Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001453.1 Hibiscus syriacus cultivar Beakdansim tig00002806_pilon, 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: 93750
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Found at i:951 original size:30 final size:30
Alignment explanation
Indices: 917--1069 Score: 135
Period size: 30 Copynumber: 5.0 Consensus size: 30
907 TAGCCTTTTC
* *
917 ACTTTCTATTTTTGTTATTTCAGTTCTTTA
1 ACTTTCTATTTTTGTTATTTTAGTCCTTTA
*
947 ACTTTCTATTTTTTTTTCTATTTTAGTCCTTTA
1 ACTTTCTA--TTTTTGT-TATTTTAGTCCTTTA
* ** *
980 ACTTTTTATTTTTACTATTTTAATCCTTTA
1 ACTTTCTATTTTTGTTATTTTAGTCCTTTA
* * * * *
1010 AGTTTCTGTTTTGGTTATTTTAGTCATATA
1 ACTTTCTATTTTTGTTATTTTAGTCCTTTA
* * *
1040 AATTTCTATTTTTGCTATTTAGAGTCCTTT
1 ACTTTCTATTTTTGTTATTT-TAGTCCTTT
1070 TTACTAAGCA
Statistics
Matches: 96, Mismatches: 23, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
30 59 0.61
31 11 0.11
32 6 0.06
33 20 0.21
ACGTcount: A:0.19, C:0.12, G:0.07, T:0.61
Consensus pattern (30 bp):
ACTTTCTATTTTTGTTATTTTAGTCCTTTA
Found at i:969 original size:33 final size:32
Alignment explanation
Indices: 917--992 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 32
907 TAGCCTTTTC
*
917 ACTTTCTA--TTTTTGTTATTTCAGTTCTTTA
1 ACTTTCTATTTTTTTGTTATTTCAGTCCTTTA
* *
947 ACTTTCTATTTTTTTTTCTATTTTAGTCCTTTA
1 ACTTTCTATTTTTTTGT-TATTTCAGTCCTTTA
*
980 ACTTTTTATTTTT
1 ACTTTCTATTTTT
993 ACTATTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 8 0.21
32 6 0.15
33 25 0.64
ACGTcount: A:0.16, C:0.13, G:0.04, T:0.67
Consensus pattern (32 bp):
ACTTTCTATTTTTTTGTTATTTCAGTCCTTTA
Found at i:4419 original size:64 final size:63
Alignment explanation
Indices: 4334--4490 Score: 154
Period size: 64 Copynumber: 2.5 Consensus size: 63
4324 TTCAGTGTGA
* * * ** * *
4334 ATCGATGCACAGGAAATGCATCGATGCACCCATTAAAAATGGGAACATCGAATGTAATTAGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCACCCATT-AAAATGAAAACATCAAAGGTAATTAGTGC
* * * * * *
4398 ATCGATGCATAAGG-AGTGCATCGGTGCACCCCCTTAAAATGAAAACATTAAAGGTGATTTGTGT
1 ATCGATGCAT-AGGTAGTGCATCGATGCA-CCCATTAAAATGAAAACATCAAAGGTAATTAGTGC
*
4462 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGTAGTGCATCGATGCAC
4491 TTCAAGGGAA
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
63 3 0.04
64 65 0.86
65 8 0.11
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (63 bp):
ATCGATGCATAGGTAGTGCATCGATGCACCCATTAAAATGAAAACATCAAAGGTAATTAGTGC
Found at i:4921 original size:20 final size:21
Alignment explanation
Indices: 4896--4946 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
4886 ATATAAACTA
*
4896 TATATGATATGATAAGA-AA-T
1 TATATGATAT-AAAAGAGAAGT
4916 TATATGAATATAAAAGAGAAGT
1 TATATG-ATATAAAAGAGAAGT
4938 TATATGATA
1 TATATGATA
4947 AGACATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.41
21 9 0.33
22 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (21 bp):
TATATGATATAAAAGAGAAGT
Found at i:5382 original size:24 final size:24
Alignment explanation
Indices: 5334--5395 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
5324 TAACTTTATA
*
5334 TGGCACTTCGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
*
5357 TGGCACTACGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
5381 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
5396 TTTATACAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 13 0.37
24 22 0.63
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCTACG
Found at i:8881 original size:45 final size:45
Alignment explanation
Indices: 8830--8933 Score: 208
Period size: 45 Copynumber: 2.3 Consensus size: 45
8820 ATGCACAGGA
8830 AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
1 AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
8875 AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
1 AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
8920 AGTGCATCGATGCA
1 AGTGCATCGATGCA
8934 TAAGGAGTGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.22
Consensus pattern (45 bp):
AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
Found at i:8943 original size:64 final size:63
Alignment explanation
Indices: 8874--9017 Score: 173
Period size: 64 Copynumber: 2.3 Consensus size: 63
8864 CGAATGCAAT
* * *
8874 TAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATTAGTGCATCGATGCATAAGG
1 TAGTGCATCGATGCACCCATT-AAAATGAAAACATCAAAGGCAATTAGTGCATCGATGCAT-AGG
* ** * * *
8939 -AGTGCATCGATGCACCCCCTTAAAATGAAAACATCAAAGGTGATTTGTGTATCGATGCATGGG
1 TAGTGCATCGATGCA-CCCATTAAAATGAAAACATCAAAGGCAATTAGTGCATCGATGCATAGG
9002 TAGTGCATCGATGCAC
1 TAGTGCATCGATGCAC
9018 TTCAAGGGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
63 3 0.04
64 60 0.88
65 5 0.07
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24
Consensus pattern (63 bp):
TAGTGCATCGATGCACCCATTAAAATGAAAACATCAAAGGCAATTAGTGCATCGATGCATAGG
Found at i:12603 original size:20 final size:20
Alignment explanation
Indices: 12578--12743 Score: 74
Period size: 21 Copynumber: 8.4 Consensus size: 20
12568 GACCAACAAA
12578 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
12598 TTCGCAAC-AG-TTTCCAAT
1 TTCGCAACGCGAATTCCAAT
**
12616 TTCGCAACGCGAATATGTAA-
1 TTCGCAACGCGAAT-TCCAAT
* ** * *
12636 ATCGCATTGCGATTTTCCAAA
1 TTCGCAACGCGA-ATTCCAAT
*** * *
12657 TTCGCGTTGCGATTTTCCAAA
1 TTCGCAACGCGA-ATTCCAAT
* *
12678 TTCGCAACGCGATAGTCAAAT
1 TTCGCAACGCGA-ATTCCAAT
* * *
12699 TT-GCAAC-TGAATTTCAAA
1 TTCGCAACGCGAATTCCAAT
*
12717 TTCGCAACGCGAATT-TAAT
1 TTCGCAACGCGAATTCCAAT
12736 TTCGCAAC
1 TTCGCAAC
12744 AGGTTTTAGT
Statistics
Matches: 110, Mismatches: 29, Indels: 15
0.71 0.19 0.10
Matches are distributed among these distances:
18 21 0.19
19 19 0.17
20 31 0.28
21 39 0.35
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:12666 original size:21 final size:21
Alignment explanation
Indices: 12637--12683 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
12627 AATATGTAAA
12637 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
12658 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
12679 TCGCA
1 TCGCA
12684 ACGCGATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:12689 original size:21 final size:21
Alignment explanation
Indices: 12574--12728 Score: 92
Period size: 20 Copynumber: 7.8 Consensus size: 21
12564 AAATGACCAA
*
12574 CAAATTCGCAACGCGA-ATTC
1 CAAATTCGCAACGCGATTTTC
* *
12594 CAATTTCGCAA--C-AGTTTC
1 CAAATTCGCAACGCGATTTTC
* * * *
12612 CAATTTCGCAACGCGAATATG
1 CAAATTCGCAACGCGATTTTC
* **
12633 TAAA-TCGCATTGCGATTTTC
1 CAAATTCGCAACGCGATTTTC
***
12653 CAAATTCGCGTTGCGATTTTC
1 CAAATTCGCAACGCGATTTTC
**
12674 CAAATTCGCAACGCGATAGT-
1 CAAATTCGCAACGCGATTTTC
* * *
12694 CAAATTTGCAAC-TGAATTT-
1 CAAATTCGCAACGCGATTTTC
12713 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
12729 ATTTAATTTC
Statistics
Matches: 103, Mismatches: 26, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
17 1 0.01
18 15 0.15
19 14 0.14
20 38 0.37
21 35 0.34
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (21 bp):
CAAATTCGCAACGCGATTTTC
Found at i:13668 original size:24 final size:24
Alignment explanation
Indices: 13636--13689 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
13626 GTATTCAAAA
*
13636 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
13660 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
13684 TTTGAT
1 TTTGAT
13690 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:16278 original size:20 final size:20
Alignment explanation
Indices: 16249--16337 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 20
16239 TGTTGCGATA
*
16249 AACGCGAAAGTCAAATTTGC
1 AACGCGAAAGTCAAATTCGC
* *
16269 AACGCAAAAGTCAAATTCAC
1 AACGCGAAAGTCAAATTCGC
* * *
16289 AATGTGAAAGACAAATTCGC
1 AACGCGAAAGTCAAATTCGC
*
16309 AACGCGATAGTCAAATTCGC
1 AACGCGAAAGTCAAATTCGC
16329 AACGCGAAA
1 AACGCGAAA
16338 TCGCAAACTG
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (20 bp):
AACGCGAAAGTCAAATTCGC
Found at i:16402 original size:20 final size:20
Alignment explanation
Indices: 16348--16486 Score: 78
Period size: 20 Copynumber: 7.2 Consensus size: 20
16338 TCGCAAACTG
** *
16348 AATTTGACTTTCATGTTGCG
1 AATTTGACTTTCGCGTTGCA
** *
16368 AATTTGACTACCGCGTAGCA
1 AATTTGACTTTCGCGTTGCA
**
16388 AATTTGACTTTCGCGTTGTG
1 AATTTGACTTTCGCGTTGCA
* ***
16408 AATTTGACTATCGCAACGC-
1 AATTTGACTTTCGCGTTGCA
16427 ---TT-A-TTTCGCGTTGCA
1 AATTTGACTTTCGCGTTGCA
*
16442 AATTT-ACCTTTCGCGTTGCG
1 AATTTGA-CTTTCGCGTTGCA
*
16462 AATTT-ACCTTTCGCGTAGCA
1 AATTTGA-CTTTCGCGTTGCA
16482 AATTT
1 AATTT
16487 ACCTTCAACA
Statistics
Matches: 90, Mismatches: 23, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
14 7 0.08
15 1 0.01
16 2 0.02
18 3 0.03
20 77 0.86
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTGCA
Found at i:16487 original size:20 final size:20
Alignment explanation
Indices: 16430--16491 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
16420 GCAACGCTTA
16430 TTTCGCGTTGCAAATTTACC
1 TTTCGCGTTGCAAATTTACC
*
16450 TTTCGCGTTGCGAATTTACC
1 TTTCGCGTTGCAAATTTACC
*
16470 TTTCGCGTAGCAAATTTACC
1 TTTCGCGTTGCAAATTTACC
16490 TT
1 TT
16492 CAACAGGTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCAAATTTACC
Found at i:17024 original size:23 final size:24
Alignment explanation
Indices: 16974--17025 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
16964 TTTCATATGT
* * *
16974 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
16998 AATTTGAG-TTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
17021 AATTT
1 AATTT
17026 CGGCTCCACT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:17363 original size:39 final size:39
Alignment explanation
Indices: 17320--17408 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
17310 TCCGATGCTC
17320 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
* * *
17359 ATCAAAATCCAAATCTCATATTGTGCCAAGCAAAAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
17398 ATCAAAATCTA
1 ATCAAAATCTA
17409 CAACTTGAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.20
Consensus pattern (39 bp):
ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:17751 original size:14 final size:14
Alignment explanation
Indices: 17714--17803 Score: 74
Period size: 14 Copynumber: 6.4 Consensus size: 14
17704 TTTTAGAAAC
* *
17714 AACAAATCAACTTT
1 AACAAATCAAATTA
*
17728 TACAACATCAAATTA
1 AACAA-ATCAAATTA
17743 AACAAATCAAATTA
1 AACAAATCAAATTA
* *
17757 AACAAATCAACTTT
1 AACAAATCAAATTA
* * *
17771 TACAAATCAATTTT
1 AACAAATCAAATTA
*
17785 TACAAATC-AATTA
1 AACAAATCAAATTA
*
17798 ATCAAA
1 AACAAA
17804 AAATAAATCT
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
13 7 0.11
14 45 0.71
15 11 0.17
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (14 bp):
AACAAATCAAATTA
Found at i:17761 original size:43 final size:41
Alignment explanation
Indices: 17714--17803 Score: 126
Period size: 43 Copynumber: 2.1 Consensus size: 41
17704 TTTTAGAAAC
17714 AACAAATCAACTTTTACAACATCAAATTAAACAAATCAAATTA
1 AACAAATCAACTTTTACAA-ATCAAATTAAACAAATC-AATTA
* **
17757 AACAAATCAACTTTTACAAATCAATTTTTACAAATCAATTA
1 AACAAATCAACTTTTACAAATCAAATTAAACAAATCAATTA
*
17798 ATCAAA
1 AACAAA
17804 AAATAAATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 10 0.23
42 14 0.33
43 19 0.44
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (41 bp):
AACAAATCAACTTTTACAAATCAAATTAAACAAATCAATTA
Found at i:21532 original size:14 final size:14
Alignment explanation
Indices: 21513--21557 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
21503 TAGTTTCGCA
21513 TTGCGAATTTGGTG
1 TTGCGAATTTGGTG
* * *
21527 TTGCGATTTTTGCG
1 TTGCGAATTTGGTG
21541 TTGCGAATTTGGTG
1 TTGCGAATTTGGTG
21555 TTG
1 TTG
21558 TGATTTAGGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.11, C:0.09, G:0.33, T:0.47
Consensus pattern (14 bp):
TTGCGAATTTGGTG
Found at i:21832 original size:22 final size:22
Alignment explanation
Indices: 21807--21849 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21797 GAGATAGATG
21807 AATTTCGTCGGAAATAGGGACA
1 AATTTCGTCGGAAATAGGGACA
* *
21829 AATTTCGTCGGAGATGGGGAC
1 AATTTCGTCGGAAATAGGGAC
21850 GGATGTCGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (22 bp):
AATTTCGTCGGAAATAGGGACA
Found at i:21994 original size:20 final size:20
Alignment explanation
Indices: 21969--22144 Score: 123
Period size: 20 Copynumber: 8.8 Consensus size: 20
21959 ATATTATGTT
21969 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
21989 TCGCGTTGCGAATTTGACTTA
1 TCGCGTTGCGAATTTGAC-TA
* *
22010 T-GTGTTGC-AATTT-ACAAA
1 TCGCGTTGCGAATTTGAC-TA
*
22028 TTCGCGTTGCGAATTTGACTT
1 -TCGCGTTGCGAATTTGACTA
* **
22049 TCGCGTTACGAATTTAGAAAA
1 TCGCGTTGCGAATTT-GACTA
* *
22070 TCACGTTGCGAAATTGGA--A
1 TCGCGTTGCG-AATTTGACTA
* * *
22089 TCTGAGTTGCGAAATTGGAAT-
1 TC-GCGTTGCG-AATTTGACTA
* *
22110 TCACGTTGCGAATTTGA-GA
1 TCGCGTTGCGAATTTGACTA
22129 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
22145 TTGGTCATTT
Statistics
Matches: 125, Mismatches: 20, Indels: 23
0.74 0.12 0.14
Matches are distributed among these distances:
18 3 0.02
19 30 0.24
20 64 0.51
21 22 0.18
22 6 0.05
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:23934 original size:21 final size:21
Alignment explanation
Indices: 23908--23952 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23898 GATTTCTGGG
* *
23908 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
23929 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
23950 CAA
1 CAA
23953 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:24556 original size:18 final size:18
Alignment explanation
Indices: 24533--24567 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24523 ATAGGAGATT
24533 TGAACATA-AAGGATAAGA
1 TGAACATATAA-GATAAGA
24551 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
24568 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:24652 original size:21 final size:22
Alignment explanation
Indices: 24623--24666 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
24613 GTTGTATGAT
24623 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
24644 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
24666 A
1 A
24667 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:24897 original size:2 final size:2
Alignment explanation
Indices: 24890--24928 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
24880 GAACATGTGA
24890 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24929 AGAGAAGGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25633 original size:149 final size:149
Alignment explanation
Indices: 25455--25758 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
25445 GAGTCGAGGG
*
25455 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAATTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
25520 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
25585 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
25604 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
25669 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
25734 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
25753 TCTACG
1 TCTACG
25759 GGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:25781 original size:23 final size:23
Alignment explanation
Indices: 25737--25781 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
25727 ATCATTATAT
*
25737 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
25760 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
25782 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:27405 original size:20 final size:20
Alignment explanation
Indices: 27377--27568 Score: 240
Period size: 20 Copynumber: 9.4 Consensus size: 20
27367 TTTTCCTAAT
27377 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
27397 TCACAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* ** *
27418 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* ** *
27439 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
27460 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
27480 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
27500 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
27520 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
27540 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
27560 TCGCAATGC
1 TCGCAATGC
27569 AAATCTGACT
Statistics
Matches: 159, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
20 104 0.65
21 55 0.35
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:27797 original size:22 final size:22
Alignment explanation
Indices: 27772--27826 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
27762 GCGACATCCA
27772 TCCCCATCTCCAACGAAATCAG
1 TCCCCATCTCCAACGAAATCAG
* *
27794 TCCCCATCGT-CGACGATATCAG
1 TCCCCATC-TCCAACGAAATCAG
*
27816 TCTCCATCTCC
1 TCCCCATCTCC
27827 GGCAAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.24, C:0.42, G:0.11, T:0.24
Consensus pattern (22 bp):
TCCCCATCTCCAACGAAATCAG
Found at i:28262 original size:20 final size:20
Alignment explanation
Indices: 28209--28263 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
28199 GATAGTCTAA
* **
28209 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
*
28229 TTCATGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
28249 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
28264 AAAGTTTCAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:28271 original size:20 final size:20
Alignment explanation
Indices: 28228--28272 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28218 CGATAGTCAT
** *
28228 TTTCATGTTGCGATTTTCAT
1 TTTCATGTTGCGATTTAAAG
*
28248 TTTCGTGTTGCGATTTAAAG
1 TTTCATGTTGCGATTTAAAG
28268 TTTCA
1 TTTCA
28273 GAAACTATTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTCATGTTGCGATTTAAAG
Found at i:30173 original size:20 final size:20
Alignment explanation
Indices: 30148--30310 Score: 129
Period size: 20 Copynumber: 8.8 Consensus size: 20
30138 AGAATAGTTT
30148 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
30168 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
30188 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
30204 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
** *
30221 AAAATCACAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
30237 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
30255 ACAATCGCAATGAGAAAATG
1 ACTATCGCAATGCGAAAATG
**
30275 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
*
30295 ACTATCACAATGCGAA
1 ACTATCGCAATGCGAA
30311 TTTAGGGATT
Statistics
Matches: 118, Mismatches: 11, Indels: 28
0.75 0.07 0.18
Matches are distributed among these distances:
14 13 0.11
16 10 0.08
17 8 0.07
18 5 0.04
19 6 0.05
20 76 0.64
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:30472 original size:20 final size:20
Alignment explanation
Indices: 30430--30476 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
30420 AAATTCAGTA
**
30430 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGAG
*
30450 TTGCGATAGTCAGATTCGAG
1 TTGCGATAGTCAGAATCGAG
30470 TTGCGAT
1 TTGCGAT
30477 TTACGTATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGAG
Found at i:30486 original size:20 final size:19
Alignment explanation
Indices: 30463--30576 Score: 111
Period size: 20 Copynumber: 5.6 Consensus size: 19
30453 CGATAGTCAG
30463 ATTCGAGTTGCGATTTACGT
1 ATTCGA-TTGCGATTTACGT
30483 ATTCGCATTGCGATTTACGT
1 ATTCG-ATTGCGATTTACGT
30503 ATTCGCATTGCGATTTACGT
1 ATTCG-ATTGCGATTTACGT
* * * **
30523 AATCACATTGCGATTTTCCAA
1 ATTC-GATTGCGA-TTTACGT
*
30544 ATTCGCGTTGCGATTTACGT
1 ATTCG-ATTGCGATTTACGT
30564 ATTCGCATTGCGA
1 ATTCG-ATTGCGA
30577 ATTAGGAAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
20 64 0.82
21 14 0.18
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (19 bp):
ATTCGATTGCGATTTACGT
Found at i:30494 original size:40 final size:38
Alignment explanation
Indices: 30450--30576 Score: 130
Period size: 40 Copynumber: 3.2 Consensus size: 38
30440 CAGAATCTCG
30450 TTGCGATAGTCAGATTCGAGTTGCGATTTACGTATTCGCA
1 TTGCGAT--TCAGATTCGAGTTGCGATTTACGTATTCGCA
* * *
30490 TTGCGATTTACGTATTCGCA-TTGCGATTTACGTAATCACA
1 TTGCGATTCA-G-ATTCG-AGTTGCGATTTACGTATTCGCA
* *
30530 TTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGA--TT-CAGATTCGAGTTGCGATTTACGTATTCGCA
30571 TTGCGA
1 TTGCGA
30577 ATTAGGAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 36 0.50
41 30 0.42
42 2 0.03
43 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (38 bp):
TTGCGATTCAGATTCGAGTTGCGATTTACGTATTCGCA
Found at i:31179 original size:2 final size:2
Alignment explanation
Indices: 31172--31225 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
31162 GAAAATTTTA
31172 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31214 AT AT AT AT AT AT
1 AT AT AT AT AT AT
31226 TAATTAGTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32525 original size:30 final size:30
Alignment explanation
Indices: 32491--32617 Score: 88
Period size: 30 Copynumber: 4.4 Consensus size: 30
32481 TTAATTTTGA
32491 ACCCTAAACTTTAAATAAAATATCATATTG
1 ACCCTAAACTTTAAATAAAATATCATATTG
* *
32521 ACCCT-AACGTTTATATTAAATATCA-ACTTG
1 ACCCTAAAC-TTTAAATAAAATATCATA-TTG
* * * * * * *
32551 A-CAT-GAGTTT--A-CAAATTTAATTTTG
1 ACCCTAAACTTTAAATAAAATATCATATTG
*
32576 ACCCTTAAACTTTAAATAAAATATCATATTA
1 ACCC-TAAACTTTAAATAAAATATCATATTG
32607 ACCCTAAACTT
1 ACCCTAAACTT
32618 ATCGATTTAT
Statistics
Matches: 71, Mismatches: 17, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
25 10 0.14
26 2 0.03
27 1 0.01
28 7 0.10
29 7 0.10
30 31 0.44
31 13 0.18
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (30 bp):
ACCCTAAACTTTAAATAAAATATCATATTG
Found at i:37873 original size:43 final size:44
Alignment explanation
Indices: 37798--37882 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 44
37788 CGTTTACCGT
37798 TGATAGTTCATTTCTTCTAAGCTTGAATGGATAATTATGATTGC
1 TGATAGTTCATTTCTTCTAAGCTTGAATGGATAATTATGATTGC
* * *
37842 TGATGGTTTATTTCTTCTAA-TTTGAATGGATAATTATGATT
1 TGATAGTTCATTTCTTCTAAGCTTGAATGGATAATTATGATT
37883 AATGAAGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 20 0.53
44 18 0.47
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (44 bp):
TGATAGTTCATTTCTTCTAAGCTTGAATGGATAATTATGATTGC
Found at i:45779 original size:35 final size:35
Alignment explanation
Indices: 45740--45814 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
45730 TGTTAAAAAA
*
45740 ATTAGTGATTGTTTGAACTAGAAGTTAACCTATTG
1 ATTAGTAATTGTTTGAACTAGAAGTTAACCTATTG
** *
45775 ATTAGTAATTGTTTGAGTTAGATGTTAACCTATTG
1 ATTAGTAATTGTTTGAACTAGAAGTTAACCTATTG
45810 ATTAG
1 ATTAG
45815 GATATGACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.43
Consensus pattern (35 bp):
ATTAGTAATTGTTTGAACTAGAAGTTAACCTATTG
Found at i:46373 original size:14 final size:15
Alignment explanation
Indices: 46354--46382 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
46344 GTTAATAATT
46354 AATATTTT-TTAAAA
1 AATATTTTATTAAAA
46368 AATATTTTATTAAAA
1 AATATTTTATTAAAA
46383 TGACAGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATTTTATTAAAA
Found at i:50989 original size:2 final size:2
Alignment explanation
Indices: 50982--51016 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
50972 GACCAATAGT
50982 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51017 TAATATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51022 original size:10 final size:11
Alignment explanation
Indices: 50981--51038 Score: 68
Period size: 12 Copynumber: 5.4 Consensus size: 11
50971 TGACCAATAG
50981 TTATATATATA
1 TTATATATATA
50992 TATATATATATA
1 T-TATATATATA
51004 TATATATATATA
1 T-TATATATATA
*
51016 TTA-ATATAAA
1 TTATATATATA
51026 TTAT-TA-ATA
1 TTATATATATA
51035 TTAT
1 TTAT
51039 TTTTCTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
9 6 0.14
10 11 0.26
11 3 0.07
12 23 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTATATATATA
Found at i:53246 original size:13 final size:14
Alignment explanation
Indices: 53228--53257 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
53218 AGTTGGACAA
53228 TCTTCATATGCA-G
1 TCTTCATATGCACG
53241 TCTTCATATGCACG
1 TCTTCATATGCACG
53255 TCT
1 TCT
53258 ATAATGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (14 bp):
TCTTCATATGCACG
Found at i:56320 original size:2 final size:2
Alignment explanation
Indices: 56303--56373 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
56293 TGTTTTGTAT
56303 TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56343 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56374 TTGTATTGTC
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 65 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56330 original size:127 final size:125
Alignment explanation
Indices: 56068--56328 Score: 370
Period size: 127 Copynumber: 2.1 Consensus size: 125
56058 TTTATTAGAC
* *
56068 ATATATATAACCTATCCCTTATAAATAGTCACTCCCATTAAATATGTATATATTATGTATGTACA
1 ATATATATAACCTATCCCTCATAAATAGTCACTCCCATTAAATATGTATATATTATGTACGTACA
* *
56133 GTATACTTTTTTTTTCAATTCGTTACATGTTAAATCATGTTTTGTATTATATATATATATAT
66 G-ATAC-TATTTTTTCAATTCGTTACATGTTAAAGCATGTTTTGTATTATATATATATATAT
* *
56195 ATATATATAACTTATCCCTCATAAATAGTCACTTCCATTAAATATGTATATATTATGTACGTACA
1 ATATATATAACCTATCCCTCATAAATAGTCACTCCCATTAAATATGTATATATTATGTACGTACA
56260 -ATA-TATTTTTT-AACTT-GTTACATATGTT-AAGCATGTTTTGTATTATATTATATTATATAT
66 GATACTATTTTTTCAA-TTCGTTAC--ATGTTAAAGCATGTTTTGTATTATA-TATA-TATATAT
56320 ATATATATA
1 ATATATATA
56329 TATATATATA
Statistics
Matches: 123, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
122 7 0.06
123 27 0.22
124 9 0.07
125 19 0.15
127 61 0.50
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (125 bp):
ATATATATAACCTATCCCTCATAAATAGTCACTCCCATTAAATATGTATATATTATGTACGTACA
GATACTATTTTTTCAATTCGTTACATGTTAAAGCATGTTTTGTATTATATATATATATAT
Found at i:68706 original size:48 final size:48
Alignment explanation
Indices: 68633--68729 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
68623 CATCGCGTAG
*
68633 GAACCGAGTTATCATCCTTCTTAAAGATGACCAAGAACTCTTCATCAC
1 GAACCGAGTTATCATCCTTCCTAAAGATGACCAAGAACTCTTCATCAC
*
68681 GAACCGAGTTATCATCTTTCCTAAAGATGACCAAGAACTCTTCATCAC
1 GAACCGAGTTATCATCCTTCCTAAAGATGACCAAGAACTCTTCATCAC
68729 G
1 G
68730 TATGAGCAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (48 bp):
GAACCGAGTTATCATCCTTCCTAAAGATGACCAAGAACTCTTCATCAC
Found at i:70221 original size:14 final size:13
Alignment explanation
Indices: 70182--70238 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
70172 TATTAATAAG
70182 TATTTATAATTAA
1 TATTTATAATTAA
**
70195 TAATAAAATAATTAGA
1 T-AT-TTATAATTA-A
70211 TATTTATAATTAA
1 TATTTATAATTAA
*
70224 TATTAAT-ATTAA
1 TATTTATAATTAA
70236 TAT
1 TAT
70239 AAAATATAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
12 8 0.22
13 8 0.22
14 9 0.25
15 9 0.25
16 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
TATTTATAATTAA
Found at i:70236 original size:12 final size:13
Alignment explanation
Indices: 70164--70238 Score: 59
Period size: 13 Copynumber: 5.8 Consensus size: 13
70154 ACCGCCTTAT
*
70164 ATAATTTATATTA
1 ATAATTAATATTA
*
70177 ATAAGT-AT-TT-
1 ATAATTAATATTA
*
70187 ATAATTAATAATAAA
1 ATAATTAAT-AT-TA
*
70202 ATAATTAGATATTT
1 ATAATTA-ATATTA
70216 ATAATTAATATTA
1 ATAATTAATATTA
70229 AT-ATTAATAT
1 ATAATTAATAT
70239 AAAATATAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
10 5 0.10
11 4 0.08
12 10 0.20
13 13 0.26
14 7 0.14
15 9 0.18
16 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
ATAATTAATATTA
Found at i:70244 original size:19 final size:20
Alignment explanation
Indices: 70190--70245 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 20
70180 AGTATTTATA
70190 ATTAATAATAAAATAATTAGAT
1 ATTAAT-ATAAAAT-ATTAGAT
70212 ATT--TATAATTAATATTA-AT
1 ATTAATATAA--AATATTAGAT
70231 ATTAATATAAAATAT
1 ATTAATATAAAATAT
70246 AGTCTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
19 14 0.47
20 5 0.17
21 8 0.27
22 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTAATATAAAATATTAGAT
Found at i:70342 original size:29 final size:31
Alignment explanation
Indices: 70225--70408 Score: 126
Period size: 31 Copynumber: 5.7 Consensus size: 31
70215 TATAATTAAT
* *
70225 ATTAATATTAATATAAAATATAGTCT-ATAAA
1 ATTAATATTAATATAAATTATAGT-TAATATA
* *
70256 ATTAATATTGATATAAACTATATGTT-ATA-A
1 ATTAATATTAATATAAATTATA-GTTAATATA
*
70286 ATTATATAGTATAGTTTATAAATTATAGTTAATATA
1 ATTA-ATA-T-TA--ATATAAATTATAGTTAATATA
* * *
70322 ATTAATATTAATA-CAA-TATAGTTTATAAA
1 ATTAATATTAATATAAATTATAGTTAATATA
*
70351 CTATATACTATATTAATATAAATTATAGTTAAGATA
1 --AT-TA--ATATTAATATAAATTATAGTTAATATA
* *
70387 ATTAACATTAATATAAACTATA
1 ATTAATATTAATATAAATTATA
70409 TAGAACATTA
Statistics
Matches: 123, Mismatches: 15, Indels: 30
0.73 0.09 0.18
Matches are distributed among these distances:
29 11 0.09
30 7 0.06
31 47 0.38
32 5 0.04
33 5 0.04
34 15 0.12
35 18 0.15
36 15 0.12
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTAATATTAATATAAATTATAGTTAATATA
Found at i:70380 original size:65 final size:65
Alignment explanation
Indices: 70229--70409 Score: 201
Period size: 65 Copynumber: 2.7 Consensus size: 65
70219 ATTAATATTA
* * *
70229 ATATTAATATAAAATATAGTCT-ATAAAATTAATATTGATATAAACTATATGTTATAAATTATAT
1 ATATTAATATAAATTATAGT-TAATATAATTAATATT-A-ATAAACTATATGTTATAAACTATAT
*
70293 AGT
63 ACT
70296 ATAGTT--TATAAATTATAGTTAATATAATTAATATTAATACAA-TATA-GTTTATAAACTATAT
1 ATA-TTAATATAAATTATAGTTAATATAATTAATATTAATA-AACTATATG-TTATAAACTATAT
70357 ACT
63 ACT
* *
70360 ATATTAATATAAATTATAGTTAAGATAATTAACATTAATATAAACTATAT
1 ATATTAATATAAATTATAGTTAATATAATTAATATT-A-ATAAACTATAT
70410 AGAACATTAA
Statistics
Matches: 98, Mismatches: 6, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
63 3 0.03
64 24 0.24
65 31 0.32
66 28 0.29
67 10 0.10
68 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (65 bp):
ATATTAATATAAATTATAGTTAATATAATTAATATTAATAAACTATATGTTATAAACTATATACT
Found at i:70449 original size:21 final size:21
Alignment explanation
Indices: 70420--70472 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
70410 AGAACATTAA
* *
70420 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
70441 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
70462 TATAAACTATA
1 TATAAACTATA
70473 TAGTACACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:70544 original size:2 final size:2
Alignment explanation
Indices: 70534--70653 Score: 95
Period size: 2 Copynumber: 59.0 Consensus size: 2
70524 TTATATAGCT
* * * *
70534 TA TA AA TA TA T- TG TA TA TA TA CA TA TA CTA TA TG T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
70575 TA TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TA CTA TA GA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA -TA
70620 TA TA TA TA TA TA TA TA CTA TA -A GT- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
70654 GTTTACATGT
Statistics
Matches: 96, Mismatches: 12, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
1 4 0.04
2 84 0.88
3 8 0.08
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:70580 original size:37 final size:37
Alignment explanation
Indices: 70534--70682 Score: 133
Period size: 37 Copynumber: 4.0 Consensus size: 37
70524 TTATATAGCT
* *
70534 TATAAATATATTGTATATATACATATACTATATGTTA
1 TATATATATATTATATATATACATATACTATATGTTA
* * * *
70571 TATATATATA-TATATATATATATATAGTTTAT-ATA
1 TATATATATATTATATATATACATATACTATATGTTA
* * *
70606 TACTATAGATAGTTTATATATATATATATACTATAAGTTA
1 TA-TATATATA--TTATATATATACATATACTATATGTTA
* * *
70646 TATATATAGT-TTACATGTATACATATACTATAGGTTA
1 TATATATA-TATTATATATATACATATACTATATGTTA
70683 CACATATTAA
Statistics
Matches: 90, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
35 4 0.04
36 25 0.28
37 32 0.36
39 24 0.27
40 5 0.06
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (37 bp):
TATATATATATTATATATATACATATACTATATGTTA
Found at i:70604 original size:51 final size:49
Alignment explanation
Indices: 70534--70640 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 49
70524 TTATATAGCT
* * *
70534 TATAAATATATTGTATATATACA-TATACTATATGTTATATATATATATATA
1 TATATATATATAGTATATATACACTATA-GATA-GTT-TATATATATATATA
* *
70585 TATATATATATAGTTTATATATACTATAGATAGTTTATATATATATATA
1 TATATATATATAGTATATATACACTATAGATAGTTTATATATATATATA
70634 TACTATA
1 TA-TATA
70641 AGTTATATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
49 16 0.33
50 7 0.14
51 22 0.45
52 4 0.08
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.48
Consensus pattern (49 bp):
TATATATATATAGTATATATACACTATAGATAGTTTATATATATATATA
Found at i:70628 original size:75 final size:75
Alignment explanation
Indices: 70515--70653 Score: 201
Period size: 75 Copynumber: 1.9 Consensus size: 75
70505 TATAGGTTAC
* * *
70515 ATATATAGTTTATATAGCTTATAAATATATTGTATATATACATATACTATATGTTATATATATAT
1 ATATATAGTTTATATAACTTATAAATATATTATATATATACATATACTATAAGTTATATATATAT
70580 ATATATATAT
66 ATATATATAT
* *
70590 ATATATAGTTTATATATAC-TATAGATAGT-TTATATATATATATATACTATAAGTTATATATAT
1 ATATATAGTTTATATA-ACTTATAAATA-TATTATATATATACATATACTATAAGTTATATATAT
70653 A
64 A
70654 GTTTACATGT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
75 55 0.96
76 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (75 bp):
ATATATAGTTTATATAACTTATAAATATATTATATATATACATATACTATAAGTTATATATATAT
ATATATATAT
Found at i:70822 original size:2 final size:2
Alignment explanation
Indices: 70809--70855 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
70799 TAATTTACTT
70809 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
70852 TA TA
1 TA TA
70856 CATAGTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:70898 original size:35 final size:36
Alignment explanation
Indices: 70857--70930 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
70847 ATATATATAC
*
70857 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
**
70892 ATAGTTTACATGTATACATATACTATAAGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
70929 AT
1 AT
70931 TAACTTGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 7 0.21
37 27 0.79
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:81624 original size:13 final size:13
Alignment explanation
Indices: 81592--81639 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
81582 ATATACTTTT
81592 TATAGTTTATACATA
1 TATAGTTTAT--ATA
81607 TATAGTTTATATA
1 TATAGTTTATATA
* *
81620 CATAGGTTATATA
1 TATAGTTTATATA
81633 TATAGTT
1 TATAGTT
81640 CACATAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 19 0.66
15 10 0.34
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:81701 original size:71 final size:68
Alignment explanation
Indices: 81621--81776 Score: 217
Period size: 71 Copynumber: 2.2 Consensus size: 68
81611 GTTTATATAC
* *
81621 ATAGGTTATATATATAGTTCACATAAACATAAT-T-TATAGCTTATAATAATTATAAAATTTATA
1 ATAGTTTATATATATAGTTCACATAAACATAATATATATAGCTTATAATAATTAT---A-TAATA
81684 ATATAAAT
62 ATAT-AAT
*
81692 ATAGTTTATATATATAGTTTACATAAACATAATATATATAGCTTATAATAATTATATAATAATAT
1 ATAGTTTATATATATAGTTCACATAAACATAATATATATAGCTTATAATAATTATATAATAATAT
81757 AAT
66 AAT
81760 ATAGTTTATATAATATA
1 ATAGTTTATAT-ATATA
81777 TTATATATAT
Statistics
Matches: 79, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
68 14 0.18
69 13 0.16
70 1 0.01
71 31 0.39
72 1 0.01
73 19 0.24
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (68 bp):
ATAGTTTATATATATAGTTCACATAAACATAATATATATAGCTTATAATAATTATATAATAATAT
AAT
Found at i:81707 original size:24 final size:23
Alignment explanation
Indices: 81680--81844 Score: 99
Period size: 24 Copynumber: 7.1 Consensus size: 23
81670 TTATAAAATT
81680 TATAATATAAATATAGTTTATATA
1 TATAATATAAATATA-TTTATATA
* * * * * *
81704 TATAGTTTACATAAACATAATATA
1 TATAATATAAATATA-TTTATATA
*
81728 TATAGCT-TATAATA-A-TTATATA
1 TATA-ATATA-AATATATTTATATA
81750 -ATAATAT-AATATAGTTTATATAA
1 TATAATATAAATATA-TTTATAT-A
* * *
81773 TATATTATATATATATATATATA
1 TATAATATAAATATATTTATATA
* *
81796 TAT-ATATATATATATATATATA
1 TATAATATAAATATATTTATATA
* *
81818 TATATATATATATATATATATATA
1 TATA-ATATAAATATATTTATATA
81842 TAT
1 TAT
81845 CAATTTTTAA
Statistics
Matches: 115, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
19 4 0.03
20 2 0.02
21 4 0.03
22 33 0.29
23 5 0.04
24 58 0.50
25 9 0.08
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TATAATATAAATATATTTATATA
Found at i:81741 original size:16 final size:14
Alignment explanation
Indices: 81720--81844 Score: 97
Period size: 14 Copynumber: 8.9 Consensus size: 14
81710 TTACATAAAC
81720 ATAATATATATAGCTT
1 ATAATATATATA--TT
*
81736 ATAATA-ATTATATA
1 ATAATATA-TATATT
81750 ATAATATAATATAGTT
1 ATAATAT-ATATA-TT
81766 -T-ATATAATATATT
1 ATAATAT-ATATATT
81779 AT-ATATATATA-T
1 ATAATATATATATT
81791 AT-ATATATATA-T
1 ATAATATATATATT
81803 AT-ATATATATA-T
1 ATAATATATATATT
81815 ATATATATATATATAT
1 ATA-ATATATATAT-T
81831 ATATATATATATAT
1 ATA-ATATATATAT
81845 CAATTTTTAA
Statistics
Matches: 98, Mismatches: 2, Indels: 18
0.83 0.02 0.15
Matches are distributed among these distances:
12 27 0.28
13 7 0.07
14 31 0.32
15 6 0.06
16 27 0.28
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (14 bp):
ATAATATATATATT
Found at i:81749 original size:2 final size:2
Alignment explanation
Indices: 81744--81844 Score: 149
Period size: 2 Copynumber: 52.5 Consensus size: 2
81734 TTATAATAAT
*
81744 TA TA TA -A TA -A TA TA -A TA TA GTT TA TA TA -A TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
81782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
81824 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
81845 CAATTTTTAA
Statistics
Matches: 91, Mismatches: 2, Indels: 12
0.87 0.02 0.11
Matches are distributed among these distances:
1 5 0.05
2 85 0.93
3 1 0.01
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:82193 original size:56 final size:56
Alignment explanation
Indices: 82126--82238 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
82116 AGTCCCTTAC
82126 CTATGTGTGTTGTTTAATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTT
1 CTATGTGTGTTGTTTAATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTT
82182 CTATGTGTGTTGTTTAATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTT
1 CTATGTGTGTTGTTTAATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTT
82238 C
1 C
82239 AATTTTGTCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (56 bp):
CTATGTGTGTTGTTTAATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTT
Found at i:82264 original size:56 final size:56
Alignment explanation
Indices: 82141--82264 Score: 187
Period size: 56 Copynumber: 2.2 Consensus size: 56
82131 TGTGTTGTTT
* ** *
82141 AATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTTCTATGTGTGTTGTTT
1 AATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTTCAATGTGTGTCATTA
*
82197 AATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTTCAAT-TTTGTCATTA
1 AATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTTCAATGTGTGTCATTA
82252 AATTTATAATTTT
1 AATTTAT-ATTTT
82265 TAAAAATTGA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 13 0.21
56 49 0.79
ACGTcount: A:0.27, C:0.06, G:0.07, T:0.60
Consensus pattern (56 bp):
AATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTTCAATGTGTGTCATTA
Found at i:84823 original size:29 final size:30
Alignment explanation
Indices: 84770--84828 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
84760 CTATTTAGTT
84770 ATTTATTTATTTTTCAGCACCTTAA-TTTC
1 ATTTATTTATTTTTCAGCACCTTAACTTTC
* *
84799 ATTTCTTTATTTTTTAGC-CCTTTAACTTTC
1 ATTTATTTATTTTTCAGCACC-TTAACTTTC
84829 CAGCATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 2 0.08
29 20 0.77
30 4 0.15
ACGTcount: A:0.20, C:0.19, G:0.03, T:0.58
Consensus pattern (30 bp):
ATTTATTTATTTTTCAGCACCTTAACTTTC
Found at i:86969 original size:20 final size:21
Alignment explanation
Indices: 86944--86988 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
86934 ATTTTGATAA
86944 AAATATAATAATAAGTTAA-G
1 AAATATAATAATAAGTTAAGG
86964 AAATATAATAATAAGTTAAGG
1 AAATATAATAATAAGTTAAGG
86985 AAAT
1 AAAT
86989 TTTATAAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (21 bp):
AAATATAATAATAAGTTAAGG
Found at i:92628 original size:20 final size:20
Alignment explanation
Indices: 92587--92644 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
92577 TTGTAAGTCT
*
92587 TAATAAATATATAGTATGAATA
1 TAATATATATATA-TAT-AATA
* *
92609 TAATGTATATCTATATAATA
1 TAATATATATATATATAATA
92629 TAATATATATATATAT
1 TAATATATATATATAT
92645 TTGTAGGATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 18 0.58
21 3 0.10
22 10 0.32
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (20 bp):
TAATATATATATATATAATA
Done.