Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012133.1 Corchorus olitorius cultivar O-4 contig12166, 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: 36173
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2722 original size:25 final size:25
Alignment explanation
Indices: 2692--2739 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2682 ATGCAATGTC
2692 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
*
2717 AAATTAGCTTTGAGCTACATGAA
1 AAATTAGATTTGAGCTACATGAA
2740 CGCAAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATG
Found at i:3351 original size:50 final size:50
Alignment explanation
Indices: 3287--3610 Score: 549
Period size: 50 Copynumber: 6.5 Consensus size: 50
3277 GAGAGATCCT
3287 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
*
3337 CGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
3387 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
*
3437 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTACGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
* *
3487 CGAGTTTGGGCTTATGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAA
1 CGAGTTT-GGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
* * * *
3538 CGAGTTCGACTTGTGGAAAAGCCTATGTTGATAATTGTCTCATATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
* *
3588 CGAGTTTGACTTATGGAAAAGCC
1 CGAGTTTGGCTTGTGGAAAAGCC
3611 AAAGCATTCG
Statistics
Matches: 259, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
50 213 0.82
51 46 0.18
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.31
Consensus pattern (50 bp):
CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAA
Found at i:3560 original size:151 final size:150
Alignment explanation
Indices: 3287--3610 Score: 549
Period size: 151 Copynumber: 2.2 Consensus size: 150
3277 GAGAGATCCT
* *
3287 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGCTTGGCTTGTG
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTACGGAAACGAGCTTGGCTTATG
* *
3352 GAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTG
66 GAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTCGACTTGTGGAAAAGCCTATGTTG
*
3417 ATAATTGACTCGTATGGAAA
131 ATAATTGACTCATATGGAAA
*
3437 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTACGGAAACGAGTTTGGGCTTAT
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTACGGAAACGAGCTT-GGCTTAT
*
3502 GGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGACTTGTGGAAAAGCCTATGTT
65 GGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTCGACTTGTGGAAAAGCCTATGTT
*
3567 GATAATTGTCTCATATGGAAA
130 GATAATTGACTCATATGGAAA
* *
3588 CGAGTTTGACTTATGGAAAAGCC
1 CGAGTTTGGCTTGTGGAAAAGCC
3611 AAAGCATTCG
Statistics
Matches: 163, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
150 55 0.34
151 108 0.66
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.31
Consensus pattern (150 bp):
CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTACGGAAACGAGCTTGGCTTATG
GAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTCGACTTGTGGAAAAGCCTATGTTG
ATAATTGACTCATATGGAAA
Found at i:4289 original size:50 final size:50
Alignment explanation
Indices: 4223--4409 Score: 266
Period size: 50 Copynumber: 3.7 Consensus size: 50
4213 AAAATCGACC
* * *
4223 TTTGGTCTTGGTCTCACAAATGGAGTGCAATCTTATTTTGAAAAGCGAAT
1 TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAAT
*
4273 TTTGATCTTGGGCTCACAAATGGAATGCAATCTCATTTTGAAAAGCGAAT
1 TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAAT
* ** * * * * *
4323 ATTGATCTTGAACTCACAAATGGAAAGCAATTTTACTTTCAGAAGCGAAT
1 TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAAT
4373 TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATT
1 TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATT
4410 GTAAATATTA
Statistics
Matches: 118, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 118 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (50 bp):
TTTGATCTTGGGCTCACAAATGGAATGCAATCTTATTTTGAAAAGCGAAT
Found at i:4995 original size:6 final size:6
Alignment explanation
Indices: 4984--5021 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
4974 ATCCATTCTC
4984 TTTTGA TTTTGA TTTTGA TTTTTGA TTTTGA -TTTGA TT
1 TTTTGA TTTTGA TTTTGA -TTTTGA TTTTGA TTTTGA TT
5022 GATTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
6 19 0.63
7 6 0.20
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTTGA
Found at i:5008 original size:19 final size:18
Alignment explanation
Indices: 4984--5060 Score: 69
Period size: 19 Copynumber: 4.6 Consensus size: 18
4974 ATCCATTCTC
4984 TTTTGATTTTGATTTTGAT
1 TTTTGATTTTGA-TTTGAT
5003 TTTTGATTTTGATTTGA-
1 TTTTGATTTTGATTTGAT
5020 --TTGATTTT--TTT--T
1 TTTTGATTTTGATTTGAT
* *
5032 TATTGACTTTGATTTGATT
1 TTTTGATTTTGATTTGA-T
5051 TTTTGATTTT
1 TTTTGATTTT
5061 TTTTTTTGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
13 3 0.06
14 7 0.15
15 8 0.17
16 3 0.06
18 5 0.11
19 21 0.45
ACGTcount: A:0.16, C:0.01, G:0.14, T:0.69
Consensus pattern (18 bp):
TTTTGATTTTGATTTGAT
Found at i:5030 original size:25 final size:25
Alignment explanation
Indices: 4986--5054 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
4976 CCATTCTCTT
* **
4986 TTGATTTTGATTTTGATTTTTGATT-
1 TTGACTTTGA-TTTGATTTTTTTTTA
5011 TTGA-TTTGA-TTGATTTTTTTTTA
1 TTGACTTTGATTTGATTTTTTTTTA
5034 TTGACTTTGATTTGATTTTTT
1 TTGACTTTGATTTGATTTTTT
5055 GATTTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 11 0.28
23 4 0.10
24 10 0.26
25 14 0.36
ACGTcount: A:0.16, C:0.01, G:0.14, T:0.68
Consensus pattern (25 bp):
TTGACTTTGATTTGATTTTTTTTTA
Found at i:5037 original size:29 final size:28
Alignment explanation
Indices: 4992--5061 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
4982 TCTTTTGATT
*
4992 TTGATTTTGATTTTTGATTTTGATTTGA
1 TTGATTTTGATTTTTGACTTTGATTTGA
**
5020 TTGATTTTTTTTTATTGACTTTGATTTGA
1 TTGATTTTGATTT-TTGACTTTGATTTGA
5049 TT--TTTTGATTTTT
1 TTGATTTTGATTTTT
5062 TTTTTTGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.06
27 7 0.19
28 11 0.31
29 16 0.44
ACGTcount: A:0.16, C:0.01, G:0.14, T:0.69
Consensus pattern (28 bp):
TTGATTTTGATTTTTGACTTTGATTTGA
Found at i:5046 original size:35 final size:32
Alignment explanation
Indices: 5004--5069 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
4994 GATTTTGATT
5004 TTTGATTTTGATTTGATTGATTTTTTTTTATTGAC
1 TTTGA-TTTGATTT-ATTGATTTTTTTTT-TTGAC
*
5039 TTTGATTTGATTTTTTGATTTTTTTTTTTGA
1 TTTGATTTGATTTATTGATTTTTTTTTTTGA
5070 AATTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 4 0.13
33 13 0.43
34 8 0.27
35 5 0.17
ACGTcount: A:0.15, C:0.02, G:0.14, T:0.70
Consensus pattern (32 bp):
TTTGATTTGATTTATTGATTTTTTTTTTTGAC
Found at i:5052 original size:24 final size:22
Alignment explanation
Indices: 4984--5054 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 22
4974 ATCCATTCTC
*
4984 TTTTGATTTTGATTTTGATTTTTGA
1 TTTTGA-TTTGA-TTTGATTTTT-T
5009 TTTTGATTTGA-TTGATTTTTTT
1 TTTTGATTTGATTTGA-TTTTTT
5031 TTATTGACTTTGATTTGATTTTTT
1 TT-TTGA-TTTGATTTGATTTTTT
5055 GATTTTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 6 0.15
23 9 0.22
24 16 0.39
25 10 0.24
ACGTcount: A:0.15, C:0.01, G:0.14, T:0.69
Consensus pattern (22 bp):
TTTTGATTTGATTTGATTTTTT
Found at i:5087 original size:14 final size:14
Alignment explanation
Indices: 5049--5088 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
5039 TTTGATTTGA
5049 TTTTTTG-ATTTTT
1 TTTTTTGAATTTTT
5062 TTTTTTGAAATTTTT
1 TTTTTTG-AATTTTT
5077 TTTTTTGAATTT
1 TTTTTTGAATTT
5089 CTTGATGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.28
14 5 0.20
15 13 0.52
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (14 bp):
TTTTTTGAATTTTT
Found at i:9222 original size:52 final size:52
Alignment explanation
Indices: 9085--9381 Score: 382
Period size: 52 Copynumber: 5.7 Consensus size: 52
9075 AACCTGATGA
* * * *
9085 GAACTTTCCCATTTTGAAATAGAGCTAGATTGAATACTTTGAAAACTTGATGG
1 GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAAC-TGGTGG
* *
9138 GAGCTTTCCCAATTTGAAAAATAGCTAAATTGAATACTTTGAAAACTGGTGG
1 GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGG
* * * * ** *
9190 AAACTTTCCTC-ACTTGAAAAAGAACTATATTGAATACTTTGAAGGCTGATGG
1 GAACTTTCC-CAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGG
* * * * *
9242 GAACTTTCCCGACTTG-AAAATAGCTAGATTGAATACTTTGAAAAATTGGTGG
1 GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG-AAAACTGGTGG
*
9294 GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAGTACTTTGAAAACTGGTGG
1 GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGG
9346 GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATA
1 GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATA
9382 TTCTTTTTGG
Statistics
Matches: 210, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
51 22 0.10
52 125 0.60
53 63 0.30
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (52 bp):
GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGG
Found at i:9278 original size:156 final size:157
Alignment explanation
Indices: 9078--9381 Score: 461
Period size: 156 Copynumber: 1.9 Consensus size: 157
9068 AAACTAAAAC
* * *
9078 CTGATGAGAACTTTCCCATTTTGAAATAGAGCTAGATTGAATACTTTGAAAACTTGATGGGAGCT
1 CTGATGAGAACTTTCCCATCTTGAAATAGAGCTAGATTGAATACTTTGAAAAATTGATGGGAACT
*
9143 TTCCCAATTTGAAAAATAGCTAAATTGAATACTTTGAAAACTGGTGGAAACTTTCCTC-ACTTGA
66 TTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGAAACTTTCC-CAACTTGA
*
9207 AAAAGAACTATATTGAATACTTTGAAGG
130 AAAAGAACTAAATTGAATACTTTGAAGG
* * *
9235 CTGATGGGAACTTTCCCGA-CTTGAAA-ATAGCTAGATTGAATACTTTGAAAAATTGGTGGGAAC
1 CTGATGAGAACTTTCCC-ATCTTGAAATAGAGCTAGATTGAATACTTTGAAAAATTGATGGGAAC
* * *
9298 TTTCCCAATTTGAAAAAGAGCTAAATTGAGTACTTTGAAAACTGGTGGGAACTTTCCCAATTTGA
65 TTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGAAACTTTCCCAACTTGA
*
9363 AAAAGAGCTAAATTGAATA
130 AAAAGAACTAAATTGAATA
9382 TTCTTTTTGG
Statistics
Matches: 133, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
155 1 0.01
156 109 0.82
157 22 0.17
158 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (157 bp):
CTGATGAGAACTTTCCCATCTTGAAATAGAGCTAGATTGAATACTTTGAAAAATTGATGGGAACT
TTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACTGGTGGAAACTTTCCCAACTTGAA
AAAGAACTAAATTGAATACTTTGAAGG
Found at i:10982 original size:1 final size:1
Alignment explanation
Indices: 10978--11007 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
10968 GTTCTTCAAA
10978 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
11008 ACTTTCACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:14327 original size:61 final size:62
Alignment explanation
Indices: 14253--14511 Score: 238
Period size: 66 Copynumber: 4.0 Consensus size: 62
14243 TGGTCGATTC
* * **
14253 TAAAAACTAAGAAAGACTAGTCTGAGGT-TTGAACTGAAG-AAGACCAGTCTGTGGTCCACTT
1 TAAAAACTAAGAAAGACT-GTCTGAGGTCTGGAACTGAAGAAAGACCAGTCTGAGGTCCAAAT
* *
14314 TAAAAACTAAGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAA
1 TAAAAACTAAGAAAGA-CTGTCTGAGGTCTGGAACTG-AAG--AAAGACCAGTCTGAGGTCCAAA
14379 T
62 T
* * *
14380 T-AAAACTGAGAAAGACTTGTCTGAGGTCTGGAACTGAAAGATAAAGA-CATATCTGAGGTCGAA
1 TAAAAACTAAGAAAGAC-TGTCTGAGGTCTGGAACTG-AAG--AAAGACCA-GTCTGAGGTCCAA
14443 AT
61 AT
* * * * *
14445 TTAAAAGTGAGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAA
1 TAAAAACTAAGAAAGA-CTGTCTGAGGTCTGGAACTG-AAG--AAAGACCAGTCTGAGGTCCAAA
14510 T
62 T
14511 T
1 T
14512 GAAAGAGAAA
Statistics
Matches: 175, Mismatches: 12, Indels: 17
0.86 0.06 0.08
Matches are distributed among these distances:
61 25 0.14
62 9 0.05
63 3 0.02
64 2 0.01
65 58 0.33
66 76 0.43
67 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (62 bp):
TAAAAACTAAGAAAGACTGTCTGAGGTCTGGAACTGAAGAAAGACCAGTCTGAGGTCCAAAT
Found at i:14401 original size:65 final size:65
Alignment explanation
Indices: 14316--14536 Score: 347
Period size: 65 Copynumber: 3.4 Consensus size: 65
14306 GTCCACTTTA
*
14316 AAAACTAAGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATT
1 AAAACTGAGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATT
* * *
14381 AAAACTGAGAAAGACTTGTCTGAGGTCTGGAACTGAAAGATAAAGACATATCTGAGGTCGAAATT
1 AAAACTGAGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAA-T
14446 T
65 T
*
14447 AAAAGTGAGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATT
1 AAAACTGAGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATT
* * *
14512 GAAA--GAGAAACACCTATCTGAGGTC
1 AAAACTGAGAAAGACCTGTCTGAGGTC
14537 GAAATTAAAA
Statistics
Matches: 144, Mismatches: 11, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
63 19 0.13
65 64 0.44
66 61 0.42
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.22
Consensus pattern (65 bp):
AAAACTGAGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATT
Found at i:14485 original size:66 final size:64
Alignment explanation
Indices: 14323--14536 Score: 340
Period size: 66 Copynumber: 3.3 Consensus size: 64
14313 TTAAAAACTA
14323 AGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAACTG
1 AGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAA-TG
* * *
14388 AGAAAGACTTGTCTGAGGTCTGGAACTGAAAGATAAAGACATATCTGAGGTCGAAATTTAAAAGT
1 AGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAA-TTAAAA-T
14453 G
64 G
*
14454 AGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTGAAA-G
1 AGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAATG
* *
14517 AGAAACACCTATCTGAGGTC
1 AGAAAGACCTGTCTGAGGTC
14537 GAAATTAAAA
Statistics
Matches: 138, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
63 19 0.14
65 58 0.42
66 61 0.44
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.22
Consensus pattern (64 bp):
AGAAAGACCTGTCTGAGGTCTGGAACTGAAAGATAAAGACCTGTCTGAGGTCGAAATTAAAATG
Found at i:14515 original size:97 final size:98
Alignment explanation
Indices: 14357--14557 Score: 262
Period size: 97 Copynumber: 2.1 Consensus size: 98
14347 ACTGAAAGAT
* * * *
14357 AAAGACCTGTCTGAGGTCGAAATTAAAACTGAGAAAGACTTGTCTGAGGTCTGGAACTGAAAGAT
1 AAAGACCTGTCTGAGGTCGAAACTAAAAC-GAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGAG
* * *
14422 AAAGACATATCTGAGGTCGAAATTTAAAAGTGAG
65 AAACACATATCTGAGGTCGAAATTAAAAACTGAG
* * * *
14456 AAAGACCTGTCTGAGGTCTGGAACTGAAA-GATAAAGACCTGTCTGAGGTC-GAAATTGAAAGAG
1 AAAGACCTGTCTGAGGTC-GAAACTAAAACGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGAG
*
14519 AAACACCTATCTGAGGTCGAAATTAAAAACTGAG
65 AAACACATATCTGAGGTCGAAATTAAAAACTGAG
14553 AAAGA
1 AAAGA
14558 TGACAAGTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
97 45 0.51
98 19 0.21
99 18 0.20
100 7 0.08
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.21
Consensus pattern (98 bp):
AAAGACCTGTCTGAGGTCGAAACTAAAACGAGAAAGACCTGTCTGAGGTCTGAAACTGAAAGAGA
AACACATATCTGAGGTCGAAATTAAAAACTGAG
Found at i:14598 original size:39 final size:39
Alignment explanation
Indices: 14548--14935 Score: 515
Period size: 39 Copynumber: 9.9 Consensus size: 39
14538 AAATTAAAAA
** *
14548 CTGAGAAAGATGACAAGTTTCCAGTCAACTTTGGTAACTG
1 CTGA-AAAGATGACCTGTTTCCAGTCAACTTTGATAACTG
*
14588 CTGAAAAGATGACCTGCTTCCAGTCAACTTTGATAACTG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTG
* * * * **
14627 TTGAAAAGATGGCATGTTTCAAACCAACTTTGATAACTG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTG
*
14666 CTGAAAAGATGATCTGTTTCCAGTCAACTTTGATAACTG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTG
* * * *
14705 CTGAAAAGATGGCATGTTTCCAGCCAACTTTGATAACTA
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTG
* * * **
14744 TTGAAAAGATGGCCTGTTTCTAACCAACTTTGATAACTG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTG
* * ** *
14783 CTGAAGAGATGGCCTGTTTCCAACCAACTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTG
*
14822 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTG
*
14861 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAGTG
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTG
*
14900 CTGAAAAGATGACCTGTTTCCAATCAACTTTGATAA
1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAA
14936 ATGTTGACTA
Statistics
Matches: 310, Mismatches: 38, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
39 306 0.99
40 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (39 bp):
CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTG
Found at i:16448 original size:17 final size:17
Alignment explanation
Indices: 16417--16517 Score: 70
Period size: 17 Copynumber: 6.2 Consensus size: 17
16407 TCCATTCTCT
**
16417 TTTGATTTTGATTTTGA
1 TTTGATTTTTTTTTTGA
16434 TTTGATTTTTTTTTT-A
1 TTTGATTTTTTTTTTGA
* * *
16450 TGATAATTTTTTTTATGA
1 T-TTGATTTTTTTTTTGA
16468 --TGA-TTTTTTTTTGA
1 TTTGATTTTTTTTTTGA
* *
16482 TGATGATCTTTTTTTT-A
1 T-TTGATTTTTTTTTTGA
*
16499 -TTGATTTTTTTTTTAA
1 TTTGATTTTTTTTTTGA
16515 TTT
1 TTT
16518 CTTAATGGAG
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
14 10 0.15
15 14 0.21
16 3 0.05
17 30 0.45
18 9 0.14
ACGTcount: A:0.18, C:0.01, G:0.11, T:0.70
Consensus pattern (17 bp):
TTTGATTTTTTTTTTGA
Found at i:16477 original size:32 final size:32
Alignment explanation
Indices: 16435--16513 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
16425 TGATTTTGAT
16435 TTGATTTTTTTTTTATGATAA--TTTTTTTTA
1 TTGATTTTTTTTTTATGATAATCTTTTTTTTA
* *
16465 TGATGATTTTTTTTTGATGATGATCTTTTTTTTA
1 T--TGATTTTTTTTTTATGATAATCTTTTTTTTA
16499 TTGATTTTTTTTTTA
1 TTGATTTTTTTTTTA
16514 ATTTCTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 1 0.02
32 31 0.74
34 10 0.24
ACGTcount: A:0.18, C:0.01, G:0.10, T:0.71
Consensus pattern (32 bp):
TTGATTTTTTTTTTATGATAATCTTTTTTTTA
Found at i:16487 original size:20 final size:21
Alignment explanation
Indices: 16464--16503 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
16454 AATTTTTTTT
*
16464 ATGATGATTTTTTT-TTGATG
1 ATGATCATTTTTTTATTGATG
*
16484 ATGATCTTTTTTTTATTGAT
1 ATGATCATTTTTTTATTGAT
16504 TTTTTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.20, C:0.03, G:0.15, T:0.62
Consensus pattern (21 bp):
ATGATCATTTTTTTATTGATG
Found at i:16493 original size:15 final size:15
Alignment explanation
Indices: 16441--16510 Score: 81
Period size: 15 Copynumber: 4.5 Consensus size: 15
16431 TGATTTGATT
*
16441 TTTTTTTTATGATAA
1 TTTTTTTTATGATGA
16456 TTTTTTTTATGATGA
1 TTTTTTTTATGATGA
16471 TTTTTTTTTGATGATGA
1 -TTTTTTTT-ATGATGA
16488 TCTTTTTTT-T-ATTGA
1 T-TTTTTTTATGA-TGA
16503 TTTTTTTT
1 TTTTTTTT
16511 TTAATTTCTT
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
14 8 0.16
15 19 0.38
16 9 0.18
17 14 0.28
ACGTcount: A:0.17, C:0.01, G:0.10, T:0.71
Consensus pattern (15 bp):
TTTTTTTTATGATGA
Found at i:16511 original size:15 final size:15
Alignment explanation
Indices: 16435--16513 Score: 79
Period size: 17 Copynumber: 5.0 Consensus size: 15
16425 TGATTTTGAT
16435 TTGATTTTTTTTTTA
1 TTGATTTTTTTTTTA
*
16450 -TGATAATTTTTTTTA
1 TTGAT-TTTTTTTTTA
*
16465 TGATGATTTTTTTTTGA
1 T--TGATTTTTTTTTTA
*
16482 TGATGATCTTTTTTTTA
1 T--TGATTTTTTTTTTA
16499 TTGATTTTTTTTTTA
1 TTGATTTTTTTTTTA
16514 ATTTCTTAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.07
15 22 0.41
17 24 0.44
18 4 0.07
ACGTcount: A:0.18, C:0.01, G:0.10, T:0.71
Consensus pattern (15 bp):
TTGATTTTTTTTTTA
Found at i:16927 original size:21 final size:22
Alignment explanation
Indices: 16903--16954 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
16893 CTTTTTTTCA
16903 TTTTCATTCAT-TTTTTTAAAT
1 TTTTCATTCATATTTTTTAAAT
* *
16924 TTTTCATTCATCATTTTTTCATT
1 TTTTCATTCAT-ATTTTTTAAAT
16947 TTTTCATT
1 TTTTCATT
16955 TTTTCATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 11 0.41
23 16 0.59
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTCATTCATATTTTTTAAAT
Found at i:16949 original size:31 final size:30
Alignment explanation
Indices: 16900--16980 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
16890 TTTCTTTTTT
16900 TCATTTTCATTCATTTTTTTAAATTTTTCATTCA
1 TCATTTT--TTCA-TTTTTTAAATTTTTCATT-A
* * *
16934 TCATTTTTTCATTTTTTCATTTTTTCATTT
1 TCATTTTTTCATTTTTTAAATTTTTCATTA
* *
16964 TGATTTTTTGATTTTTT
1 TCATTTTTTCATTTTTT
16981 GATTTTTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 15 0.36
31 16 0.38
32 4 0.10
34 7 0.17
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.69
Consensus pattern (30 bp):
TCATTTTTTCATTTTTTAAATTTTTCATTA
Found at i:16956 original size:30 final size:29
Alignment explanation
Indices: 16922--16987 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
16912 ATTTTTTTAA
16922 ATTTTTCATTCATCATTTTTTCATTTTTTC
1 ATTTTTCATT-ATCATTTTTTCATTTTTTC
* * * *
16952 ATTTTTTCATTTTGATTTTTTGATTTTTTG
1 A-TTTTTCATTATCATTTTTTCATTTTTTC
16982 ATTTTT
1 ATTTTT
16988 TGATTTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 5 0.16
30 17 0.55
31 9 0.29
ACGTcount: A:0.15, C:0.09, G:0.05, T:0.71
Consensus pattern (29 bp):
ATTTTTCATTATCATTTTTTCATTTTTTC
Found at i:17121 original size:8 final size:8
Alignment explanation
Indices: 16936--17108 Score: 287
Period size: 8 Copynumber: 21.6 Consensus size: 8
16926 TTCATTCATC
*
16936 ATTTTTTC
1 ATTTTTTG
*
16944 ATTTTTTC
1 ATTTTTTG
*
16952 ATTTTTTC
1 ATTTTTTG
16960 A--TTTTG
1 ATTTTTTG
16966 ATTTTTTG
1 ATTTTTTG
16974 ATTTTTTG
1 ATTTTTTG
16982 ATTTTTTG
1 ATTTTTTG
16990 ATTTTTTG
1 ATTTTTTG
16998 ATTTTTTG
1 ATTTTTTG
17006 ATTTTTTG
1 ATTTTTTG
17014 ATTTTTTG
1 ATTTTTTG
17022 ATTTTTTG
1 ATTTTTTG
17030 ATTTTTTG
1 ATTTTTTG
17038 ATTTTTTG
1 ATTTTTTG
17046 ATTTTTTG
1 ATTTTTTG
17054 ATTTTTTG
1 ATTTTTTG
17062 ATTTTTTG
1 ATTTTTTG
17070 ATTTTTTG
1 ATTTTTTG
17078 ATTTTTTG
1 ATTTTTTG
17086 ATTTTTTTG
1 A-TTTTTTG
17095 ATTTTTTTG
1 A-TTTTTTG
17104 ATTTT
1 ATTTT
17109 ATTTTTTTGT
Statistics
Matches: 161, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
6 5 0.03
8 139 0.86
9 17 0.11
ACGTcount: A:0.13, C:0.02, G:0.10, T:0.75
Consensus pattern (8 bp):
ATTTTTTG
Found at i:25373 original size:19 final size:19
Alignment explanation
Indices: 25361--25398 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
25351 TACTTATTTT
*
25361 GGTCTTGTGTACTTGGTGA
1 GGTCTTGTGTACTTAGTGA
*
25380 GGTCTTGTGTACTTGGTGA
1 GGTCTTGTGTACTTAGTGA
25399 ATATTTGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.37, T:0.42
Consensus pattern (19 bp):
GGTCTTGTGTACTTAGTGA
Found at i:26019 original size:28 final size:28
Alignment explanation
Indices: 25923--26041 Score: 161
Period size: 27 Copynumber: 4.3 Consensus size: 28
25913 AGGTGATCCT
***
25923 AAAATGACCAAAATGCCCCT-GAACATG
1 AAAATGACCAAAATGCCCCTGGATTTTG
* *
25950 CAAATGACCAAAATGCCCCTGGA-TGTG
1 AAAATGACCAAAATGCCCCTGGATTTTG
**
25977 CGAATGACCAAAATGCCCCTGGATTTTG
1 AAAATGACCAAAATGCCCCTGGATTTTG
26005 AAAATGACCAAAATGCCCCTGGATTTTG
1 AAAATGACCAAAATGCCCCTGGATTTTG
26033 AAAATGACC
1 AAAATGACC
26042 CAAGATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
27 43 0.52
28 40 0.48
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGGATTTTG
Found at i:26024 original size:55 final size:54
Alignment explanation
Indices: 25925--26028 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 54
25915 GTGATCCTAA
*
25925 AATGACCAAAATGCCCCTGAACATGCAAATGACCAAAATGCCCCTGGATGTGCG
1 AATGACCAAAATGCCCCTGAACATGAAAATGACCAAAATGCCCCTGGATGTGCG
***
25979 AATGACCAAAATGCCCCTGGATTTTGAAAATGACCAAAATGCCCCTGGAT
1 AATGACCAAAATGCCCCT-GAACATGAAAATGACCAAAATGCCCCTGGAT
26029 TTTGAAAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 18 0.40
55 27 0.60
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (54 bp):
AATGACCAAAATGCCCCTGAACATGAAAATGACCAAAATGCCCCTGGATGTGCG
Found at i:26714 original size:19 final size:18
Alignment explanation
Indices: 26690--26736 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 18
26680 GTTCAACGAT
26690 ATCTCCATG-TTCTTCTTGC
1 ATCTCCATGCTTC--CTTGC
26709 ATCTCCATGCTTCCTTGC
1 ATCTCCATGCTTCCTTGC
26727 A-CTCCATGCT
1 ATCTCCATGCT
26737 CATCCTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.33
18 6 0.22
19 9 0.33
20 3 0.11
ACGTcount: A:0.13, C:0.36, G:0.11, T:0.40
Consensus pattern (18 bp):
ATCTCCATGCTTCCTTGC
Found at i:29528 original size:2 final size:2
Alignment explanation
Indices: 29521--29547 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29511 CTCACAAATA
29521 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
29548 ATTACCAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:29967 original size:21 final size:21
Alignment explanation
Indices: 29943--29983 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29933 AGAACCCTAA
29943 TTTGAACCACTTAAATCCAAT
1 TTTGAACCACTTAAATCCAAT
* * *
29964 TTTGTACCATTTGAATCCAA
1 TTTGAACCACTTAAATCCAA
29984 CAGGGTTCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (21 bp):
TTTGAACCACTTAAATCCAAT
Found at i:30097 original size:19 final size:18
Alignment explanation
Indices: 30073--30111 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
30063 ATTTCAATCC
30073 AATTAGGGCTAATTGCACA
1 AATTAGGGC-AATTGCACA
**
30092 AATTAGTTCAATTGCACA
1 AATTAGGGCAATTGCACA
30110 AA
1 AA
30112 ACCAAGAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (18 bp):
AATTAGGGCAATTGCACA
Found at i:32086 original size:27 final size:27
Alignment explanation
Indices: 32056--32128 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
32046 AGGGTCACCT
*
32056 AGGGGCATTTTGGTTATTTTTACACTA
1 AGGGGCATTTTGGTCATTTTTACACTA
* * * *
32083 A-GGGCATTTTGGTCATTTATGCATTC
1 AGGGGCATTTTGGTCATTTTTACACTA
*
32109 AGGGGCATGTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
32129 AAGTCCACTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.42
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTTACACTA
Found at i:32308 original size:25 final size:25
Alignment explanation
Indices: 32280--32338 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
32270 GTATTGTTAC
32280 ATTTTAATCATGTA-GCTCAAATCTA
1 ATTTTAATCATGTACG-TCAAATCTA
* *
32305 ATTTCATTCATGTACGTCAAATCTA
1 ATTTTAATCATGTACGTCAAATCTA
32330 A-TTTAATCA
1 ATTTTAATCA
32339 ACTAATTGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 6 0.21
25 22 0.76
26 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.41
Consensus pattern (25 bp):
ATTTTAATCATGTACGTCAAATCTA
Found at i:35030 original size:20 final size:20
Alignment explanation
Indices: 34982--35047 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
34972 GATTGATTTG
*
34982 TAAAT-AAAGATTGAATTTT
1 TAAATAAAAGATTGAATCTT
* *
35001 TAAGTGAAAGATTGAATCTT
1 TAAATAAAAGATTGAATCTT
35021 TAAATAAAAGA-TGAAATCTT
1 TAAATAAAAGATTG-AATCTT
*
35041 TGAATAA
1 TAAATAA
35048 TGTGAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
19 6 0.15
20 34 0.85
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.35
Consensus pattern (20 bp):
TAAATAAAAGATTGAATCTT
Done.