Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004036.1 Kokia drynarioides strain JFW-HI SEQ_117172, 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: 140064
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 18 characters in sequence are not A, C, G, or T
Found at i:729 original size:29 final size:28
Alignment explanation
Indices: 697--759 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
687 AAATGAGATT
* *
697 TTTGGATACCCAAGGGGCAAAATGGTAAC
1 TTTGGACACCCAA-GGGCAAAATAGTAAC
* * *
726 TTTGGACACTCGAGGGCAAAATAGTAAT
1 TTTGGACACCCAAGGGCAAAATAGTAAC
754 TTTGGA
1 TTTGGA
760 AAAGTGGTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.25
Consensus pattern (28 bp):
TTTGGACACCCAAGGGCAAAATAGTAAC
Found at i:832 original size:30 final size:28
Alignment explanation
Indices: 791--870 Score: 81
Period size: 30 Copynumber: 2.8 Consensus size: 28
781 TTTTAGACAT
*
791 TCGGGGATAAAATGGTACTTTTGGGATGAA
1 TCGGGG-TAAAATGGTAATTTTGGGATG-A
* *
821 TCGGGGTTAAAAATGG-AATTTTTGGATGT
1 TCGGGG-T-AAAATGGTAATTTTGGGATGA
*
850 TCAGGGTAAAATGGTAATTTT
1 TCGGGGTAAAATGGTAATTTT
871 TAAAAAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 7 0.16
28 7 0.16
29 5 0.12
30 17 0.40
31 7 0.16
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (28 bp):
TCGGGGTAAAATGGTAATTTTGGGATGA
Found at i:843 original size:59 final size:58
Alignment explanation
Indices: 765--1051 Score: 268
Period size: 58 Copynumber: 4.9 Consensus size: 58
755 TTGGAAAAGT
* * * * * *
765 GGTCAAAAAATGGAGTTTTTAGACA-TTCGGGGATAAAATGGT-ACTTTTGGGATGAATCGG
1 GGTC-AAAAATGGAATTTTTAGA-AGTTCAGGG-TAAAATGGTAATTTTTGAGA-AAATCGA
* * * * * *
825 GGTTAAAAATGGAATTTTTGGATGTTCAGGGTAAAATGGTAATTTTTAAAAAAAAT-AA
1 GGTCAAAAATGGAATTTTTAGAAGTTCAGGGTAAAATGGTAATTTTT-GAGAAAATCGA
* * *
883 GGTTAAAAATGGAATTTTTGGAAGTTTAGGGATAAAATGGTAATTTTTGAGAAAATCGA
1 GGTCAAAAATGGAATTTTTAGAAGTTCAGGG-TAAAATGGTAATTTTTGAGAAAATCGA
942 GGTCAAAAATGGAA-TTTTAGAAAGTTCAGGGGTAAAA-GTGTAATTTTTG-GAAAATCGA
1 GGTCAAAAATGGAATTTTTAG-AAGTTCA-GGGTAAAATG-GTAATTTTTGAGAAAATCGA
*
1000 GGTCAAAAATGGAA-TTTTGGAAGTTCAAGGGTAACAAT-GTAATTTTTG-GAAA
1 GGTCAAAAATGGAATTTTTAGAAGTTC-AGGGTAA-AATGGTAATTTTTGAGAAA
1052 GTTTAGGGGT
Statistics
Matches: 195, Mismatches: 21, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
57 26 0.13
58 81 0.42
59 81 0.42
60 7 0.04
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (58 bp):
GGTCAAAAATGGAATTTTTAGAAGTTCAGGGTAAAATGGTAATTTTTGAGAAAATCGA
Found at i:887 original size:58 final size:57
Alignment explanation
Indices: 765--1051 Score: 269
Period size: 59 Copynumber: 4.9 Consensus size: 57
755 TTGGAAAAGT
* * * * ** * *
765 GGTCAAAAAATGGAGTTTTTAGACA-TTCGGGGATAAAATGGTACTTTTGGGATGAATCGG
1 GGTC-AAAAATGGAATTTTTGGA-AGTTCAGGG-TAAAATGGTAATTTTTAGA-AAATCGA
* * * *
825 GGTTAAAAATGGAATTTTTGGATGTTCAGGGTAAAATGGTAATTTTTAAAAAAAAT-AA
1 GGTCAAAAATGGAATTTTTGGAAGTTCAGGGTAAAATGGTAATTTTT--AGAAAATCGA
* *
883 GGTTAAAAATGGAATTTTTGGAAGTTTAGGGATAAAATGGTAATTTTTGAGAAAATCGA
1 GGTCAAAAATGGAATTTTTGGAAGTTCAGGG-TAAAATGGTAATTTTT-AGAAAATCGA
* * *
942 GGTCAAAAATGGAATTTTAGAAAGTTCAGGGGTAAAA-GTGTAATTTTTGGAAAATCGA
1 GGTCAAAAATGGAATTTTTGGAAGTTCA-GGGTAAAATG-GTAATTTTTAGAAAATCGA
*
1000 GGTCAAAAATGGAA-TTTTGGAAGTTCAAGGGTAACAAT-GTAATTTTTGGAAA
1 GGTCAAAAATGGAATTTTTGGAAGTTC-AGGGTAA-AATGGTAATTTTTAGAAA
1052 GTTTAGGGGT
Statistics
Matches: 193, Mismatches: 24, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
57 30 0.16
58 76 0.39
59 80 0.41
60 7 0.04
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (57 bp):
GGTCAAAAATGGAATTTTTGGAAGTTCAGGGTAAAATGGTAATTTTTAGAAAATCGA
Found at i:901 original size:117 final size:118
Alignment explanation
Indices: 770--1051 Score: 278
Period size: 117 Copynumber: 2.4 Consensus size: 118
760 AAAGTGGTCA
* * * * * *
770 AAAAATGGAGTTTTTAGACA-TTCGGGGATAAAATGGT-ACTTTTGGGATGAATCGGGGTTAAAA
1 AAAAATGGAATTTTTAGA-AGTTCAGGGATAAAATGGTAACTTTTGAGA-AAATCGAGGTCAAAA
* * *
833 ATGGAATTTTTGGATGTTCA-GGGTAAAA-TGGTAATTTTTAAAAAAAATAAGGTT
64 ATGGAATTTTAGAAAGTTCAGGGGTAAAAGT-GTAATTTTTAAAAAAAATAAGGTT
* * *
887 AAAAATGGAATTTTTGGAAGTTTAGGGATAAAATGGTAATTTTTGAGAAAATCGAGGTCAAAAAT
1 AAAAATGGAATTTTTAGAAGTTCAGGGATAAAATGGTAACTTTTGAGAAAATCGAGGTCAAAAAT
** * *
952 GGAATTTTAGAAAGTTCAGGGGTAAAAGTGTAATTTTT--GGAAAATCGAGGTC
66 GGAATTTTAGAAAGTTCAGGGGTAAAAGTGTAATTTTTAAAAAAAAT-AAGGTT
* *
1004 AAAAATGGAA-TTTTGGAAGTTCAAGGG-TAACAAT-GTAATTTTTG-GAAA
1 AAAAATGGAATTTTTAGAAGTTC-AGGGATAA-AATGGTAACTTTTGAGAAA
1052 GTTTAGGGGT
Statistics
Matches: 141, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
115 4 0.03
116 30 0.21
117 81 0.57
118 25 0.18
119 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (118 bp):
AAAAATGGAATTTTTAGAAGTTCAGGGATAAAATGGTAACTTTTGAGAAAATCGAGGTCAAAAAT
GGAATTTTAGAAAGTTCAGGGGTAAAAGTGTAATTTTTAAAAAAAATAAGGTT
Found at i:919 original size:29 final size:28
Alignment explanation
Indices: 828--1142 Score: 178
Period size: 29 Copynumber: 10.9 Consensus size: 28
818 GAATCGGGGT
* *
828 TAAAAATGGAATTTTTGGATGTTCAGGG
1 TAAAAATGGAATTTTTGGAAGTTTAGGG
** ** * *
856 T-AAAATGGTAATTTTTAAAAAAAATAAGGT
1 TAAAAATGG-AATTTTT--GGAAGTTTAGGG
886 TAAAAATGGAATTTTTGGAAGTTTAGGG
1 TAAAAATGGAATTTTTGGAAGTTTAGGG
** *
914 -ATAAAATGGTAATTTTTGAGAA-AATCGAGG
1 TA-AAAATGG-AATTTTTG-GAAGTTTAG-GG
* * *
944 TCAAAAATGGAATTTTAGAAAGTTCAGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTA-GGG
* * ** *
974 TAAAAGTGTAATTTTTGGAA-AATCGAGG
1 TAAAAATGGAATTTTTGGAAGTTTAG-GG
*
1002 TCAAAAATGGAA-TTTTGGAAGTTCAAGGG
1 T-AAAAATGGAATTTTTGGAAGTT-TAGGG
* *
1031 TAACAATGTAATTTTTGGAAAGTTTAGGGG
1 TAAAAATGGAATTTTTGG-AAGTTTA-GGG
*
1061 T-AAAATGTAATTTTTGGAAAGTTT-GGG
1 TAAAAATGGAATTTTTGG-AAGTTTAGGG
1088 TAAAAAATGGAA-TTTTGGAAAGTTTGAGGG
1 T-AAAAATGGAATTTTTGG-AAGTTT-AGGG
* *
1118 TAAAAATGTAATTTTAGGAAAGTTT
1 TAAAAATGGAATTTTTGG-AAGTTT
1143 GGGGGTCGAA
Statistics
Matches: 220, Mismatches: 43, Indels: 46
0.71 0.14 0.15
Matches are distributed among these distances:
27 13 0.06
28 53 0.24
29 84 0.38
30 54 0.25
31 15 0.07
32 1 0.00
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (28 bp):
TAAAAATGGAATTTTTGGAAGTTTAGGG
Found at i:1065 original size:87 final size:87
Alignment explanation
Indices: 946--1148 Score: 268
Period size: 87 Copynumber: 2.3 Consensus size: 87
936 AATCGAGGTC
* * * *
946 AAAAATGGAA-TTTTAGAAAGTTCAGGGGTAAAAGTGTAATTTTTGGAAA-ATCGAGGTCAAAAA
1 AAAAATGTAATTTTTGGAAAGTTTAGGGGTAAAA-TGTAATTTTTGGAAAGATCG-GGTAAAAAA
1009 TGGAATTTTGG-AAGTTCAAGGGT
64 TGGAATTTTGGAAAGTTCAAGGGT
* * *
1032 AACAATGTAATTTTTGGAAAGTTTAGGGGTAAAATGTAATTTTTGGAAAGTTTGGGTAAAAAATG
1 AAAAATGTAATTTTTGGAAAGTTTAGGGGTAAAATGTAATTTTTGGAAAGATCGGGTAAAAAATG
**
1097 GAATTTTGGAAAGTTTGAGGGT
66 GAATTTTGGAAAGTTCAAGGGT
* *
1119 AAAAATGTAATTTTAGGAAAGTTTGGGGGT
1 AAAAATGTAATTTTTGGAAAGTTTAGGGGT
1149 CGAAGTATGA
Statistics
Matches: 102, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
86 42 0.41
87 60 0.59
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (87 bp):
AAAAATGTAATTTTTGGAAAGTTTAGGGGTAAAATGTAATTTTTGGAAAGATCGGGTAAAAAATG
GAATTTTGGAAAGTTCAAGGGT
Found at i:1066 original size:57 final size:56
Alignment explanation
Indices: 830--1092 Score: 233
Period size: 58 Copynumber: 4.6 Consensus size: 56
820 ATCGGGGTTA
* ** ** * *
830 AAAATGGAATTTTTGGATGTTCAGGGTAAAATGGTAATTTTTAAAAAAAATAAGGTT
1 AAAATGGAATTTTTGGAAGTTCAGGGTAAAAT-GTAATTTTTGGAAAATCTAGGGCT
* * * *
887 AAAAATGGAATTTTTGGAAGTTTAGGGATAAAATGGTAATTTTTGAGAAAATCGAGGTCA
1 -AAAATGGAATTTTTGGAAGTTCAGGG-TAAAAT-GTAATTTTTG-GAAAATCTAGGGCT
* * * * *
947 AAAATGGAATTTTAGAAAGTTCAGGGGTAAAAGTGTAATTTTTGGAAAATCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTCA-GGGTAAAA-TGTAATTTTTGGAAAATCTAGGGCT
* * *
1005 AAAATGGAA-TTTTGGAAGTTCAAGGGTAACAATGTAATTTTTGGAAAGTTTAGGGGT
1 AAAATGGAATTTTTGGAAGTTC-AGGGTAA-AATGTAATTTTTGGAAAATCTAGGGCT
* *
1062 AAAATGTAATTTTTGGAAAGTT-TGGGTAAAA
1 AAAATGGAATTTTTGG-AAGTTCAGGGTAAAA
1093 AATGGAATTT
Statistics
Matches: 173, Mismatches: 24, Indels: 18
0.80 0.11 0.08
Matches are distributed among these distances:
56 2 0.01
57 49 0.28
58 56 0.32
59 56 0.32
60 10 0.06
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.33
Consensus pattern (56 bp):
AAAATGGAATTTTTGGAAGTTCAGGGTAAAATGTAATTTTTGGAAAATCTAGGGCT
Found at i:4057 original size:16 final size:16
Alignment explanation
Indices: 4019--4060 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
4009 ATTTAATCAT
4019 TTAAAATTTATAAAAA
1 TTAAAATTTATAAAAA
4035 -TATAAA-TTATTAAAAA
1 TTA-AAATTTA-TAAAAA
4051 TTAAAATTTA
1 TTAAAATTTA
4061 ATTCTGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
15 5 0.23
16 12 0.55
17 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAAATTTATAAAAA
Found at i:4549 original size:28 final size:29
Alignment explanation
Indices: 4518--4581 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
4508 ATTAATAAAA
4518 ATAAAATTATAATTT-ATCTT-TAAAAATG
1 ATAAAATT-TAATTTAATCTTCTAAAAATG
*
4546 ATAAAAATTTAATTTAATCTTCTAAAAATT
1 AT-AAAATTTAATTTAATCTTCTAAAAATG
4576 ATAAAA
1 ATAAAA
4582 GATAAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 8 0.25
29 15 0.47
30 9 0.28
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (29 bp):
ATAAAATTTAATTTAATCTTCTAAAAATG
Found at i:4552 original size:29 final size:30
Alignment explanation
Indices: 4520--4581 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
4510 TAATAAAAAT
4520 AAAATTATAATTT-ATCTT-TAAAAATGATA
1 AAAATT-TAATTTAATCTTCTAAAAATGATA
*
4549 AAAATTTAATTTAATCTTCTAAAAATTATA
1 AAAATTTAATTTAATCTTCTAAAAATGATA
4579 AAA
1 AAA
4582 GATAAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 6 0.20
29 11 0.37
30 13 0.43
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (30 bp):
AAAATTTAATTTAATCTTCTAAAAATGATA
Found at i:6651 original size:26 final size:27
Alignment explanation
Indices: 6600--6651 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
6590 CCAATTTAAT
**
6600 AATTTTTATATTTTTAGATTTTTTATG
1 AATTTTTATATTTTTAGATTAATTATG
6627 AATTTTT-TATTATTTA-ATTAATTAT
1 AATTTTTATATT-TTTAGATTAATTAT
6652 TATTGATCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (27 bp):
AATTTTTATATTTTTAGATTAATTATG
Found at i:8724 original size:30 final size:30
Alignment explanation
Indices: 8690--8765 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
8680 CACGATTTGG
** *
8690 CACATGACTGTGTG-CTCAGCCTGTGTGGCT
1 CACATGACTGTGTGTC-CAGCCCATGTGACT
* *
8720 CACATGGCTGTGTGTCCATCCCATGTGACT
1 CACATGACTGTGTGTCCAGCCCATGTGACT
8750 CACATGACTGTGTGTC
1 CACATGACTGTGTGTC
8766 TAGTCCGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 38 0.97
31 1 0.03
ACGTcount: A:0.16, C:0.28, G:0.26, T:0.30
Consensus pattern (30 bp):
CACATGACTGTGTGTCCAGCCCATGTGACT
Found at i:21983 original size:30 final size:30
Alignment explanation
Indices: 21949--22005 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
21939 TGCATTTCCA
21949 TTCTGCTGCTGAATTTGAGGAGCCAAAATG
1 TTCTGCTGCTGAATTTGAGGAGCCAAAATG
*
21979 TTCTGGTGCTGAATTTGAGGAGCCAAA
1 TTCTGCTGCTGAATTTGAGGAGCCAAA
22006 GGATACAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (30 bp):
TTCTGCTGCTGAATTTGAGGAGCCAAAATG
Found at i:26650 original size:2 final size:2
Alignment explanation
Indices: 26637--26674 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
26627 TAATTCTAAA
*
26637 AG AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
26675 AACTGGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:31713 original size:42 final size:42
Alignment explanation
Indices: 31649--31730 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
31639 GCTTATTGTA
*
31649 TTTTCAATTTGTTTGTTGTTTTACGAATTGTTTTAATATTCG
1 TTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAATATTCG
* * *
31691 TTTTTAATTTGTTTGTTGTTTTAATATTTGTTTTAATATT
1 TTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAATATT
31731 TTTAAATGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.20, C:0.04, G:0.12, T:0.65
Consensus pattern (42 bp):
TTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAATATTCG
Found at i:31723 original size:12 final size:12
Alignment explanation
Indices: 31706--31731 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31696 AATTTGTTTG
31706 TTGTTTTAATAT
1 TTGTTTTAATAT
31718 TTGTTTTAATAT
1 TTGTTTTAATAT
31730 TT
1 TT
31732 TTAAATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:32119 original size:21 final size:20
Alignment explanation
Indices: 32086--32125 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
32076 TATATTATAA
32086 AAATATTAAAATTGATAAAAT
1 AAATATTAAAATT-ATAAAAT
**
32107 AAATATTTTAATTATAAAA
1 AAATATTAAAATTATAAAA
32126 ATTCGTAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATATTAAAATTATAAAAT
Found at i:48440 original size:45 final size:45
Alignment explanation
Indices: 48299--48442 Score: 108
Period size: 45 Copynumber: 3.3 Consensus size: 45
48289 TTCATGTCGG
*
48299 TGAATTCATTAAGTCCGTCTCAATAAGACCACCCAACTTGGGATA
1 TGAACTCATTAAGTCCGTCTCAATAAGACCACCCAACTTGGGATA
** *** *
48344 TGAACCTCATTAA--AAG---CAATAA-ACTCAACCTTTCATGTCGG---
1 TGAA-CTCATTAAGTCCGTCTCAATAAGAC-C-ACCCAAC-T-TGGGATA
*
48385 TGAATTCATTAAGTCCGTCTCAATAAGACCACCCAACTTGGGATA
1 TGAACTCATTAAGTCCGTCTCAATAAGACCACCCAACTTGGGATA
48430 TGAACTCATTAAG
1 TGAACTCATTAAG
48443 AGCGAGAACT
Statistics
Matches: 70, Mismatches: 15, Indels: 28
0.62 0.13 0.25
Matches are distributed among these distances:
40 9 0.13
41 11 0.16
42 8 0.11
43 2 0.03
44 8 0.11
45 23 0.33
46 9 0.13
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (45 bp):
TGAACTCATTAAGTCCGTCTCAATAAGACCACCCAACTTGGGATA
Found at i:48467 original size:86 final size:85
Alignment explanation
Indices: 48212--48459 Score: 381
Period size: 86 Copynumber: 2.9 Consensus size: 85
48202 TTAAGTTCGA
* * * * * *
48212 TGAATTCATCAAGTCTGTCACAATAGGACCACCCAAACTCTAGGATATGAATTCATTAAAAGCAA
1 TGAATTCATTAAGTCCGTCTCAATAAGACCACCC-AACT-TGGGATATGAACTCATTAAAAGCAA
48277 TAAACTCAACCTTTCATGTCGG
64 TAAACTCAACCTTTCATGTCGG
48299 TGAATTCATTAAGTCCGTCTCAATAAGACCACCCAACTTGGGATATGAACCTCATTAAAAGCAAT
1 TGAATTCATTAAGTCCGTCTCAATAAGACCACCCAACTTGGGATATGAA-CTCATTAAAAGCAAT
48364 AAACTCAACCTTTCATGTCGG
65 AAACTCAACCTTTCATGTCGG
* * *
48385 TGAATTCATTAAGTCCGTCTCAATAAGACCACCCAACTTGGGATATGAACTCATTAAGAGCGA-G
1 TGAATTCATTAAGTCCGTCTCAATAAGACCACCCAACTTGGGATATGAACTCATTAAAAGCAATA
48449 AACTCAACCTT
66 AACTCAACCTT
48460 ATGCATGTAC
Statistics
Matches: 151, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
84 11 0.07
85 22 0.15
86 88 0.58
87 30 0.20
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (85 bp):
TGAATTCATTAAGTCCGTCTCAATAAGACCACCCAACTTGGGATATGAACTCATTAAAAGCAATA
AACTCAACCTTTCATGTCGG
Found at i:51309 original size:17 final size:17
Alignment explanation
Indices: 51287--51327 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
51277 TGTGGATATA
*
51287 ATTTTTTAAATATTATT-
1 ATTTTTTAAAT-TGATTG
51304 A-TTTTTAAATTGATTG
1 ATTTTTTAAATTGATTG
51320 ATTTTTTA
1 ATTTTTTA
51328 TTTCTTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.19
16 10 0.48
17 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
ATTTTTTAAATTGATTG
Found at i:52127 original size:24 final size:25
Alignment explanation
Indices: 52095--52141 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
52085 TTTTAAAAGT
52095 AAAACTTAATTCAATTTTTAATTAC
1 AAAACTTAATTCAATTTTTAATTAC
* *
52120 AAAA-TTAATTTATTTTTTAATT
1 AAAACTTAATTCAATTTTTAATT
52142 TAATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (25 bp):
AAAACTTAATTCAATTTTTAATTAC
Found at i:84430 original size:16 final size:16
Alignment explanation
Indices: 84409--84440 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
84399 GTTTCAATTT
84409 TGATTGAAGGTAGAAC
1 TGATTGAAGGTAGAAC
*
84425 TGATTGAAGGTGGAAC
1 TGATTGAAGGTAGAAC
84441 ATTTTGGTTG
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:0.34, C:0.06, G:0.34, T:0.25
Consensus pattern (16 bp):
TGATTGAAGGTAGAAC
Found at i:89732 original size:20 final size:21
Alignment explanation
Indices: 89696--89736 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
89686 TTATATATAA
89696 TTACATGATGAATTTTTTTTT
1 TTACATGATGAATTTTTTTTT
89717 TTACAT-ATGACATTTTTTTT
1 TTACATGATGA-ATTTTTTTT
89737 ATGATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.61
Consensus pattern (21 bp):
TTACATGATGAATTTTTTTTT
Found at i:97901 original size:23 final size:24
Alignment explanation
Indices: 97848--97906 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
97838 ATATTGTTCG
**
97848 TGAACATGTTCGATTATATATTTA
1 TGAACATGTTCGATTATATATAAA
97872 TGAACATGTTCGATTA-AGT-TAAA
1 TGAACATGTTCGATTATA-TATAAA
97895 TGAACATGTTCG
1 TGAACATGTTCG
97907 TGGAAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (24 bp):
TGAACATGTTCGATTATATATAAA
Found at i:97916 original size:23 final size:23
Alignment explanation
Indices: 97848--97917 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
97838 ATATTGTTCG
* *
97848 TGAACATGTTCGATTATATATT-TA
1 TGAACATGTTCGATGA-A-ATTAAA
* *
97872 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
97895 TGAACATGTTCG-TGGAAATTAAA
1 TGAACATGTTCGAT-GAAATTAAA
97918 CAAATGAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 3 0.08
23 21 0.52
24 16 0.40
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:107786 original size:31 final size:29
Alignment explanation
Indices: 107706--107786 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 29
107696 GTGTAATTTA
*
107706 ATACATAAACTTTGGTTTAGTATAATTAT
1 ATACATAAACTTTGGTTTTGTATAATTAT
* *** *
107735 ATACATTAAACATAAATTTTGTATCATATAT
1 ATACA-TAAACTTTGGTTTTGTATAAT-TAT
107766 ATACATGAAACTTTGGTTTTG
1 ATACAT-AAACTTTGGTTTTG
107787 ATTCAATTGT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
29 5 0.13
30 16 0.41
31 18 0.46
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (29 bp):
ATACATAAACTTTGGTTTTGTATAATTAT
Found at i:107961 original size:30 final size:32
Alignment explanation
Indices: 107927--107998 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 32
107917 AAATTAAATC
107927 AAATCAAAATTTCATATAT-AAAAT-CACAAA
1 AAATCAAAATTTCATATATGAAAATACACAAA
* * **
107957 AAATCAAAA-TTCATGTATGAAATTACACATT
1 AAATCAAAATTTCATATATGAAAATACACAAA
107988 AAATCAAAATT
1 AAATCAAAATT
107999 AATGTATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 8 0.23
30 13 0.37
31 13 0.37
32 1 0.03
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (32 bp):
AAATCAAAATTTCATATATGAAAATACACAAA
Found at i:107979 original size:29 final size:31
Alignment explanation
Indices: 107927--108007 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
107917 AAATTAAATC
*
107927 AAATCAAAATTTCATATATAAAA-T-CACAAA
1 AAATCAAAA-TTCATGTATAAAATTACACAAA
* **
107957 AAATCAAAATTCATGTATGAAATTACACATT
1 AAATCAAAATTCATGTATAAAATTACACAAA
*
107988 AAATCAAAATTAATGTATAA
1 AAATCAAAATTCATGTATAA
108008 TTTTAATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 11 0.26
30 10 0.23
31 22 0.51
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.30
Consensus pattern (31 bp):
AAATCAAAATTCATGTATAAAATTACACAAA
Found at i:124062 original size:28 final size:30
Alignment explanation
Indices: 124028--124088 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
124018 ATTGTAATGA
124028 TTTTAAAAATACTT-TAAA-ATA-TTAATTT
1 TTTTAAAAAT-CTTATAAATATATTTAATTT
* *
124056 TTTTAAATATTTTATAAATATATTTAATTT
1 TTTTAAAAATCTTATAAATATATTTAATTT
124086 TTT
1 TTT
124089 GGACGATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.07
28 13 0.46
29 3 0.11
30 10 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTTAAAAATCTTATAAATATATTTAATTT
Found at i:133811 original size:2 final size:2
Alignment explanation
Indices: 133804--133833 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
133794 GAAGGGCACT
133804 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
133834 TCAAACTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:139429 original size:20 final size:20
Alignment explanation
Indices: 139406--139447 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
139396 TTATCTAAGT
139406 AATAAATTATATATCATTAA
1 AATAAATTATATATCATTAA
*
139426 AATAAATTATATCTCATTAA
1 AATAAATTATATATCATTAA
139446 AA
1 AA
139448 ATATTCCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAAATTATATATCATTAA
Done.