Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015782.1 Corchorus olitorius cultivar O-4 contig15815, 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: 68884
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:284 original size:154 final size:154
Alignment explanation
Indices: 1--799 Score: 1159
Period size: 154 Copynumber: 5.1 Consensus size: 154
* *
1 AACTTCAAAGTGGACTAATCTCACCAAAATGTTTATAGTTAAGCCATAAACAATGGAAAGAAAAG
1 AACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * ** * *
66 CATTGAGGTTTGCCAAATCGAAGAAGATTCGATACGTCACTAATGGACCCCGATAGGACAAAAAT
66 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAAAAT
131 AACAAGTGTTCCAAATGAGATAAA
131 AACAAGTGTTCCAAATGAGATAAA
*
155 AACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAATGAAAAG
1 AACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
*
220 CATTGAGGTTAGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAAAAT
66 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAAAAT
* * *
285 AACAAGTGTTCTAAATCAGCTAAA
131 AACAAGTGTTCCAAATGAGATAAA
* * *
309 AACTTCACAGTGGACTAATATCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * ** * * *
374 CATTGAGGTTTGCCAAATCGATGAAGATTCAATACGTCATTAATGGGCCCCGATTGGCCCAAAAT
66 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAAAAT
* * *
439 ATCAAGGGTTCCAAATGAGATAAG
131 AACAAGTGTTCCAAATGAGATAAA
**
463 AACTTCACGGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
528 CATTGAGGTTTGCCAAATCGAATACGATTACAAAACGTCAACAAATCGGACCCCGATAGGACCCA
66 CATTGAGGTTTGCCAAATCGAAGACGATT-CAAAACG-GAACTAAT-GGACCCCGATAGG-CCCA
* * *
593 AAATAACAAGTGTTCCCAATGAGCTAGA
127 AAATAACAAGTGTTCCAAATGAGATAAA
*
621 AACTTCAAAGTTGACTAATCTCAACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAGAAA
1 AACTTCAAAGTGGACTAATCTC-ACCAAAATGATTATAGTTAGGCCATAAACAATGG-AAAGAAA
*
686 AGCATTGAGGTTTGCTAAATCGAAGACGATTACAAAACGGAACTAATCGGACCCCGATAGGCCCA
64 AGCATTGAGGTTTGCCAAATCGAAGACGATT-CAAAACGGAACTAAT-GGACCCCGATAGGCCCA
751 AAATAACAAGTGTTCCAAATGA-ACTAAA
127 AAATAACAAGTGTTCCAAATGAGA-TAAA
*
779 AACTTCATAGTGGACTAATCT
1 AACTTCAAAGTGGACTAATCT
800 AATATAAATT
Statistics
Matches: 574, Mismatches: 64, Indels: 10
0.89 0.10 0.02
Matches are distributed among these distances:
154 363 0.63
155 6 0.01
156 4 0.01
157 11 0.02
158 92 0.16
159 54 0.09
160 44 0.08
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
AACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAAAAT
AACAAGTGTTCCAAATGAGATAAA
Found at i:5738 original size:153 final size:157
Alignment explanation
Indices: 5548--5864 Score: 443
Period size: 157 Copynumber: 2.0 Consensus size: 157
5538 ACTTATAATT
* * * *
5548 ATTAAATGTTATTGGATTTGTTGGTAAATGTAATTTTTTTTATAATTTTATAACGT-TTTTTAGT
1 ATTAAATGTTACTGGAATTGTTGATAAATGTAA-TTTTTTTATAATTATATAA--TATTTTTAGT
* * *
5612 AA-T-TGT-GTATTA-TA-A-ATTTGATAGCCCGTTACCTAATTTATTTATAATGAAAATTTACT
63 AACTCTATAGTATTATTATAGATATAATAGCCCGTTACCTAATTTATTTATAATGAAAATTTACT
*
5671 AAATTTGATGGTTCTTG-TATAGTACTTATA
128 AAATTTGATGGTTC-AGATATAGTACTTATA
5701 ATTAAATGTTACTGGAATTGTTGATAAATGTAATTTTTTTATAATTATATAATATTTTTAGTAAC
1 ATTAAATGTTACTGGAATTGTTGATAAATGTAATTTTTTTATAATTATATAATATTTTTAGTAAC
*
5766 TCTATATTATTATTATAGATATAATAGCCCGTTACCTAATTTATTTATAATGAAAATTTACTAAA
66 TCTATAGTATTATTATAGATATAATAGCCCGTTACCTAATTTATTTATAATGAAAATTTACTAAA
* *
5831 TTTGATGGTTCAGATATAGTACTTTTG
131 TTTGATGGTTCAGATATAGTACTTATA
5858 ATTAAAT
1 ATTAAAT
5865 ATATTATATG
Statistics
Matches: 145, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
150 1 0.01
151 10 0.07
152 19 0.13
153 32 0.22
154 5 0.03
155 2 0.01
156 2 0.01
157 74 0.51
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (157 bp):
ATTAAATGTTACTGGAATTGTTGATAAATGTAATTTTTTTATAATTATATAATATTTTTAGTAAC
TCTATAGTATTATTATAGATATAATAGCCCGTTACCTAATTTATTTATAATGAAAATTTACTAAA
TTTGATGGTTCAGATATAGTACTTATA
Found at i:13120 original size:39 final size:39
Alignment explanation
Indices: 13063--13138 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
13053 ACCGGCTTTA
13063 CTGGTTTTGAAAGCCTGGCCTAGAGTAAAATCAATGGAG
1 CTGGTTTTGAAAGCCTGGCCTAGAGTAAAATCAATGGAG
*
13102 CTGGTTTTGAAAGGCTGGCCTAGAGTAAAATCAATGG
1 CTGGTTTTGAAAGCCTGGCCTAGAGTAAAATCAATGG
13139 TTAAGTAGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.26
Consensus pattern (39 bp):
CTGGTTTTGAAAGCCTGGCCTAGAGTAAAATCAATGGAG
Found at i:14899 original size:6 final size:6
Alignment explanation
Indices: 14888--14920 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
14878 TTCTTTCTGT
14888 ATATTA ATATTA ATATTA ATATTA ATATTA ATA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATA
14921 ATCAAAGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:17281 original size:21 final size:21
Alignment explanation
Indices: 17242--17281 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17232 GCTCATGAGC
* * *
17242 ATATGTGGAGACATTTGGTTG
1 ATATGTGGACAAATATGGTTG
17263 ATATGTGGACAAATATGGT
1 ATATGTGGACAAATATGGT
17282 CACATGAAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (21 bp):
ATATGTGGACAAATATGGTTG
Found at i:19709 original size:31 final size:33
Alignment explanation
Indices: 19669--19736 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 33
19659 AAGACAAGAT
*
19669 CTTGCGAGAAAAATAAAG-AGAAAAGCACAGGG
1 CTTGCGAGAAAAATAAAGTAGAAAAGCACAGAG
*
19701 CTTG-GAGAAAAATAAAGTTGAAAAGCACAGAG
1 CTTGCGAGAAAAATAAAGTAGAAAAGCACAGAG
19733 CTTG
1 CTTG
19737 AGTTTTACGC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.47, C:0.12, G:0.26, T:0.15
Consensus pattern (33 bp):
CTTGCGAGAAAAATAAAGTAGAAAAGCACAGAG
Found at i:21017 original size:11 final size:11
Alignment explanation
Indices: 21001--21025 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20991 CATCTTTTAA
21001 TTTTTTCATTT
1 TTTTTTCATTT
21012 TTTTTTCATTT
1 TTTTTTCATTT
21023 TTT
1 TTT
21026 AATTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:21017 original size:19 final size:19
Alignment explanation
Indices: 20995--21031 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20985 TTATTACATC
*
20995 TTTTAATTTTTTCATTTTT
1 TTTTAATTTTTTAATTTTT
*
21014 TTTTCATTTTTTAATTTT
1 TTTTAATTTTTTAATTTT
21032 AAAATTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTAATTTTTTAATTTTT
Found at i:36224 original size:66 final size:66
Alignment explanation
Indices: 36118--36309 Score: 267
Period size: 66 Copynumber: 2.9 Consensus size: 66
36108 TGCCTTCTTG
* ** * **
36118 TCAATTTTCTCTGCAAACACTCTATTGAAATCTCTGTGATTTCCCGATGTTTATTTGAGGCTCCT
1 TCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGAGGCTCCT
36183 A
66 A
* * * * *
36184 TCAATTTTCTATGCAGACACTCTGCTAAAATCTCCGTGATTTCCCGATATTTATTAGAGGCTTCT
1 TCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGAGGCTCCT
36249 A
66 A
* *
36250 TCAACTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCTGATGTTTATCAGAGG
1 TCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGAGG
36310 TTTTAACGCT
Statistics
Matches: 111, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 111 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (66 bp):
TCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGAGGCTCCT
A
Found at i:36551 original size:66 final size:66
Alignment explanation
Indices: 36366--36633 Score: 401
Period size: 66 Copynumber: 4.0 Consensus size: 66
36356 ATCTCTGTGC
*
36366 TTCCTTATCAATTTTCCCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGA
1 TTCC-TATCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGA
36431 GG
65 GG
* * *
36433 CTCCTATTCAATTTTCTCTGTAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAAA
1 TTCCTA-TCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGA
36498 GG
65 GG
* * * ** * * *
36500 TTTCTATCAACTTTCTCTACAGACACTCTAATGAAATCTCTGAGATTTCCCGATGTTTATCAGGG
1 TTCCTATCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGAG
36565 G
66 G
*
36566 TTCCTGTCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGAG
1 TTCCTATCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGAG
36631 G
66 G
36632 TT
1 TT
36634 TTAACACGCT
Statistics
Matches: 176, Mismatches: 24, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
66 112 0.64
67 64 0.36
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (66 bp):
TTCCTATCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGAG
G
Found at i:37505 original size:35 final size:35
Alignment explanation
Indices: 37458--37558 Score: 148
Period size: 35 Copynumber: 2.9 Consensus size: 35
37448 TAGATAAAAC
* *
37458 AATACTAACTCTTCTGGAGCCTTCAATCAAATTTG
1 AATACTAGCTCTTCTGGAGCCTTCAATCAAATGTG
* *
37493 AATACTAGCTCTTCTAGAGCCTCCAATCAAATGTG
1 AATACTAGCTCTTCTGGAGCCTTCAATCAAATGTG
* *
37528 AATGCTAGCTCTTTTGGAGCCTTCAATCAAA
1 AATACTAGCTCTTCTGGAGCCTTCAATCAAA
37559 ATTGCACTAC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (35 bp):
AATACTAGCTCTTCTGGAGCCTTCAATCAAATGTG
Found at i:38413 original size:26 final size:26
Alignment explanation
Indices: 38384--38437 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
38374 CTCTTTCTCT
38384 TAATTGTGTCTTCA-GAACCATTTACA
1 TAATTGTGTCTTCATG-ACCATTTACA
38410 TAATTGTGTCTTCATGACCATTTACA
1 TAATTGTGTCTTCATGACCATTTACA
38436 TA
1 TA
38438 TTTCAACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (26 bp):
TAATTGTGTCTTCATGACCATTTACA
Found at i:39550 original size:27 final size:28
Alignment explanation
Indices: 39502--39562 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
39492 CATTTTTTTC
*
39502 AAAT-ATATTTTTAGATTGCCATTATT-
1 AAATAATATTTTAAGATTGCCATTATTA
39528 AAATAATATTTTAATGATT-CCATTATTA
1 AAATAATATTTTAA-GATTGCCATTATTA
39556 AAATAAT
1 AAATAAT
39563 GGAAATTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 4 0.13
27 16 0.52
28 11 0.35
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.46
Consensus pattern (28 bp):
AAATAATATTTTAAGATTGCCATTATTA
Found at i:40373 original size:20 final size:20
Alignment explanation
Indices: 40334--40374 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40324 AGGGGTGAGC
* **
40334 ATCGGGTCGGTTTCGGTCCA
1 ATCGGGTCGGTTCCACTCCA
40354 ATCGGGTCGGTTCCACTCCA
1 ATCGGGTCGGTTCCACTCCA
40374 A
1 A
40375 AACCGACAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGGGTCGGTTCCACTCCA
Found at i:40493 original size:18 final size:19
Alignment explanation
Indices: 40448--40504 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
40438 AACCGAGAGG
* *
40448 ATTTATATATTA-ATTTAA
1 ATTTATATATTATAATTAT
*
40466 ATTTAAATATTATAATTAT
1 ATTTATATATTATAATTAT
*
40485 A-TTATATATGATTAATTAT
1 ATTTATATATTA-TAATTAT
40504 A
1 A
40505 AAAAAAAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 19 0.59
19 13 0.41
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTTATATATTATAATTAT
Found at i:40548 original size:25 final size:25
Alignment explanation
Indices: 40520--40573 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
40510 AAACAAAACA
40520 TATAATTATA-TATATATAAATATAT
1 TATAATTATATTATATATAAATA-AT
*
40545 TATAATTATATTATATATAATTAAT
1 TATAATTATATTATATATAAATAAT
40570 TATA
1 TATA
40574 TAACAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TATAATTATATTATATATAAATAAT
Found at i:40590 original size:63 final size:65
Alignment explanation
Indices: 40472--40605 Score: 191
Period size: 69 Copynumber: 2.0 Consensus size: 65
40462 TTAAATTTAA
*
40472 ATATTATAATTATATTATATATGATTAATTATAAAAAAAAACAAAACATATAATTATATATATAT
1 ATATTATAATTATATTATATATAATTAATTAT----AAAAACAAAACATATAATTATATATATAT
40537 AAAT
62 AAAT
* *
40541 ATATTATAATTATATTATATATAATTAATTAT-ATAAC-AAATATATAATTATATATATATAAAT
1 ATATTATAATTATATTATATATAATTAATTATAAAAACAAAACATATAATTATATATATATAAAT
40604 AT
1 AT
40606 TTAAAAAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
63 27 0.44
64 4 0.06
69 31 0.50
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (65 bp):
ATATTATAATTATATTATATATAATTAATTATAAAAACAAAACATATAATTATATATATATAAAT
Found at i:42817 original size:21 final size:22
Alignment explanation
Indices: 42791--42869 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
42781 CATATGGAGT
*
42791 TTATCACAATTTCATA-GGTAA
1 TTATCAAAATTTCATAGGGTAA
*
42812 TTATCAAAATTTCATAGGGTAG
1 TTATCAAAATTTCATAGGGTAA
*** *
42834 TTATCTTTATTTAATAGGGTAA
1 TTATCAAAATTTCATAGGGTAA
42856 TTATCAAAATTTCA
1 TTATCAAAATTTCA
42870 AAAAAATATT
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 15 0.33
22 31 0.67
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGTAA
Found at i:42838 original size:43 final size:44
Alignment explanation
Indices: 42769--42869 Score: 118
Period size: 43 Copynumber: 2.3 Consensus size: 44
42759 CATAATTAGG
* *
42769 TTAT-AAAAGTTTCATATGGAGTTTATCACAATTTCATA-GGTAA
1 TTATCAAAA-TTTCATAGGGAGTTTATCACAATTTAATAGGGTAA
***
42812 TTATCAAAATTTCATAGGGTAG-TTATCTTTATTTAATAGGGTAA
1 TTATCAAAATTTCATAGGG-AGTTTATCACAATTTAATAGGGTAA
42856 TTATCAAAATTTCA
1 TTATCAAAATTTCA
42870 AAAAAATATT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
43 25 0.50
44 25 0.50
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.42
Consensus pattern (44 bp):
TTATCAAAATTTCATAGGGAGTTTATCACAATTTAATAGGGTAA
Found at i:55945 original size:196 final size:196
Alignment explanation
Indices: 55596--56034 Score: 751
Period size: 196 Copynumber: 2.3 Consensus size: 196
55586 AGTTGCAAAA
* *
55596 TTTGCAATTAA-GGCCGCGACATACTAGGGTTTAGGTTATTCATCAAATTGGGTTTTATACTTAT
1 TTTGCAATTAAGGGCTGCGACATACTAGGGTTTAGGTTATTCATCAAATTGGGTTTTAGACTTAT
55660 GAAATTTAACCTAATTTCATATATTTAAACCTAATTTAACATTAATTTATTAGGTAATTTCATCA
66 GAAATTTAACCTAATTTCATATATTTAAACCTAATTTAACATTAATTTATTAGGTAATTTCATCA
55725 ATAGGGCCAAAAATAGCAAAATTCCTAAACCTAGAAATTAAATTACAAGCCGCCAAGGTTGTAAT
131 ATAGGGCCAAAAATAGCAAAATTCCTAAACCTAGAAATTAAATTACAAGCCGCCAAGGTTGTAAT
55790 T
196 T
*
55791 TTTGCAAATAAGGGCTGCGACATACTAGGGTTTAGGTTATTCATCAAATTGGGTTTTAGACTTAT
1 TTTGCAATTAAGGGCTGCGACATACTAGGGTTTAGGTTATTCATCAAATTGGGTTTTAGACTTAT
55856 GAAATTTAACCTAATTTCATATATTTAAACCTAATTTAACATTAATTTATT-GGCTAATTTCATC
66 GAAATTTAACCTAATTTCATATATTTAAACCTAATTTAACATTAATTTATTAGG-TAATTTCATC
* *
55920 AATTGGGCCAAAAATAGCAAAATTCCTAAACCTAGAAATTGAATTACAAGCCGCCAAGGTTGTAA
130 AATAGGGCCAAAAATAGCAAAATTCCTAAACCTAGAAATTAAATTACAAGCCGCCAAGGTTGTAA
55985 TT
195 TT
* * * * *
55987 TATGCAATTAAGGGCTGCGGCTTGCTAGGGTTT-GG-AATTCATCAAATT
1 TTTGCAATTAAGGGCTGCGACATACTAGGGTTTAGGTTATTCATCAAATT
56035 AGGTCTCCAT
Statistics
Matches: 231, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
194 12 0.05
195 14 0.06
196 205 0.89
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (196 bp):
TTTGCAATTAAGGGCTGCGACATACTAGGGTTTAGGTTATTCATCAAATTGGGTTTTAGACTTAT
GAAATTTAACCTAATTTCATATATTTAAACCTAATTTAACATTAATTTATTAGGTAATTTCATCA
ATAGGGCCAAAAATAGCAAAATTCCTAAACCTAGAAATTAAATTACAAGCCGCCAAGGTTGTAAT
T
Found at i:60107 original size:26 final size:26
Alignment explanation
Indices: 60052--60107 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
60042 CATAAAGAAG
* * *
60052 TTATCCCATTTGTCCTCCTCTCAATG
1 TTATCCCATTCGTCCTCCTCACAATA
* *
60078 TTATCCCATTCGTCCTTCTCACATTA
1 TTATCCCATTCGTCCTCCTCACAATA
60104 TTAT
1 TTAT
60108 TTTGGGTGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.18, C:0.32, G:0.05, T:0.45
Consensus pattern (26 bp):
TTATCCCATTCGTCCTCCTCACAATA
Found at i:60293 original size:16 final size:16
Alignment explanation
Indices: 60272--60302 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60262 CAGATCGTCT
*
60272 ATCAATAGGGTGTGTG
1 ATCAATAGGATGTGTG
60288 ATCAATAGGATGTGT
1 ATCAATAGGATGTGT
60303 AGAGACTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (16 bp):
ATCAATAGGATGTGTG
Found at i:66976 original size:23 final size:21
Alignment explanation
Indices: 66936--66978 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
66926 AATGAGCACC
*
66936 TATATATTATATTTTTAATAA
1 TATATATTATATTGTTAATAA
66957 TATATATATATATATGTTAATA
1 TATATAT-TATAT-TGTTAATA
66979 TTCAAATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TATATATTATATTGTTAATAA
Done.