Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007392.1 Kokia drynarioides strain JFW-HI SEQ_122010, 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: 44238
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Warning! 246 characters in sequence are not A, C, G, or T
Found at i:599 original size:20 final size:20
Alignment explanation
Indices: 574--612 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
564 TTGGATAGCA
574 AGTGGTGGAGTTTGTTTGGC
1 AGTGGTGGAGTTTGTTTGGC
594 AGTGGTGGAGTTTGTTTGG
1 AGTGGTGGAGTTTGTTTGG
613 TAGTTAGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.03, G:0.46, T:0.41
Consensus pattern (20 bp):
AGTGGTGGAGTTTGTTTGGC
Found at i:1340 original size:16 final size:16
Alignment explanation
Indices: 1319--1349 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1309 TTAAACACAT
1319 AAAATTCTCCAAAAAC
1 AAAATTCTCCAAAAAC
*
1335 AAAATTCTCTAAAAA
1 AAAATTCTCCAAAAA
1350 TGTGTGTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATTCTCCAAAAAC
Found at i:1474 original size:24 final size:24
Alignment explanation
Indices: 1447--1503 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1437 CTAATAAAAT
*
1447 TTTAATTGAAACAAATTGA-TAGAG
1 TTTAATTGAAACAAA-TAATTAGAG
* *
1471 TTTAATTAAAATAAATAATTAGAG
1 TTTAATTGAAACAAATAATTAGAG
1495 TTTAATTGA
1 TTTAATTGA
1504 GAGATTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39
Consensus pattern (24 bp):
TTTAATTGAAACAAATAATTAGAG
Found at i:6993 original size:55 final size:56
Alignment explanation
Indices: 6908--7043 Score: 168
Period size: 55 Copynumber: 2.4 Consensus size: 56
6898 TTGTTATTAA
* * * * *
6908 ATTTTAATA-AGATTGTTATTAAATATAATTTAAT-AGTAATAAATAATTTAATCAT
1 ATTTTAATATA-ATTATTATTAAATACAATTTAATAAATAATAAATAATTTAATAAC
* *
6963 ATTTTAATATAATTTTTATTAAATACAATTTAATAAAATAATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATACAATTTAAT-AAATAATAAATAATTTAATAAC
7020 ATTCTTAATATAATTATTATTAAA
1 ATT-TTAATATAATTATTATTAAA
7044 ATATGAATCA
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
55 30 0.43
56 1 0.01
57 20 0.29
58 19 0.27
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (56 bp):
ATTTTAATATAATTATTATTAAATACAATTTAATAAATAATAAATAATTTAATAAC
Found at i:7075 original size:58 final size:58
Alignment explanation
Indices: 6923--7043 Score: 131
Period size: 57 Copynumber: 2.1 Consensus size: 58
6913 AATAAGATTG
* * * * * * * *
6923 TTATTAAATATAATTTAAT--AGTAATAAATAATTTAATCATATT-TTAATATAATTT
1 TTATTAAATACAATTCAATAAAATAATATATAATATAATAACATTCTTAATATAATTA
* *
6978 TTATTAAATACAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATAATTA
1 TTATTAAATACAATTCAATAAAATAATATATAATATAATAACATTCTTAATATAATTA
7036 TTATTAAA
1 TTATTAAA
7044 ATATGAATCA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
55 18 0.32
57 20 0.35
58 19 0.33
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (58 bp):
TTATTAAATACAATTCAATAAAATAATATATAATATAATAACATTCTTAATATAATTA
Found at i:11873 original size:23 final size:22
Alignment explanation
Indices: 11843--11886 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
11833 ATATTTGATA
*
11843 GGAAATAATAAA-GAAGAAAAAT
1 GGAAATAA-AAAGGAAAAAAAAT
11865 GGAAGATAAAAAGGAAAAAAAA
1 GGAA-ATAAAAAGGAAAAAAAA
11887 AAAAGAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.09
Consensus pattern (22 bp):
GGAAATAAAAAGGAAAAAAAAT
Found at i:19286 original size:13 final size:13
Alignment explanation
Indices: 19280--19307 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19270 ATTTTTACAC
19280 AATATTTTTCAAA
1 AATATTTTTCAAA
19293 AATATTTTTCAAA
1 AATATTTTTCAAA
19306 AA
1 AA
19308 CAATATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (13 bp):
AATATTTTTCAAA
Found at i:21590 original size:14 final size:13
Alignment explanation
Indices: 21566--21595 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
21556 ACGGCGGCGA
21566 ACGACGGTGGATG
1 ACGACGGTGGATG
21579 ACGACTGGTGGATG
1 ACGAC-GGTGGATG
21593 ACG
1 ACG
21596 GGTTGACGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.23, C:0.17, G:0.43, T:0.17
Consensus pattern (13 bp):
ACGACGGTGGATG
Found at i:21696 original size:13 final size:14
Alignment explanation
Indices: 21669--21697 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21659 AGAGTTTTGT
21669 AAAATGAAAAGAAA
1 AAAATGAAAAGAAA
21683 AAAATGAAAA-AAA
1 AAAATGAAAAGAAA
21696 AA
1 AA
21698 GGTTTAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (14 bp):
AAAATGAAAAGAAA
Found at i:22231 original size:21 final size:21
Alignment explanation
Indices: 22205--22247 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
22195 TTGAATTTTC
*
22205 CAAAAATT-ACATTTTTACTCT
1 CAAAAATTAAAATTTTT-CTCT
22226 CAAAAATTAAAATTTTTCTCT
1 CAAAAATTAAAATTTTTCTCT
22247 C
1 C
22248 GAACTTCTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.42
Consensus pattern (21 bp):
CAAAAATTAAAATTTTTCTCT
Found at i:22327 original size:58 final size:58
Alignment explanation
Indices: 22238--22615 Score: 228
Period size: 57 Copynumber: 6.6 Consensus size: 58
22228 AAAATTAAAA
* *
22238 TTTTTCTCTCGAACTTCTCGAAAATTACATTTTTACCCCTGAACTT-TATAAAATCACAT
1 TTTTTCCCTCGAACTTC-CAAAAATTACATTTTTACCCCTGAACTTCTA-AAAATCACAT
* * * * *
22297 TTTTTCCCTCGAAATTCCAAAAATCACA-TTTTAGCCCTCAAACTTCTCAAAAATTACAT
1 TTTTTCCCTCGAACTTCCAAAAATTACATTTTTACCCCT-GAACTTCT-AAAAATCACAT
** * ** * * *
22356 TTTACCCCT-AAACTTTTAAAAATTATATTTTTACCCTTAAACTTCTCAAAAAAT-ACAT
1 TTTTTCCCTCGAACTTCCAAAAATTACATTTTTACCCCTGAACTTCT--AAAAATCACAT
* * *
22414 TTTTCCCCT-GAACTTCTCTAAAATTACATTTTT--CCCTCGAAAATT-TAAAAATCACA-
1 TTTTTCCCTCGAACTTC-CAAAAATTACATTTTTACCCCT-G-AACTTCTAAAAATCACAT
* ** * * * *
22470 TTTTTGCCTCGAACTTTAAAAAATTACATTTTTGCCTC-GAACTTCCAAAAACCACAT
1 TTTTTCCCTCGAACTTCCAAAAATTACATTTTTACCCCTGAACTTCTAAAAATCACAT
** * * * * *
22527 TTTGGCTCC-CGAACTTCCAAAAATCATATTTTTA-CCCTCGAATTTC-CAAAATTACCA-
1 TTTTTC-CCTCGAACTTCCAAAAATTACATTTTTACCCCT-GAACTTCTAAAAATCA-CAT
* *
22584 TTTTGCCCTCGAACATCC-AAAATTATCATTTT
1 TTTTTCCCTCGAACTTCCAAAAATTA-CATTTT
22616 GCCCCCAAAC
Statistics
Matches: 246, Mismatches: 53, Indels: 42
0.72 0.16 0.12
Matches are distributed among these distances:
55 4 0.02
56 47 0.19
57 67 0.27
58 64 0.26
59 63 0.26
60 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (58 bp):
TTTTTCCCTCGAACTTCCAAAAATTACATTTTTACCCCTGAACTTCTAAAAATCACAT
Found at i:22568 original size:29 final size:29
Alignment explanation
Indices: 22237--22605 Score: 228
Period size: 29 Copynumber: 12.8 Consensus size: 29
22227 AAAAATTAAA
* * *
22237 ATTTTT-CTCTCGAACTTCTCGAAAATTAC
1 ATTTTTACCCTCGAACTTC-CAAAAATCAC
*
22266 ATTTTTACCC-CTGAACTT-TATAAAATCAC
1 ATTTTTACCCTC-GAACTTCCA-AAAATCAC
* *
22295 ATTTTTTCCCTCGAAATTCCAAAAATCAC
1 ATTTTTACCCTCGAACTTCCAAAAATCAC
* *
22324 A-TTTTAGCCCTCAAACTTCTCAAAAATTAC
1 ATTTTTA-CCCTCGAACTTC-CAAAAATCAC
* ** * *
22354 A-TTTTACCC-CTAAACTTTTAAAAATTAT
1 ATTTTTACCCTC-GAACTTCCAAAAATCAC
**
22382 ATTTTTACCCTTAAACTTCTCAAAAAAT-AC
1 ATTTTTACCCTCGAACTTC-C-AAAAATCAC
* * *
22412 ATTTTTCCCCT-GAACTTCTCTAAAATTAC
1 ATTTTTACCCTCGAACTTC-CAAAAATCAC
* *
22441 ATTTTT-CCCTCGAAAATT-TAAAAATCAC
1 ATTTTTACCCTCG-AACTTCCAAAAATCAC
* ** *
22469 ATTTTT-GCCTCGAACTTTAAAAAATTAC
1 ATTTTTACCCTCGAACTTCCAAAAATCAC
* *
22497 ATTTTT-GCCTCGAACTTCCAAAAACCAC
1 ATTTTTACCCTCGAACTTCCAAAAATCAC
** *
22525 ATTTTGGCTCC-CGAACTTCCAAAAATCAT
1 ATTTTTAC-CCTCGAACTTCCAAAAATCAC
* *
22554 ATTTTTACCCTCGAATTTCC-AAAATTACC
1 ATTTTTACCCTCGAACTTCCAAAAATCA-C
* *
22583 A-TTTTGCCCTCGAACATCCAAAA
1 ATTTTTACCCTCGAACTTCCAAAA
22606 TTATCATTTT
Statistics
Matches: 274, Mismatches: 45, Indels: 42
0.76 0.12 0.12
Matches are distributed among these distances:
27 4 0.01
28 101 0.37
29 121 0.44
30 42 0.15
31 6 0.02
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (29 bp):
ATTTTTACCCTCGAACTTCCAAAAATCAC
Found at i:22616 original size:28 final size:27
Alignment explanation
Indices: 22245--22700 Score: 181
Period size: 29 Copynumber: 15.9 Consensus size: 27
22235 AAATTTTTCT
*
22245 CTCGAACTTCTCGAAAATTACATTTTTACC
1 CTCGAACTTC-C-AAAATTACA-TTTTGCC
** * *
22275 C-CTGAACTTTATAAAATCACATTTTTTCC
1 CTC-GAAC-TTCCAAAATTACA-TTTTGCC
* *
22304 CTCGAAATTCCAAAAATCACATTTTAGCC
1 CTCGAACTTCC-AAAATTACATTTT-GCC
* *
22333 CTCAAACTTCTCAAAAATTACATTTTACC
1 CTCGAACTTC-C-AAAATTACATTTTGCC
* ** * *
22362 C-CTAAACTTTTAAAAATTATATTTTTACC
1 CTC-GAAC-TTCCAAAATTACA-TTTTGCC
** * *
22391 CTTAAACTTCTCAAAAAATACATTTTTCC
1 CTCGAACTTC-C-AAAATTACATTTTGCC
*
22420 C-CTGAACTTCTCTAAAATTACATTTTTCC
1 CTC-GAACTTC-C-AAAATTACATTTTGCC
* ** *
22449 CTCGAAAATTTAAAAATCACATTTTTG-C
1 CTCG-AACTTCCAAAATTACA-TTTTGCC
**
22477 CTCGAACTTTAAAAAATTACATTTTTG-C
1 CTCGAAC-TTCCAAAATTACA-TTTTGCC
**
22505 CTCGAACTTCCAAAAACCACATTTTGGCTC
1 CTCGAACTTCC-AAAATTACATTTT-GC-C
* * *
22535 C-CGAACTTCCAAAAATCATATTTTTACC
1 CTCGAACTTCC-AAAATTACA-TTTTGCC
*
22563 CTCGAATTTCCAAAATTACCATTTTGCC
1 CTCGAACTTCCAAAATTA-CATTTTGCC
*
22591 CTCGAACATCCAAAATTATCATTTTGCC
1 CTCGAACTTCCAAAATTA-CATTTTGCC
* * *
22619 CCCAAACATCCAAAACTTACCATTTTGCTC
1 CTCGAACTTCCAAAA-TTA-CATTTTGC-C
* * *
22649 CT--AAATTCCAAAAGTCACATTTTCGAC
1 CTCGAACTTCCAAAA-TTACATTTT-GCC
* *
22676 CTCAAACTTTCCAAAATTACGTTTT
1 CTCGAAC-TTCCAAAATTACATTTT
22701 AACCCCAAAC
Statistics
Matches: 337, Mismatches: 59, Indels: 61
0.74 0.13 0.13
Matches are distributed among these distances:
27 17 0.05
28 127 0.38
29 141 0.42
30 50 0.15
31 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (27 bp):
CTCGAACTTCCAAAATTACATTTTGCC
Found at i:22863 original size:14 final size:14
Alignment explanation
Indices: 22840--22869 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
22830 CGTATTTCAT
*
22840 TTTTCTTATATTTA
1 TTTTCCTATATTTA
22854 TTTTCCTATATTTA
1 TTTTCCTATATTTA
22868 TT
1 TT
22870 CATTTGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTCCTATATTTA
Found at i:27623 original size:12 final size:11
Alignment explanation
Indices: 27595--27677 Score: 60
Period size: 11 Copynumber: 7.0 Consensus size: 11
27585 AAATAAATAG
*
27595 AAAAGAAAGAA
1 AAAAAAAAGAA
*
27606 AGAAAAAAGGAA
1 A-AAAAAAAGAA
27618 AAAAAAAAGAA
1 AAAAAAAAGAA
27629 AAAAAGAAA-AA
1 AAAAA-AAAGAA
**
27640 AGGAAAAAGAA
1 AAAAAAAAGAA
27651 AATAGAAAAAGGAGA
1 AA-A-AAAAA-GA-A
27666 AAAAGAAAAGAA
1 AAAA-AAAAGAA
27678 GAGGTCGAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
10 3 0.05
11 23 0.40
12 13 0.23
13 8 0.14
14 7 0.12
15 3 0.05
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:27628 original size:19 final size:20
Alignment explanation
Indices: 27593--27660 Score: 77
Period size: 19 Copynumber: 3.4 Consensus size: 20
27583 ATAAATAAAT
27593 AGAAAAGAAAGAAAGAAAAAA
1 AGAAAA-AAAGAAAGAAAAAA
*
27614 GGAAAAAAA-AAAGAAAAAA
1 AGAAAAAAAGAAAGAAAAAA
*
27633 AGAAAAAAGGAAA-AAGAAAA
1 AGAAAAAAAGAAAGAA-AAAA
27653 TAGAAAAA
1 -AGAAAAA
27661 GGAGAAAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 19 0.46
20 10 0.24
21 12 0.29
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (20 bp):
AGAAAAAAAGAAAGAAAAAA
Found at i:27634 original size:27 final size:28
Alignment explanation
Indices: 27595--27669 Score: 107
Period size: 27 Copynumber: 2.6 Consensus size: 28
27585 AAATAAATAG
*
27595 AAAAGAAAGAAAGAAAAAAGGAAAAA-A
1 AAAAGAAAAAAAGAAAAAAGGAAAAAGA
27622 AAAAGAAAAAAAGAAAAAAGGAAAAAGA
1 AAAAGAAAAAAAGAAAAAAGGAAAAAGA
*
27650 AAATAGAAAAAGGAGAAAAA
1 AAA-AGAAAAA-AAGAAAAA
27670 GAAAAGAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 25 0.58
28 4 0.09
29 7 0.16
30 7 0.16
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (28 bp):
AAAAGAAAAAAAGAAAAAAGGAAAAAGA
Found at i:27646 original size:6 final size:6
Alignment explanation
Indices: 27600--27661 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
27590 AATAGAAAAG
* * *
27600 AAAGAA AGAA-AA AAGGAA AAA-AA AAAGAA AAA-AA GAA-AA AAGGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
27645 AAAGAA AATAGAA AAAG
1 AAAGAA AA-AGAA AAAG
27662 GAGAAAAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
5 13 0.29
6 24 0.53
7 8 0.18
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:27646 original size:22 final size:21
Alignment explanation
Indices: 27604--27674 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 21
27594 GAAAAGAAAG
27604 AAAGAAAAAAGGAAAA--AAA
1 AAAGAAAAAAGGAAAAAGAAA
* *
27623 AAAGAAAAAAAGAAAAAAGGAA
1 AAAG-AAAAAAGGAAAAAGAAA
*
27645 AAAGAAAATA-GAAAAAGGAGAA
1 AAAGAAAAAAGGAAAAA-GA-AA
27667 AAAGAAAA
1 AAAGAAAA
27675 GAAGAGGTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
19 4 0.10
20 16 0.38
21 6 0.14
22 16 0.38
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.01
Consensus pattern (21 bp):
AAAGAAAAAAGGAAAAAGAAA
Found at i:27660 original size:8 final size:7
Alignment explanation
Indices: 27575--27679 Score: 88
Period size: 7 Copynumber: 14.6 Consensus size: 7
27565 AAATTCAATG
27575 AAGAAAA
1 AAGAAAA
*
27582 AATAAATA
1 AAGAAA-A
* *
27590 AATAGAA
1 AAGAAAA
27597 AAGAAAGA
1 AAGAAA-A
27605 AAGAAAA
1 AAGAAAA
*
27612 AAG-GAA
1 AAGAAAA
27618 AA-AAAA
1 AAGAAAA
27624 AAGAAAAA
1 AAG-AAAA
27632 AAGAAAA
1 AAGAAAA
*
27639 AAGGAAA
1 AAGAAAA
27646 AAGAAAA
1 AAGAAAA
*
27653 TAGAAAA
1 AAGAAAA
*
27660 AGGAGAAA
1 AAGA-AAA
27668 AAGAAAA
1 AAGAAAA
27675 GAAGA
1 -AAGA
27680 GGTCGAGATG
Statistics
Matches: 79, Mismatches: 12, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
6 8 0.10
7 41 0.52
8 30 0.38
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (7 bp):
AAGAAAA
Found at i:27677 original size:20 final size:20
Alignment explanation
Indices: 27604--27674 Score: 72
Period size: 22 Copynumber: 3.4 Consensus size: 20
27594 GAAAAGAAAG
27604 AAAGAAAAAAGGAAAAA-AA
1 AAAGAAAAAAGGAAAAAGAA
*
27623 AAAGAAAAAAAGAAAAAAGGAA
1 AAAG-AAAAAAGGAAAAA-GAA
* *
27645 AAAGAAAATAGAAAAAGGAGAA
1 AAAGAAAAAAGGAAAA--AGAA
27667 AAAGAAAA
1 AAAGAAAA
27675 GAAGAGGTCG
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.09
20 12 0.27
21 11 0.24
22 17 0.38
23 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAAGGAAAAAGAA
Found at i:28550 original size:50 final size:49
Alignment explanation
Indices: 28496--28795 Score: 255
Period size: 50 Copynumber: 6.0 Consensus size: 49
28486 AATGACAAAC
* * *
28496 TCGGTACCTAAGAAGATGTGACGGGAAAGGTTAAGGCCACAACGGCGAAA
1 TCGGTACCTAA-AAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAAA
*
28546 TCGGTACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACAGCGAAA
1 TCGGTACC-TAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAAA
* * * * *
28596 TTGATACCTTAAAAGATGTGACGGGAAAGGTTGAGGCCGCAACGACGAAC
1 TCGGTACC-TAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAAA
* * * * * * *
28646 CCGGTACC-ATGAAGATTTGAAGGGAAAGATTGAGGCCGCGATGGTG-AA
1 TCGGTACCTA-AAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAAA
* * * * * * * *
28694 TCCCGTACCTCAGAAGATTTGAAGGTAAAGGTTGAGGCTGCAATGACGAAC
1 T-CGGTACCT-AAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAAA
* * * **
28745 TCGGTACTTTAAAAGATGTGACGCGAAAGGTTGAGATCGCAACGGC-AAA
1 TCGGTAC-CTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAAA
28794 TC
1 TC
28796 CGATACCTTA
Statistics
Matches: 199, Mismatches: 44, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
48 2 0.01
49 38 0.19
50 152 0.76
51 7 0.04
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.18
Consensus pattern (49 bp):
TCGGTACCTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAAA
Found at i:28969 original size:49 final size:49
Alignment explanation
Indices: 28835--28950 Score: 171
Period size: 49 Copynumber: 2.4 Consensus size: 49
28825 TTGAAGCCGT
* * * *
28835 AATGGCGAATCTTATACCATAAAGTCGAAGAGGAGAAAATTGAAGTTGC
1 AATGGAGAATCTTATACCATAAAGTCGAAAAGAAGCAAATTGAAGTTGC
28884 AATGGAGAATCTTATACCATAAAGTCGAAAAGAAGCAAATTGAAGTTGC
1 AATGGAGAATCTTATACCATAAAGTCGAAAAGAAGCAAATTGAAGTTGC
*
28933 AATGGCA-AATCTTCTACC
1 AATGG-AGAATCTTATACC
28951 TCGAAGTTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
49 60 0.98
50 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (49 bp):
AATGGAGAATCTTATACCATAAAGTCGAAAAGAAGCAAATTGAAGTTGC
Found at i:29180 original size:39 final size:39
Alignment explanation
Indices: 29134--29668 Score: 330
Period size: 39 Copynumber: 13.7 Consensus size: 39
29124 TGAAGATTCG
*
29134 ATCTCTTACCCCGAGCCTAGGGCAGATCATCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCA
* * *
29173 ATATCTTACCCCGAGCCTGGGGCAGATCACCATTAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCA
** * * * * *
29212 ATCTCTTACCCTTAGCTTGGGGTAGAT--TGCAGCCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAT-CA-TCAGCCA
* * * *
29251 ATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCA
* * * * ** * * *
29290 ATCTTTTACCCCAAGCTTGAGGCAGATTGT-AGCCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCA-TCAGCCA
* * * *
29329 ATCTTTTACCCCAAGCCTGGGGCAAATCACCATCAGCTC-
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGC-CA
* * *
29368 ATCTTTTACCCCGAGCCTGTGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCA
* * ** *
29407 ATCTCTTACCCGGAGCCTGAGGCAGAT--TGCATCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAT-CAT-CAGCCA
* * * *
29446 ATCTTTTACACCGAGCTTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCA
** * ** **
29485 ATCTCTTATGCCGAGCTTGGGGCAGATTGT-ATCCATTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCAT-CAGCCA
* * * *
29524 ATCTTTTACCCCGAGCTTGGGGTAGATCATCTCTCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATC-ATCAGCCA
* * ** ** *
29564 ATCTCTTACCCCGAGCCTGAGGCAAATTGT-ATTCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCA-TCAGCCA
* * * * * * *
29603 ATCTTTTACCTCGAGCTTGGGGCAAATCACCACCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCA
* *
29642 ATCTCTTACCCTGAGCCAGGGGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
29669 TGCAACCACC
Statistics
Matches: 375, Mismatches: 104, Indels: 34
0.73 0.20 0.07
Matches are distributed among these distances:
38 9 0.02
39 330 0.88
40 35 0.09
41 1 0.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCA
Found at i:29416 original size:78 final size:77
Alignment explanation
Indices: 29134--29668 Score: 388
Period size: 78 Copynumber: 6.9 Consensus size: 77
29124 TGAAGATTCG
* * * * *
29134 ATCTCTTACCCCGAGCCTAGGGCAGATCATCATCAGCCAATATCTTACCCCGAGCCTGGGGCAGA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
*
29199 TCACCATTAGC-CA
66 T-ACCATCA-CTCA
* ** * * * * *
29212 ATCTCTTACCCTTAGCTTGGGGTAGATTGCAGCCAT---CCGATCTTTTACCCCGAGCTTAGGGC
1 ATCTTTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGCCAATCTCTTACCCCGAGCCTGGGGC
29274 AGATCACCATCAGC-CA
63 AGAT-ACCATCA-CTCA
* * * * * *
29290 ATCTTTTACCCCAAGCTTGAGGCAGATTGTAGCCAT---CCGATCTTTTACCCCAAGCCTGGGGC
1 ATCTTTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGCCAATCTCTTACCCCGAGCCTGGGGC
*
29352 AAATCACCATCAGCTC-
63 AGAT-ACCATCA-CTCA
* * * *
29368 ATCTTTTACCCCGAGCCTGTGGCAGATCACCATCAGCCAATCTCTTACCCGGAGCCTGAGGCAGA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
** * *
29433 TTGCATCCATTCG
66 TACCAT-CACTCA
* ** *
29446 ATCTTTTACACCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTATGCCGAGCTTGGGGCAGA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
*** *
29511 TTGTATCCATTCA
66 TACCAT-CACTCA
* *
29524 ATCTTTTACCCCGAGCTTGGGGTAGATCATCTC-TCAGCCAATCTCTTACCCCGAGCCTGAGGCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCA-C-CATCAGCCAATCTCTTACCCCGAGCCTGGGGCA
* *** * *
29588 AATTGTATTCATTCG
64 GATACCA-TCACTCA
* * * * * *
29603 ATCTTTTACCTCGAGCTTGGGGCAAATCACCACCAACCAATCTCTTACCCTGAGCCAGGGGCAGA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
29668 T
66 T
29669 TGCAACCACC
Statistics
Matches: 382, Mismatches: 62, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
75 4 0.01
76 1 0.00
77 7 0.02
78 296 0.77
79 67 0.18
80 4 0.01
81 3 0.01
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (77 bp):
ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
TACCATCACTCA
Found at i:29481 original size:117 final size:114
Alignment explanation
Indices: 29134--29511 Score: 379
Period size: 117 Copynumber: 3.2 Consensus size: 114
29124 TGAAGATTCG
* * * *
29134 ATCTCTTACCCCGAGCCTAGGGCAGATCATCATCAGCCAATATCTTACCCCGAGCCTGGGGCAGA
1 ATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAGA
* * * * *
29199 -T-CACCATTAGCCAATCTCTTACCCTTAGCTTGGGGTAGATTGCAGCCATC--CG
66 TTGCACCATT---CGATCTTTTACCC-AAGCTTGGGGCAGA-T-CA-CCATCAGCC
* * * *
29251 ATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGCCAATCTTTTACCCCAAGCTTGAGGCAGA
1 ATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAGA
* * * *
29316 TTGTAGCCATCCGATCTTTTACCCCAAGCCTGGGGCAAATCACCATCAGCTC
66 TTGCA-CCATTCGATCTTTTA-CCCAAGCTTGGGGCAGATCACCATCAGC-C
*
29368 ATCTTTTACCCCGAGCCT-GTGGCAGATCACCATCAGCCAATCTCTTACCCGGAGCCTGAGGCAG
1 ATCTTTTACCCCGAGCCTAG-GGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAG
*
29432 ATTGCATCCATTCGATCTTTTACACCGAGCTTGGGGCAGATCACCATCAGCC
65 ATTGCA-CCATTCGATCTTTTAC-CCAAGCTTGGGGCAGATCACCATCAGCC
* ** * *
29484 AATCTCTTATGCCGAGCTTGGGGCAGAT
1 -ATCTTTTACCCCGAGCCTAGGGCAGAT
29512 TGTATCCATT
Statistics
Matches: 218, Mismatches: 32, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
114 5 0.02
115 2 0.01
116 5 0.02
117 196 0.90
118 5 0.02
119 1 0.00
120 4 0.02
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (114 bp):
ATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAGA
TTGCACCATTCGATCTTTTACCCAAGCTTGGGGCAGATCACCATCAGCC
Found at i:29610 original size:157 final size:156
Alignment explanation
Indices: 29368--29649 Score: 433
Period size: 157 Copynumber: 1.8 Consensus size: 156
29358 CCATCAGCTC
* * *
29368 ATCTTTTACCCCGAGCCTGTGGCAGATCACCATCAGCCAATCTCTTACCCGGAGCCTGAGGCAGA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAAA
* * *
29433 TTGCATCCATTCGATCTTTTACAC-CGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTATGCC
66 TTGCATCCATTCGATCTTTTAC-CTCGAGCTTGGGGCAAATCACCACCAACCAATCTCTTATGCC
29497 GAGCTTGGGGCAGATTGTATCCATTCA
130 GAGCTTGGGGCAGATTGTATCCATTCA
* *
29524 ATCTTTTACCCCGAGCTTGGGGTAGATCATCTC-TCAGCCAATCTCTTACCCCGAGCCTGAGGCA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCA-C-CATCAGCCAATCTCTTACCCCGAGCCTGAGGCA
* *
29588 AATTGTATTCATTCGATCTTTTACCTCGAGCTTGGGGCAAATCACCACCAACCAATCTCTTA
64 AATTGCATCCATTCGATCTTTTACCTCGAGCTTGGGGCAAATCACCACCAACCAATCTCTTA
29650 CCCTGAGCCA
Statistics
Matches: 113, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
156 27 0.24
157 85 0.75
158 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (156 bp):
ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAAA
TTGCATCCATTCGATCTTTTACCTCGAGCTTGGGGCAAATCACCACCAACCAATCTCTTATGCCG
AGCTTGGGGCAGATTGTATCCATTCA
Found at i:30279 original size:30 final size:30
Alignment explanation
Indices: 30236--30546 Score: 209
Period size: 29 Copynumber: 10.8 Consensus size: 30
30226 TTTAACCCTA
*
30236 AACTTCT-AAAAATTACATTTTTACCCCCA
1 AACTTCTCAAAAATTACATTTTTACCCCCG
* * *
30265 AACTTCTCAAAAATTACA-TTTTGCCTCTG
1 AACTTCTCAAAAATTACATTTTTACCCCCG
* * * * *
30294 AACTTCTCAAAAATTAAAATTTTGCTCTCG
1 AACTTCTCAAAAATTACATTTTTACCCCCG
* **
30324 AACTTC-CAAAAATCACATTTTGGCCCCCG
1 AACTTCTCAAAAATTACATTTTTACCCCCG
* * *
30353 AACTTCTCAAAATTTATATTTTTACCCTCG
1 AACTTCTCAAAAATTACATTTTTACCCCCG
* *
30383 AACTT-T--AAAATTAC-TTTTTTCTCCCG
1 AACTTCTCAAAAATTACATTTTTACCCCCG
* * **
30409 AACTT-TCAAAAATCACATTTTTGCTTCCG
1 AACTTCTCAAAAATTACATTTTTACCCCCG
* * *
30438 AACTTCT-AAAAATCATATTTTTACCCTCG
1 AACTTCTCAAAAATTACATTTTTACCCCCG
* * ** *
30467 AACTT-TCAAAAATCATATTTTGGCCCTCG
1 AACTTCTCAAAAATTACATTTTTACCCCCG
* * *
30496 AACTT-T-AAAAATCATATTTTTACCCCTTG
1 AACTTCTCAAAAATTACATTTTTACCCC-CG
*
30525 AA-TT-TCCAAAATTACCATTTTT
1 AACTTCTCAAAAATTA-CATTTTT
30547 CTCCCAAATT
Statistics
Matches: 228, Mismatches: 43, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
26 15 0.07
27 6 0.03
28 28 0.12
29 127 0.56
30 52 0.23
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTCTCAAAAATTACATTTTTACCCCCG
Found at i:30439 original size:29 final size:29
Alignment explanation
Indices: 30243--30602 Score: 206
Period size: 29 Copynumber: 12.5 Consensus size: 29
30233 CTAAACTTCT
* * * *
30243 AAAAATTACATTTTTACCCCCAAACTTCTC
1 AAAAATCACATTTTTGCCCTCGAACTT-TC
*
30273 AAAAATTACA-TTTTG-CCTCTGAACTTCTC
1 AAAAATCACATTTTTGCCCTC-GAACTT-TC
* * * * *
30302 AAAAATTAAAATTTTGCTCTCGAACTTCC
1 AAAAATCACATTTTTGCCCTCGAACTTTC
* *
30331 AAAAATCACATTTTGGCCCCCGAACTTCTC
1 AAAAATCACATTTTTGCCCTCGAACTT-TC
* * * *
30361 AAAATTTATATTTTTACCCTCGAACTTT-
1 AAAAATCACATTTTTGCCCTCGAACTTTC
* *
30389 -AAAATTAC-TTTTTTCTCC-CGAACTTTC
1 AAAAATCACATTTTTGC-CCTCGAACTTTC
*
30416 AAAAATCACATTTTTG-CTTCCGAAC-TTC
1 AAAAATCACATTTTTGCCCT-CGAACTTTC
* *
30444 TAAAAATCATATTTTTACCCTCGAACTTTC
1 -AAAAATCACATTTTTGCCCTCGAACTTTC
* *
30474 AAAAATCATATTTTGGCCCTCGAACTTT-
1 AAAAATCACATTTTTGCCCTCGAACTTTC
* * *
30502 AAAAATCATATTTTTACCCCTTGAA-TTTC
1 AAAAATCACATTTTT-GCCCTCGAACTTTC
* * *
30531 CAAAATTACCATTTTT-CTCC-C-AAATTTCC
1 AAAAATCA-CATTTTTGC-CCTCGAACTTT-C
* * * * *
30560 TAAAGTCACATTTTCGACCTCAAACTTTC
1 AAAAATCACATTTTTGCCCTCGAACTTTC
* *
30589 CAAAATTACATTTT
1 AAAAATCACATTTT
30603 AACCCTAAAC
Statistics
Matches: 262, Mismatches: 46, Indels: 45
0.74 0.13 0.13
Matches are distributed among these distances:
26 14 0.05
27 11 0.04
28 42 0.16
29 133 0.51
30 59 0.23
31 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAAATCACATTTTTGCCCTCGAACTTTC
Found at i:30439 original size:85 final size:85
Alignment explanation
Indices: 30236--30477 Score: 247
Period size: 85 Copynumber: 2.8 Consensus size: 85
30226 TTTAACCCTA
* * ** * * * *
30236 AACTTCTAAAAATTACATTTTTACCCCCAAACTTCTCAAAAATTACA-TTTT-GCCTCTGAACTT
1 AACTTCCAAAAATCACATTTTGGCCCCCGAACTTCT-AAAAATCATATTTTTACCCTC-GAACTT
** *
30299 CTCAAAAATTAAAATTTTGCTCTCG
64 -TC-AAAATT-ACTTTTTGCTCCCG
* *
30324 AACTTCCAAAAATCACATTTTGGCCCCCGAACTTCTCAAAATTTATATTTTTACCCTCGAACTTT
1 AACTTCCAAAAATCACATTTTGGCCCCCGAACTTCT-AAAAATCATATTTTTACCCTCGAACTTT
*
30389 -AAAATTACTTTTTTCTCCCG
65 CAAAATTACTTTTTGCTCCCG
* * **
30409 AACTTTCAAAAATCACATTTTTGCTTCCGAACTTCTAAAAATCATATTTTTACCCTCGAACTTTC
1 AACTTCCAAAAATCACATTTTGGCCCCCGAACTTCTAAAAATCATATTTTTACCCTCGAACTTTC
30474 AAAA
66 AAAA
30478 ATCATATTTT
Statistics
Matches: 133, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
84 26 0.20
85 46 0.35
86 6 0.05
88 41 0.31
89 10 0.08
90 4 0.03
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (85 bp):
AACTTCCAAAAATCACATTTTGGCCCCCGAACTTCTAAAAATCATATTTTTACCCTCGAACTTTC
AAAATTACTTTTTGCTCCCG
Found at i:30474 original size:58 final size:57
Alignment explanation
Indices: 30243--30546 Score: 219
Period size: 59 Copynumber: 5.3 Consensus size: 57
30233 CTAAACTTCT
* * * * * *
30243 AAAAATTACATTTTTACCCCCAAACTTCTCAAAAATTACA-TTTT-GCCTCTGAACTTCTC
1 AAAAATTACATTTTTGCCCTCGAACTT-T-AAAAATCATATTTTTACCCTC-GAACTT-TC
* * * * * ** *
30302 AAAAATTAAAATTTTGCTCTCGAACTTCCAAAAATCACATTTTGGCCCCCGAACTTCTC
1 AAAAATTACATTTTTGCCCTCGAACTT-TAAAAATCATATTTTTACCCTCGAACTT-TC
* * * *
30361 AAAATTTATATTTTTACCCTCGAACTTT-AAAAT--TACTTTTTTCTCC-CGAACTTTC
1 AAAAATTACATTTTTGCCCTCGAACTTTAAAAATCATA-TTTTTAC-CCTCGAACTTTC
* *
30416 AAAAATCACATTTTTG-CTTCCGAACTTCTAAAAATCATATTTTTACCCTCGAACTTTC
1 AAAAATTACATTTTTGCCCT-CGAACTT-TAAAAATCATATTTTTACCCTCGAACTTTC
* * * *
30474 AAAAATCATATTTTGGCCCTCGAACTTTAAAAATCATATTTTTACCCCTTGAA-TTTC
1 AAAAATTACATTTTTGCCCTCGAACTTTAAAAATCATATTTTTA-CCCTCGAACTTTC
*
30531 CAAAATTACCATTTTT
1 AAAAATTA-CATTTTT
30547 CTCCCAAATT
Statistics
Matches: 198, Mismatches: 34, Indels: 27
0.76 0.13 0.10
Matches are distributed among these distances:
54 2 0.01
55 22 0.11
56 13 0.07
57 41 0.21
58 57 0.29
59 60 0.30
60 3 0.02
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (57 bp):
AAAAATTACATTTTTGCCCTCGAACTTTAAAAATCATATTTTTACCCTCGAACTTTC
Found at i:30477 original size:143 final size:142
Alignment explanation
Indices: 30244--30573 Score: 362
Period size: 143 Copynumber: 2.3 Consensus size: 142
30234 TAAACTTCTA
* * * *
30244 AAAATTACATTTTTACCCCCAAACTTCTCAAAAATTACA-TTTTGCCTCTGAACTTCTCAAAAAT
1 AAAATTAC-TTTTTTCTCCC-AACTT-TCAAAAATCACATTTTTGCCTCCGAACTTCTCAAAAAT
* * * * *
30308 TAAAATTTTGCTCTCGAACTTCCAAAAATCACATTTTGGCCCCCGAACTTCTCAAAATTTATATT
63 CAAAATTTTACCCTCGAACTTCCAAAAATCACATTTTGGCCCCCGAACTT-T-AAAAATCATATT
30373 TTTA-CCCTCGAACTTT-
126 TTTACCCCTCGAA-TTTC
*
30389 AAAATTACTTTTTTCTCCCGAACTTTCAAAAATCACATTTTTGCTTCCGAACTTCT-AAAAATCA
1 AAAATTACTTTTTTCTCCC-AACTTTCAAAAATCACATTTTTGCCTCCGAACTTCTCAAAAATCA
* * * * *
30453 TATTTTTACCCTCGAACTTTCAAAAATCATATTTTGGCCCTCGAACTTTAAAAATCATATTTTTA
65 AAATTTTACCCTCGAACTTCCAAAAATCACATTTTGGCCCCCGAACTTTAAAAATCATATTTTTA
*
30518 CCCCTTGAATTTCC
130 CCCCTCGAATTT-C
* * * *
30532 AAAATTACCATTTTTCTCCCAAATTTCCTAAAGTCACATTTT
1 AAAATTA-CTTTTTTCTCCCAACTTT-CAAAAATCACATTTT
30574 CGACCTCAAA
Statistics
Matches: 158, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
141 17 0.11
142 8 0.05
143 71 0.45
144 54 0.34
145 8 0.05
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (142 bp):
AAAATTACTTTTTTCTCCCAACTTTCAAAAATCACATTTTTGCCTCCGAACTTCTCAAAAATCAA
AATTTTACCCTCGAACTTCCAAAAATCACATTTTGGCCCCCGAACTTTAAAAATCATATTTTTAC
CCCTCGAATTTC
Found at i:30516 original size:114 final size:115
Alignment explanation
Indices: 30293--30505 Score: 279
Period size: 114 Copynumber: 1.9 Consensus size: 115
30283 TTTTGCCTCT
* *
30293 GAACTTCTCAAAAATTAAAATTTTGCTCTCGAACTTCCAAAAATCACATTTTGGCCCCCGAACTT
1 GAACTTCTCAAAAATCAAAATTTTGCTCTCGAACTTCCAAAAATCACATTTTGACCCCCGAACTT
* * * *
30358 CTCAAAATTTATATTTTTACCCTCGAACTTTAAAATTACTTTTTTCTCCC
66 CTCAAAAATCATATTTTGACCCTCGAACTTTAAAATCACTTTTTTCTCCC
* * * * * *
30408 GAACTT-TCAAAAATCACATTTTTGCT-TCCGAACTTCTAAAAATCATATTTTTACCCTCGAACT
1 GAACTTCTCAAAAATCAAAATTTTGCTCT-CGAACTTCCAAAAATCACATTTTGACCCCCGAACT
*
30471 T-TCAAAAATCATATTTTGGCCCTCGAACTTTAAAA
65 TCTCAAAAATCATATTTTGACCCTCGAACTTTAAAA
30506 ATCATATTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
113 31 0.36
114 48 0.56
115 6 0.07
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.37
Consensus pattern (115 bp):
GAACTTCTCAAAAATCAAAATTTTGCTCTCGAACTTCCAAAAATCACATTTTGACCCCCGAACTT
CTCAAAAATCATATTTTGACCCTCGAACTTTAAAATCACTTTTTTCTCCC
Found at i:30762 original size:14 final size:14
Alignment explanation
Indices: 30739--30768 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
30729 CGTATTTCAT
*
30739 TTTTCTTATATTTA
1 TTTTCGTATATTTA
30753 TTTTCGTATATTTA
1 TTTTCGTATATTTA
30767 TT
1 TT
30769 CATTTGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTTCGTATATTTA
Found at i:31974 original size:18 final size:18
Alignment explanation
Indices: 31938--31988 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
31928 TTCTCTCAAT
*
31938 AAAA-ATTTAAAAAAATC
1 AAAATATTTATAAAAATC
*
31955 AAAATAATTT-TAAAATTC
1 AAAAT-ATTTATAAAAATC
31973 AAAATATTTATAAAAA
1 AAAATATTTATAAAAA
31989 ATTTAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 8 0.29
18 16 0.57
19 4 0.14
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATATTTATAAAAATC
Found at i:32003 original size:24 final size:24
Alignment explanation
Indices: 31976--32026 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
31966 AAAATTCAAA
* *
31976 ATATTTATAAAAA-ATTTAAAATTT
1 ATATTT-TAAAAATATATAAAAATT
32000 ATATTTTAAAAATATATAAAAATT
1 ATATTTTAAAAATATATAAAAATT
32024 ATA
1 ATA
32027 AAAAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATTTTAAAAATATATAAAAATT
Found at i:32462 original size:28 final size:29
Alignment explanation
Indices: 32420--32492 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
32410 TGTTCAAAAC
*
32420 ATATTATTTTGGTAAATAA-CTTTTATCT
1 ATATTATTTTAGTAAATAATCTTTTATCT
* * *
32448 ATATTATTTTAGTAATTAATTTTTTATTT
1 ATATTATTTTAGTAAATAATCTTTTATCT
* *
32477 ATATTATATTAATAAA
1 ATATTATTTTAGTAAA
32493 AAGCCAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 17 0.46
29 20 0.54
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (29 bp):
ATATTATTTTAGTAAATAATCTTTTATCT
Found at i:33046 original size:22 final size:22
Alignment explanation
Indices: 33014--33055 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
33004 ATATAATAAT
*
33014 GCACCATAGTG-TAAATCAAAGG
1 GCACCAAAGTGCT-AATCAAAGG
33036 GCACCAAAGTGCTAATCAAA
1 GCACCAAAGTGCTAATCAAA
33056 ACAAAGAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (22 bp):
GCACCAAAGTGCTAATCAAAGG
Found at i:33160 original size:28 final size:28
Alignment explanation
Indices: 33111--33221 Score: 152
Period size: 28 Copynumber: 4.0 Consensus size: 28
33101 TAGTAAACAC
* *
33111 CAAAATGCAATCACGTAACAATAAGCA-
1 CAAAGTGCAATCACGTAGCAATAAGCAT
*
33138 CTAAAGTGCATTCACGTAGCAATAAGCAT
1 C-AAAGTGCAATCACGTAGCAATAAGCAT
* *
33167 CGAAGTGTAATCACGTAGCAATAAGCAT
1 CAAAGTGCAATCACGTAGCAATAAGCAT
*
33195 CAAAGTGCAATCACGTAGCAGTAAGCA
1 CAAAGTGCAATCACGTAGCAATAAGCA
33222 CCGAAATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
27 1 0.01
28 71 0.97
29 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (28 bp):
CAAAGTGCAATCACGTAGCAATAAGCAT
Found at i:35383 original size:18 final size:19
Alignment explanation
Indices: 35348--35386 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
35338 AATAAATATA
35348 AATACAATTTAAATTTAAT
1 AATACAATTTAAATTTAAT
35367 AATA-AATTGTAAA-TTAAT
1 AATACAATT-TAAATTTAAT
35385 AA
1 AA
35387 AAACAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AATACAATTTAAATTTAAT
Found at i:40744 original size:21 final size:21
Alignment explanation
Indices: 40718--40772 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
40708 TTTTCGGATA
* * *
40718 CTTCTACTGATACAAGTGAAG
1 CTTCTACCGATACAAATCAAG
* *
40739 CTTCTACCGAAACAAATCATG
1 CTTCTACCGATACAAATCAAG
40760 CTTCTACCGATAC
1 CTTCTACCGATAC
40773 TAAAAACTCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (21 bp):
CTTCTACCGATACAAATCAAG
Found at i:41477 original size:36 final size:36
Alignment explanation
Indices: 41430--41557 Score: 211
Period size: 36 Copynumber: 3.6 Consensus size: 36
41420 GGTCATGCTT
41430 ACTCCCTGTTGACCCAAAGGTCACGATGCTCATTTC
1 ACTCCCTGTTGACCCAAAGGTCACGATGCTCATTTC
*
41466 ACTCCTTGTTGACCCAAAGGTCACGATGCTCATTTC
1 ACTCCCTGTTGACCCAAAGGTCACGATGCTCATTTC
* * *
41502 ACTCCTTGTTGACCCAAAGGTCATGATGCTCATTTT
1 ACTCCCTGTTGACCCAAAGGTCACGATGCTCATTTC
*
41538 ACTCCCTGTTGATCCAAAGG
1 ACTCCCTGTTGACCCAAAGG
41558 CCATGCCTGT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 87 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (36 bp):
ACTCCCTGTTGACCCAAAGGTCACGATGCTCATTTC
Found at i:43341 original size:59 final size:59
Alignment explanation
Indices: 43228--43438 Score: 228
Period size: 59 Copynumber: 3.5 Consensus size: 59
43218 AAGGATACGA
** * * * *
43228 GTCAAAACATAATTTTAGAAAATTTTAAGGGGTAAAAATGTAATTTTAGGAAAGTTTGAG
1 GTCAAAATGTAATTTTAGAAAAGTTT-AGGGGTTAAAATGCAATTTTAGAAAAGTTTGAG
*
43288 GTCAAAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGCAATTTTAGAAAAGTTTAAAG
1 GTCAAAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGCAATTTTAGAAAAGTTT-GAG
* * * * * * *
43348 GTTAAAATGTAATTTTGGAGAAGTTT-GAGGTTAAAATACAATTTTGGAAAAGTATGAG
1 GTCAAAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGCAATTTTAGAAAAGTTTGAG
* *
43406 GATTAAAATGTAATTTTTA-AAAATTTTAGGGGT
1 G-TCAAAATGTAA-TTTTAGAAAAGTTTAGGGGT
43439 CTTAATGTGA
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
58 3 0.02
59 69 0.54
60 56 0.44
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.35
Consensus pattern (59 bp):
GTCAAAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGCAATTTTAGAAAAGTTTGAG
Found at i:43391 original size:89 final size:90
Alignment explanation
Indices: 43238--43422 Score: 241
Period size: 89 Copynumber: 2.1 Consensus size: 90
43228 GTCAAAACAT
* * **
43238 AATTTTAGAAAATTTTAAGGGGTAAAAATGTAATTTTAGGAAAGTTTGAGGTCAAAATGTAATTT
1 AATTTTAGAAAAGTTTAAGAGGTAAAAATGTAATTTTAGGAAAGTTTGAGGTCAAAATACAATTT
* *
43303 TAGAAAAGT-TTAGGGGTTAAAATGC
66 TAGAAAAGTATGA-GGATTAAAATGC
* *
43328 AATTTTAGAAAAGTTTAA-AGGTTAAAATGTAATTTT-GGAGAAGTTTGAGGTTAAAATACAATT
1 AATTTTAGAAAAGTTTAAGAGGTAAAAATGTAATTTTAGGA-AAGTTTGAGGTCAAAATACAATT
* *
43391 TTGGAAAAGTATGAGGATTAAAATGT
65 TTAGAAAAGTATGAGGATTAAAATGC
43417 AATTTT
1 AATTTT
43423 TAAAAATTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
88 3 0.04
89 61 0.73
90 19 0.23
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.36
Consensus pattern (90 bp):
AATTTTAGAAAAGTTTAAGAGGTAAAAATGTAATTTTAGGAAAGTTTGAGGTCAAAATACAATTT
TAGAAAAGTATGAGGATTAAAATGC
Found at i:43427 original size:29 final size:29
Alignment explanation
Indices: 43237--43422 Score: 201
Period size: 30 Copynumber: 6.2 Consensus size: 29
43227 AGTCAAAACA
* * *
43237 TAATTTTAGAAAATTTTAAGGGGTAAAAATG
1 TAATTTTAGAAAAGTTT--GAGGTTAAAATG
* *
43268 TAATTTTAGGAAAGTTTGAGGTCAAAATG
1 TAATTTTAGAAAAGTTTGAGGTTAAAATG
*
43297 TAATTTTAGAAAAGTTTAGGGGTTAAAATG
1 TAATTTTAGAAAAGTTT-GAGGTTAAAATG
* *
43327 CAATTTTAGAAAAGTTTAAAGGTTAAAATG
1 TAATTTTAGAAAAGTTT-GAGGTTAAAATG
* * *
43357 TAATTTTGGAGAAGTTTGAGGTTAAAATA
1 TAATTTTAGAAAAGTTTGAGGTTAAAATG
* * *
43386 CAATTTTGGAAAAGTATGAGGATTAAAATG
1 TAATTTTAGAAAAGTTTGAGG-TTAAAATG
43416 TAATTTT
1 TAATTTT
43423 TAAAAATTTT
Statistics
Matches: 133, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
29 54 0.41
30 64 0.48
31 15 0.11
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (29 bp):
TAATTTTAGAAAAGTTTGAGGTTAAAATG
Found at i:43446 original size:89 final size:88
Alignment explanation
Indices: 43238--43452 Score: 229
Period size: 89 Copynumber: 2.4 Consensus size: 88
43228 GTCAAAACAT
* **
43238 AATTTTAGAAAATTTTAAGGGGTAAAAATGTAATTTTAGGAAAGTTTGAGGTCAAAATGTAATTT
1 AATTTTAGAAAATTTT-AGGGGT-TAAATGTAATTTTAGGAAAGTTTGAGGTCAAAATACAATTT
* *
43303 TAGAAAAGTTTAGGGGTTAAAATGC
64 TAGAAAAGTTGAGGGATTAAAATGC
* ** *
43328 AATTTTAGAAAAGTTTAAAGGTTAAAATGTAATTTT-GGAGAAGTTTGAGGTTAAAATACAATTT
1 AATTTTAGAAAATTTTAGGGGTT-AAATGTAATTTTAGGA-AAGTTTGAGGTCAAAATACAATTT
* *
43392 TGGAAAAGTATGA-GGATTAAAATGT
64 TAGAAAAGT-TGAGGGATTAAAATGC
* *
43417 AATTTTTA-AAAATTTTAGGGGTCTTAATGTGATTTT
1 AA-TTTTAGAAAATTTTAGGGGT-TAAATGTAATTTT
43453 CAAAGAAAAT
Statistics
Matches: 104, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
88 3 0.03
89 78 0.75
90 23 0.22
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (88 bp):
AATTTTAGAAAATTTTAGGGGTTAAATGTAATTTTAGGAAAGTTTGAGGTCAAAATACAATTTTA
GAAAAGTTGAGGGATTAAAATGC
Done.