Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015878.1 Corchorus capsularis cultivar CVL-1 contig15899, 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: 67627
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8198 original size:40 final size:38
Alignment explanation
Indices: 8103--8198 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 38
8093 GATTAAAAAA
* * *
8103 AAAAGTAGTAATCAGTCAATTGGTAATTAAGAGGAAGT
1 AAAAGTAGTAATCAGTAAATTGATAATTAAGAGGAAGC
* * *
8141 AAAAGAATTAATTAGTAAATTGATAATTAAGAGAGGAAGC
1 AAAAGTAGTAATCAGTAAATTGATAATT-A-AGAGGAAGC
*
8181 AAAAGTAGCAATCAGTAA
1 AAAAGTAGTAATCAGTAA
8199 TTAAGGGTCA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
38 23 0.50
39 1 0.02
40 22 0.48
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (38 bp):
AAAAGTAGTAATCAGTAAATTGATAATTAAGAGGAAGC
Found at i:8217 original size:32 final size:32
Alignment explanation
Indices: 8181--8249 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
8171 GAGAGGAAGC
*
8181 AAAAGTAGCAA-TCAGTAATTAAGGGTCAAAGT
1 AAAAG-AGCAAGTCAGTAATTAAGAGTCAAAGT
* * *
8213 AAAAGGGTAAGTCAGTAATTAAGAGTCAAGGT
1 AAAAGAGCAAGTCAGTAATTAAGAGTCAAAGT
8245 AAAAG
1 AAAAG
8250 GATTAATAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 3 0.09
32 29 0.91
ACGTcount: A:0.48, C:0.07, G:0.25, T:0.20
Consensus pattern (32 bp):
AAAAGAGCAAGTCAGTAATTAAGAGTCAAAGT
Found at i:8405 original size:32 final size:32
Alignment explanation
Indices: 8363--8439 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
8353 AAGAAAAGAG
* * *
8363 GAAGTGATCAGTAGAATGGGGTGAAAGTAAAA
1 GAAGTAATCAGTAGAATAGAGTGAAAGTAAAA
*
8395 GAAGTAATCAGTAGAATAGAGTGAAAGTAAAT
1 GAAGTAATCAGTAGAATAGAGTGAAAGTAAAA
8427 GAAGTAATCAGTA
1 GAAGTAATCAGTA
8440 AGTTGGTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.47, C:0.04, G:0.29, T:0.21
Consensus pattern (32 bp):
GAAGTAATCAGTAGAATAGAGTGAAAGTAAAA
Found at i:8462 original size:40 final size:40
Alignment explanation
Indices: 8412--8522 Score: 161
Period size: 40 Copynumber: 2.8 Consensus size: 40
8402 TCAGTAGAAT
* * **
8412 AGAGTGAAAGTAAATGAAGTAATCAGTAAGTTGGTAATTA
1 AGAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTA
8452 AGAGTAAAAGTAAAAGAAGTAATCA-TAAAAATGGTAATTA
1 AGAGTAAAAGTAAAAGAAGTAATCAGT-AAAATGGTAATTA
*
8492 AGAGTAACAGTAAAAGAAGTAATCAGTAAAA
1 AGAGTAAAAGTAAAAGAAGTAATCAGTAAAA
8523 GTAAAGAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.02
40 62 0.97
41 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.23
Consensus pattern (40 bp):
AGAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTA
Found at i:8518 original size:16 final size:15
Alignment explanation
Indices: 8494--8523 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
8484 GGTAATTAAG
8494 AGTAACAGTAAAAGA
1 AGTAACAGTAAAAGA
8509 AGTAATCAGTAAAAG
1 AGTAA-CAGTAAAAG
8524 TAAAGAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.07, G:0.20, T:0.17
Consensus pattern (15 bp):
AGTAACAGTAAAAGA
Found at i:8652 original size:7 final size:7
Alignment explanation
Indices: 8636--8942 Score: 182
Period size: 7 Copynumber: 43.6 Consensus size: 7
8626 AAGAAAAATG
*
8636 GTAAAAA
1 GTAAAGA
8643 GTAAAGA
1 GTAAAGA
**
8650 GTAATCA
1 GTAAAGA
8657 GTAAAG-
1 GTAAAGA
* *
8663 GAAAAATA
1 G-TAAAGA
8671 GTAAAGA
1 GTAAAGA
8678 GTAAAGA
1 GTAAAGA
8685 GTAAAGA
1 GTAAAGA
8692 GTAAAGA
1 GTAAAGA
**
8699 GTAATCA
1 GTAAAGA
8706 GTAAAGA
1 GTAAAGA
*
8713 -AAAATG-
1 GTAAA-GA
*
8719 GTAAAAA
1 GTAAAGA
8726 GTAAAGA
1 GTAAAGA
8733 GTAATCAGA
1 GTAA--AGA
*
8742 -AAAAG-
1 GTAAAGA
* *
8747 GAAAATA
1 GTAAAGA
8754 GTAAAGA
1 GTAAAGA
8761 GTAAAGA
1 GTAAAGA
8768 GTAAAGA
1 GTAAAGA
8775 GTAAAGA
1 GTAAAGA
8782 GTAAAGA
1 GTAAAGA
**
8789 GTAATTA
1 GTAAAGA
* *
8796 TTAAAAA
1 GTAAAGA
8803 TGGTAAAGA
1 --GTAAAGA
8812 GTAAAGA
1 GTAAAGA
**
8819 GTAATCA
1 GTAAAGA
8826 GTAAAG-
1 GTAAAGA
*
8832 G-AAAAA
1 GTAAAGA
*
8838 TGGTGAAGA
1 --GTAAAGA
8847 GTAAAGA
1 GTAAAGA
* **
8854 ATAATCA
1 GTAAAGA
*
8861 GTAAGGA
1 GTAAAGA
**
8868 GTAATTA
1 GTAAAGA
8875 GTAAAGA
1 GTAAAGA
8882 GTAAAAAGA
1 GT--AAAGA
8891 GTAAAGA
1 GTAAAGA
8898 GTAAAGA
1 GTAAAGA
**
8905 GTAATCA
1 GTAAAGA
8912 GTAAAGA
1 GTAAAGA
*
8919 -AAAATG-
1 GTAAA-GA
*
8925 GTAAAAA
1 GTAAAGA
8932 GTAAAGA
1 GTAAAGA
8939 GTAA
1 GTAA
8943 TCAGTAAAAG
Statistics
Matches: 226, Mismatches: 54, Indels: 40
0.71 0.17 0.12
Matches are distributed among these distances:
5 3 0.01
6 14 0.06
7 187 0.83
8 4 0.02
9 18 0.08
ACGTcount: A:0.57, C:0.02, G:0.23, T:0.18
Consensus pattern (7 bp):
GTAAAGA
Found at i:8910 original size:51 final size:49
Alignment explanation
Indices: 8811--8918 Score: 146
Period size: 51 Copynumber: 2.2 Consensus size: 49
8801 AATGGTAAAG
*
8811 AGTAAAGAGTAATCAGTAAAGGAAAAATGGTGAAGAGTAAAGAATAATC
1 AGTAAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATC
* * *
8860 AGTAAGGAGTAATTAGTAAAGAGTAAAAA-GAGTAAAGAGTAAAGAGTAATC
1 AGTAAAGAGTAATCAGTAAAG-G-AAAAATG-GTAAAGAGTAAAGAATAATC
8911 AGTAAAGA
1 AGTAAAGA
8919 AAAATGGTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
49 19 0.37
50 2 0.04
51 30 0.59
ACGTcount: A:0.54, C:0.03, G:0.25, T:0.19
Consensus pattern (49 bp):
AGTAAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATC
Found at i:8960 original size:35 final size:35
Alignment explanation
Indices: 8860--9021 Score: 193
Period size: 35 Copynumber: 4.6 Consensus size: 35
8850 AAGAATAATC
* * * *
8860 AGTAAGGAGTAATTAGTAAAGAGTAA-AAAGAGTAAAG
1 AGTAAAGAGTAATCAGTAAA-AG-AAGAATG-GTAAAA
*
8897 AGTAAAGAGTAATCAGT-AAAGAAAAATGGTAAAA
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
8931 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
* * *
8966 AGTAAAGTGTAATCAGTAAAGGAAGAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
* *
9001 AGTGAAGGGTAATCAGTAAAA
1 AGTAAAGAGTAATCAGTAAAA
9022 AGATAATTAG
Statistics
Matches: 112, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
34 24 0.21
35 71 0.63
36 2 0.02
37 15 0.13
ACGTcount: A:0.54, C:0.02, G:0.25, T:0.19
Consensus pattern (35 bp):
AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
Found at i:9164 original size:22 final size:22
Alignment explanation
Indices: 9081--9227 Score: 122
Period size: 22 Copynumber: 6.8 Consensus size: 22
9071 ATAATAATGA
*
9081 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGTAAAAAGTAAAATAG
* * * *
9103 TAGTTAGT-AAGAGCAAAAT-G
1 TAATCAGTAAAAAGTAAAATAG
* ** *
9123 ATAATCAGT-GAGGGTAAAATGG
1 -TAATCAGTAAAAAGTAAAATAG
9145 TAATCAGTAAAAAGTAAAATAG
1 TAATCAGTAAAAAGTAAAATAG
*
9167 TAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAAAGTAA-AATAG
* * *
9189 AAATCAGTAAAGAGTAAGATAG
1 TAATCAGTAAAAAGTAAAATAG
*
9211 TAATCAGTAAAAGGTAA
1 TAATCAGTAAAAAGTAA
9228 TCAGTAAGAG
Statistics
Matches: 98, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.01
21 31 0.32
22 64 0.65
23 2 0.02
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.22
Consensus pattern (22 bp):
TAATCAGTAAAAAGTAAAATAG
Found at i:9168 original size:15 final size:15
Alignment explanation
Indices: 9150--9213 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
9140 AATGGTAATC
9150 AGTAAAAAGTAAAAT
1 AGTAAAAAGTAAAAT
**
9165 AGTAATCAGTAAAA-
1 AGTAAAAAGTAAAAT
* *
9179 AGTAAGAAG-GAAAT
1 AGTAAAAAGTAAAAT
* *
9193 CAGTAAAGAGTAAGAT
1 -AGTAAAAAGTAAAAT
9209 AGTAA
1 AGTAA
9214 TCAGTAAAAG
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
13 3 0.08
14 7 0.19
15 24 0.65
16 3 0.08
ACGTcount: A:0.58, C:0.03, G:0.20, T:0.19
Consensus pattern (15 bp):
AGTAAAAAGTAAAAT
Found at i:9249 original size:35 final size:37
Alignment explanation
Indices: 9179--9254 Score: 111
Period size: 35 Copynumber: 2.1 Consensus size: 37
9169 ATCAGTAAAA
*
9179 AGTAAGAAGGAAATCAGTAAAGAGTAAGATAGTAATC
1 AGTAAGAAGGAAATCAGTAAAGAGTAAAATAGTAATC
* *
9216 AGTAA-AAGGTAATCAGT-AAGAGTAAAATGGTAATC
1 AGTAAGAAGGAAATCAGTAAAGAGTAAAATAGTAATC
9251 AGTA
1 AGTA
9255 TGAGCAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 20 0.56
36 11 0.31
37 5 0.14
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.21
Consensus pattern (37 bp):
AGTAAGAAGGAAATCAGTAAAGAGTAAAATAGTAATC
Found at i:9263 original size:21 final size:20
Alignment explanation
Indices: 9112--9317 Score: 122
Period size: 21 Copynumber: 10.1 Consensus size: 20
9102 GTAGTTAGTA
* *
9112 AGAGCAAAATGATAATCAGT
1 AGAGTAAAATGGTAATCAGT
*
9132 GAGGGTAAAATGGTAATCAGT
1 -AGAGTAAAATGGTAATCAGT
* *
9153 AAAAAGTAAAATAGTAATCAGT
1 --AGAGTAAAATGGTAATCAGT
* *
9175 AAAAAGTAAGAA-GGAAATCAGT
1 --AGAGTAA-AATGGTAATCAGT
* *
9197 AAAGAGTAAGATAGTAATC---
1 --AGAGTAAAATGGTAATCAGT
9216 --AGTAAAA-GGTAATCAGT
1 AGAGTAAAATGGTAATCAGT
9233 AAGAGTAAAATGGTAATCAGT
1 -AGAGTAAAATGGTAATCAGT
* *
9254 ATGAGCAAAATGGTAATTAGT
1 A-GAGTAAAATGGTAATCAGT
*
9275 CAGAGTAAAATAGTAATCAGT
1 -AGAGTAAAATGGTAATCAGT
*
9296 AAAGAGTAAAA-GGTGATCAGT
1 --AGAGTAAAATGGTAATCAGT
9317 A
1 A
9318 ATTCAAAGAG
Statistics
Matches: 149, Mismatches: 23, Indels: 28
0.75 0.12 0.14
Matches are distributed among these distances:
14 6 0.04
15 6 0.04
19 1 0.01
20 8 0.05
21 69 0.46
22 57 0.38
23 2 0.01
ACGTcount: A:0.50, C:0.06, G:0.23, T:0.22
Consensus pattern (20 bp):
AGAGTAAAATGGTAATCAGT
Found at i:9438 original size:27 final size:27
Alignment explanation
Indices: 9379--9457 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
9369 GGTAATCAAT
* *
9379 AAAAGAGAGTAAGAAAAGAGTAATTAGTG
1 AAAA-AGAGTAAGAAAAGAGTAA-AAATG
9408 -AAAAGAGTAAGAAAAGAGTAAAAATG
1 AAAAAGAGTAAGAAAAGAGTAAAAATG
*
9434 AAAAA-AGT-AGCAAA-AGTAAAAATG
1 AAAAAGAGTAAGAAAAGAGTAAAAATG
9458 GTAATCAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 10 0.22
25 5 0.11
26 6 0.13
27 22 0.48
28 3 0.07
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.14
Consensus pattern (27 bp):
AAAAAGAGTAAGAAAAGAGTAAAAATG
Found at i:17474 original size:21 final size:21
Alignment explanation
Indices: 17450--17500 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
17440 TCAAGATTTG
*
17450 AAGGAAAAGCAAAAAA-GAAGA
1 AAGGAAAAG-AAAAAATGAAAA
17471 AAGGAAAAGAAAAAATGAAAA
1 AAGGAAAAGAAAAAATGAAAA
17492 AATGGAAAA
1 AA-GGAAAA
17501 ATCAGAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 6 0.22
21 15 0.56
22 6 0.22
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.04
Consensus pattern (21 bp):
AAGGAAAAGAAAAAATGAAAA
Found at i:22889 original size:10 final size:11
Alignment explanation
Indices: 22865--22899 Score: 56
Period size: 10 Copynumber: 3.4 Consensus size: 11
22855 ACCCTTAGGA
22865 AAAACTAGAAG
1 AAAACTAGAAG
22876 AAAACTAG-AG
1 AAAACTAGAAG
22886 AAAA-TAGAAG
1 AAAACTAGAAG
22896 AAAA
1 AAAA
22900 GAAATTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 3 0.13
10 12 0.52
11 8 0.35
ACGTcount: A:0.69, C:0.06, G:0.17, T:0.09
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:23510 original size:15 final size:16
Alignment explanation
Indices: 23475--23559 Score: 93
Period size: 16 Copynumber: 5.4 Consensus size: 16
23465 GGCAGTTTTC
23475 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
23491 TCGGGTCA-TCTGGG-T
1 TCGGGTCATTC-GGGTT
*
23506 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
23522 TCGGGTCATACGAGTT
1 TCGGGTCATTCGGGTT
* * *
23538 TTGGGTCATTTGGGTC
1 TCGGGTCATTCGGGTT
23554 TCGGGT
1 TCGGGT
23560 TGGACGGGTT
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
15 13 0.23
16 43 0.77
ACGTcount: A:0.08, C:0.16, G:0.38, T:0.38
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:24009 original size:17 final size:16
Alignment explanation
Indices: 23980--24013 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
23970 TCATTACTTC
*
23980 AATTATTATTAATATA
1 AATTATTAATAATATA
23996 AATTAATTAATAATATA
1 AATT-ATTAATAATATA
24013 A
1 A
24014 CTACCCATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTATTAATAATATA
Found at i:24379 original size:16 final size:15
Alignment explanation
Indices: 24359--24477 Score: 89
Period size: 16 Copynumber: 7.5 Consensus size: 15
24349 AGATAAGGGT
*
24359 TTCGGGTCATACGGG
1 TTCGGGTCATTCGGG
24374 TCTCGGGTCACTT-GGG
1 T-TCGGGTCA-TTCGGG
24390 TTACGGGTCA-TCTGGG
1 TT-CGGGTCATTC-GGG
* *
24406 TTACGAGTCATTTGGG
1 TT-CGGGTCATTCGGG
*
24422 TCTCGGGTCATTTGGG
1 T-TCGGGTCATTCGGG
24438 TTGCGGGTCATTCGGG
1 TT-CGGGTCATTCGGG
***
24454 TCTCGGGTCGGGCGGG
1 T-TCGGGTCATTCGGG
24470 TTCGGGTC
1 TTCGGGTC
24478 GTTTACTTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
14 1 0.01
15 10 0.11
16 72 0.83
17 4 0.05
ACGTcount: A:0.08, C:0.20, G:0.40, T:0.31
Consensus pattern (15 bp):
TTCGGGTCATTCGGG
Found at i:24421 original size:32 final size:31
Alignment explanation
Indices: 24355--24462 Score: 112
Period size: 32 Copynumber: 3.4 Consensus size: 31
24345 TAAAAGATAA
* *
24355 GGGTTTCGGGTCATAC-GGGTCTCGGGTCACTT
1 GGGTCTCGGGTCAT-CTGGGT-TCGGGTCATTT
*
24387 GGGT-TACGGGTCATCTGGGTTACGAGTCATTT
1 GGGTCT-CGGGTCATCTGGGTT-CGGGTCATTT
* *
24419 GGGTCTCGGGTCATTTGGGTTGCGGGTCATTC
1 GGGTCTCGGGTCATCTGGGTT-CGGGTCATTT
24451 GGGTCTCGGGTC
1 GGGTCTCGGGTC
24463 GGGCGGGTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
31 3 0.05
32 62 0.94
33 1 0.02
ACGTcount: A:0.09, C:0.19, G:0.39, T:0.32
Consensus pattern (31 bp):
GGGTCTCGGGTCATCTGGGTTCGGGTCATTT
Found at i:24518 original size:15 final size:16
Alignment explanation
Indices: 24498--24533 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
24488 TCTGATCAAA
24498 TCGGGTT-GGGCGGGT
1 TCGGGTTCGGGCGGGT
24513 TCGGGTTCGGGCGGGT
1 TCGGGTTCGGGCGGGT
24529 T-GGGT
1 TCGGGT
24534 GGGTTCTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.00, C:0.14, G:0.58, T:0.28
Consensus pattern (16 bp):
TCGGGTTCGGGCGGGT
Found at i:24675 original size:19 final size:18
Alignment explanation
Indices: 24638--24677 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
24628 TTATTGAAAT
*
24638 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
24656 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
24675 AAT
1 AAT
24678 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:29552 original size:88 final size:87
Alignment explanation
Indices: 29445--29614 Score: 322
Period size: 88 Copynumber: 1.9 Consensus size: 87
29435 CTCTTTGCAT
29445 AGAGGGGTGCGGCAACTCTAGGGATTCCGCCCCCTTCAAGTTTTGTAAGTTTTCTTATGCCTCTC
1 AGAGGGGTGCGGCAACTCTAGGGATTCCGCCCCCTTCAAGTTTTGTAAGTTTTCTTATGCCTCTC
29510 ATGGATTTTGAGAAATCGGCAA
66 ATGGATTTTGAGAAATCGGCAA
*
29532 AGAGAGGGTGCGGCACCTCTAGGGATTCCGCCCCCTTCAAGTTTTGTAAGTTTTCTTATGCCTCT
1 AGAG-GGGTGCGGCAACTCTAGGGATTCCGCCCCCTTCAAGTTTTGTAAGTTTTCTTATGCCTCT
29597 CATGGATTTTGAGAAATC
65 CATGGATTTTGAGAAATC
29615 CATGAGCAGC
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
87 4 0.05
88 77 0.95
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (87 bp):
AGAGGGGTGCGGCAACTCTAGGGATTCCGCCCCCTTCAAGTTTTGTAAGTTTTCTTATGCCTCTC
ATGGATTTTGAGAAATCGGCAA
Found at i:36388 original size:19 final size:19
Alignment explanation
Indices: 36353--36391 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
36343 AAAGGGTAGT
*
36353 TAAAAAAAAATCTTTTTCA
1 TAAAAAAAAATCGTTTTCA
36372 TAAAAAAAAAGT-GTTTTCA
1 TAAAAAAAAA-TCGTTTTCA
36391 T
1 T
36392 GCAAGAGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (19 bp):
TAAAAAAAAATCGTTTTCA
Found at i:44125 original size:303 final size:303
Alignment explanation
Indices: 43573--44158 Score: 823
Period size: 303 Copynumber: 1.9 Consensus size: 303
43563 TCAAGCAGAA
* * * *
43573 GATGATGAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTTTGTACTCTTCTTTGCACTTGC
1 GATGATGAAATGTCGATAACTGACGCACATGTGTTCCACGTTTTTATACTCTTCTTTGCAATTGC
* * * * *
43638 TGGCTCACTCAAATTTTTATATATAGGGTCTTAAAGAGTCTTCTTTACAAATGCATCGTGAAAAA
66 TGACTCACTCAAATCTTTATATAAAGGATCTTAAAGAGTCTTCTTAACAAATGCATCGTGAAAAA
** * * *
43703 CTTTACCCAATACCTTGAGTTCACCGCAAAAATTCTTATTGAAAGCTCCGGTCTTGAATATACTT
131 CTTTACCCAATACCACGAGTTCACCGCAAAAATTCTTAGTGAAAGCTCCGGTATAGAATATACTT
* * ** * *
43768 GTGAAAACTTCCCTGGCACAGGGTAGTTCCATTTTTGTTTTGCAATTGTTTTCCTTAATAATCAA
196 GTGAAAACTTCCCTGGAACAGGGCAGGCCCATTTTTGTCTTGCAATTATTTTCCTTAATAATCAA
*
43833 GTCGGGGTTCTT-TGCAGGTGAAATGACTCCGCTTGCAGAAGAG
261 GTCGGGGTT-TTCTGCAGATGAAATGACTCCGCTTGCAGAAGAG
* * * *
43876 GATGGTGAAATGTCGATAAGTGACGCACATGTGTTCCATGTTTTTATACTCTTCTTTGCAATTGT
1 GATGATGAAATGTCGATAACTGACGCACATGTGTTCCACGTTTTTATACTCTTCTTTGCAATTGC
* * * * *
43941 TGACTCGCTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCATCGTGACAAA
66 TGACTCACTCAAATCTTTATATAAAGGATCTTAAAGAGTCTTCTTAACAAATGCATCGTGAAAAA
* * * * *
44006 CTTTACCCTATACCACGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAGAATATTCTT
131 CTTTACCCAATACCACGAGTTCACCGCAAAAATTCTTAGTGAAAGCTCCGGTATAGAATATACTT
*
44071 GTGAAAACTTCCCTGGAACAGGGCAGGCCCATTTTTGTCTTGCAATTATTTTCCTTAATAATTAA
196 GTGAAAACTTCCCTGGAACAGGGCAGGCCCATTTTTGTCTTGCAATTATTTTCCTTAATAATCAA
*
44136 GTCTGGGTTTTCTGCAGATGAAA
261 GTCGGGGTTTTCTGCAGATGAAA
44159 CATCTCCACT
Statistics
Matches: 245, Mismatches: 37, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
302 2 0.01
303 243 0.99
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (303 bp):
GATGATGAAATGTCGATAACTGACGCACATGTGTTCCACGTTTTTATACTCTTCTTTGCAATTGC
TGACTCACTCAAATCTTTATATAAAGGATCTTAAAGAGTCTTCTTAACAAATGCATCGTGAAAAA
CTTTACCCAATACCACGAGTTCACCGCAAAAATTCTTAGTGAAAGCTCCGGTATAGAATATACTT
GTGAAAACTTCCCTGGAACAGGGCAGGCCCATTTTTGTCTTGCAATTATTTTCCTTAATAATCAA
GTCGGGGTTTTCTGCAGATGAAATGACTCCGCTTGCAGAAGAG
Found at i:49872 original size:30 final size:31
Alignment explanation
Indices: 49838--49912 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
49828 CCAGTTGTGC
** *
49838 CCGGTCTTGTGCGATTGGC-CCATGCCATGG
1 CCGGTCTTGTGCGATTCCCTCCATGCAATGG
* *
49868 CCGGTCATGTGGGA-TCCCTCCATGCAATGG
1 CCGGTCTTGTGCGATTCCCTCCATGCAATGG
*
49898 CTGGTCTTGTGCGAT
1 CCGGTCTTGTGCGAT
49913 GGCATCCTCT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 2 0.06
30 33 0.94
ACGTcount: A:0.12, C:0.28, G:0.32, T:0.28
Consensus pattern (31 bp):
CCGGTCTTGTGCGATTCCCTCCATGCAATGG
Found at i:58992 original size:303 final size:303
Alignment explanation
Indices: 58431--59031 Score: 907
Period size: 303 Copynumber: 2.0 Consensus size: 303
58421 AGCTTCTCAA
58431 GCAGAAGAAGATGGTCAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTTTGTACTCTTCTT
1 GCAGAAGAAGATGGTCAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTTTGTACTCTTCTT
* * * * * *
58496 TGCAATTGCTGACTCACTCAAATTTTTATATATAGGGTCTTCAAGAGTCTTCTTTACAAATGCAT
66 CGCAATTGCTGACTCACTCAAATCTTTATACAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
* * **
58561 CGTGACAAACTTCACCCAATACCTTGAGATCACCGCAACACTTCTTAGTGACAGCTCCGGTTTTG
131 CGTGACAAACTTCACCCAATACCATGAGATCACCGCAACACTTCTTAGTGACAGCTCCGGTATAA
* ** *
58626 AATATACTTGTGAAAACTTCCCTGGCACAGGGCAGTTCCAGTTTTGTTTAGCAATTGTTTTCCTT
196 AATATACTTGTGAAAACTTCCCTGGAACAGGGCAGGCCCAGTTTTGTTTAGCAATTATTTTCCTT
* * * *
58691 AATAATCAAGTCGGGGTTTTTTGTAGGTGAAATGACTCCACTT
261 AATAATCAAGTCGGGGTTTTCTGCAGATGAAACGACTCCACTT
* * * *
58734 GCAGAAGAGGATGGTGAAATGTCGATGACTGAGGCACATGTGTTCCATGTTTTTGTACTTTTCTT
1 GCAGAAGAAGATGGTCAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTTTGTACTCTTCTT
* * * *
58799 CGCAATTGTTGACTCGCTTAAGTCTTTATACAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
66 CGCAATTGCTGACTCACTCAAATCTTTATACAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
* *
58864 CGTGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAA
131 CGTGACAAACTTCACCCAATACCATGAGATCACCGCAACACTTCTTAGTGACAGCTCCGGTATAA
* *
58929 AATATTCTTGTGAAAACTTCCCTGGAACAGGGCAGGCCCATTTTTGTCTT-GCAATTATTTTCCT
196 AATATACTTGTGAAAACTTCCCTGGAACAGGGCAGGCCCAGTTTTGT-TTAGCAATTATTTTCCT
*
58993 TAATAATCAAGTCTGGGTTTTCTGCAGATGAAACGACTC
260 TAATAATCAAGTCGGGGTTTTCTGCAGATGAAACGACTC
59032 TGCTTGTTAA
Statistics
Matches: 266, Mismatches: 31, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
303 264 0.99
304 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (303 bp):
GCAGAAGAAGATGGTCAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTTTGTACTCTTCTT
CGCAATTGCTGACTCACTCAAATCTTTATACAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
CGTGACAAACTTCACCCAATACCATGAGATCACCGCAACACTTCTTAGTGACAGCTCCGGTATAA
AATATACTTGTGAAAACTTCCCTGGAACAGGGCAGGCCCAGTTTTGTTTAGCAATTATTTTCCTT
AATAATCAAGTCGGGGTTTTCTGCAGATGAAACGACTCCACTT
Found at i:60831 original size:303 final size:303
Alignment explanation
Indices: 60279--60863 Score: 893
Period size: 303 Copynumber: 1.9 Consensus size: 303
60269 TGCTTCTCAA
* *
60279 GCAGAAGAAGATGGTGAAATGTCGATGACTGAGGCACATGTGTTCCACGTTTTCGTACTCTTCTT
1 GCAGAAGAAGATGGTGAAATATCGATGACTGAGGCACATGTGTTCCACGTTTTCATACTCTTCTT
* * * *
60344 TGCAATTGCTGACTCACTCAAATTTTTATATATAGGGTCTTCAAGAGTCTTCTTTACAAATGCAT
66 TGCAATTGCTGACTCACTCAAATCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
* *
60409 CGTGACAAACTTTACCCAATACCTTGAGATCACCGCAACACTTCTTAGTGACAGCTCCGGTTTTG
131 CGTGACAAACTTTACCCAATACCATGAGATCACCGCAACACTTCTTAGTGACAGCTCCGGTTATG
* ** * * *
60474 AATATACTTGTGAAAACTTCCCTGGCACAGGGCAGTTCTAGTTTTGTTTTGCAATTGCTTTCCTT
196 AATATACTTGTGAAAACTTCCCTGGAACAGGGCAGACCCAGTTTTGTCTTGCAATTACTTTCCTT
60539 AATAATCAAGTCGGGGTTTTCTGCAGGTGAAATAACTCCGCTT
261 AATAATCAAGTCGGGGTTTTCTGCAGGTGAAATAACTCCGCTT
* ** * *
60582 GCAGAAGAGGATGGTGAAATATTTATGACTGAGGCACATGTGTTCCATGTTTTTATACTCTTCTT
1 GCAGAAGAAGATGGTGAAATATCGATGACTGAGGCACATGTGTTCCACGTTTTCATACTCTTCTT
* * * *
60647 TGCAATTGTTGACTCGCTTAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
66 TGCAATTGCTGACTCACTCAAATCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
* * *
60712 CGTGACAAACTTTACCTAATACCATGAGTTCACTGCAACACTTCTTAGTGACAGCTCCGG-TATG
131 CGTGACAAACTTTACCCAATACCATGAGATCACCGCAACACTTCTTAGTGACAGCTCCGGTTATG
* *
60776 AAATATACTTGTGAAAACTTCCCTGGAACAGGGCAGACCCATTTTTGTCTTGCAATTATTTTCCT
196 -AATATACTTGTGAAAACTTCCCTGGAACAGGGCAGACCCAGTTTTGTCTTGCAATTACTTTCCT
*
60841 TAATAATCAAGTCTGGGTTTTCT
260 TAATAATCAAGTCGGGGTTTTCT
60864 ACAGCTGAGT
Statistics
Matches: 252, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
302 3 0.01
303 249 0.99
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (303 bp):
GCAGAAGAAGATGGTGAAATATCGATGACTGAGGCACATGTGTTCCACGTTTTCATACTCTTCTT
TGCAATTGCTGACTCACTCAAATCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
CGTGACAAACTTTACCCAATACCATGAGATCACCGCAACACTTCTTAGTGACAGCTCCGGTTATG
AATATACTTGTGAAAACTTCCCTGGAACAGGGCAGACCCAGTTTTGTCTTGCAATTACTTTCCTT
AATAATCAAGTCGGGGTTTTCTGCAGGTGAAATAACTCCGCTT
Found at i:60875 original size:21 final size:21
Alignment explanation
Indices: 60850--60892 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
60840 TTAATAATCA
60850 AGTCTGGGTTTTCTACAGCTG
1 AGTCTGGGTTTTCTACAGCTG
60871 AGTCTGGGTTTTCTACAGCTG
1 AGTCTGGGTTTTCTACAGCTG
60892 A
1 A
60893 AATGACTCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.37
Consensus pattern (21 bp):
AGTCTGGGTTTTCTACAGCTG
Found at i:62947 original size:18 final size:19
Alignment explanation
Indices: 62924--62975 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
62914 TTTCCCTTTT
62924 TTATTTCCTTATTTCTC-C
1 TTATTTCCTTATTTCTCTC
62942 TTATTTTCCTTA-TTCTCTC
1 TTA-TTTCCTTATTTCTCTC
*
62961 TT-TTTCCTTTTTTCT
1 TTATTTCCTTATTTCT
62976 TTACTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.23
18 12 0.40
19 11 0.37
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTCCTTATTTCTCTC
Found at i:65680 original size:303 final size:303
Alignment explanation
Indices: 65128--65712 Score: 861
Period size: 303 Copynumber: 1.9 Consensus size: 303
65118 TGCTTCTCAA
* *
65128 GCAGAAGAAGATGGTTAAATGTCGATGACTGAGACACATGTGTTCCACGTTTTTGTACTCTTCTT
1 GCAGAAGAAGATGGTGAAATGTCGATGACTGAGACACATGTGTTCCACGTTTTTATACTCTTCTT
* * * *
65193 TGCAATTGCTGACTCACTCAAACTTTTATATATAGGGTCCTCAAGAGTCTTCTTTACAAATGCAT
66 CGCAATTGCTGACTCACTCAAACTTTTATATAAAGGATCCTCAAGAGTCTTCTTAACAAATGCAT
* * **
65258 CGTGACAAATTTTACCCAATACCTCGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTTTTG
131 CGTGACAAACTTTACCCAATACCTCGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAA
* * ** * *
65323 AATATACTTGTGAAAACTTACCTGGCACAGGGCCGTTCCAGTTTTGTTTTGCAATTGTTTTCCTT
196 AATATACTTGTGAAAACTTACCTGGAACAGGGCAGGCCCAGTTTTGTCTTGCAATTATTTTCCTT
*
65388 AATAATCAAGTCGGGGTTTTCTGTAGGTGCAATGACTCCGCTT
261 AAAAATCAAGTCGGGGTTTTCTGTAGGTGCAATGACTCCGCTT
* * * *
65431 GCAGAAGAGGATGGTGAAATGTCGATGACTGAGGCACATGTGTTCCATGTTTTTATACTGTTCTT
1 GCAGAAGAAGATGGTGAAATGTCGATGACTGAGACACATGTGTTCCACGTTTTTATACTCTTCTT
* * * * *
65496 CGCAATTGTTGACTCGCT-TAAGTCTTTATATAAAGGATCTTCAAGAGTCTTCTTAACAAATGCA
66 CGCAATTGCTGACTCACTCAAACT-TTTATATAAAGGATCCTCAAGAGTCTTCTTAACAAATGCA
*
65560 TCGTTACAAACTTTACCCAATACCAT-GAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTAT
130 TCGTGACAAACTTTACCCAATACC-TCGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTAT
*
65624 AAAATATACTTGTGAAAACTTCCCTGGAACAGGGCAGGCCCA-TTTTGGTCTTGCAATTATTTTC
194 AAAATATACTTGTGAAAACTTACCTGGAACAGGGCAGGCCCAGTTTT-GTCTTGCAATTATTTTC
*
65688 CTTAAAAATCAAGTCTGGGTTTTCT
258 CTTAAAAATCAAGTCGGGGTTTTCT
65713 ACAGCTGAAA
Statistics
Matches: 250, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
302 7 0.03
303 242 0.97
304 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (303 bp):
GCAGAAGAAGATGGTGAAATGTCGATGACTGAGACACATGTGTTCCACGTTTTTATACTCTTCTT
CGCAATTGCTGACTCACTCAAACTTTTATATAAAGGATCCTCAAGAGTCTTCTTAACAAATGCAT
CGTGACAAACTTTACCCAATACCTCGAGTTCACCGCAACACTTCTTAGTGACAGCTCCGGTATAA
AATATACTTGTGAAAACTTACCTGGAACAGGGCAGGCCCAGTTTTGTCTTGCAATTATTTTCCTT
AAAAATCAAGTCGGGGTTTTCTGTAGGTGCAATGACTCCGCTT
Done.