Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009578.1 Kokia drynarioides strain JFW-HI SEQ_124292, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 229893
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 120 characters in sequence are not A, C, G, or T
Found at i:427 original size:18 final size:19
Alignment explanation
Indices: 389--439 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
379 CATTAATAGG
389 TATTAATAAAATATTTATTAA
1 TATTAATAAAA-A-TTATTAA
410 TATTAATAAAAA-TATTAA
1 TATTAATAAAAATTATTAA
*
428 TAATAATAAAAA
1 TATTAATAAAAA
440 AGGGAACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 17 0.59
20 1 0.03
21 11 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTAATAAAAATTATTAA
Found at i:1417 original size:29 final size:29
Alignment explanation
Indices: 1369--1637 Score: 273
Period size: 29 Copynumber: 9.1 Consensus size: 29
1359 GAGGTCCTTA
**
1369 AACTATCCAAAAATTTTATTTTTACCCCTG
1 AACT-TCCAAAAATCCTATTTTTACCCCTG
*
1399 AACTTCCAAAAATCCTATTTTTGA-CCCTAA
1 AACTTCCAAAAATCCTATTTTT-ACCCCT-G
1429 AACTTCCAAAAATTCC-ATTTTTA-CCCTCG
1 AACTTCCAAAAA-TCCTATTTTTACCCCT-G
*
1458 AACTTTCAAAAATCCTATTTTTGACCCC-G
1 AACTTCCAAAAATCCTATTTTT-ACCCCTG
* * *
1487 AAACTTCCAAGAATTCTATTTTTA-TCCTCG
1 -AACTTCCAAAAATCCTATTTTTACCCCT-G
*
1517 AACTTCCAAAAATCCTATTTTTGACCTC-G
1 AACTTCCAAAAATCCTATTTTT-ACCCCTG
*
1546 AAACTTCCAAAAATTCTATTTTTACCCCTG
1 -AACTTCCAAAAATCCTATTTTTACCCCTG
**
1576 AACTTCCAAAAATCCTATTTTTAACCCCAA
1 AACTTCCAAAAATCCTATTTTT-ACCCCTG
*
1606 AACTTCCAAAAATTCC-ATTTTTACCCTTG
1 AACTTCCAAAAA-TCCTATTTTTACCCCTG
1635 AAC
1 AAC
1638 CTCTAAAATC
Statistics
Matches: 202, Mismatches: 22, Indels: 31
0.79 0.09 0.12
Matches are distributed among these distances:
28 5 0.02
29 97 0.48
30 90 0.45
31 10 0.05
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
AACTTCCAAAAATCCTATTTTTACCCCTG
Found at i:1645 original size:29 final size:29
Alignment explanation
Indices: 1369--1637 Score: 250
Period size: 30 Copynumber: 9.1 Consensus size: 29
1359 GAGGTCCTTA
**
1369 AACTATCCAAAAATTTTATTTTTACCC-CTG
1 AACT-TCCAAAAATTCCATTTTTACCCTC-G
**
1399 AACTTCCAAAAA-TCCTATTTTTGACCCTAA
1 AACTTCCAAAAATTCC-ATTTTT-ACCCTCG
1429 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
1458 AACTTTCAAAAA-TCCTATTTTTGACCC-CG
1 AACTTCCAAAAATTCC-ATTTTT-ACCCTCG
* * *
1487 AAACTTCCAAGAATTCTATTTTTATCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
1517 AACTTCCAAAAA-TCCTATTTTTGA-CCTCG
1 AACTTCCAAAAATTCC-ATTTTT-ACCCTCG
*
1546 AAACTTCCAAAAATTCTATTTTTACCC-CTG
1 -AACTTCCAAAAATTCCATTTTTACCCTC-G
*
1576 AACTTCCAAAAA-TCCTATTTTTAACCC-CAA
1 AACTTCCAAAAATTCC-ATTTTT-ACCCTC-G
*
1606 AACTTCCAAAAATTCCATTTTTACCCTTG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
1635 AAC
1 AAC
1638 CTCTAAAATC
Statistics
Matches: 201, Mismatches: 19, Indels: 39
0.78 0.07 0.15
Matches are distributed among these distances:
28 8 0.04
29 90 0.45
30 93 0.46
31 10 0.05
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:1668 original size:59 final size:59
Alignment explanation
Indices: 1368--1637 Score: 396
Period size: 59 Copynumber: 4.6 Consensus size: 59
1358 GGAGGTCCTT
* * **
1368 AAACTATCCAAAAATTTTATTTTTACCCCTGAACTTCCAAAAATCCTATTTTTGACCCTA
1 AAACT-TCCAAAAATTCTATTTTTACCCTTGAACTTCCAAAAATCCTATTTTTGACCCCG
* * *
1428 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTCAAAAATCCTATTTTTGACCCCG
1 AAACTTCCAAAAATTCTATTTTTACCCTTGAACTTCCAAAAATCCTATTTTTGACCCCG
* * * *
1487 AAACTTCCAAGAATTCTATTTTTATCCTCGAACTTCCAAAAATCCTATTTTTGACCTCG
1 AAACTTCCAAAAATTCTATTTTTACCCTTGAACTTCCAAAAATCCTATTTTTGACCCCG
* * *
1546 AAACTTCCAAAAATTCTATTTTTACCCCTGAACTTCCAAAAATCCTATTTTTAACCCCA
1 AAACTTCCAAAAATTCTATTTTTACCCTTGAACTTCCAAAAATCCTATTTTTGACCCCG
*
1605 AAACTTCCAAAAATTCCATTTTTACCCTTGAAC
1 AAACTTCCAAAAATTCTATTTTTACCCTTGAAC
1638 CTCTAAAATC
Statistics
Matches: 189, Mismatches: 21, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
59 184 0.97
60 5 0.03
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
AAACTTCCAAAAATTCTATTTTTACCCTTGAACTTCCAAAAATCCTATTTTTGACCCCG
Found at i:1675 original size:118 final size:118
Alignment explanation
Indices: 1368--1668 Score: 401
Period size: 118 Copynumber: 2.5 Consensus size: 118
1358 GGAGGTCCTT
* * * *
1368 AAACTATCCAAAAATTTTATTTTTACCCCTGAACTTCCAAAAATCCTATTTTTGACCCTAAAACT
1 AAACT-TCCAAAAATTCTATTTTTACCCTTGAACTTCCAAAAATCCTATTTTTGACCTTGAAACT
* * *
1433 TCCAAAAATTCCATTTTTACCCTCGAACTTTCAAAAATCCTATTTTTGACCCCG
65 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCTATTTTTAACCCCA
* * * *
1487 AAACTTCCAAGAATTCTATTTTTATCCTCGAACTTCCAAAAATCCTATTTTTGACCTCGAAACTT
1 AAACTTCCAAAAATTCTATTTTTACCCTTGAACTTCCAAAAATCCTATTTTTGACCTTGAAACTT
*
1552 CCAAAAATTCTATTTTTACCC-CTGAACTTCCAAAAATCCTATTTTTAACCCCA
66 CCAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATCCTATTTTTAACCCCA
* * * *
1605 AAACTTCCAAAAATTCCATTTTTACCCTTGAACCT-CTAAAAT-CTTTGTTTTCGACCTTGAAAC
1 AAACTTCCAAAAATTCTATTTTTACCCTTGAACTTCCAAAAATCCTAT-TTTT-GACCTTGAAAC
1668 T
64 T
1669 CTCAAAATCA
Statistics
Matches: 159, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
116 3 0.02
117 11 0.07
118 140 0.88
119 5 0.03
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.36
Consensus pattern (118 bp):
AAACTTCCAAAAATTCTATTTTTACCCTTGAACTTCCAAAAATCCTATTTTTGACCTTGAAACTT
CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCTATTTTTAACCCCA
Found at i:1752 original size:28 final size:28
Alignment explanation
Indices: 1699--1757 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1689 CTCTGAATTT
*
1699 TCCAAAATTACCATTTTTGCCTCGAGAA
1 TCCAAAATTACCATTTTTGCCCCGAGAA
* *
1727 TCCAAAATTACTA-TTTTGCCCCCGAGTA
1 TCCAAAATTACCATTTTTG-CCCCGAGAA
1755 TCC
1 TCC
1758 GAGAAGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (28 bp):
TCCAAAATTACCATTTTTGCCCCGAGAA
Found at i:12891 original size:205 final size:206
Alignment explanation
Indices: 12539--13130 Score: 848
Period size: 205 Copynumber: 2.9 Consensus size: 206
12529 CAGCGATATG
* * *
12539 ATCATCTTCCTGATGAGATACTGAGAAGGAGACCAAATCAAGCTCACGCTCGATGTGAGCAAATC
1 ATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCCCGATGTGAGCAAATC
* * * ** *
12604 TTCGAACCCCAGCTTCCTGATGAGATACGGAGAAGCAGGGTGAATCAAT-AAGAGGTTAGCTTCC
66 TTCGAACCTCAACTTCCTGATGAGATACAGAGAAGCAGGACGAAGCAATAAAGAGGTTAGCTTCC
* *
12668 TGATGAGATACTGAGAAGTAAACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAA
131 TGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAA
*
12733 CAAACGATGCA
196 CAAACGACGCA
* * *
12744 ATCATCTTCCTGATGAGATACTGAGAATAAGACCAAATCAAACTCATGCCCGATGTTAGCAAATC
1 ATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCCCGATGTGAGCAAATC
* *
12809 TTCAAACCTCAACTTCCTGATGAGATACAGAGAAGCAGGACGAAGCAATAAAG-GGTTTGCTTCC
66 TTCGAACCTCAACTTCCTGATGAGATACAGAGAAGCAGGACGAAGCAATAAAGAGGTTAGCTTCC
* *
12873 TGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGAATTGAAA
131 TGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAA
*
12938 CAAACGACGTA
196 CAAACGACGCA
* * * *
12949 GTCATCTTCCTGACGAGATACTAAGAAGAAGACCAAATCAAACTCACGCCCGATATGAGCAAATC
1 ATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCCCGATGTGAGCAAATC
* * * * * *
13014 TTCGAACCTTAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAGTGGTTAGCTCCC
66 TTCGAACCTCAACTTCCTGATGAGATACAGAGAAGCAGGACGAAGCAATAAAGAGGTTAGCTTCC
* * * *
13079 TGATGAGATA-TAGAGAAGTGAACCAAATCCGTCTTCTTGATGAAACACAGAG
131 TGATGAGATACT-GAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
13131 GAATGGATCA
Statistics
Matches: 344, Mismatches: 40, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
205 288 0.84
206 56 0.16
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (206 bp):
ATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCCCGATGTGAGCAAATC
TTCGAACCTCAACTTCCTGATGAGATACAGAGAAGCAGGACGAAGCAATAAAGAGGTTAGCTTCC
TGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAA
CAAACGACGCA
Found at i:13548 original size:17 final size:18
Alignment explanation
Indices: 13525--13636 Score: 104
Period size: 17 Copynumber: 6.4 Consensus size: 18
13515 CCAAACTCAT
**
13525 TTTAAATTTATTTTACGA
1 TTTAAATTTATTTTAAAA
* *
13543 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAAA
13560 TTTAAATTTATTTT-AAA
1 TTTAAATTTATTTTAAAA
* *
13577 TTTAAATTTAATTT-AAG
1 TTTAAATTTATTTTAAAA
*
13594 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAAA
** *
13612 TTTAAAAATATTATAAAA
1 TTTAAATTTATTTTAAAA
*
13630 TTAAAAT
1 TTTAAAT
13637 AAATAAAGTT
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
17 44 0.58
18 32 0.42
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:13564 original size:35 final size:34
Alignment explanation
Indices: 13525--13617 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 34
13515 CCAAACTCAT
* *
13525 TTTAAATTTATTTTACGA-TTAAATTT-GTTTAAAAA
1 TTTAAATTTATTTTA-AATTTAAATTTAATTT--AAA
*
13560 TTTAAATTTATTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
13594 TTTAAATTTATTTTCAAATTTAAA
1 TTTAAATTTATTTT-AAATTTAAA
13618 AATATTATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
34 17 0.33
35 32 0.62
36 3 0.06
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
Found at i:13568 original size:6 final size:6
Alignment explanation
Indices: 13557--13617 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
13547 ATTTGTTTAA
* *
13557 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
13603 -ATTTT CAAATTT AAA
1 AAATTT -AAATTT AAA
13618 AATATTATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
5 13 0.29
6 28 0.62
7 4 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:13576 original size:11 final size:11
Alignment explanation
Indices: 13560--13615 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
13550 TGTTTAAAAA
13560 TTTAAATTTAT
1 TTTAAATTTAT
*
13571 TTTAAATTTAAA
1 TTTAAATTT-AT
*
13583 TTT-AATTTAAG
1 TTTAAATTT-AT
13594 TTTAAATTTAT
1 TTTAAATTTAT
13605 TTTCAAATTTA
1 TTT-AAATTTA
13616 AAAATATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
11 23 0.59
12 16 0.41
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:13634 original size:52 final size:52
Alignment explanation
Indices: 13526--13634 Score: 128
Period size: 52 Copynumber: 2.1 Consensus size: 52
13516 CAAACTCATT
* * * ** * *
13526 TTAAATTTATTTTACGATTAAATTTGTTTAAAAATTTAAATTTATTTTAAAT
1 TTAAATTTAATTTAAGATTAAATTTATTTAAAAATTTAAAAATATTATAAAA
* **
13578 TTAAATTTAATTTAAGTTTAAATTTATTTTCAAATTTAAAAATATTATAAAA
1 TTAAATTTAATTTAAGATTAAATTTATTTAAAAATTTAAAAATATTATAAAA
13630 TTAAA
1 TTAAA
13635 ATAAATAAAG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (52 bp):
TTAAATTTAATTTAAGATTAAATTTATTTAAAAATTTAAAAATATTATAAAA
Found at i:14059 original size:33 final size:33
Alignment explanation
Indices: 14017--14082 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
14007 AGATTCAAAA
14017 GAAATCAATACAAAGTCTCAACATTCGCAACAT
1 GAAATCAATACAAAGTCTCAACATTCGCAACAT
14050 GAAATCAATACAAAGTCTCAACATTCGCAACAT
1 GAAATCAATACAAAGTCTCAACATTCGCAACAT
14083 ACTTTCTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.21
Consensus pattern (33 bp):
GAAATCAATACAAAGTCTCAACATTCGCAACAT
Found at i:14395 original size:21 final size:21
Alignment explanation
Indices: 14353--14396 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
14343 CATTAATAGT
* *
14353 TATTAATAAAATATTTATTAA
1 TATTAATAAAATATCTAATAA
14374 TATTAATAAAA-ATACTAATAA
1 TATTAATAAAATAT-CTAATAA
14395 TA
1 TA
14397 ATAAAAAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TATTAATAAAATATCTAATAA
Found at i:15437 original size:29 final size:29
Alignment explanation
Indices: 15395--15556 Score: 152
Period size: 29 Copynumber: 5.5 Consensus size: 29
15385 TTAAACTATT
**
15395 CAAAAATTTTATTTTTACCCCCGAACTTC
1 CAAAAATCCTATTTTTACCCCCGAACTTC
**
15424 CAAAAATCCTATTTTTGACCCCAAAACTTC
1 CAAAAATCCTATTTTT-ACCCCCGAACTTC
* *
15454 CAAGAATTCC-ATTTTTACCCTCGAACTTC
1 CAA-AAATCCTATTTTTACCCCCGAACTTC
*
15483 CAAAAATCCTATTTTTGA-CCCAGAAACTTC
1 CAAAAATCCTATTTTT-ACCCCCG-AACTTC
* *
15513 CAAAAATTCC-ATTTTTACCCTCGAACCT-
1 CAAAAA-TCCTATTTTTACCCCCGAACTTC
*
15541 CTAAAATCTCTATTTT
1 CAAAAATC-CTATTTT
15557 CGACCTCAAA
Statistics
Matches: 109, Mismatches: 15, Indels: 18
0.77 0.11 0.13
Matches are distributed among these distances:
27 2 0.02
28 11 0.10
29 46 0.42
30 42 0.39
31 8 0.07
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (29 bp):
CAAAAATCCTATTTTTACCCCCGAACTTC
Found at i:15452 original size:30 final size:29
Alignment explanation
Indices: 15395--15532 Score: 140
Period size: 30 Copynumber: 4.7 Consensus size: 29
15385 TTAAACTATT
** **
15395 CAAAAATTTTATTTTTACCCCCGAACTTC
1 CAAAAATCCTATTTTTACCCCAAAACTTC
15424 CAAAAATCCTATTTTTGACCCCAAAACTTC
1 CAAAAATCCTATTTTT-ACCCCAAAACTTC
* *
15454 CAAGAATTCC-ATTTTTACCCTC-GAACTTC
1 CAA-AAATCCTATTTTTACCC-CAAAACTTC
15483 CAAAAATCCTATTTTTGA-CCCAGAAACTTC
1 CAAAAATCCTATTTTT-ACCCCA-AAACTTC
15513 CAAAAATTCC-ATTTTTACCC
1 CAAAAA-TCCTATTTTTACCC
15533 TCGAACCTCT
Statistics
Matches: 92, Mismatches: 8, Indels: 17
0.79 0.07 0.15
Matches are distributed among these distances:
28 6 0.07
29 36 0.39
30 42 0.46
31 8 0.09
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
CAAAAATCCTATTTTTACCCCAAAACTTC
Found at i:15480 original size:59 final size:59
Alignment explanation
Indices: 15395--15569 Score: 246
Period size: 59 Copynumber: 3.0 Consensus size: 59
15385 TTAAACTATT
** *
15395 CAAAAATTTTATTTTTACCCCCGAACTTCCAAAAATCCTATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCTATTTTTGACCCCAAAACTTC
*
15454 CAAGAATTCCATTTTTACCCTCGAACTTCCAAAAATCCTATTTTTGA-CCCAGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCTATTTTTGACCCCA-AAACTTC
* * * *
15513 CAAAAATTCCATTTTTACCCTCGAACCT-CTAAAATCTCTATTTTCGACCTCAAAACT
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATC-CTATTTTTGACCCCAAAACT
15570 CTCAAAATCA
Statistics
Matches: 104, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
58 11 0.11
59 90 0.87
60 3 0.03
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (59 bp):
CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCTATTTTTGACCCCAAAACTTC
Found at i:15633 original size:28 final size:28
Alignment explanation
Indices: 15600--15663 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
15590 CTCCGAATTT
* *
15600 TCCAAAATTACCATTTTTGCCTCGAGAA
1 TCCAAAATTACCATTTTTCCCCCGAGAA
*
15628 TCCAAAATTACCATTTTTCCCCCGAGTA
1 TCCAAAATTACCATTTTTCCCCCGAGAA
15656 TCCGAAAA
1 TCC-AAAA
15664 GTCTTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.30
Consensus pattern (28 bp):
TCCAAAATTACCATTTTTCCCCCGAGAA
Found at i:18107 original size:15 final size:16
Alignment explanation
Indices: 18087--18120 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
18077 AATGTATATC
*
18087 TAAAAATTAA-TTTAA
1 TAAAAATAAAGTTTAA
18102 TAAAAATAAAGTTTAA
1 TAAAAATAAAGTTTAA
18118 TAA
1 TAA
18121 TCAAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TAAAAATAAAGTTTAA
Found at i:18708 original size:31 final size:31
Alignment explanation
Indices: 18621--18708 Score: 74
Period size: 31 Copynumber: 2.8 Consensus size: 31
18611 ATTTCTTTAA
* * *
18621 ATGTGAATGATTGAATCAAAATT-AAAGTTTC
1 ATGTGTATAATTG-ATCAAAATTAAAAGTTGC
* * *
18652 ATGTATATAATTGAACTACAA-TAAAAGTTGC
1 ATGTGTATAATTGATC-AAAATTAAAAGTTGC
18683 ATGTGTATAATTGCATC-AAATTAAAA
1 ATGTGTATAATTG-ATCAAAATTAAAA
18709 TTCATATATC
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
30 5 0.11
31 37 0.84
32 2 0.05
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (31 bp):
ATGTGTATAATTGATCAAAATTAAAAGTTGC
Found at i:19817 original size:3 final size:3
Alignment explanation
Indices: 19809--19849 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
19799 ATATTCGCAC
*
19809 TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
19850 CTGCACTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:22730 original size:44 final size:44
Alignment explanation
Indices: 22654--22738 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
22644 TAATTTAGGG
* **
22654 TTGGTAAGAGAAATATCTGCCTTGGTAGTTGGATGTATTTAGTA
1 TTGGGAAGAGAAATATCTGCCTTAATAGTTGGATGTATTTAGTA
*
22698 TTGGGAAGAGAAATATCTGCTTTAAT-GATTGGATGTATTTA
1 TTGGGAAGAGAAATATCTGCCTTAATAG-TTGGATGTATTTA
22739 TAGTAATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 1 0.03
44 35 0.97
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (44 bp):
TTGGGAAGAGAAATATCTGCCTTAATAGTTGGATGTATTTAGTA
Found at i:25437 original size:55 final size:57
Alignment explanation
Indices: 25377--25482 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 57
25367 AATGGCTGGC
*
25377 ACCAAAAAACACGAAT-AAAAAATATT-TTTTGAGTGTTTGGCAACTAATGATCGGT
1 ACCAAAAAACACGAATAAAAAAATATTATTTTGAGTGTTTGACAACTAATGATCGGT
* * *
25432 ACCAAAAAGCATGAATAAAAAAATATTATTTTGCGTGTTTGACAACTAATG
1 ACCAAAAAACACGAATAAAAAAATATTATTTTGAGTGTTTGACAACTAATG
25483 GCCAACACCA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
55 14 0.31
56 10 0.22
57 21 0.47
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29
Consensus pattern (57 bp):
ACCAAAAAACACGAATAAAAAAATATTATTTTGAGTGTTTGACAACTAATGATCGGT
Found at i:25493 original size:57 final size:55
Alignment explanation
Indices: 25376--25506 Score: 154
Period size: 57 Copynumber: 2.3 Consensus size: 55
25366 TAATGGCTGG
* * **
25376 CACCAAAAAACACGAATAAAAAATATTTTTTGAGTGTTTGGCAACTAATGATCGG
1 CACCAAAAAACACGAATAAAAAATATTTTTTGAGTGTTTGACAACTAATGACCAA
* * * * *
25431 TACCAAAAAGCATGAATAAAAAAATATTATTTTGCGTGTTTGACAACTAATGGCCAA
1 CACCAAAAAACACGAAT-AAAAAATATT-TTTTGAGTGTTTGACAACTAATGACCAA
*
25488 CACCAAAAAACACAAATAA
1 CACCAAAAAACACGAATAA
25507 TTTTTTTTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
55 14 0.23
56 12 0.20
57 35 0.57
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (55 bp):
CACCAAAAAACACGAATAAAAAATATTTTTTGAGTGTTTGACAACTAATGACCAA
Found at i:29578 original size:24 final size:24
Alignment explanation
Indices: 29528--29704 Score: 221
Period size: 24 Copynumber: 7.4 Consensus size: 24
29518 ATTTAGCCCA
*
29528 TACGAGCCCAGAA-GGTTAGCTCC
1 TACGAGCCCAGAACGGTTAGCTCT
* *
29551 TACGAGCCCAAAACGATTAGCTCT
1 TACGAGCCCAGAACGGTTAGCTCT
* * *
29575 TACGAGCCCAGAATGATTAGCTCC
1 TACGAGCCCAGAACGGTTAGCTCT
29599 TACGAGCCCAGAACGGTTAGCTCT
1 TACGAGCCCAGAACGGTTAGCTCT
* ** * *
29623 TACAAGCAGAGAATGGTTAGCTCC
1 TACGAGCCCAGAACGGTTAGCTCT
*
29647 TACGAGCCAAGAACGGTTAGCTCT
1 TACGAGCCCAGAACGGTTAGCTCT
*
29671 TACGAGCCCAGAATGGTTAGCTCT
1 TACGAGCCCAGAACGGTTAGCTCT
*
29695 TACGATCCCA
1 TACGAGCCCA
29705 AAATCAGAAT
Statistics
Matches: 131, Mismatches: 22, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
23 12 0.09
24 119 0.91
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.21
Consensus pattern (24 bp):
TACGAGCCCAGAACGGTTAGCTCT
Found at i:29608 original size:48 final size:48
Alignment explanation
Indices: 29528--29707 Score: 265
Period size: 48 Copynumber: 3.8 Consensus size: 48
29518 ATTTAGCCCA
*
29528 TACGAGCCCAGAA-GGTTAGCTCCTACGAGCCCAAAACGATTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCCTACGAGCCCAAAACGGTTAGCTCT
* *
29575 TACGAGCCCAGAATGATTAGCTCCTACGAGCCCAGAACGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCCTACGAGCCCAAAACGGTTAGCTCT
* **
29623 TACAAGCAGAGAATGGTTAGCTCCTACGAG-CCAAGAACGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCCTACGAGCCCAA-AACGGTTAGCTCT
* *
29671 TACGAGCCCAGAATGGTTAGCTCTTACGATCCCAAAA
1 TACGAGCCCAGAATGGTTAGCTCCTACGAGCCCAAAA
29708 TCAGAATAAT
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
47 16 0.14
48 97 0.83
49 4 0.03
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (48 bp):
TACGAGCCCAGAATGGTTAGCTCCTACGAGCCCAAAACGGTTAGCTCT
Found at i:32653 original size:26 final size:26
Alignment explanation
Indices: 32615--32665 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
32605 ACTCTGAAGA
* * * *
32615 TATATTGAGTTGGCTCGTAGGAGCGC
1 TATACTGAATTGGCTCATAAGAGCGC
32641 TATACTGAATTGGCTCATAAGAGCG
1 TATACTGAATTGGCTCATAAGAGCG
32666 ATTGATTTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
TATACTGAATTGGCTCATAAGAGCGC
Found at i:35478 original size:18 final size:20
Alignment explanation
Indices: 35440--35482 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
35430 CTTCATCTTT
35440 TTCTTTTTCCTTCTCTTCTC
1 TTCTTTTTCCTTCTCTTCTC
*
35460 TTCTTTTT-C-TCTTTTCTC
1 TTCTTTTTCCTTCTCTTCTC
35478 TTCTT
1 TTCTT
35483 CTTCAATACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.59
19 1 0.05
20 8 0.36
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (20 bp):
TTCTTTTTCCTTCTCTTCTC
Found at i:35482 original size:21 final size:20
Alignment explanation
Indices: 35435--35485 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
35425 AATGTCTTCA
*
35435 TCTTTTTCTTTTTCCTTCTC
1 TCTTCTTCTTTTTCCTTCTC
*
35455 T-TCTCTTCTTTTTCTCTTTTC
1 TCT-TCTTCTTTTTC-CTTCTC
35476 TCTTCTTCTT
1 TCTTCTTCTT
35486 CAATACCCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 11 0.42
21 13 0.50
22 1 0.04
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTTCTTCTTTTTCCTTCTC
Found at i:37507 original size:15 final size:16
Alignment explanation
Indices: 37481--37510 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
37471 GCATGACCAT
37481 CTGGAGTGCAATTTTC
1 CTGGAGTGCAATTTTC
37497 CTGGA-TGCAATTTT
1 CTGGAGTGCAATTTT
37511 AAACATGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (16 bp):
CTGGAGTGCAATTTTC
Found at i:44648 original size:26 final size:26
Alignment explanation
Indices: 44611--44719 Score: 119
Period size: 26 Copynumber: 4.2 Consensus size: 26
44601 TGCTATCAGT
* *
44611 GATATACTAAACTGGCTCGTAAGAGC
1 GATATACTAAACTGACTCATAAGAGC
*
44637 GATATACAAAACTGACTCATAAGAGC
1 GATATACTAAACTGACTCATAAGAGC
* * * *
44663 GATATACTGAGCTGACTCGTAAGAAC
1 GATATACTAAACTGACTCATAAGAGC
* * *
44689 GATATATTGAACTGGCTCATAAGAGC
1 GATATACTAAACTGACTCATAAGAGC
*
44715 AATAT
1 GATAT
44720 CCTGACTGGG
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 69 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (26 bp):
GATATACTAAACTGACTCATAAGAGC
Found at i:44692 original size:52 final size:52
Alignment explanation
Indices: 44611--44724 Score: 138
Period size: 52 Copynumber: 2.2 Consensus size: 52
44601 TGCTATCAGT
* * *
44611 GATATACTAAACTGGCTCGTAAGAGCGATATACAAAACTGACTCATAAGAGC
1 GATATACTGAACTGACTCGTAAGAACGATATACAAAACTGACTCATAAGAGC
* *** *
44663 GATATACTGAGCTGACTCGTAAGAACGATATATTGAACTGGCTCATAAGAGC
1 GATATACTGAACTGACTCGTAAGAACGATATACAAAACTGACTCATAAGAGC
* *
44715 AATATCCTGA
1 GATATACTGA
44725 CTGGGCTGGT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (52 bp):
GATATACTGAACTGACTCGTAAGAACGATATACAAAACTGACTCATAAGAGC
Found at i:44742 original size:26 final size:26
Alignment explanation
Indices: 44713--44763 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
44703 GCTCATAAGA
44713 GCAATATCCTGACTGGGCTGGTATGT
1 GCAATATCCTGACTGGGCTGGTATGT
* * *
44739 GCAATATCTTTACTGGGCTTGTATG
1 GCAATATCCTGACTGGGCTGGTATG
44764 AGCTAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (26 bp):
GCAATATCCTGACTGGGCTGGTATGT
Found at i:49166 original size:22 final size:22
Alignment explanation
Indices: 49109--49152 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
49099 CGATCTGAGG
49109 AAAAATAAAAGAAAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
*
49131 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAACAGAATT
49153 GAAAGAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAGAAAACAGAATT
Found at i:54129 original size:12 final size:14
Alignment explanation
Indices: 54101--54141 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
54091 TTTAAACTCT
54101 AAAAGATAAATACA
1 AAAAGATAAATACA
54115 AAAAGAT-AA-ACA
1 AAAAGATAAATACA
*
54127 AAAA-TTAAATACA
1 AAAAGATAAATACA
54140 AA
1 AA
54142 TTTAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
11 1 0.04
12 9 0.38
13 7 0.29
14 7 0.29
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAAGATAAATACA
Found at i:54156 original size:19 final size:19
Alignment explanation
Indices: 54132--54174 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54122 AAACAAAAAT
54132 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
54151 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
54170 TAAAT
1 TAAAT
54175 CTTGATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:59075 original size:12 final size:14
Alignment explanation
Indices: 59047--59087 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
59037 TTTAAACTCT
59047 AAAAGATAAATACA
1 AAAAGATAAATACA
59061 AAAAGAT-AA-ACA
1 AAAAGATAAATACA
*
59073 AAAA-TTAAATACA
1 AAAAGATAAATACA
59086 AA
1 AA
59088 TTTAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
11 1 0.04
12 9 0.38
13 7 0.29
14 7 0.29
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAAGATAAATACA
Found at i:59102 original size:19 final size:19
Alignment explanation
Indices: 59078--59120 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
59068 AAACAAAAAT
59078 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
59097 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
59116 TAAAT
1 TAAAT
59121 CCTAATACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:59347 original size:24 final size:24
Alignment explanation
Indices: 59320--59370 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
59310 TTTAATAGAA
*
59320 TAATACTCTAAAAATATAT-ATATT
1 TAATA-TCCAAAAATATATCATATT
* *
59344 TAATATCCAAAAGTATGTCATATT
1 TAATATCCAAAAATATATCATATT
59368 TAA
1 TAA
59371 GCATTATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (24 bp):
TAATATCCAAAAATATATCATATT
Found at i:67525 original size:87 final size:87
Alignment explanation
Indices: 67379--67564 Score: 284
Period size: 87 Copynumber: 2.1 Consensus size: 87
67369 TTTTATCTTT
* *
67379 TTGATGCAACTGTGTGTGCTTTGATTGACCCAAGGTTGACTCATTCTTATATTTGTACTACTCTA
1 TTGATGCAACTGTGTGTGCTTTGATTGACCCAAGGTCGACTCATTCTTATATATGTACTACTCTA
* *
67444 GCGAGTGATAAAAATTTGTCTG
66 GCAAGTGATAAAAATTTGTCTA
* * * *
67466 TTGATGTAATTGTGTGTGCTTTGGTTGACCCAAGGTCGACTCATTCTTTTATATGTACTACTCTA
1 TTGATGCAACTGTGTGTGCTTTGATTGACCCAAGGTCGACTCATTCTTATATATGTACTACTCTA
67531 GCAAGTGATAAAAATTTGTCTA
66 GCAAGTGATAAAAATTTGTCTA
67553 TTGA-GTCAACTG
1 TTGATG-CAACTG
67565 AATTTGATGT
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 1 0.01
87 87 0.99
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (87 bp):
TTGATGCAACTGTGTGTGCTTTGATTGACCCAAGGTCGACTCATTCTTATATATGTACTACTCTA
GCAAGTGATAAAAATTTGTCTA
Found at i:68727 original size:30 final size:30
Alignment explanation
Indices: 68691--68864 Score: 176
Period size: 30 Copynumber: 5.9 Consensus size: 30
68681 CCAGAAGATT
* *
68691 CTTAAACTATCCAAAAATTACATTTTGACA
1 CTTAAACTTTCCAAAAATTACATTTTGACC
*
68721 CTTAAACTTTCCAAAAATTATATTTTGACC
1 CTTAAACTTTCCAAAAATTACATTTTGACC
** * *
68751 CACAAACTTT-AAAAAATTACACTTTGACC
1 CTTAAACTTTCCAAAAATTACATTTTGACC
* ***
68780 CTTAAAATTTTTGAAAATTACAATTTT-ACC
1 CTTAAACTTTCCAAAAATTAC-ATTTTGACC
* * *
68810 CTCAAACTTTTCAAAAATTACATTTTTACC
1 CTTAAACTTTCCAAAAATTACATTTTGACC
68840 C-TAAAC-TTCCAAAAATTACCATTTT
1 CTTAAACTTTCCAAAAATTA-CATTTT
68865 TATCCTCAAG
Statistics
Matches: 120, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
28 11 0.09
29 38 0.32
30 67 0.56
31 4 0.03
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (30 bp):
CTTAAACTTTCCAAAAATTACATTTTGACC
Found at i:68872 original size:59 final size:57
Alignment explanation
Indices: 68702--68930 Score: 183
Period size: 59 Copynumber: 3.9 Consensus size: 57
68692 TTAAACTATC
* * * *
68702 CAAAAATTACATTTTGACACTTAAACTTTCCAAAAATTATATTTTGACCCACAAACTTT
1 CAAAAATTACATTTTGAC-CCTAAAC-TTCCAAAAATTACATTTTTACCCTCAAACTTT
* * * *** *
68761 AAAAAATTACACTTTGACCCTTAAAATTTTTGAAAATTACAATTTTACCCTCAAACTTTT
1 CAAAAATTACATTTTGACCC-T-AAACTTCCAAAAATTACATTTTTACCCTCAAAC-TTT
* * *
68821 CAAAAATTACATTTTTACCCTAAACTTCCAAAAATTACCATTTTTATCCTC-AAGTTT
1 CAAAAATTACATTTTGACCCTAAACTTCCAAAAATTA-CATTTTTACCCTCAAACTTT
*** *
68878 CAAAAAATTACCATTTACCCCCGAATGA-TGTCCAAAAATTACATTTTTACCCT
1 C-AAAAATTA-CATTTTGACCCTAA--ACT-TCCAAAAATTACATTTTTACCCT
68931 GAATGTCCAA
Statistics
Matches: 135, Mismatches: 26, Indels: 17
0.76 0.15 0.10
Matches are distributed among these distances:
57 4 0.03
58 23 0.17
59 61 0.45
60 35 0.26
61 12 0.09
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (57 bp):
CAAAAATTACATTTTGACCCTAAACTTCCAAAAATTACATTTTTACCCTCAAACTTT
Found at i:68914 original size:89 final size:88
Alignment explanation
Indices: 68821--68990 Score: 247
Period size: 89 Copynumber: 1.9 Consensus size: 88
68811 TCAAACTTTT
* *
68821 CAAAAATTACATTTTTACCCTAAACT-TCCAAAAATTACCATTTTTATCCTCAAG-TTTCAAAAA
1 CAAAAATTACATTTTTACCCTAAA-TGTCCAAAAATTACC-GTTTTA-CCCCAAGTTTTC-AAAA
68884 ATTACCA-TTTACCCCCGAATGATGTC
62 ATTACCATTTTACCCCCGAATGATGTC
* *
68910 CAAAAATTACATTTTTACCCTGAATGTCCAAAAATTACCGTTTTACCCCGAGTTTTCAAAAATTA
1 CAAAAATTACATTTTTACCCTAAATGTCCAAAAATTACCGTTTTACCCCAAGTTTTCAAAAATTA
68975 CCATTTTACCCCCGAA
66 CCATTTTACCCCCGAA
68991 CATTTGAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
87 16 0.22
88 22 0.30
89 36 0.49
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (88 bp):
CAAAAATTACATTTTTACCCTAAATGTCCAAAAATTACCGTTTTACCCCAAGTTTTCAAAAATTA
CCATTTTACCCCCGAATGATGTC
Found at i:68986 original size:28 final size:28
Alignment explanation
Indices: 68793--68986 Score: 135
Period size: 28 Copynumber: 6.7 Consensus size: 28
68783 AAAATTTTTG
* * *
68793 AAAATTACAATTTTACCCTCAAACTTTTCA
1 AAAATTACCATTTTACCC-C-AAGTTTCCA
* **
68823 AAAATTA-CATTTTTACCCTAAACTTCCA
1 AAAATTACCA-TTTTACCCCAAGTTTCCA
* *
68851 AAAATTACCATTTTTATCCTCAAGTTTCAA
1 AAAATTACCA-TTTTA-CCCCAAGTTTCCA
*
68881 AAAATTACCA-TTTACCCCCGAATGATGTCCA
1 AAAATTACCATTTTA-CCCC-AA-G-TTTCCA
* *
68912 AAAATTA-CATTTTTACCCTGAA-TGTCCA
1 AAAATTACCA-TTTTACCC-CAAGTTTCCA
* * *
68940 AAAATTACCGTTTTACCCCGAGTTTTCA
1 AAAATTACCATTTTACCCCAAGTTTCCA
68968 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTACCCC
68987 CGAACATTTG
Statistics
Matches: 132, Mismatches: 21, Indels: 24
0.75 0.12 0.14
Matches are distributed among these distances:
27 1 0.01
28 63 0.48
29 12 0.09
30 36 0.27
31 16 0.12
32 4 0.03
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCAAGTTTCCA
Found at i:74322 original size:26 final size:26
Alignment explanation
Indices: 74281--74524 Score: 283
Period size: 26 Copynumber: 9.4 Consensus size: 26
74271 AGACTCTGAA
* *
74281 GATATATTGAACTGGCTCGTAAGAGT
1 GATATACTGAACTGGCTCGTAAGAGC
* * *
74307 AATATACTAAATTGGCTCGTAAGAGC
1 GATATACTGAACTGGCTCGTAAGAGC
*
74333 GATATACTGAACTGGCTTGTAAGAGC
1 GATATACTGAACTGGCTCGTAAGAGC
* *
74359 GATCTATTGAACTGGCTCGTAAGAGC
1 GATATACTGAACTGGCTCGTAAGAGC
* *
74385 GATATACTGGACTGGCTCGTAAGAAC
1 GATATACTGAACTGGCTCGTAAGAGC
* * **
74411 GATATACAGAACTAGCTCGT-AGAAAT
1 GATATACTGAACTGGCTCGTAAG-AGC
*
74437 GATATACTGAACTGGCTCGTAAAAGC
1 GATATACTGAACTGGCTCGTAAGAGC
*
74463 GATATACTGAACTGGCTCGTAAGAGA
1 GATATACTGAACTGGCTCGTAAGAGC
* * * *
74489 GTTATACTAAACTAGCTCGTAAGAGT
1 GATATACTGAACTGGCTCGTAAGAGC
*
74515 GATATCCTGA
1 GATATACTGA
74525 CTAGGCTTGT
Statistics
Matches: 182, Mismatches: 34, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
25 2 0.01
26 179 0.98
27 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (26 bp):
GATATACTGAACTGGCTCGTAAGAGC
Found at i:92612 original size:17 final size:17
Alignment explanation
Indices: 92574--92619 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
92564 AAAAATAAGA
92574 GAAAAGAGAAGAAGAAG
1 GAAAAGAGAAGAAGAAG
92591 G--AAGAGAAG-AGAAG
1 GAAAAGAGAAGAAGAAG
*
92605 GAAAA-AGAAAAAGAA
1 GAAAAGAGAAGAAGAA
92620 AAAGAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 6 0.24
15 12 0.48
16 6 0.24
17 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GAAAAGAGAAGAAGAAG
Found at i:92616 original size:6 final size:6
Alignment explanation
Indices: 92605--92630 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
92595 AGAAGAGAAG
92605 GAAAAA GAAAAA GAAAAA GAAAAA GA
1 GAAAAA GAAAAA GAAAAA GAAAAA GA
92631 CATTGTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:105573 original size:22 final size:22
Alignment explanation
Indices: 105548--105612 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
105538 ATAACACAAT
105548 TTCATTTATATACAACATCATA
1 TTCATTTATATACAACATCATA
* * *
105570 TTCA-TCATCT-CAA-AGC---
1 TTCATTTATATACAACATCATA
105586 TTCATTTATATACAACATCATA
1 TTCATTTATATACAACATCATA
105608 TTCAT
1 TTCAT
105613 CATCTCAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 12
0.63 0.12 0.24
Matches are distributed among these distances:
16 4 0.13
17 4 0.13
18 3 0.10
19 4 0.13
20 3 0.10
21 4 0.13
22 9 0.29
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.40
Consensus pattern (22 bp):
TTCATTTATATACAACATCATA
Found at i:105590 original size:38 final size:38
Alignment explanation
Indices: 105548--105625 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
105538 ATAACACAAT
105548 TTCATTTATATACAACATCATATTCATCATCTCAAAGC
1 TTCATTTATATACAACATCATATTCATCATCTCAAAGC
105586 TTCATTTATATACAACATCATATTCATCATCTCAAAGC
1 TTCATTTATATACAACATCATATTCATCATCTCAAAGC
105624 TT
1 TT
105626 TCAAGTATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (38 bp):
TTCATTTATATACAACATCATATTCATCATCTCAAAGC
Found at i:108985 original size:8 final size:9
Alignment explanation
Indices: 108952--108982 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
108942 TTATTTTAAT
108952 TTTTTAAAA
1 TTTTTAAAA
108961 TTTTTAAAA
1 TTTTTAAAA
108970 TTTTTAAAA
1 TTTTTAAAA
108979 TTTT
1 TTTT
108983 AAACTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:126222 original size:24 final size:24
Alignment explanation
Indices: 126195--126243 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
126185 AGACTGTTGT
126195 AACTTTTTGATGTTATAAAACTTA
1 AACTTTTTGATGTTATAAAACTTA
126219 AACTTTTTGATGTTATAAAACTTA
1 AACTTTTTGATGTTATAAAACTTA
126243 A
1 A
126244 CATATAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (24 bp):
AACTTTTTGATGTTATAAAACTTA
Found at i:126260 original size:14 final size:14
Alignment explanation
Indices: 126243--126269 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
126233 ATAAAACTTA
126243 ACATATAGATTATG
1 ACATATAGATTATG
126257 ACATATAGATTAT
1 ACATATAGATTAT
126270 ATTTGAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (14 bp):
ACATATAGATTATG
Found at i:126513 original size:37 final size:38
Alignment explanation
Indices: 126443--126514 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
126433 TAATTCATAT
* * *
126443 TTTAATAGTAATTATATTAAGAATGTTATTAAATTGTA
1 TTTAATAATAATCATATTAAGAATGTGATTAAATTGTA
*
126481 TTTAATAATAATCATGTTAA-AATGTGATTAAATT
1 TTTAATAATAATCATATTAAGAATGTGATTAAATT
126515 ATTTATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 13 0.43
38 17 0.57
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (38 bp):
TTTAATAATAATCATATTAAGAATGTGATTAAATTGTA
Found at i:130050 original size:13 final size:13
Alignment explanation
Indices: 130032--130064 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
130022 AGATGAGGAA
*
130032 GGAAGCCACCGTG
1 GGAAGCCACCATG
130045 GGAAGCCACCATG
1 GGAAGCCACCATG
130058 GGAAGCC
1 GGAAGCC
130065 GCAAGGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.30, G:0.36, T:0.06
Consensus pattern (13 bp):
GGAAGCCACCATG
Found at i:142986 original size:439 final size:439
Alignment explanation
Indices: 142168--143028 Score: 1386
Period size: 439 Copynumber: 2.0 Consensus size: 439
142158 ATTGGTGGCC
* *
142168 TGGTCTTAAACGTGAAGTGATCGAATATGTGTCTTAATGTTTGACTTGACAACAGGTTAAAGCTG
1 TGGTCTTAAACGTGAAGTGACCGAATATGTGTCTAAATGTTTGACTTGACAACAGGTTAAAGCTG
* *
142233 AACATTAATTCCCATCAGGGTTACTTCAACCAATTCAAATTCCAAAGTGGAAGTGGGAAAGAGTG
66 AACATCAATTCCCATCAGGGTTACTTCAACCAATTCAAATTCCAAAGTGGAAATGGGAAAGAGTG
*
142298 TCAATGGATTTTGTTAATGGGCTACCTTTGACACCTACTAAGAAAGATTCAGGTTGGATTGTGGT
131 TCAATGGATTTTGTTAATGGGCTACCTTTGAAACCTACTAAGAAAGATTCAGGTTGGATTGTGGT
* * * *
142363 GGATAGATTGACTAAGTCCACCCATTTTGTACTTGTTCGCACCGATTATTCTCTTTAGAAGTTAG
196 GGATAGATTGACTAAGTCCACCCATTTTATACCTGTTCGCACCGAGTATTCTCTTCAGAAGTTAG
* * *
142428 CTAAGCTTTATATCTCCGAGATAGTGAGATTACATGGTGTGTCGGTGTCAATTATTGCAGATCAG
261 CTAAGCTTTATATCTCCAAGATAGTGAGATTACATGGTGTGTCAGTGTCAATTATTACAGATCAG
* *
142493 GATCCTAGATTCACTTCTCGATTCTGGAAGAAATTGCACAAGGCTTTGGGTACTCAATTAGATTT
326 GATCCTAGATTCACTTCTCAATTCTGGAAGAAATTGCACAAGGCTTTAGGTACTCAATTAGATTT
* *
142558 CAGTACGACATTCCATGCACAAATTGATGGTCTAAATTAGGGATAATCT
391 CAGTACGACATTCCATCCACAAACTGATGGTCTAAATTAGGGATAATCT
* *
142607 TGGTCTTAAACGTGAAGTGACCGAATATGTGTCTAAATGTTTGACTT-ACCAATAGGTTAAAGTT
1 TGGTCTTAAACGTGAAGTGACCGAATATGTGTCTAAATGTTTGACTTGA-CAACAGGTTAAAGCT
* * * *
142671 GAGCATCAATTCCCATCGGGGTTACTTCAACCAATTCGAATTCCACAGTGGAAATGGGAAAGAGT
65 GAACATCAATTCCCATCAGGGTTACTTCAACCAATTCAAATTCCAAAGTGGAAATGGGAAAGAGT
* * *
142736 GTTAATGGATTTTGTTAGTGGGCTACCTTTGAAACCTACTAAGAAAGATT-ATGTTTGGATTGTG
130 GTCAATGGATTTTGTTAATGGGCTACCTTTGAAACCTACTAAGAAAGATTCA-GGTTGGATTGTG
*
142800 GTGGATAGATTGACTAAGTCCGCCCATTTTATACCTGTTCGCACCGAGTATTCTCTTCAGAAGTT
194 GTGGATAGATTGACTAAGTCCACCCATTTTATACCTGTTCGCACCGAGTATTCTCTTCAGAAGTT
*
142865 AGCTAAGCTTTATATCTCCAAGATAGTGAGATTACATGGTGTG-CTAGTGTCGATTATTACAGAT
259 AGCTAAGCTTTATATCTCCAAGATAGTGAGATTACATGGTGTGTC-AGTGTCAATTATTACAGAT
* * **
142929 CTGGATCCTAGATTCACTTCTCAATTCTGGAAGAAATTGCACGAGGCTTTAGGTACTCGGTTAGA
323 CAGGATCCTAGATTCACTTCTCAATTCTGGAAGAAATTGCACAAGGCTTTAGGTACTCAATTAGA
*
142994 TTTCAGTACGACATTTCATCCACAAACTGATGGTC
388 TTTCAGTACGACATTCCATCCACAAACTGATGGTC
143029 AGTCAGAAAG
Statistics
Matches: 387, Mismatches: 32, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
438 3 0.01
439 384 0.99
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (439 bp):
TGGTCTTAAACGTGAAGTGACCGAATATGTGTCTAAATGTTTGACTTGACAACAGGTTAAAGCTG
AACATCAATTCCCATCAGGGTTACTTCAACCAATTCAAATTCCAAAGTGGAAATGGGAAAGAGTG
TCAATGGATTTTGTTAATGGGCTACCTTTGAAACCTACTAAGAAAGATTCAGGTTGGATTGTGGT
GGATAGATTGACTAAGTCCACCCATTTTATACCTGTTCGCACCGAGTATTCTCTTCAGAAGTTAG
CTAAGCTTTATATCTCCAAGATAGTGAGATTACATGGTGTGTCAGTGTCAATTATTACAGATCAG
GATCCTAGATTCACTTCTCAATTCTGGAAGAAATTGCACAAGGCTTTAGGTACTCAATTAGATTT
CAGTACGACATTCCATCCACAAACTGATGGTCTAAATTAGGGATAATCT
Found at i:144005 original size:15 final size:16
Alignment explanation
Indices: 143980--144018 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
143970 TTCGTTGTTT
143980 TTTTCTAATTAAA-TTA
1 TTTT-TAATTAAATTTA
143996 TTTTTAATTAAATTTA
1 TTTTTAATTAAATTTA
144012 TTTTTAA
1 TTTTTAA
144019 GATTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTAATTAAATTTA
Found at i:148072 original size:15 final size:15
Alignment explanation
Indices: 148033--148072 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
148023 ATTTATTTTC
*
148033 TTTTTTTCTTCAATT
1 TTTTTTTTTTCAATT
* *
148048 TTTTTCTTTTCGATT
1 TTTTTTTTTTCAATT
148063 TTTTTTTTTT
1 TTTTTTTTTT
148073 GAATAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.07, C:0.10, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTTTTTTTCAATT
Found at i:151927 original size:18 final size:16
Alignment explanation
Indices: 151897--151935 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
151887 AAGTTTAATC
*
151897 AATTTTTTTTTTTTGT
1 AATTTTTTTTTTTTGG
151913 AATTTTTTATATTTTTGG
1 AATTTTTT-T-TTTTTGG
151931 AATTT
1 AATTT
151936 CGGTACTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 1 0.05
18 11 0.55
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (16 bp):
AATTTTTTTTTTTTGG
Found at i:152944 original size:24 final size:24
Alignment explanation
Indices: 152909--152971 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
152899 CGATAAGCTA
*
152909 GCGAGCGAAAACGTATTCATGCTG
1 GCGAGCGTAAACGTATTCATGCTG
152933 GCGAGCGTAAACGTATTCATGCTG
1 GCGAGCGTAAACGTATTCATGCTG
* *
152957 ACGAGCATAAACGTA
1 GCGAGCGTAAACGTA
152972 ATGAATTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.21
Consensus pattern (24 bp):
GCGAGCGTAAACGTATTCATGCTG
Found at i:155158 original size:20 final size:21
Alignment explanation
Indices: 155126--155198 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
155116 GAATACAAAA
155126 ATTAAATTAAAAATAAAAATT
1 ATTAAATTAAAAATAAAAATT
155147 ATTAAATTAAAAATAAAAA-T
1 ATTAAATTAAAAATAAAAATT
* *
155167 ATTAAATTATAAATTAAAAATG
1 ATTAAATTA-AAAATAAAAATT
*
155189 ACTAAATTAA
1 ATTAAATTAA
155199 TAGAAATAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
20 10 0.21
21 29 0.62
22 8 0.17
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (21 bp):
ATTAAATTAAAAATAAAAATT
Found at i:155159 original size:15 final size:14
Alignment explanation
Indices: 155129--155198 Score: 56
Period size: 15 Copynumber: 5.0 Consensus size: 14
155119 TACAAAAATT
*
155129 AAATTA-AAAATAA
1 AAATTATAAATTAA
155142 AAATTATTAAATTAA
1 AAATTA-TAAATTAA
* *
155157 AAA-TA-AAAATATT
1 AAATTATAAATTA-A
155170 AAATTATAAATTAA
1 AAATTATAAATTAA
*
155184 AAATGACTAAATTAA
1 AAATTA-TAAATTAA
155199 TAGAAATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
12 5 0.11
13 9 0.20
14 9 0.20
15 22 0.49
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (14 bp):
AAATTATAAATTAA
Found at i:155198 original size:27 final size:28
Alignment explanation
Indices: 155124--155187 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
155114 TAGAATACAA
* *
155124 AAATT-AAATTAAAAATA-AAAATTATT
1 AAATTAAAAATAAAAATATTAAATTATT
155150 AAATTAAAAATAAAAATATTAAATTA-T
1 AAATTAAAAATAAAAATATTAAATTATT
155177 AAATTAAAAAT
1 AAATTAAAAAT
155188 GACTAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 5 0.15
27 23 0.68
28 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
AAATTAAAAATAAAAATATTAAATTATT
Found at i:162470 original size:34 final size:34
Alignment explanation
Indices: 162427--162495 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
162417 TACAATAAGT
*
162427 AAACAATATATACAAATCTCATAAATTACTCCTA
1 AAACAATATATACAAATCCCATAAATTACTCCTA
*
162461 AAACAATATATACAAATCCCATAAGTTACTCCTA
1 AAACAATATATACAAATCCCATAAATTACTCCTA
162495 A
1 A
162496 CACCCCCCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.28
Consensus pattern (34 bp):
AAACAATATATACAAATCCCATAAATTACTCCTA
Found at i:181962 original size:15 final size:15
Alignment explanation
Indices: 181942--181972 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
181932 TTTATCAAAG
*
181942 AACAAAATATTAAAA
1 AACAAAATATGAAAA
181957 AACAAAATATGAAAA
1 AACAAAATATGAAAA
181972 A
1 A
181973 GGCAGTAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.16
Consensus pattern (15 bp):
AACAAAATATGAAAA
Found at i:186924 original size:32 final size:32
Alignment explanation
Indices: 186888--186948 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
186878 TTTTTGGTCC
186888 AATTTGATA-CTCAAACTTAACATTTTTTTCTT
1 AATTTGATACCT-AAACTTAACATTTTTTTCTT
* *
186920 AATTTGGTACCTAAACTTGACATTTTTTT
1 AATTTGATACCTAAACTTAACATTTTTTT
186949 TAAAGTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.49
Consensus pattern (32 bp):
AATTTGATACCTAAACTTAACATTTTTTTCTT
Found at i:186958 original size:31 final size:32
Alignment explanation
Indices: 186900--186960 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
186890 TTTGATACTC
* *
186900 AAACTTAACATTTTTTTCTTAATTTGGTACCT
1 AAACTTAACATTTTTTTCTAAAGTTGGTACCT
*
186932 AAACTTGACATTTTTTT-TAAAGTTGGTAC
1 AAACTTAACATTTTTTTCTAAAGTTGGTAC
186961 TTAATCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (32 bp):
AAACTTAACATTTTTTTCTAAAGTTGGTACCT
Found at i:187273 original size:29 final size:28
Alignment explanation
Indices: 187241--187335 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 28
187231 GTTCAAGTAT
187241 CAAATTGGGTCCAAAAAAAGTTTAGGTAC
1 CAAATTGGGT-CAAAAAAAGTTTAGGTAC
*
187270 CAAATTAGG--AAAAATGTCAAGTTTTAGGTAC
1 CAAATTGGGTCAAAAA----AAG-TTTAGGTAC
*
187301 CAAATTGGGTCAAAAAAAAGTTTAGGTAT
1 CAAATTGGGTC-AAAAAAAGTTTAGGTAC
187330 CAAATT
1 CAAATT
187336 AGGAAAAAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
26 5 0.09
29 22 0.40
30 6 0.11
31 17 0.31
34 5 0.09
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (28 bp):
CAAATTGGGTCAAAAAAAGTTTAGGTAC
Found at i:187297 original size:31 final size:32
Alignment explanation
Indices: 187261--187354 Score: 101
Period size: 31 Copynumber: 3.0 Consensus size: 32
187251 CCAAAAAAAG
187261 TTTAGGTACCAAATTAGG-AAAAATGTCAAGT
1 TTTAGGTACCAAATTAGGAAAAAATGTCAAGT
*
187292 TTTAGGTACCAAATTGGGTCAAAAAA----AAG-
1 TTTAGGTACCAAATTAGG--AAAAAATGTCAAGT
*
187321 TTTAGGTATCAAATTAGGAAAAAGATGTCAAGT
1 TTTAGGTACCAAATTAGGAAAAA-ATGTCAAGT
187354 T
1 T
187355 CAGATACCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
27 5 0.10
28 1 0.02
29 16 0.31
30 3 0.06
31 17 0.33
32 3 0.06
33 1 0.02
34 5 0.10
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.29
Consensus pattern (32 bp):
TTTAGGTACCAAATTAGGAAAAAATGTCAAGT
Found at i:187319 original size:62 final size:61
Alignment explanation
Indices: 187190--187366 Score: 218
Period size: 60 Copynumber: 2.9 Consensus size: 61
187180 ATTGAATCTT
** * *
187190 AAAAAAAAACTTAGGTACCAAATTGGTGAAAAAAATGTCAAG-TTCAAGTATCAAATTGGGTC
1 AAAAAAAAGTTTAGGTACCAAATTAG-G-AAAAAATGTCAAGTTTCAAGTACCAAATTGGGTC
* * *
187252 CAAAAAAAGTTTAGGTACCAAATTAGG-AAAAATGTCAAGTTTTAGGTACCAAATTGGGTC
1 AAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTTCAAGTACCAAATTGGGTC
*
187312 AAAAAAAAGTTTAGGTATCAAATTAGGAAAAAGATGTCAAG-TTC-AGATACCAAAT
1 AAAAAAAAGTTTAGGTACCAAATTAGGAAAAA-ATGTCAAGTTTCAAG-TACCAAAT
187367 ATTTTATTAA
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
59 12 0.12
60 43 0.43
61 15 0.15
62 30 0.30
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTTCAAGTACCAAATTGGGTC
Found at i:188927 original size:54 final size:54
Alignment explanation
Indices: 188868--188975 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
188858 GCACTCTTGT
188868 GTTAGGATTTTTTTGGAGAGTAAAACATTATTGTAAGTGAGGCTATTTGGGGTA
1 GTTAGGATTTTTTTGGAGAGTAAAACATTATTGTAAGTGAGGCTATTTGGGGTA
188922 GTTAGGATTTTTTTGGAGAGTAAAACATTATTGTAAGTGAGGCTATTTGGGGTA
1 GTTAGGATTTTTTTGGAGAGTAAAACATTATTGTAAGTGAGGCTATTTGGGGTA
188976 AGTGATTTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.28, C:0.04, G:0.30, T:0.39
Consensus pattern (54 bp):
GTTAGGATTTTTTTGGAGAGTAAAACATTATTGTAAGTGAGGCTATTTGGGGTA
Found at i:190122 original size:22 final size:22
Alignment explanation
Indices: 190097--190141 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
190087 TGCAAAACTT
190097 GTTCAAACAATGAATGGAACAA
1 GTTCAAACAATGAATGGAACAA
190119 GTTCAAACAATGAATGGAACAA
1 GTTCAAACAATGAATGGAACAA
190141 G
1 G
190142 AAGACCACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.20, T:0.18
Consensus pattern (22 bp):
GTTCAAACAATGAATGGAACAA
Found at i:191263 original size:29 final size:29
Alignment explanation
Indices: 191200--191593 Score: 316
Period size: 29 Copynumber: 13.8 Consensus size: 29
191190 TTTGACTCTA
* *
191200 AAAATGGGATTTTTAGAAGTTTTGGGGTT
1 AAAATGGAATTTTTGGAAGTTTTGGGGTT
* * *
191229 AAAAATGGAATTTTTAGAAGTTTCGAGGTT
1 -AAAATGGAATTTTTGGAAGTTTTGGGGTT
* * *
191259 AAAATGGGATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTT
*
191288 AAAATGGAATTTTTAGAAGTTTTGGGGTT
1 AAAATGGAATTTTTGGAAGTTTTGGGGTT
*
191317 AAAAATAGGAA-TTTTGGAAGTTTTGGGGTA
1 -AAAAT-GGAATTTTTGGAAGTTTTGGGGTT
*
191347 AAAATGGAATTTTTGGAAGTTTTGGGATT
1 AAAATGGAATTTTTGGAAGTTTTGGGGTT
* *
191376 AAAAT-GAGATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTTG-GGGTT
191405 AAAATGGAATTTTTGGAAGTTTTGGGGTT
1 AAAATGGAATTTTTGGAAGTTTTGGGGTT
* ** *
191434 AAAATGGGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTT
*
191463 AAAATGGGA---TT-----TTTT-GGGTT
1 AAAATGGAATTTTTGGAAGTTTTGGGGTT
* *
191483 AAAATGGGATTTTTGGAAG-TTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTT
* *
191512 AAAATAGTATTTTT--AATTGTTTTGGGGTT
1 AAAATGGAATTTTTGGAA--GTTTTGGGGTT
* * ** *
191541 AAAAATGGGATTCTTGGAAGTTCGGGGGTA
1 -AAAATGGAATTTTTGGAAGTTTTGGGGTT
* *
191571 AAAATGGGATTCTTGGAAAGTTT
1 AAAATGGAATTTTTGG-AAGTTT
191594 AGTGACCTCC
Statistics
Matches: 300, Mismatches: 38, Indels: 52
0.77 0.10 0.13
Matches are distributed among these distances:
20 13 0.04
21 2 0.01
23 2 0.01
26 2 0.01
27 5 0.02
28 13 0.04
29 173 0.58
30 84 0.28
31 4 0.01
32 2 0.01
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTT
Found at i:191291 original size:88 final size:87
Alignment explanation
Indices: 191198--191476 Score: 384
Period size: 88 Copynumber: 3.2 Consensus size: 87
191188 AATTTGACTC
* * *
191198 TAAAAATGGGATTTTTAGAAGTTTTGGGGTTAAAAATGGAATTTTTAGAAGTTTCGAGGTTAAAA
1 TAAAAATGGGATTTTTAGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAA
191263 TGGGATTTTTGGAAGTTCGAGGG
66 TGGGATTTTTGGAAGTTCG-GGG
* *
191286 TAAAAATGGAATTTTTAGAAGTTTTGGGGTTAAAAATAGGAA-TTTTGGAAGTTTTGGGGTAAAA
1 TAAAAATGGGATTTTTAGAAGTTTTGGGGTTAAAAAT-GGAATTTTTGGAAGTTTTGGGGTTAAA
* * *
191350 ATGGAATTTTTGGAAGTTTTGGGA
65 ATGGGATTTTTGGAAG-TTCGGGG
* * * *
191374 TTAAAATGAGATTTTTGGAAG-TTCGAGGG-TAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAA
1 TAAAAATGGGATTTTTAGAAGTTTTG-GGGTTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAA
191437 ATGGGATTTTTGGAAGTTCGGGGG
65 ATGGGATTTTTGGAAGTTC-GGGG
191461 TAAAAATGGGATTTTT
1 TAAAAATGGGATTTTT
191477 TGGGTTAAAA
Statistics
Matches: 167, Mismatches: 19, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
86 6 0.04
87 63 0.38
88 91 0.54
89 7 0.04
ACGTcount: A:0.32, C:0.01, G:0.30, T:0.37
Consensus pattern (87 bp):
TAAAAATGGGATTTTTAGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAA
TGGGATTTTTGGAAGTTCGGGG
Found at i:191305 original size:58 final size:58
Alignment explanation
Indices: 191200--191577 Score: 447
Period size: 58 Copynumber: 6.6 Consensus size: 58
191190 TTTGACTCTA
* * * *
191200 AAAATGGGATTTTTAGAAGTTTTG-GGGTTAAAAATGGAATTTTTAGAAGTTTCGAGGTT
1 AAAATGGGATTTTTGGAAG-TTCGAGGG-TAAAAATGGAATTTTTAGAAGTTTTGGGGTT
191259 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTT
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTT
* * * * *
191317 AAAAATAGGAATTTTGGAAGTTTTG-GGGTAAAAATGGAATTTTTGGAAGTTTTGGGATT
1 -AAAATGGGATTTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTT
* *
191376 AAAATGAGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTT
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTT
* *
191434 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGA---TT-----TTTT-GGGTT
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTT
* * * *
191483 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAAATAGTATTTTTA-ATTGTTTTGGGGTT
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGA-AGTTTTGGGGTT
* *
191541 AAAAATGGGATTCTTGGAAGTTCGGGGGTAAAAATGG
1 -AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGG
191578 GATTCTTGGA
Statistics
Matches: 280, Mismatches: 25, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
49 39 0.14
50 4 0.01
52 2 0.01
55 2 0.01
57 7 0.03
58 121 0.43
59 102 0.36
60 3 0.01
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.37
Consensus pattern (58 bp):
AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTT
Found at i:191419 original size:49 final size:48
Alignment explanation
Indices: 191360--191525 Score: 161
Period size: 49 Copynumber: 3.2 Consensus size: 48
191350 ATGGAATTTT
* *
191360 TGGAAGTTTTGGGATTAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAA
1 TGGAATTTTTGGG-TTAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAA
*
191409 TGGAATTTTTGGAAGTTTTGGGGTTAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAA
1 TGGAA----T-----TTTT-GGGTTAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAA
* *
191467 TGGGATTTTTTGGGTTAAAATGGGATTTTTGGAAGTTTGAGGGTAAAAA
1 T-GGAATTTTTGGGTTAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAA
* *
191516 TAGTATTTTT
1 TGGAATTTTT
191526 AATTGTTTTG
Statistics
Matches: 97, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
48 6 0.06
49 42 0.43
50 4 0.04
55 1 0.01
58 38 0.39
59 6 0.06
ACGTcount: A:0.30, C:0.01, G:0.31, T:0.38
Consensus pattern (48 bp):
TGGAATTTTTGGGTTAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAA
Found at i:191498 original size:19 final size:20
Alignment explanation
Indices: 191458--191496 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
191448 GGAAGTTCGG
191458 GGGTAAAAATGGGATTTTTT
1 GGGTAAAAATGGGATTTTTT
*
191478 GGGTTAAAATGGGATTTTT
1 GGGTAAAAATGGGATTTTT
191497 GGAAGTTTGA
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:0.00, G:0.31, T:0.41
Consensus pattern (20 bp):
GGGTAAAAATGGGATTTTTT
Found at i:191539 original size:78 final size:78
Alignment explanation
Indices: 191400--191552 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 78
191390 GGAAGTTCGA
* *
191400 GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAATGGGATTTTTGGAAGTTCGGGGG-TAA
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTAAAAATAGGATTTTT-GAAGTTCGGGGGTTAA
191464 AAATGGGATTTTTT
65 AAATGGGATTTTTT
* * * **
191478 GGGTTAAAATGGGATTTTTGGAAG-TTTGAGGGTAAAAATAGTATTTTT-AATTGTTTTGGGGTT
1 GGGTAAAAATGGAATTTTTGGAAGTTTTG-GGGTAAAAATAGGATTTTTGAA--GTTCGGGGGTT
191541 AAAAATGGGATT
63 AAAAATGGGATT
191553 CTTGGAAGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
76 2 0.03
77 4 0.06
78 45 0.70
79 13 0.20
ACGTcount: A:0.29, C:0.01, G:0.31, T:0.39
Consensus pattern (78 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTAAAAATAGGATTTTTGAAGTTCGGGGGTTAAA
AATGGGATTTTTT
Found at i:193258 original size:18 final size:18
Alignment explanation
Indices: 193237--193322 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 18
193227 TTTTTTAATT
193237 AATTAAATTTTAAA-TTCA
1 AATTAAATTTTAAACTT-A
193255 AATT-AATTTTAAACTTA
1 AATTAAATTTTAAACTTA
*
193272 ATTTAAA-TTTAAACTTAA
1 AATTAAATTTTAAACTT-A
** *
193290 AAGAAAAGTTTAAACTTTA
1 AATTAAATTTTAAAC-TTA
*
193309 AACTAAA-TTTAAAC
1 AATTAAATTTTAAAC
193323 CCAAAATGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
17 22 0.39
18 20 0.35
19 13 0.23
20 2 0.04
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (18 bp):
AATTAAATTTTAAACTTA
Found at i:194039 original size:86 final size:84
Alignment explanation
Indices: 193884--194049 Score: 194
Period size: 86 Copynumber: 2.0 Consensus size: 84
193874 CGTGGGTTTG
** * *
193884 ATTTGATCTTCTTCTCAGTATCTCATAAGGAAGATGACCACGTCGTTTGCTTCAATCCGCTTCTC
1 ATTTGATCCACTTCTCAGTATCTCATAAGGAAGATGAACACGTCGTTTACTTCAATCCGCTTCTC
193949 TGTATCTCATCAGGAAGACGA
66 TGTA--TCATCAGGAAGACGA
* * * *
193970 ATTTGATCCACTTCTCAGTATCTCATCAGGAAGCT-AAC-CGT-TTATTACTTCAATCTGCTTCT
1 ATTTGATCCACTTCTCAGTATCTCATAAGGAAGATGAACACGTCGT-TTACTTCAATCCGCTTCT
194032 CGGTGTATCATCAGGAAG
65 C--TGTATCATCAGGAAG
194050 CTGGGATTCA
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
83 1 0.01
84 31 0.45
85 2 0.03
86 35 0.51
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (84 bp):
ATTTGATCCACTTCTCAGTATCTCATAAGGAAGATGAACACGTCGTTTACTTCAATCCGCTTCTC
TGTATCATCAGGAAGACGA
Found at i:194122 original size:205 final size:205
Alignment explanation
Indices: 193677--194332 Score: 868
Period size: 205 Copynumber: 3.2 Consensus size: 205
193667 TCTGGTTTCA
* * * * ** ** *
193677 TTGACTTGGCCTTCTTCTCAGTATCTCATCGGGAAGATGACCATATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCGTTTGTTTCAATCCGCTT
* * * * ** * * * *
193742 CTCTGTGTTTCATCAGGAAGATGATTTTGGTTTACTTCCCCGTATTTCATCAAGAAGCTAACCGT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCG-
* * ** * * *
193807 TTTATTACTTCGACCTGCTTCTCAGTACCTCATCAGGAAGCT-AGAGTTCGAAGATTT-GT-TCA
130 TTTATTACTTCGATCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGA-TTCGAAGATTTACTCACA
193869 TCAAGCGTGGGT
194 TCAAGCGTGGGT
* * * *
193881 TTGATTTGATCTTCTTCTCAGTATCTCATAAGGAAGATGACCACGTCGTTTGCTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCGTTTGTTTCAATCCGCTT
*
193946 CTCTGTATCTCATCAGGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
* * *
194011 TTATTACTTCAATCTGCTTCTCGGTGTATCATCAGGAAGCTGGGATTCAAAGATTTACTCACATC
131 TTATTACTTCGATCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGATTCGAAGATTTACTCACATC
194076 AAGCGTGGGT
196 AAGCGTGGGT
* *
194086 TTGATTTGGTCTTCTTCTCGGTATCTCATCAGGAAGATGACTACATCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCGTTTGTTTCAATCCGCTT
* *
194151 CTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCGT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
* * *
194216 TTATTGCTTCGATCTGCTTCTCGGTGTCTCATCAAGAAGCTGGGATTCGAAGTTTTACTCACATC
131 TTATTACTTCGATCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGATTCGAAGATTTACTCACATC
* *
194281 GAGCGTGTGT
196 AAGCGTGGGT
* *
194291 TTGATTTGGTCTTCTTCTCAGTATTTCATCAAGAAGATGACC
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACC
194333 GTATCGCTAT
Statistics
Matches: 394, Mismatches: 55, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
203 46 0.12
204 108 0.27
205 240 0.61
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (205 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCGTTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
TTATTACTTCGATCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGATTCGAAGATTTACTCACATC
AAGCGTGGGT
Found at i:207599 original size:16 final size:14
Alignment explanation
Indices: 207561--207603 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 14
207551 ATTAAAGTAA
207561 AATATATGAAT-AT
1 AATATATGAATCAT
207574 AATATAATGAATCAT
1 AATAT-ATGAATCAT
207589 ATATATGATGAATCA
1 A-ATAT-ATGAATCA
207604 ACTAAGTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 5 0.19
14 6 0.23
15 3 0.12
16 12 0.46
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (14 bp):
AATATATGAATCAT
Found at i:209326 original size:20 final size:20
Alignment explanation
Indices: 209301--209338 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
209291 GGTTACTCAA
209301 AAAAAGTCAACGATCAACCT
1 AAAAAGTCAACGATCAACCT
*
209321 AAAAAGTCAACGGTCAAC
1 AAAAAGTCAACGATCAAC
209339 GGTTAATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.24, G:0.13, T:0.13
Consensus pattern (20 bp):
AAAAAGTCAACGATCAACCT
Found at i:216004 original size:21 final size:21
Alignment explanation
Indices: 215978--216017 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
215968 AAGACATTAG
*
215978 TAATGGTCAACGGTCAACTTC
1 TAATGGTCAACAGTCAACTTC
*
215999 TAATGGTCAATAGTCAACT
1 TAATGGTCAACAGTCAACT
216018 GTCAACGGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (21 bp):
TAATGGTCAACAGTCAACTTC
Found at i:216027 original size:21 final size:21
Alignment explanation
Indices: 215990--216030 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
215980 ATGGTCAACG
*
215990 GTCAACTTCTAATGGTCAATA
1 GTCAACTTCTAACGGTCAATA
216011 GTCAACTGTC-AACGGTCAAT
1 GTCAACT-TCTAACGGTCAAT
216031 GGGTCGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (21 bp):
GTCAACTTCTAACGGTCAATA
Found at i:216057 original size:18 final size:18
Alignment explanation
Indices: 216026--216061 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
216016 CTGTCAACGG
*
216026 TCAATGGGTCGGGTTCGA
1 TCAATAGGTCGGGTTCGA
*
216044 TCAATAGGTTGGGTTCGA
1 TCAATAGGTCGGGTTCGA
216062 GCCGATCAGG
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:0.14, G:0.36, T:0.31
Consensus pattern (18 bp):
TCAATAGGTCGGGTTCGA
Found at i:221459 original size:29 final size:30
Alignment explanation
Indices: 221404--221462 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
221394 ATCTCAAAAT
*
221404 TATACATGAACTTTAATTTAATGTACAATTG
1 TATACATGAACTTTAATTT-AGGTACAATTG
221435 TATACATGAACTTTAATTT-GGTACAATT
1 TATACATGAACTTTAATTTAGGTACAATT
221463 ATACACGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 8 0.30
31 19 0.70
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (30 bp):
TATACATGAACTTTAATTTAGGTACAATTG
Found at i:221473 original size:29 final size:29
Alignment explanation
Indices: 221401--221514 Score: 92
Period size: 31 Copynumber: 3.8 Consensus size: 29
221391 TAAATCTCAA
221401 AATTATACA-TG-AACTTTAATTTAATGTAC
1 AATTATACACTGAAACTTTAATTT-A-GTAC
*
221430 AATTGTATACA-TG-AACTTTAATTTGGTAC
1 AA-T-TATACACTGAAACTTTAATTTAGTAC
* *
221459 AATTATACACGTGAAACTCTAATTGTAGTTC
1 AATTATACAC-TGAAACTTTAATT-TAGTAC
* *
221490 AAATATATACTTGAAACTTTAATTT
1 AATTATACAC-TGAAACTTTAATTT
221515 TGATTTAATC
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
27 6 0.08
28 1 0.01
29 10 0.14
30 11 0.15
31 43 0.61
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (29 bp):
AATTATACACTGAAACTTTAATTTAGTAC
Found at i:226812 original size:16 final size:16
Alignment explanation
Indices: 226791--226822 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
226781 TTTGATTTGT
*
226791 TGGTTTAATCGTTTTA
1 TGGTTTAATCATTTTA
226807 TGGTTTAATCATTTTA
1 TGGTTTAATCATTTTA
226823 AGTTTTGGGG
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:0.22, C:0.06, G:0.16, T:0.56
Consensus pattern (16 bp):
TGGTTTAATCATTTTA
Found at i:228459 original size:33 final size:34
Alignment explanation
Indices: 228405--228473 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 34
228395 TGTAACTTCA
228405 AAAAAAATGTATAAAAGAATATATTGAAACTATG
1 AAAAAAATGTATAAAAGAATATATTGAAACTATG
228439 AAAAAAATGTATAAAA-AATATATTGAAACTATG
1 AAAAAAATGTATAAAAGAATATATTGAAACTATG
228472 AA
1 AA
228474 TTAATAACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 19 0.54
34 16 0.46
ACGTcount: A:0.61, C:0.03, G:0.10, T:0.26
Consensus pattern (34 bp):
AAAAAAATGTATAAAAGAATATATTGAAACTATG
Found at i:229336 original size:28 final size:28
Alignment explanation
Indices: 229304--229357 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
229294 ATCAATAATC
229304 TAGAAATATTAAACCCATAATTAAGCTT
1 TAGAAATATTAAACCCATAATTAAGCTT
*
229332 TAGAAATATTAAACCCGTAATTAAGC
1 TAGAAATATTAAACCCATAATTAAGC
229358 ACACATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (28 bp):
TAGAAATATTAAACCCATAATTAAGCTT
Done.