Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018062.1 Corchorus olitorius cultivar O-4 contig18095, 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: 71152
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3481 original size:29 final size:30
Alignment explanation
Indices: 3446--3503 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
3436 TATAAATAAT
*
3446 ATAATAAAATTAAATAA-TTATATTTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
*
3475 ATAATAAAATTGAATAATTTATATGTATA
1 ATAATAAAATTAAATAATTTATATGTATA
3504 TATTAATTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (30 bp):
ATAATAAAATTAAATAATTTATATGTATAC
Found at i:5554 original size:9 final size:9
Alignment explanation
Indices: 5540--5600 Score: 61
Period size: 9 Copynumber: 6.7 Consensus size: 9
5530 AGTGTGCCAT
5540 AGAGATGGA
1 AGAGATGGA
5549 AGAGATGG-
1 AGAGATGGA
* **
5557 AGACATTATCA
1 AGAGA-T-GGA
5568 AGAGATGGA
1 AGAGATGGA
*
5577 AGAGATAGA
1 AGAGATGGA
5586 AGAGATGGA
1 AGAGATGGA
5595 AGAGAT
1 AGAGAT
5601 AGAGACATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
8 4 0.10
9 32 0.78
10 1 0.02
11 4 0.10
ACGTcount: A:0.46, C:0.03, G:0.36, T:0.15
Consensus pattern (9 bp):
AGAGATGGA
Found at i:9190 original size:14 final size:13
Alignment explanation
Indices: 9171--9209 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
9161 ACTCAACACT
9171 AACTGACTCGAAAA
1 AACTGACTC-AAAA
*
9185 AACTGACTCAACA
1 AACTGACTCAAAA
9198 AACTGACT-AAAA
1 AACTGACTCAAAA
9210 CCCGATAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 3 0.13
13 11 0.48
14 9 0.39
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.15
Consensus pattern (13 bp):
AACTGACTCAAAA
Found at i:9202 original size:13 final size:13
Alignment explanation
Indices: 9160--9205 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
9150 GTCAGACTCA
9160 GACTCAACACTAACT
1 GACTCAACA--AACT
*
9175 GACTCGAAAAAACT
1 GACTC-AACAAACT
9189 GACTCAACAAACT
1 GACTCAACAAACT
9202 GACT
1 GACT
9206 AAAACCCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.17
Consensus pattern (13 bp):
GACTCAACAAACT
Found at i:11076 original size:15 final size:16
Alignment explanation
Indices: 11056--11086 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
11046 TTTTGTCAAA
11056 TTTTTCTTTTC-TTTT
1 TTTTTCTTTTCATTTT
11071 TTTTTCTTTTCATTTT
1 TTTTTCTTTTCATTTT
11087 ACAGCCAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTCTTTTCATTTT
Found at i:32316 original size:16 final size:15
Alignment explanation
Indices: 32278--32319 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
32268 ACAGAGATTG
* *
32278 ACAGAAAGCAATTAA
1 ACAGAAAACAATGAA
32293 ACAGAAAACAATGAA
1 ACAGAAAACAATGAA
32308 ACTAGAAAACAA
1 AC-AGAAAACAA
32320 AGCAAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.64, C:0.14, G:0.12, T:0.10
Consensus pattern (15 bp):
ACAGAAAACAATGAA
Found at i:33716 original size:19 final size:18
Alignment explanation
Indices: 33687--33722 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
33677 TTGAAATAAA
33687 TCTTCAATGGTCTTCAAG
1 TCTTCAATGGTCTTCAAG
33705 TCTTCAAATGGTCTTCAA
1 TCTTC-AATGGTCTTCAA
33723 ATGGTTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAG
Found at i:33720 original size:11 final size:11
Alignment explanation
Indices: 33687--33734 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
33677 TTGAAATAAA
33687 TCTTC-AATGG
1 TCTTCAAATGG
33697 TCTTC-AA--G
1 TCTTCAAATGG
33705 TCTTCAAATGG
1 TCTTCAAATGG
33716 TCTTCAAATGG
1 TCTTCAAATGG
*
33727 TTTTCAAA
1 TCTTCAAA
33735 CACGAACTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
8 6 0.18
9 2 0.06
10 7 0.21
11 19 0.56
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (11 bp):
TCTTCAAATGG
Found at i:36047 original size:21 final size:22
Alignment explanation
Indices: 36012--36057 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
36002 TCAGTTTCAA
36012 TTTCTGAACCTGTTTTGATCAG
1 TTTCTGAACCTGTTTTGATCAG
*
36034 TTTCTG-ATCTGTTTTGATCAG
1 TTTCTGAACCTGTTTTGATCAG
36055 TTT
1 TTT
36058 ATGTGTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.52
Consensus pattern (22 bp):
TTTCTGAACCTGTTTTGATCAG
Found at i:36051 original size:10 final size:10
Alignment explanation
Indices: 36023--36057 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
36013 TTCTGAACCT
36023 GTTTTGATCA
1 GTTTTGATCA
*
36033 GTTTCTGATCT
1 GTTT-TGATCA
36044 GTTTTGATCA
1 GTTTTGATCA
36054 GTTT
1 GTTT
36058 ATGTGTTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.54
Consensus pattern (10 bp):
GTTTTGATCA
Found at i:38559 original size:14 final size:14
Alignment explanation
Indices: 38540--38583 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
38530 ACTTGAGTCA
*
38540 TTGATTTGCTGTTT
1 TTGATTTCCTGTTT
*
38554 TTGATTTCCTATTT
1 TTGATTTCCTGTTT
* *
38568 GTGAGTTCCTGTTT
1 TTGATTTCCTGTTT
38582 TT
1 TT
38584 TAGTTCCTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.09, C:0.11, G:0.18, T:0.61
Consensus pattern (14 bp):
TTGATTTCCTGTTT
Found at i:38588 original size:14 final size:14
Alignment explanation
Indices: 38548--38591 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
38538 CATTGATTTG
*
38548 CTGTTTTTGATTTC
1 CTGTTTTTGAGTTC
* *
38562 CTATTTGTGAGTTC
1 CTGTTTTTGAGTTC
*
38576 CTGTTTTTTAGTTC
1 CTGTTTTTGAGTTC
38590 CT
1 CT
38592 TACTTGCTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.59
Consensus pattern (14 bp):
CTGTTTTTGAGTTC
Found at i:38954 original size:63 final size:63
Alignment explanation
Indices: 38569--38961 Score: 381
Period size: 63 Copynumber: 6.2 Consensus size: 63
38559 TTCCTATTTG
* * * *
38569 TGAGTTCCTGTTTTTTAGTTCCTTACTTGCTGTTTTTGAG--CCTGTTTATTTAACTG-TTTT
1 TGAGTTCTTGTTTTTTAGTTCATTACTTCCTGTTTTTGAGTTCCTGTTTGTTTAACTGTTTTT
* * ** *
38629 T-AGTTCCTGTTTTTTTAGTTCCTTACTTCCTGTTTTTGAGCCTGTTTAGTGTTTATTTAACTGT
1 TGAGTTCTTG-TTTTTTAGTTCATTACTTCCTGTTTTTGA----G-TTCCTGTTTGTTTAACTGT
38693 TTTT
60 TTTT
* * * * * *
38697 TG-GTTCCTGTTTTTTAGTTCATTACCTCCTATTTTTAAGTTCCTGCTGGTTTAACTGTTTTT
1 TGAGTTCTTGTTTTTTAGTTCATTACTTCCTGTTTTTGAGTTCCTGTTTGTTTAACTGTTTTT
* * *
38759 TTAGTT-TCTGTTTTTTAGTTCATTACTTCCTGTTTTTGAGTTCCTGCTGGTTTAACTGTTTTT
1 TGAGTTCT-TGTTTTTTAGTTCATTACTTCCTGTTTTTGAGTTCCTGTTTGTTTAACTGTTTTT
* **
38822 TTAGTT-TCTGTTTTTTAGTTCATTACTTCCTGTTTTTG-GATTCCCCTTTGTTTAACTGTTTTT
1 TGAGTTCT-TGTTTTTTAGTTCATTACTTCCTGTTTTTGAG-TTCCTGTTTGTTTAACTG-TTTT
38885 T
63 T
* * * * *
38886 TGAGTTCTTG-TTTTTAGTTCCTTACTTGCTGTTTTTGGGTTGCTGTTTCTTTAACTGTTTTT
1 TGAGTTCTTGTTTTTTAGTTCATTACTTCCTGTTTTTGAGTTCCTGTTTGTTTAACTGTTTTT
*
38948 TGGAGTTCCTGTTT
1 T-GAGTTCTTGTTT
38962 AACTGTTTTT
Statistics
Matches: 286, Mismatches: 29, Indels: 32
0.82 0.08 0.09
Matches are distributed among these distances:
59 8 0.03
60 29 0.10
62 26 0.09
63 155 0.54
64 16 0.06
65 1 0.00
67 39 0.14
68 12 0.04
ACGTcount: A:0.11, C:0.15, G:0.16, T:0.58
Consensus pattern (63 bp):
TGAGTTCTTGTTTTTTAGTTCATTACTTCCTGTTTTTGAGTTCCTGTTTGTTTAACTGTTTTT
Found at i:38975 original size:22 final size:23
Alignment explanation
Indices: 38935--38983 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
38925 TTGCTGTTTC
38935 TTTAACTGTTTTTTGGAGTTCCTG
1 TTTAACTGTTTTTTGGAGTT-CTG
38959 TTTAACTG-TTTTT-GAGTTCTG
1 TTTAACTGTTTTTTGGAGTTCTG
38980 TTTA
1 TTTA
38984 TGACTTGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.28
22 5 0.20
23 5 0.20
24 8 0.32
ACGTcount: A:0.14, C:0.10, G:0.18, T:0.57
Consensus pattern (23 bp):
TTTAACTGTTTTTTGGAGTTCTG
Found at i:43366 original size:29 final size:30
Alignment explanation
Indices: 43319--43378 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
43309 GAAGTTCGTG
* *
43319 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
43350 TTTGAAGA-CATTGAAGAATTATTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
43379 GGAAAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:44755 original size:16 final size:15
Alignment explanation
Indices: 44734--44772 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
44724 TTGCTTTGTT
44734 TTGTTTCCTAGTTTAA
1 TTGTTTCCT-GTTTAA
*
44750 TTGTTTTCTGTTTAA
1 TTGTTTCCTGTTTAA
44765 TTGCTTTC
1 TTG-TTTC
44773 TTTCAACCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.62
Consensus pattern (15 bp):
TTGTTTCCTGTTTAA
Found at i:44764 original size:15 final size:16
Alignment explanation
Indices: 44734--44773 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
44724 TTGCTTTGTT
*
44734 TTGTTTCCTAGTTTAA
1 TTGTTTTCTAGTTTAA
44750 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
44765 TTGCTTTCT
1 TTGTTTTCT
44774 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:51312 original size:16 final size:16
Alignment explanation
Indices: 51291--51324 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
51281 ACTTCCATTA
51291 TTATTATT-TTATTTAT
1 TTATTATTATT-TTTAT
51307 TTATTATTATTTTTAT
1 TTATTATTATTTTTAT
51323 TT
1 TT
51325 TACGGGCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTATTATTTTTAT
Found at i:52037 original size:113 final size:111
Alignment explanation
Indices: 51879--52312 Score: 329
Period size: 113 Copynumber: 3.8 Consensus size: 111
51869 TAGCTGAGAT
* ** ** * * *
51879 CCTAAGCAGGTTTACTTAAATGGAAGCTCTAAATAGTGACCTAAGCAGGTT-TTAAACGAAAATT
1 CCTAAGCAGGTTTGCTTAAACAGAAATTCTACACAGAGACCTAAGCAGGTTATTAAACGAAAATT
* * * **
51943 CTAAACAGAGACCTAAGTAGGTTTAATCAAACGAGATTCTAAGCGGGGA
66 CTAAACAGAGACCTAAGCAGGTTTAAACAAA--A-ATTCTAAACAAGGA
* * *
51992 CCTAAGCAGGTTTTCTTAAACATAAATTCTA-AGCCGAGACCTAAGCAGGTTTGATTAAAC-AAG
1 CCTAAGCAGGTTTGCTTAAACAGAAATTCTACA-CAGAGACCTAAGCAGG-TT-ATTAAACGAA-
*
52055 AATTCTAAACAGAGACCTAAGCAGGTTTAAACGAAAATTCTAAACAAGGA
62 AATTCTAAACAGAGACCTAAGCAGGTTTAAACAAAAATTCTAAACAAGGA
* * *
52105 CCTAAGCAGGTTTGCTTAAACAGAAGTTCTACACAGGGACCTAAGCAGGTTCGATTAAACGAAAC
1 CCTAAGCAGGTTTGCTTAAACAGAAATTCTACACAGAGACCTAAGCAGGTT--ATTAAACGAAAA
* * * ** * * *
52170 TCCTAAACATAGACTTAAGCAGGTTTACTTAAACGGAAGTTCTACACAGGGA
64 TTCTAAACAGAGACCTAAGCAGG--T--TTAAACAAAAATTCTAAACAAGGA
* * * * * * *
52222 CCTAAGTAGGTTCGATTAAAC-GAAACTCCTAAAC-GTAGACTTAAGCAGGTTTACTTAAACGGA
1 CCTAAGCAGGTTTGCTTAAACAGAAA-TTCTACACAG-AGACCTAAGCAGG-TTA-TTAAACGAA
* * * *
52285 AGTTCTACACAGGGACCTAAACAGGTTT
62 AATTCTAAACAGAGACCTAAGCAGGTTT
52313 GCTTAAATGA
Statistics
Matches: 261, Mismatches: 44, Indels: 32
0.77 0.13 0.09
Matches are distributed among these distances:
112 3 0.01
113 122 0.47
114 6 0.02
115 4 0.02
116 43 0.16
117 81 0.31
118 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (111 bp):
CCTAAGCAGGTTTGCTTAAACAGAAATTCTACACAGAGACCTAAGCAGGTTATTAAACGAAAATT
CTAAACAGAGACCTAAGCAGGTTTAAACAAAAATTCTAAACAAGGA
Found at i:52135 original size:152 final size:150
Alignment explanation
Indices: 51835--52330 Score: 491
Period size: 152 Copynumber: 3.2 Consensus size: 150
51825 TATTGTAAAG
* * * * * * * *
51835 AGGGACCTCAGTAGGTTTACTTAAACGAAACTCTTAGCTGAGATCCTAAGCAGGTTTACTTAAAT
1 AGGGACCTAAGCAGGTTTGCTTAAACAAAATTCTAAGCAGAGA-CCTAAGCAGGTTTACTTAAAC
* * * *
51900 GGAAGCTCTAAATAGTGACCTAAGCAGGTTTTAAACGAAAATTCTAAACAGAGACCTAAGTAGGT
65 GGAAGTTCTAAACAGAGACCTAAGCAGGTTTTAAACGAAAATTCTAAACAG-GACCTAAGCAGGT
* *
51965 TTAATCAAACG-AGATTCTA-AGC
129 TTACTTAAACGAAG-TTCTACA-C
* * *
51987 GGGGACCTAAGCAGGTTTTCTTAAACATAAATTCTAAGCCGAGACCTAAGCAGGTTTGA-TTAAA
1 AGGGACCTAAGCAGGTTTGCTTAAACA-AAATTCTAAGCAGAGACCTAAGCAGGTTT-ACTTAAA
*
52051 CAAGAA-TTCTAAACAGAGACCTAAGCAGG-TTTAAACGAAAATTCTAAACAAGGACCTAAGCAG
64 C-GGAAGTTCTAAACAGAGACCTAAGCAGGTTTTAAACGAAAATTCTAAAC-AGGACCTAAGCAG
*
52114 GTTTGCTTAAACAGAAGTTCTACAC
127 GTTTACTTAAAC-GAAGTTCTACAC
* * * * * * *
52139 AGGGACCTAAGCAGGTTCGATTAAACGAAACTCCTAAACATAGACTTAAGCAGGTTTACTTAAAC
1 AGGGACCTAAGCAGGTTTGCTTAAAC-AAAATTCTAAGCAGAGACCTAAGCAGGTTTACTTAAAC
* * * * * *
52204 GGAAGTTCTACACAGGGACCTAAGTAGGTTCGATTAAACGAAACTCCTAAAC-GTAGACTTAAGC
65 GGAAGTTCTAAACAGAGACCTAAGCAGGTT---TTAAACGAAAATTCTAAACAG--GACCTAAGC
52268 AGGTTTACTTAAACGGAAGTTCTACAC
125 AGGTTTACTTAAAC-GAAGTTCTACAC
* **
52295 AGGGACCTAAACAGGTTTGCTTAAATGAAATTCTAA
1 AGGGACCTAAGCAGGTTTGCTTAAACAAAATTCTAA
52331 TGAAACTTCT
Statistics
Matches: 285, Mismatches: 43, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
151 43 0.15
152 140 0.49
153 22 0.08
154 1 0.00
155 7 0.02
156 72 0.25
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (150 bp):
AGGGACCTAAGCAGGTTTGCTTAAACAAAATTCTAAGCAGAGACCTAAGCAGGTTTACTTAAACG
GAAGTTCTAAACAGAGACCTAAGCAGGTTTTAAACGAAAATTCTAAACAGGACCTAAGCAGGTTT
ACTTAAACGAAGTTCTACAC
Found at i:52193 original size:78 final size:75
Alignment explanation
Indices: 51874--52312 Score: 437
Period size: 78 Copynumber: 5.7 Consensus size: 75
51864 ACTCTTAGCT
* * * * *
51874 GAGATCCTAAGCAGGTTTACTTAAATGGAAGCTCTAAATAGTGACCTAAGCAGGTTTTAAACGAA
1 GAGA-CCTAAGCAGGTTTACTTAAACGGAAGTTCTACACAGGGACCTAAGCAGGTTTTAAACGAA
51939 AATTCTAAACA
65 AATTCTAAACA
* * * *
51950 GAGACCTAAGTAGGTTTAATCAAAC-G-AGATTCTA-AGCGGGGACCTAAGCAGGTTTTCTTAAA
1 GAGACCTAAGCAGGTTTACTTAAACGGAAG-TTCTACA-CAGGGACCTAAGCAGG--TT-TTAAA
* *
52012 C-ATAAATTCTAAGCC
61 CGA-AAATTCTAAACA
* * *
52027 GAGACCTAAGCAGGTTTGA-TTAAACAAGAA-TTCTAAACAGAGACCTAAGCAGG-TTTAAACGA
1 GAGACCTAAGCAGGTTT-ACTTAAAC-GGAAGTTCTACACAGGGACCTAAGCAGGTTTTAAACGA
52089 AAATTCTAAACA
64 AAATTCTAAACA
* *
52101 -AGGACCTAAGCAGGTTTGCTTAAACAGAAGTTCTACACAGGGACCTAAGCAGGTTCGATTAAAC
1 GA-GACCTAAGCAGGTTTACTTAAACGGAAGTTCTACACAGGGACCTAAGCAGGTT---TTAAAC
* *
52165 GAAACTCCTAAACA
62 GAAAATTCTAAACA
* * *
52179 TAGACTTAAGCAGGTTTACTTAAACGGAAGTTCTACACAGGGACCTAAGTAGGTTCGATTAAACG
1 GAGACCTAAGCAGGTTTACTTAAACGGAAGTTCTACACAGGGACCTAAGCAGGTT---TTAAACG
* *
52244 AAACTCCTAAAC-
63 AAAATTCTAAACA
* *
52256 GTAGACTTAAGCAGGTTTACTTAAACGGAAGTTCTACACAGGGACCTAAACAGGTTT
1 G-AGACCTAAGCAGGTTTACTTAAACGGAAGTTCTACACAGGGACCTAAGCAGGTTT
52313 GCTTAAATGA
Statistics
Matches: 314, Mismatches: 28, Indels: 43
0.82 0.07 0.11
Matches are distributed among these distances:
73 8 0.03
74 76 0.24
75 21 0.07
76 7 0.02
77 37 0.12
78 161 0.51
79 3 0.01
80 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (75 bp):
GAGACCTAAGCAGGTTTACTTAAACGGAAGTTCTACACAGGGACCTAAGCAGGTTTTAAACGAAA
ATTCTAAACA
Found at i:52312 original size:39 final size:39
Alignment explanation
Indices: 51838--52319 Score: 330
Period size: 39 Copynumber: 12.6 Consensus size: 39
51828 TGTAAAGAGG
* * ** * * *
51838 GACCTCAGTAGGTTTACTTAAAC-GAAACTCTTAGCTGA
1 GACCTAAGCAGGTTTACTTAAACGGAAGTTCTAAACAGA
* * * *
51876 GATCCTAAGCAGGTTTACTTAAATGGAAGCTCTAAATAGT
1 GA-CCTAAGCAGGTTTACTTAAACGGAAGTTCTAAACAGA
* *
51916 GACCTAAGCAGG-TT--TTAAACGAAAATTCTAAACAGA
1 GACCTAAGCAGGTTTACTTAAACGGAAGTTCTAAACAGA
* * * * * *
51952 GACCTAAGTAGGTTTAATCAAAC-G-AGATTCTAAGCGGG
1 GACCTAAGCAGGTTTACTTAAACGGAAG-TTCTAAACAGA
* ** * * *
51990 GACCTAAGCAGGTTTTCTTAAACATAAATTCTAAGCCGA
1 GACCTAAGCAGGTTTACTTAAACGGAAGTTCTAAACAGA
*
52029 GACCTAAGCAGGTTTGA-TTAAACAAGAA-TTCTAAACAGA
1 GACCTAAGCAGGTTT-ACTTAAAC-GGAAGTTCTAAACAGA
* *
52068 GACCTAAGCAGG--T--TTAAACGAAAATTCTAAACA-A
1 GACCTAAGCAGGTTTACTTAAACGGAAGTTCTAAACAGA
* * * *
52102 GGACCTAAGCAGGTTTGCTTAAACAGAAGTTCTACACAGG
1 -GACCTAAGCAGGTTTACTTAAACGGAAGTTCTAAACAGA
* * * * *
52142 GACCTAAGCAGGTTCGA-TTAAACGAAACTCCTAAACATA
1 GACCTAAGCAGGTT-TACTTAAACGGAAGTTCTAAACAGA
* * *
52181 GACTTAAGCAGGTTTACTTAAACGGAAGTTCTACACAGG
1 GACCTAAGCAGGTTTACTTAAACGGAAGTTCTAAACAGA
* * * * *
52220 GACCTAAGTAGGTTCGA-TTAAACGAAACTCCTAAAC-GTA
1 GACCTAAGCAGGTT-TACTTAAACGGAAGTTCTAAACAG-A
* * *
52259 GACTTAAGCAGGTTTACTTAAACGGAAGTTCTACACAGG
1 GACCTAAGCAGGTTTACTTAAACGGAAGTTCTAAACAGA
* *
52298 GACCTAAACAGGTTTGCTTAAA
1 GACCTAAGCAGGTTTACTTAAA
52320 TGAAATTCTA
Statistics
Matches: 344, Mismatches: 77, Indels: 45
0.74 0.17 0.10
Matches are distributed among these distances:
34 3 0.01
35 27 0.08
36 27 0.08
37 5 0.01
38 34 0.10
39 231 0.67
40 17 0.05
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (39 bp):
GACCTAAGCAGGTTTACTTAAACGGAAGTTCTAAACAGA
Found at i:52319 original size:78 final size:78
Alignment explanation
Indices: 51835--52330 Score: 436
Period size: 78 Copynumber: 6.5 Consensus size: 78
51825 TATTGTAAAG
* * * * * *
51835 AGGGACCTCAGTAGGTTTACTTAAACG-AAACTCTTAGC-TGAGATCCTAAGCAGGTTTACTTAA
1 AGGGACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACGT-AGA-CCTAAGCAGGTTTACTTAA
* * * *
51898 ATGGAAGCTCTAAAT
64 ACGGAAGTTCTACAC
* * * *
51913 AGTGACCTAAGCAGG-TT--TTAAACGAAAATTCTAAACAG-AGACCTAAGTAGGTTTAATCAAA
1 AGGGACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAAC-GTAGACCTAAGCAGGTTTACTTAAA
51974 C-G-AGATTCTA-AGC
65 CGGAAG-TTCTACA-C
* * *
51987 GGGGACCTAAGCAGGTTTTCTTAAAC-ATAAATTCTAAGCCG-AGACCTAAGCAGGTTTGA-TTA
1 AGGGACCTAAGCAGGTTTGCTTAAACGA-AAATTCTAA-ACGTAGACCTAAGCAGGTTT-ACTTA
* *
52049 AACAAGAA-TTCTAAAC
63 AAC-GGAAGTTCTACAC
* * *
52065 AGAGACCTAAGCAGG--T--TTAAACGAAAATTCTAAAC-AAGGACCTAAGCAGGTTTGCTTAAA
1 AGGGACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACGTA-GACCTAAGCAGGTTTACTTAAA
*
52125 CAGAAGTTCTACAC
65 CGGAAGTTCTACAC
* * * * * *
52139 AGGGACCTAAGCAGGTTCGATTAAACGAAACTCCTAAACATAGACTTAAGCAGGTTTACTTAAAC
1 AGGGACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACGTAGACCTAAGCAGGTTTACTTAAAC
52204 GGAAGTTCTACAC
66 GGAAGTTCTACAC
* * * * * *
52217 AGGGACCTAAGTAGGTTCGATTAAACGAAACTCCTAAACGTAGACTTAAGCAGGTTTACTTAAAC
1 AGGGACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACGTAGACCTAAGCAGGTTTACTTAAAC
52282 GGAAGTTCTACAC
66 GGAAGTTCTACAC
* *
52295 AGGGACCTAAACAGGTTTGCTTAAATG-AAATTCTAA
1 AGGGACCTAAGCAGGTTTGCTTAAACGAAAATTCTAA
52331 TGAAACTTCT
Statistics
Matches: 354, Mismatches: 39, Indels: 51
0.80 0.09 0.11
Matches are distributed among these distances:
73 9 0.03
74 75 0.21
75 27 0.08
76 13 0.04
77 45 0.13
78 181 0.51
79 3 0.01
80 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (78 bp):
AGGGACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACGTAGACCTAAGCAGGTTTACTTAAAC
GGAAGTTCTACAC
Found at i:56913 original size:2 final size:2
Alignment explanation
Indices: 56906--56947 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
56896 AGATGGCAAG
56906 AT AT AT AT AT -T 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
56947 A
1 A
56948 CATAGAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68602 original size:15 final size:16
Alignment explanation
Indices: 68569--68608 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
68559 TTTGTTTGTT
68569 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
68585 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
68600 TTGCTTTCT
1 TTGTTTTCT
68609 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Done.