATTACACAATG-A
* * ** * * * *
28619878 TTGACTGGTACTAACAATTAATA-ATTTGATATAATTTA
1 AT-AATTTTACTAACAATTAATACAATT-ACACAA-TGA
28619916 ATAATTTTACTAACAATTAATACAATTA-ACAATGA
1 ATAATTTTACTAACAATTAATACAATTACACAATGA
*
28619951 ATAATTTGACTAACAA
1 ATAATTTTACTAACAA
28619967 AATGTTAGAT
Statistics
Matches: 92, Mismatches: 28, Indels: 16
0.68 0.21 0.12
Matches are distributed among these distances:
35 30 0.33
36 9 0.10
37 24 0.26
38 14 0.15
39 7 0.08
40 8 0.09
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (36 bp):
ATAATTTTACTAACAATTAATACAATTACACAATGA
Found at i:28619989 original size:112 final size:111
Alignment explanation
Indices: 28619787--28620031 Score: 409
Period size: 112 Copynumber: 2.2 Consensus size: 111
28619777 ACCCTAACCC
* *
28619787 TAATCTGATATAATTTCATAATTTTACTAACAATTAATACAATTAACAATGAATAATTTGACTAA
1 TAATTTGATATAATTTAATAATTTTACTAACAATTAATACAATTAACAATGAATAATTTGACTAA
* * *
28619852 CAAAATGTTAGATTTTACAAAATGTTTTGACTGGTACTAACAATTAA
66 CAAAATGTTAGATTTTACAAAATGTTTTGACTGGTACAAAAAAAT-A
28619899 TAATTTGATATAATTTAATAATTTTACTAACAATTAATACAATTAACAATGAATAATTTGACTAA
1 TAATTTGATATAATTTAATAATTTTACTAACAATTAATACAATTAACAATGAATAATTTGACTAA
*
28619964 CAAAATGTTAGATTTTACAAAATGTTTTGATTGGTACAAAAAAATA
66 CAAAATGTTAGATTTTACAAAATGTTTTGACTGGTACAAAAAAATA
*
28620010 TAATTTGATAAAATTTTAATAA
1 TAATTTGATATAA-TTTAATAA
28620032 CAATTAGTTT
Statistics
Matches: 125, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
111 13 0.10
112 112 0.90
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (111 bp):
TAATTTGATATAATTTAATAATTTTACTAACAATTAATACAATTAACAATGAATAATTTGACTAA
CAAAATGTTAGATTTTACAAAATGTTTTGACTGGTACAAAAAAATA
Found at i:28620046 original size:22 final size:23
Alignment explanation
Indices: 28620003--28620067 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 23
28619993 ATTGGTACAA
28620003 AAAAATATAATTTGATAAAATTTTAAT
1 AAAAATATAATTT--T--AATTTTAAT
* *
28620030 AACAAT-TAGTTTTAATTTTAAT
1 AAAAATATAATTTTAATTTTAAT
28620052 AAAAATATAATTTTAA
1 AAAAATATAATTTTAA
28620068 ATACCCAGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 14 0.42
23 8 0.24
24 1 0.03
26 5 0.15
27 5 0.15
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (23 bp):
AAAAATATAATTTTAATTTTAAT
Found at i:28620630 original size:11 final size:11
Alignment explanation
Indices: 28620614--28620639 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28620604 TAAATTTTAA
28620614 TTTTAAAATAT
1 TTTTAAAATAT
28620625 TTTTAAAATAT
1 TTTTAAAATAT
28620636 TTTT
1 TTTT
28620640 TTATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:28627011 original size:55 final size:53
Alignment explanation
Indices: 28626922--28627031 Score: 139
Period size: 55 Copynumber: 2.0 Consensus size: 53
28626912 ACTTCACCTG
* *
28626922 AAGAAGGAGAAGGGACCAACGTGAAAACCCGCAAAGGGCGCTTTGAGTTTCAAAA
1 AAGAAGAAGAAGGGACCAACGTGAAAACCCGCAAAGAGCGCTTTGAG--TCAAAA
* * * * *
28626977 AAGAAGAAGAGGGGATCAAGGTGAAAACCTGCAAATAGCGCTTTGAGTCAAAA
1 AAGAAGAAGAAGGGACCAACGTGAAAACCCGCAAAGAGCGCTTTGAGTCAAAA
28627030 AA
1 AA
28627032 ATGATGAAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 8 0.17
55 40 0.83
ACGTcount: A:0.43, C:0.15, G:0.28, T:0.14
Consensus pattern (53 bp):
AAGAAGAAGAAGGGACCAACGTGAAAACCCGCAAAGAGCGCTTTGAGTCAAAA
Found at i:28628380 original size:44 final size:43
Alignment explanation
Indices: 28628331--28628474 Score: 128
Period size: 44 Copynumber: 3.3 Consensus size: 43
28628321 GATAGCAGAT
*
28628331 CTTGCCTTCCTGCATCGACAGAGAAGCAGATTGAAGACACCAGC
1 CTTGCCTTCCT-CATCGACAGTGAAGCAGATTGAAGACACCAGC
* * * * * * * * * *
28628375 CTTGCCTCCCTCGGTTG-CAGTGGATCCGGTTGAAGATAGCAGAT
1 CTTGCCTTCCTC-ATCGACAGTGAAGCAGATTGAAGACACCAG-C
* *
28628419 CTTGCCTTCCTACACCGACAGTGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCT-CATCGACAGTGAAGCAGATTGAAGACACCAGC
28628463 CTTGCCTTCCTC
1 CTTGCCTTCCTC
28628475 GGTTACAGTG
Statistics
Matches: 73, Mismatches: 23, Indels: 9
0.70 0.22 0.09
Matches are distributed among these distances:
43 20 0.27
44 34 0.47
45 19 0.26
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (43 bp):
CTTGCCTTCCTCATCGACAGTGAAGCAGATTGAAGACACCAGC
Found at i:28628466 original size:88 final size:88
Alignment explanation
Indices: 28628317--28628563 Score: 343
Period size: 88 Copynumber: 2.8 Consensus size: 88
28628307 AACAGATCAG
* *
28628317 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGAGAAGCAGATTGAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGCAACGACAGAGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
28628382 CCCTCGGTTGCAGTGGATCCGGT
66 CCCTCGGTTACAGTGGAACAGGT
* * *
28628405 TGAAGATAGCAGATCTTGCCTTCCTACACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGCAACGACAGAGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
28628470 TCCTCGGTTACAGTGGAACATGT
66 CCCTCGGTTACAGTGGAACAGGT
* * *
28628493 TGAAGATAGCAGATCTTGCCCCTTCTTGCAATGACA-ACGAAGCAGATCGAAGATACCAGCCTTG
1 TGAAGATAGCAGATCTTG--CCTTCCTGCAACGACAGA-GAAGCAGATCGAAGACACCAGCCTTG
28628557 CCTCCCT
63 CCTCCCT
28628564 GACCAGCAGT
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
88 97 0.69
90 43 0.31
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (88 bp):
TGAAGATAGCAGATCTTGCCTTCCTGCAACGACAGAGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTCGGTTACAGTGGAACAGGT
Found at i:28628511 original size:44 final size:43
Alignment explanation
Indices: 28628317--28628512 Score: 114
Period size: 44 Copynumber: 4.5 Consensus size: 43
28628307 AACAGATCAG
* * *
28628317 TGAAGATAGCAGATCTTGCCTTCCT-GCATCGACAG-AGAAGCAGAT
1 TGAAGATAGCAGATCTTGCCTTCCTCG-GT-TACAGTGGAA-CAG-T
* * * * * * *
28628362 TGAAGACACCAG-CCTTGCCTCCCTCGGTTGCAGTGGATCCGGT
1 TGAAGATAGCAGATCTTGCCTTCCTCGGTTACAGTGGA-ACAGT
****
28628405 TGAAGATAGCAGATCTTGCCTTCCTACACCGACAGT-GAAGCAGAT
1 TGAAGATAGCAGATCTTGCCTTCCT-CGGTTACAGTGGAA-CAG-T
* * * *
28628450 CGAAGACACCAG-CCTTGCCTTCCTCGGTTACAGTGGAACATGT
1 TGAAGATAGCAGATCTTGCCTTCCTCGGTTACAGTGGAACA-GT
28628493 TGAAGATAGCAGATCTTGCC
1 TGAAGATAGCAGATCTTGCC
28628513 CCTTCTTGCA
Statistics
Matches: 108, Mismatches: 33, Indels: 21
0.67 0.20 0.13
Matches are distributed among these distances:
43 32 0.30
44 50 0.46
45 26 0.24
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (43 bp):
TGAAGATAGCAGATCTTGCCTTCCTCGGTTACAGTGGAACAGT
Found at i:28628607 original size:44 final size:43
Alignment explanation
Indices: 28628558--28629065 Score: 642
Period size: 44 Copynumber: 11.6 Consensus size: 43
28628548 CCAGCCTTGC
28628558 CTCCCTGACCAGCAGTGGAATAGGCTGAAGATTGTAAGTCCTAT
1 CTCCCTGACCAGCAGTGGAATAGG-TGAAGATTGTAAGTCCTAT
*
28628602 CTCCCTGACCAGTAGTGGAATAGGCTGAAGATTGTAAGTCCTAT
1 CTCCCTGACCAGCAGTGGAATAGG-TGAAGATTGTAAGTCCTAT
* *
28628646 CTCCCTGACCAGCAGTGAAATAGGTTGAAGATTGCAAGTCCTAT
1 CTCCCTGACCAGCAGTGGAATAGG-TGAAGATTGTAAGTCCTAT
*
28628690 CTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCCTAT
1 CTCCCTGACCAGCAGTGGAATAGG-TGAAGATTGTAAGTCCTAT
* * *
28628734 CTCCCTAACCAGCAGTGGAATAGGTCGAAGATGGTAAGCCCTAT
1 CTCCCTGACCAGCAGTGGAATAGGT-GAAGATTGTAAGTCCTAT
* * * *
28628778 CTTCCTGAACAGCAGTGGAATAGGTCGAAGATTGTAAGTCTTAG
1 CTCCCTGACCAGCAGTGGAATAGGT-GAAGATTGTAAGTCCTAT
* * * *
28628822 CTCCCTGAACAACAGTGGAATAGGTCGAAGATGGTAAGCCCTAT
1 CTCCCTGACCAGCAGTGGAATAGGT-GAAGATTGTAAGTCCTAT
* * *
28628866 CTCCCT-AACAGCAGTGGAATAGATCGAAGATTGTAAGTCCTAA
1 CTCCCTGACCAGCAGTGGAATAGGT-GAAGATTGTAAGTCCTAT
* * *
28628909 CTCCCTGAACAGCAGTGGAATAGGTTGAAGATGGTAAGCCCTAT
1 CTCCCTGACCAGCAGTGGAATAGG-TGAAGATTGTAAGTCCTAT
* *
28628953 CTCCCTGAACAACAGTGGAATAGGTCGAAGATTGTAAGTCCTAT
1 CTCCCTGACCAGCAGTGGAATAGGT-GAAGATTGTAAGTCCTAT
* *
28628997 CTCCCTGACCAGCAGTGGAATAGTTTGAAGATTGT-AGACCTTAT
1 CTCCCTGACCAGCAGTGGAATAG-GTGAAGATTGTAAGTCC-TAT
* * *
28629041 CTCCCTGAGCAGTAGTGGAGTAGGT
1 CTCCCTGACCAGCAGTGGAATAGGT
28629066 CAAAAATTAC
Statistics
Matches: 415, Mismatches: 43, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
43 45 0.11
44 368 0.89
45 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (43 bp):
CTCCCTGACCAGCAGTGGAATAGGTGAAGATTGTAAGTCCTAT
Found at i:28629090 original size:88 final size:88
Alignment explanation
Indices: 28628558--28629066 Score: 709
Period size: 88 Copynumber: 5.8 Consensus size: 88
28628548 CCAGCCTTGC
* * * * *
28628558 CTCCCTGACCAGCAGTGGAATAGGCTGAAGATTGTAAGTCCTATCTCCCTGACCAGTAGTGGAAT
1 CTCCCTGACCAGCAGTGGAATAGGTTGAAGATGGTAAGCCCTATCTCCCTGAACAGCAGTGGAAT
28628623 AGG-CTGAAGATTGTAAGTCCTAT
66 AGGTC-GAAGATTGTAAGTCCTAT
* * * * *
28628646 CTCCCTGACCAGCAGTGAAATAGGTTGAAGATTGCAAGTCCTATCTCCCTGACCAGCAGTGGAAT
1 CTCCCTGACCAGCAGTGGAATAGGTTGAAGATGGTAAGCCCTATCTCCCTGAACAGCAGTGGAAT
* *
28628711 AGGTTGAAGATTGCAAGTCCTAT
66 AGGTCGAAGATTGTAAGTCCTAT
* * *
28628734 CTCCCTAACCAGCAGTGGAATAGGTCGAAGATGGTAAGCCCTATCTTCCTGAACAGCAGTGGAAT
1 CTCCCTGACCAGCAGTGGAATAGGTTGAAGATGGTAAGCCCTATCTCCCTGAACAGCAGTGGAAT
* *
28628799 AGGTCGAAGATTGTAAGTCTTAG
66 AGGTCGAAGATTGTAAGTCCTAT
* * *
28628822 CTCCCTGAACAACAGTGGAATAGGTCGAAGATGGTAAGCCCTATCTCCCT-AACAGCAGTGGAAT
1 CTCCCTGACCAGCAGTGGAATAGGTTGAAGATGGTAAGCCCTATCTCCCTGAACAGCAGTGGAAT
* *
28628886 AGATCGAAGATTGTAAGTCCTAA
66 AGGTCGAAGATTGTAAGTCCTAT
* *
28628909 CTCCCTGAACAGCAGTGGAATAGGTTGAAGATGGTAAGCCCTATCTCCCTGAACAACAGTGGAAT
1 CTCCCTGACCAGCAGTGGAATAGGTTGAAGATGGTAAGCCCTATCTCCCTGAACAGCAGTGGAAT
28628974 AGGTCGAAGATTGTAAGTCCTAT
66 AGGTCGAAGATTGTAAGTCCTAT
* * * * * *
28628997 CTCCCTGACCAGCAGTGGAATAGTTTGAAGATTGT-AGACCTTATCTCCCTGAGCAGTAGTGGAG
1 CTCCCTGACCAGCAGTGGAATAGGTTGAAGATGGTAAG-CCCTATCTCCCTGAACAGCAGTGGAA
28629061 TAGGTC
65 TAGGTC
28629067 AAAAATTACA
Statistics
Matches: 380, Mismatches: 38, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
87 84 0.22
88 296 0.78
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (88 bp):
CTCCCTGACCAGCAGTGGAATAGGTTGAAGATGGTAAGCCCTATCTCCCTGAACAGCAGTGGAAT
AGGTCGAAGATTGTAAGTCCTAT
Found at i:28641035 original size:16 final size:18
Alignment explanation
Indices: 28641000--28641037 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28640990 ATCCTTATTT
*
28641000 AAATAAAATACAGTAGTA
1 AAATAAAATACAGAAGTA
28641018 AAATAAAATA-A-AAGTA
1 AAATAAAATACAGAAGTA
28641034 AAAT
1 AAAT
28641038 CTATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAGAAGTA
Found at i:28641465 original size:15 final size:17
Alignment explanation
Indices: 28641445--28641476 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28641435 CAAAGGAAAA
28641445 AAAAT-ATT-TTTTTAT
1 AAAATAATTGTTTTTAT
28641460 AAAATAATTGTTTTTAT
1 AAAATAATTGTTTTTAT
28641477 TAATTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 3 0.20
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
AAAATAATTGTTTTTAT
Found at i:28641887 original size:3 final size:3
Alignment explanation
Indices: 28641879--28641912 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28641869 AGCCACGTAT
28641879 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28641913 AATTGATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28646218 original size:20 final size:20
Alignment explanation
Indices: 28646180--28646218 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28646170 TAACATTATA
* *
28646180 AAAATAAATGATATCAAATT
1 AAAATAAAAGAAATCAAATT
*
28646200 AAAATAAAAGAAATTAAAT
1 AAAATAAAAGAAATCAAAT
28646219 ATCAAATTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAATAAAAGAAATCAAATT
Found at i:28652421 original size:3 final size:3
Alignment explanation
Indices: 28652413--28652438 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28652403 AGAACCATGA
28652413 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
28652439 ATGATGGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:28652446 original size:9 final size:9
Alignment explanation
Indices: 28652410--28652452 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
28652400 ACCAGAACCA
28652410 TGATGGTGG
1 TGATGGTGG
*
28652419 TGGTGGTGG
1 TGATGGTGG
*
28652428 TGGTGGTGG
1 TGATGGTGG
*
28652437 TGATGATGG
1 TGATGGTGG
*
28652446 TCATGGT
1 TGATGGT
28652453 CATGGTCATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.09, C:0.02, G:0.53, T:0.35
Consensus pattern (9 bp):
TGATGGTGG
Found at i:28653050 original size:6 final size:6
Alignment explanation
Indices: 28653039--28653105 Score: 53
Period size: 6 Copynumber: 10.2 Consensus size: 6
28653029 TATTTCTCCC
* * *
28653039 TATTTT TATTTT TATTTT CATTTT CATTTAT ATAAATTCT TATTTT TATTATT
1 TATTTT TATTTT TATTTT TATTTT TATTT-T -T--ATTTT TATTTT TATT-TT
28653092 TATTATT TATTTT T
1 TATT-TT TATTTT T
28653106 GTAAAATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
6 33 0.63
7 14 0.27
8 1 0.02
9 1 0.02
10 3 0.06
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (6 bp):
TATTTT
Found at i:28654273 original size:15 final size:15
Alignment explanation
Indices: 28654253--28654284 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28654243 CATTTCACTA
*
28654253 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
28654268 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
28654283 TT
1 TT
28654285 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:28669950 original size:116 final size:116
Alignment explanation
Indices: 28669744--28670022 Score: 408
Period size: 116 Copynumber: 2.4 Consensus size: 116
28669734 NNNNNNNNNN
* * *
28669744 CATCAAATATACAATAGATGTAC--ATATATATAT-ACATATTCTAACTTCATTTATGTGTATAT
1 CATCAAATATACAATAGATATACATATATATATATAACATATTCGAACTTCATTTA-GTGCATAT
*
28669806 ATATAACATTTATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCT
65 ATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCT
28669858 CATCAAATATACAATAGATATACATATATATATATACACATATTCGAACTTCATTTA-TGCATAT
1 CATCAAATATACAATAGATATACATATATATATATA-ACATATTCGAACTTCATTTAGTGCATAT
* *
28669922 ATATATCATTCATACTTAACTAATTTCAATTCGTATACTTTTAATTATAGCT
65 ATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCT
* * *
28669974 CATCAAATGTACAATAGTTA-ACATACATAT-TATATACATATTCGAACTT
1 CATCAAATATACAATAGATATACATATATATATATA-ACATATTCGAACTT
28670023 NNNNNNNNNN
Statistics
Matches: 151, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
114 40 0.26
115 9 0.06
116 83 0.55
118 19 0.13
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.41
Consensus pattern (116 bp):
CATCAAATATACAATAGATATACATATATATATATAACATATTCGAACTTCATTTAGTGCATATA
TATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCT
Found at i:28672883 original size:15 final size:15
Alignment explanation
Indices: 28672859--28672888 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28672849 ATTAATTTTG
28672859 ATCAAGTAAAATTAA
1 ATCAAGTAAAATTAA
*
28672874 ATCAATTAAAATTAA
1 ATCAAGTAAAATTAA
28672889 TATGATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (15 bp):
ATCAAGTAAAATTAA
Found at i:28685447 original size:28 final size:29
Alignment explanation
Indices: 28685380--28685448 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 29
28685370 ATTTAAATCA
** * **
28685380 GCCTATTTCCCTAATTAATTTTAAAATTG
1 GCCTATTGGCCTAATTAATTTAAAAAAAG
**
28685409 GCCTAAAGGCCTAATTAA-TTAAAAAAAG
1 GCCTATTGGCCTAATTAATTTAAAAAAAG
28685437 GCCTATTGGCCT
1 GCCTATTGGCCT
28685449 TATTTTGCCA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (29 bp):
GCCTATTGGCCTAATTAATTTAAAAAAAG
Found at i:28688809 original size:27 final size:27
Alignment explanation
Indices: 28688779--28688942 Score: 213
Period size: 27 Copynumber: 6.1 Consensus size: 27
28688769 AGGCTATCCC
* * *
28688779 TTCATATTTCACCATAAAGGTTTTTCT
1 TTCATATTTCGCCACAAAGGCTTTTCT
* *
28688806 TTCATATTTCGCCAGAAAGACTTTTCT
1 TTCATATTTCGCCACAAAGGCTTTTCT
28688833 TTCATGA-TTCGCCACAAAGGCTTTTCT
1 TTCAT-ATTTCGCCACAAAGGCTTTTCT
*
28688860 TTCATGTTTCGCCACAAAGGCTTTTCT
1 TTCATATTTCGCCACAAAGGCTTTTCT
* * *
28688887 TTTATATTTCGCCAGAAAGACTTTTCT
1 TTCATATTTCGCCACAAAGGCTTTTCT
**
28688914 TTCATATTTTTCCACAAAGGCTTTTCT
1 TTCATATTTCGCCACAAAGGCTTTTCT
28688941 TT
1 TT
28688943 TATGACATGT
Statistics
Matches: 119, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
27 118 0.99
28 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (27 bp):
TTCATATTTCGCCACAAAGGCTTTTCT
Found at i:28688936 original size:81 final size:81
Alignment explanation
Indices: 28688779--28688942 Score: 249
Period size: 81 Copynumber: 2.0 Consensus size: 81
28688769 AGGCTATCCC
* *
28688779 TTCATATTTCACCATAAAGGTTTTTCTTTCATATTTCGCCAGAAAGACTTTTCTTTCATGATTCG
1 TTCATATTTCACCACAAAGGCTTTTCTTTCATATTTCGCCAGAAAGACTTTTCTTTCATGATTCG
28688844 CCACAAAGGCTTTTCT
66 CCACAAAGGCTTTTCT
* * * *
28688860 TTCATGTTTCGCCACAAAGGCTTTTCTTTTATATTTCGCCAGAAAGACTTTTCTTTCAT-ATTTT
1 TTCATATTTCACCACAAAGGCTTTTCTTTCATATTTCGCCAGAAAGACTTTTCTTTCATGA-TTC
*
28688924 TCCACAAAGGCTTTTCT
65 GCCACAAAGGCTTTTCT
28688941 TT
1 TT
28688943 TATGACATGT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
80 1 0.01
81 74 0.99
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (81 bp):
TTCATATTTCACCACAAAGGCTTTTCTTTCATATTTCGCCAGAAAGACTTTTCTTTCATGATTCG
CCACAAAGGCTTTTCT
Found at i:28691213 original size:41 final size:41
Alignment explanation
Indices: 28691168--28691287 Score: 118
Period size: 41 Copynumber: 3.0 Consensus size: 41
28691158 AATTGAGTTG
* * *
28691168 TTATGGCGGTGTATTGTATTGGGCCTTGGGCCTAGCAGGCT
1 TTATGGCGGTGTATTATATCGGGCCTTGAGCCTAGCAGGCT
** * *
28691209 TTATGTTGGTGTATTATATCGGGCCTTGAGCCTAGCAAGCC
1 TTATGGCGGTGTATTATATCGGGCCTTGAGCCTAGCAGGCT
** * * *
28691250 TCGTGTCGGTG-ACT-TATCGGGCTTTGAGCCTAGCAGGC
1 TTATGGCGGTGTATTATATCGGGCCTTGAGCCTAGCAGGC
28691288 CTCGGCCGGT
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
39 22 0.33
40 2 0.03
41 42 0.64
ACGTcount: A:0.15, C:0.20, G:0.33, T:0.33
Consensus pattern (41 bp):
TTATGGCGGTGTATTATATCGGGCCTTGAGCCTAGCAGGCT
Found at i:28691321 original size:37 final size:38
Alignment explanation
Indices: 28691225--28691333 Score: 132
Period size: 39 Copynumber: 2.8 Consensus size: 38
28691215 TGGTGTATTA
* *
28691225 TATCGGGCCTTGAGCCTAGCAAGCCTCGTGTCGGTGACT
1 TATCGGG-CTTGAGCCTAGCAGGCCTCGTGCCGGTGACT
*
28691264 TATCGGGCTTTGAGCCTAGCAGGCCTCG-GCCGGTG-TT
1 TATCGGGC-TTGAGCCTAGCAGGCCTCGTGCCGGTGACT
* *
28691301 TATCGGGCTTGATGCTTAGCAGGCTTCGTGCCG
1 TATCGGGCTTGA-GCCTAGCAGGCCTCGTGCCG
28691334 CTTTAACAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
36 4 0.06
37 22 0.35
38 11 0.18
39 25 0.40
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.28
Consensus pattern (38 bp):
TATCGGGCTTGAGCCTAGCAGGCCTCGTGCCGGTGACT
Found at i:28692027 original size:54 final size:54
Alignment explanation
Indices: 28691928--28692031 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 54
28691918 ATTAAGTTGA
* * **
28691928 ACACGGTCTAGCACACGGCCTACGATACGACCGTGTGAGGGTATTTTGAATGTT
1 ACACGGGCTAGCACACGGCCTACGATACGACCATGTGAAAGTATTTTGAATGTT
* ** * *
28691982 ACACGGGCTAGCACACGGTCTGTGATACGATCATGTGAAATTATTTTGAA
1 ACACGGGCTAGCACACGGCCTACGATACGACCATGTGAAAGTATTTTGAA
28692032 GGGTACATGG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (54 bp):
ACACGGGCTAGCACACGGCCTACGATACGACCATGTGAAAGTATTTTGAATGTT
Found at i:28710945 original size:54 final size:54
Alignment explanation
Indices: 28710886--28711008 Score: 142
Period size: 54 Copynumber: 2.3 Consensus size: 54
28710876 TGCCTTCACC
****
28710886 CGTGTAACTCACTGAGTAGGGTCACACGACCGTGTAG-CAGGACT-TGTGCCAGGT
1 CGTGTAACTCACTGAGTAGCCAAACACGACCGTGT-GCCAGG-CTGTGTGCCAGGT
* * * *
28710940 TGTGTAACTCTCTGAGTTGCCAAACACGACCGTGTGCCAGGCTGTGTGCTAGGT
1 CGTGTAACTCACTGAGTAGCCAAACACGACCGTGTGCCAGGCTGTGTGCCAGGT
28710994 CGTGTAACTCACTGA
1 CGTGTAACTCACTGA
28711009 CTTGAAACAC
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
53 3 0.05
54 54 0.95
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.25
Consensus pattern (54 bp):
CGTGTAACTCACTGAGTAGCCAAACACGACCGTGTGCCAGGCTGTGTGCCAGGT
Found at i:28714605 original size:36 final size:32
Alignment explanation
Indices: 28714538--28714602 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
28714528 ATATATTAAG
28714538 CCATCAACGAAGTAGAATTAATTACTCTCTTT
1 CCATCAACGAAGTAGAATTAATTACTCTCTTT
*
28714570 CCATCAACGAAGTAGAATTAATTATTCTCTTT
1 CCATCAACGAAGTAGAATTAATTACTCTCTTT
28714602 C
1 C
28714603 TTTTTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.35
Consensus pattern (32 bp):
CCATCAACGAAGTAGAATTAATTACTCTCTTT
Found at i:28719649 original size:29 final size:29
Alignment explanation
Indices: 28719607--28719664 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28719597 CACTTATCTA
28719607 ATCTTATAGTTACAATTAAACTAATTTAG
1 ATCTTATAGTTACAATTAAACTAATTTAG
28719636 ATCTTATAGTTACAATTAAACTAATTTAG
1 ATCTTATAGTTACAATTAAACTAATTTAG
28719665 GTGAACCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (29 bp):
ATCTTATAGTTACAATTAAACTAATTTAG
Found at i:28721577 original size:68 final size:66
Alignment explanation
Indices: 28721448--28721586 Score: 199
Period size: 68 Copynumber: 2.1 Consensus size: 66
28721438 GGCGCTATCC
* * * *
28721448 AAAAAGCGCTGCTAATGCTTGACTTTTGCGGCATTTCTAGAAAGCTCCACTAATGTCTCTAAAGC
1 AAAAAGCACCGCTAATACTTGACTTTTGCGGCATTTCTAAAAAGCTCCACTAATGTCTCTAAAGC
28721513 T
66 T
*
28721514 CAAAAGCACCGCTAATACTTGACTTTTTGCGGCATTTTCTAAAAAG-TGCCACTAATGTCTCTAA
1 AAAAAGCACCGCTAATACTTGAC-TTTTGCGGCA-TTTCTAAAAAGCT-CCACTAATGTCTCTAA
28721578 AGCT
63 AGCT
28721582 AAAAA
1 AAAAA
28721587 CAAACCGAGC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
66 19 0.30
67 11 0.17
68 34 0.53
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (66 bp):
AAAAAGCACCGCTAATACTTGACTTTTGCGGCATTTCTAAAAAGCTCCACTAATGTCTCTAAAGC
T
Found at i:28722194 original size:13 final size:13
Alignment explanation
Indices: 28722176--28722208 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
28722166 TTCTTCATTA
28722176 CTTTTGAGAAGTG
1 CTTTTGAGAAGTG
28722189 CTTTTGAGAAGTG
1 CTTTTGAGAAGTG
28722202 CTTTTGA
1 CTTTTGA
28722209 AAAATTTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.09, G:0.27, T:0.42
Consensus pattern (13 bp):
CTTTTGAGAAGTG
Found at i:28727435 original size:63 final size:63
Alignment explanation
Indices: 28727361--28727487 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
28727351 AAACCATATA
*
28727361 TATATTTAATAAGTAATTGAAATTAAAAAATTTTAAGCATAGTATTAATTAATAAATTGAAAT
1 TATATTTAATAAGTAATTGAAATTAAAAAATTTTAAGCATAGTATTAATTAATAAATAGAAAT
28727424 TATATTTAATAAGTAATTGAAATTAAAAAATTTTAAGCATAGTATTAATTAATAAATAGAAAT
1 TATATTTAATAAGTAATTGAAATTAAAAAATTTTAAGCATAGTATTAATTAATAAATAGAAAT
28727487 T
1 T
28727488 CTTTTATTAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (63 bp):
TATATTTAATAAGTAATTGAAATTAAAAAATTTTAAGCATAGTATTAATTAATAAATAGAAAT
Found at i:28730809 original size:13 final size:12
Alignment explanation
Indices: 28730793--28730855 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 12
28730783 TTTAAATCAA
28730793 ACTTTTCAAAATC
1 ACTTTTCAAAA-C
28730806 ACTTCTT-AAAAGC
1 ACTT-TTCAAAA-C
*
28730819 ACTTTTCCACAAC
1 ACTTTT-CAAAAC
*
28730832 ACTTTTCCACAAC
1 ACTTTT-CAAAAC
28730845 ACTTTTCAAAA
1 ACTTTTCAAAA
28730856 GTAATGAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
12 6 0.14
13 33 0.75
14 5 0.11
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.33
Consensus pattern (12 bp):
ACTTTTCAAAAC
Found at i:28732554 original size:303 final size:303
Alignment explanation
Indices: 28732078--28732683 Score: 1212
Period size: 303 Copynumber: 2.0 Consensus size: 303
28732068 TTCTATAAAA
28732078 ACACAAATAGGTATTTTGGATCATTTTATAATCCTCCTTTAACTACTATTTACCACATATATTCA
1 ACACAAATAGGTATTTTGGATCATTTTATAATCCTCCTTTAACTACTATTTACCACATATATTCA
28732143 AATTATTTCAATTCCTATAAATGAACAATTTCTCAAGAATTTCAATATGCTTCTAGCATCCTAAA
66 AATTATTTCAATTCCTATAAATGAACAATTTCTCAAGAATTTCAATATGCTTCTAGCATCCTAAA
28732208 TCCTTCAAGGATTTTAATATAAGCTTTACTATATAATGGTTCATAAAAGGTTGTAACAACAACCA
131 TCCTTCAAGGATTTTAATATAAGCTTTACTATATAATGGTTCATAAAAGGTTGTAACAACAACCA
28732273 TTAGATGCAAGTTAAATCTTTTATGAATTGTTAAAATAATATATCTAAAAGTTATTGCATCCACC
196 TTAGATGCAAGTTAAATCTTTTATGAATTGTTAAAATAATATATCTAAAAGTTATTGCATCCACC
28732338 ACAAAAGAATATTTTATCTTTTTATAACCAATGCTAGGACTTC
261 ACAAAAGAATATTTTATCTTTTTATAACCAATGCTAGGACTTC
28732381 ACACAAATAGGTATTTTGGATCATTTTATAATCCTCCTTTAACTACTATTTACCACATATATTCA
1 ACACAAATAGGTATTTTGGATCATTTTATAATCCTCCTTTAACTACTATTTACCACATATATTCA
28732446 AATTATTTCAATTCCTATAAATGAACAATTTCTCAAGAATTTCAATATGCTTCTAGCATCCTAAA
66 AATTATTTCAATTCCTATAAATGAACAATTTCTCAAGAATTTCAATATGCTTCTAGCATCCTAAA
28732511 TCCTTCAAGGATTTTAATATAAGCTTTACTATATAATGGTTCATAAAAGGTTGTAACAACAACCA
131 TCCTTCAAGGATTTTAATATAAGCTTTACTATATAATGGTTCATAAAAGGTTGTAACAACAACCA
28732576 TTAGATGCAAGTTAAATCTTTTATGAATTGTTAAAATAATATATCTAAAAGTTATTGCATCCACC
196 TTAGATGCAAGTTAAATCTTTTATGAATTGTTAAAATAATATATCTAAAAGTTATTGCATCCACC
28732641 ACAAAAGAATATTTTATCTTTTTATAACCAATGCTAGGACTTC
261 ACAAAAGAATATTTTATCTTTTTATAACCAATGCTAGGACTTC
28732684 GCGAAAAACT
Statistics
Matches: 303, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
303 303 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (303 bp):
ACACAAATAGGTATTTTGGATCATTTTATAATCCTCCTTTAACTACTATTTACCACATATATTCA
AATTATTTCAATTCCTATAAATGAACAATTTCTCAAGAATTTCAATATGCTTCTAGCATCCTAAA
TCCTTCAAGGATTTTAATATAAGCTTTACTATATAATGGTTCATAAAAGGTTGTAACAACAACCA
TTAGATGCAAGTTAAATCTTTTATGAATTGTTAAAATAATATATCTAAAAGTTATTGCATCCACC
ACAAAAGAATATTTTATCTTTTTATAACCAATGCTAGGACTTC
Found at i:28738629 original size:16 final size:17
Alignment explanation
Indices: 28738600--28738634 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
28738590 AGCATATTTG
28738600 ATAAAAATAATTTAATC
1 ATAAAAATAATTTAATC
*
28738617 ATAAAAA-ATTTTAATC
1 ATAAAAATAATTTAATC
28738633 AT
1 AT
28738635 CCAAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAAAATAATTTAATC
Found at i:28739231 original size:135 final size:136
Alignment explanation
Indices: 28739017--28739289 Score: 539
Period size: 135 Copynumber: 2.0 Consensus size: 136
28739007 GAGCAAAAAA
28739017 GAGCATATTTTATTGATCAATCAGAATATTTACAAAGCTTCTTCAAAGTCTCTATTTATAGGCAT
1 GAGCATATTTTATTGATCAATCAGAATATTTACAAAGCTTCTTCAAAGTCTCTATTTATAGGCAT
28739082 AAGAAGTATAAATGAAGTAGAGATCTACTTTTAATGACTATTAGAATTTGAAGCACATC-AAACT
66 AAGAAGTATAAATGAAGTAGAGATCTACTTTTAATGACTATTAGAATTTGAAGCACATCAAAACT
28739146 TATCTT
131 TATCTT
28739152 GAGCATATTTTATTGATCAATCAGAATATTTACAAAGCTTCTTCAAAGTCTCTATTTATAGGCAT
1 GAGCATATTTTATTGATCAATCAGAATATTTACAAAGCTTCTTCAAAGTCTCTATTTATAGGCAT
28739217 AAGAAGTATAAATGAAGTAGAGATCTACTTTTAATGACTATTAGAATTTGAAGCACATCAAAACT
66 AAGAAGTATAAATGAAGTAGAGATCTACTTTTAATGACTATTAGAATTTGAAGCACATCAAAACT
28739282 TATCTT
131 TATCTT
28739288 GA
1 GA
28739290 TCTTGATGGA
Statistics
Matches: 137, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
135 124 0.91
136 13 0.09
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (136 bp):
GAGCATATTTTATTGATCAATCAGAATATTTACAAAGCTTCTTCAAAGTCTCTATTTATAGGCAT
AAGAAGTATAAATGAAGTAGAGATCTACTTTTAATGACTATTAGAATTTGAAGCACATCAAAACT
TATCTT
Found at i:28747729 original size:25 final size:25
Alignment explanation
Indices: 28747695--28747745 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
28747685 TAGGAACATC
28747695 ACTCAAAGTAAAGAGCATCGTCCTA
1 ACTCAAAGTAAAGAGCATCGTCCTA
28747720 ACTCAAAGTAAAGAGCATCGTCCTA
1 ACTCAAAGTAAAGAGCATCGTCCTA
28747745 A
1 A
28747746 GGTGATATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.20
Consensus pattern (25 bp):
ACTCAAAGTAAAGAGCATCGTCCTA
Found at i:28752869 original size:15 final size:16
Alignment explanation
Indices: 28752849--28752879 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28752839 ACAAAAAGAA
28752849 ATAGAAA-GAAACAGG
1 ATAGAAACGAAACAGG
28752864 ATAGAAACGAAACAGG
1 ATAGAAACGAAACAGG
28752880 GAGAAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.58, C:0.10, G:0.26, T:0.06
Consensus pattern (16 bp):
ATAGAAACGAAACAGG
Found at i:28752912 original size:13 final size:15
Alignment explanation
Indices: 28752884--28752924 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
28752874 AACAGGGAGA
*
28752884 AAAAGAAAGA-AAAG
1 AAAAGAAGGAGAAAG
28752898 AAAA-AAGG-GAAAG
1 AAAAGAAGGAGAAAG
28752911 AAAAGAAGGAGAAA
1 AAAAGAAGGAGAAA
28752925 TTAGGGTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 11 0.48
14 8 0.35
15 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAAGAAGGAGAAAG
Found at i:28754337 original size:13 final size:13
Alignment explanation
Indices: 28754319--28754346 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28754309 AGAAGGCTTC
28754319 ATAATTCATATTA
1 ATAATTCATATTA
28754332 ATAATTCATATTA
1 ATAATTCATATTA
28754345 AT
1 AT
28754347 TATGAATGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATTCATATTA
Found at i:28754683 original size:13 final size:13
Alignment explanation
Indices: 28754665--28754690 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28754655 TTTTAATTTA
28754665 TATATATTTAAAT
1 TATATATTTAAAT
28754678 TATATATTTAAAT
1 TATATATTTAAAT
28754691 GATAAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATTTAAAT
Found at i:28756274 original size:40 final size:40
Alignment explanation
Indices: 28756225--28756332 Score: 162
Period size: 40 Copynumber: 2.7 Consensus size: 40
28756215 GGTGTTACAA
* * *
28756225 TATAACTATTTCCATATAACAGATTCATATAACCATTCTG
1 TATATCTATTTCCATATAACTGATTCATATAACCATTCCG
* *
28756265 TATATCTATTTACTTATAACTGATTCATATAACCATTCCG
1 TATATCTATTTCCATATAACTGATTCATATAACCATTCCG
*
28756305 TATATCTATTTCCATATAGCTGATTCAT
1 TATATCTATTTCCATATAACTGATTCAT
28756333 TTATTCATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (40 bp):
TATATCTATTTCCATATAACTGATTCATATAACCATTCCG
Found at i:28758949 original size:12 final size:11
Alignment explanation
Indices: 28758919--28758949 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
28758909 TTTATTTTTT
28758919 TATTTTTAAAA
1 TATTTTTAAAA
28758930 TATTTTTAAAA
1 TATTTTTAAAA
28758941 TATTCTTTA
1 TATT-TTTA
28758950 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTTTTAAAA
Done.