Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020722.1 Corchorus olitorius cultivar O-4 contig20755, 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: 64053
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:113 original size:19 final size:18
Alignment explanation
Indices: 87--124 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
77 ATTCAAAGTT
87 TGAATAAT-TATACACAAA
1 TGAATAATCTATACA-AAA
105 TGAATTAATCTATACAAAA
1 TGAA-TAATCTATACAAAA
124 T
1 T
125 AAGAAACTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
TGAATAATCTATACAAAA
Found at i:232 original size:13 final size:14
Alignment explanation
Indices: 214--242 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
204 AATTGACAAC
214 AAAAGAAAA-GTAA
1 AAAAGAAAAGGTAA
227 AAAAGAAAAGGTAA
1 AAAAGAAAAGGTAA
241 AA
1 AA
243 TCCCAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAAGAAAAGGTAA
Found at i:30144 original size:28 final size:27
Alignment explanation
Indices: 30110--30184 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
30100 GTACCGTTTT
* *
30110 GACATTTTGCCCTTAAATTTTAATGTTG
1 GACATTTTGCCCATAAA-CTTAATGTTG
*
30138 GACATTTTGTCCCATAAACTTAATTTTG
1 GACATTTTG-CCCATAAACTTAATGTTG
30166 GACATTTTGCACC-TAAACT
1 GACATTTTGC-CCATAAACT
30185 CTCAATTTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 7 0.17
28 28 0.67
29 7 0.17
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (27 bp):
GACATTTTGCCCATAAACTTAATGTTG
Found at i:30193 original size:28 final size:26
Alignment explanation
Indices: 30110--30196 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 26
30100 GTACCGTTTT
* *
30110 GACATTTTGCCCTTAAATTTTAATGTTG
1 GACATTTTGCCCATAAA-CTTAAT-TTG
30138 GACATTTTGTCCCATAAACTTAATTTTG
1 GACATTTTG-CCCATAAACTTAA-TTTG
30166 GACATTTTGCACC-TAAACTCTCAATTTG
1 GACATTTTGC-CCATAAACT-T-AATTTG
30194 GAC
1 GAC
30197 CCTTTTTAGC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
27 7 0.13
28 35 0.67
29 10 0.19
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (26 bp):
GACATTTTGCCCATAAACTTAATTTG
Found at i:32433 original size:21 final size:20
Alignment explanation
Indices: 32405--32443 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
32395 ACAGGTTAGT
* *
32405 TTTAATATTATAATAATATA
1 TTTAATATAATAAAAATATA
32425 TTTATATATAATAAAAATA
1 TTTA-ATATAATAAAAATA
32444 AAAAATTACT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTAATATAATAAAAATATA
Found at i:32633 original size:22 final size:22
Alignment explanation
Indices: 32589--32634 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
32579 AAAGAAGAAT
**
32589 AAAAAAATTAAGAAATTGCCTA
1 AAAAAAATTAAGAAATTAACTA
*
32611 AAAAAAATTAAGGAATTAACTA
1 AAAAAAATTAAGAAATTAACTA
32633 AA
1 AA
32635 GTTAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.22
Consensus pattern (22 bp):
AAAAAAATTAAGAAATTAACTA
Found at i:35713 original size:29 final size:29
Alignment explanation
Indices: 35680--35741 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
35670 CGTTTTGATG
*
35680 TTTTGCCCCATAAACTTTAATTTTGGACA
1 TTTTGCCCCATAAACTTTAATTTTGCACA
* **
35709 TTTTGCCCCTTAATTTTTAATTTTGCACA
1 TTTTGCCCCATAAACTTTAATTTTGCACA
35738 TTTT
1 TTTT
35742 ACCTTCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.50
Consensus pattern (29 bp):
TTTTGCCCCATAAACTTTAATTTTGCACA
Found at i:37086 original size:31 final size:31
Alignment explanation
Indices: 37024--37089 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
37014 CAAGCTTATC
** *
37024 AAATATTTATATAGCTTATAGTACCACTAAA
1 AAATATTTATATAGCTTATAGTAAAAATAAA
37055 AAATATTTATATAGCTTATA-TATAAAATAAA
1 AAATATTTATATAGCTTATAGTA-AAAATAAA
37086 AAAT
1 AAAT
37090 CTGTTTGGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.36
Consensus pattern (31 bp):
AAATATTTATATAGCTTATAGTAAAAATAAA
Found at i:37487 original size:16 final size:16
Alignment explanation
Indices: 37468--37502 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
37458 ATTGAATAAT
37468 TAATGTCTAATTTGGG
1 TAATGTCTAATTTGGG
37484 TAATGTCTAATTTGGG
1 TAATGTCTAATTTGGG
37500 TAA
1 TAA
37503 CATGTATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (16 bp):
TAATGTCTAATTTGGG
Found at i:38868 original size:3 final size:3
Alignment explanation
Indices: 38860--38892 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
38850 GTATTGTGAA
38860 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
38893 TACATATTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:40756 original size:2 final size:2
Alignment explanation
Indices: 40749--40774 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40739 ATTGGAATTA
40749 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
40775 GCTAGAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43256 original size:17 final size:17
Alignment explanation
Indices: 43236--43274 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
43226 CATTAACCTC
43236 CTTTTCTTATTAAGAAA
1 CTTTTCTTATTAAGAAA
* *
43253 CTTTTTTTTTTAAGAAA
1 CTTTTCTTATTAAGAAA
43270 CTTTT
1 CTTTT
43275 TTTTTTAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.56
Consensus pattern (17 bp):
CTTTTCTTATTAAGAAA
Found at i:43276 original size:16 final size:17
Alignment explanation
Indices: 43245--43281 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
43235 CCTTTTCTTA
43245 TTAAGAAACTTTTTTTT
1 TTAAGAAACTTTTTTTT
43262 TTAAGAAACTTTTTTTT
1 TTAAGAAACTTTTTTTT
43279 TTA
1 TTA
43282 GTGGTACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (17 bp):
TTAAGAAACTTTTTTTT
Found at i:43336 original size:98 final size:99
Alignment explanation
Indices: 43170--43362 Score: 316
Period size: 98 Copynumber: 1.9 Consensus size: 99
43160 TAAGAACATT
* *
43170 CTTTTTTCTTTAGTGGTACAAGTGAAATCATATATAGATTATGCTGTTTGGATTTTCATTAACCT
1 CTTTTTTCTTTAGTGGTACAAGTGAAATCA-ATATAGATTATGATGTCTGGATTTTCATTAACCT
* * *
43235 CCTTTTCTTATTAAGAAACTTTTTTTTTTAAGAAA
65 CCTTTCCTTATTAAGAAAATTTTTGTTTTAAGAAA
*
43270 CTTTTTTTTTTAGTGGTACAAGTGAAATC-ATATAGATTATGATGTCTGGATTTTCATTAACCTC
1 CTTTTTTCTTTAGTGGTACAAGTGAAATCAATATAGATTATGATGTCTGGATTTTCATTAACCTC
43334 CTTTCCTTATTAAGAAAATTTTTGTTTTA
66 CTTTCCTTATTAAGAAAATTTTTGTTTTA
43363 GTGGTACAAG
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 59 0.68
100 28 0.32
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (99 bp):
CTTTTTTCTTTAGTGGTACAAGTGAAATCAATATAGATTATGATGTCTGGATTTTCATTAACCTC
CTTTCCTTATTAAGAAAATTTTTGTTTTAAGAAA
Found at i:43379 original size:81 final size:81
Alignment explanation
Indices: 43262--43460 Score: 281
Period size: 81 Copynumber: 2.4 Consensus size: 81
43252 ACTTTTTTTT
* *
43262 TTAAGAAACTTTTTTTTTTAGTGGTACAAGTGAAATCATATAGATTATGATGTCTGGATTTTCAT
1 TTAAGAAAATTTTTTTTTTAGTGGTACAAGTGAAATCATACAGATTATGATGTCTGGATTTTCAT
* * *
43327 TAACCTCCTTTCCTTA
66 TAACATACTTTACTTA
* * *
43343 TTAAGAAAATTTTTGTTTTAGTGGTACAAGTGAAATCATACAGATTCTGCTGTCTGGATTTTCAT
1 TTAAGAAAATTTTTTTTTTAGTGGTACAAGTGAAATCATACAGATTATGATGTCTGGATTTTCAT
*
43408 TAATATACTTTACTTA
66 TAACATACTTTACTTA
* * *
43424 TTAAGAACATTCTTTTTTTTAGTGGTATAAGTTAAAT
1 TTAAGAAAATT-TTTTTTTTAGTGGTACAAGTGAAAT
43461 TTCATTACAA
Statistics
Matches: 104, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
81 82 0.79
82 22 0.21
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (81 bp):
TTAAGAAAATTTTTTTTTTAGTGGTACAAGTGAAATCATACAGATTATGATGTCTGGATTTTCAT
TAACATACTTTACTTA
Found at i:43756 original size:6 final size:7
Alignment explanation
Indices: 43741--43769 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
43731 AGTTACACCC
43741 TTTTCTT
1 TTTTCTT
43748 TTTTCTT
1 TTTTCTT
43755 TTTTC-T
1 TTTTCTT
43761 TTTTCTT
1 TTTTCTT
43768 TT
1 TT
43770 CTATTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTCTT
Found at i:43763 original size:13 final size:14
Alignment explanation
Indices: 43741--43769 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
43731 AGTTACACCC
43741 TTTTCTTTTTTCTT
1 TTTTCTTTTTTCTT
43755 TTTTC-TTTTTCTT
1 TTTTCTTTTTTCTT
43768 TT
1 TT
43770 CTATTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTCTTTTTTCTT
Found at i:46717 original size:59 final size:58
Alignment explanation
Indices: 46613--46723 Score: 186
Period size: 59 Copynumber: 1.9 Consensus size: 58
46603 ATAGCATCAT
*
46613 GCCTCAGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCCATAA
1 GCCTCAGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCCATAA
* *
46671 GCCTCAGTCCGAAAACGTCTTTTTTTATGCATCTAATAAAAGAACATGTCACT
1 GCCTCAGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGTCACT
46724 TGATGTTTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
58 18 0.37
59 31 0.63
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (58 bp):
GCCTCAGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCCATAA
Found at i:47715 original size:19 final size:21
Alignment explanation
Indices: 47693--47732 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
47683 CCTTATACTA
47693 TATAAATTTT-T-ATAACCTT
1 TATAAATTTTCTAATAACCTT
*
47712 TATAACTTTTCTAATAACCTT
1 TATAAATTTTCTAATAACCTT
47733 AAAGAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
TATAAATTTTCTAATAACCTT
Found at i:48420 original size:22 final size:21
Alignment explanation
Indices: 48390--48447 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
48380 ATTATTAATT
*
48390 ATTATTAATAATAACAATTTAA
1 ATTAATAATAATAACAA-TTAA
*
48412 ATTAATAATAATTAATAATTAA
1 ATTAATAATAA-TAACAATTAA
48434 A-TAATTAATAATAA
1 ATTAA-TAATAATAA
48448 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 6 0.19
22 21 0.66
23 5 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTAATAATAATAACAATTAA
Found at i:48429 original size:7 final size:7
Alignment explanation
Indices: 48378--48445 Score: 52
Period size: 7 Copynumber: 9.6 Consensus size: 7
48368 TTTTGTTTTT
*
48378 TAATTAT
1 TAATTAA
48385 TAATT-A
1 TAATTAA
*
48391 TTATTAA
1 TAATTAA
48398 TAA-TAA
1 TAATTAA
*
48404 CAATTTAAA
1 TAA-TT-AA
48413 TTAA-TAA
1 -TAATTAA
48420 TAATTAA
1 TAATTAA
48427 TAATTAAA
1 TAATT-AA
48435 TAATTAA
1 TAATTAA
48442 TAAT
1 TAAT
48446 AATTAAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
6 12 0.24
7 24 0.49
8 9 0.18
9 2 0.04
10 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATTAA
Found at i:48438 original size:18 final size:17
Alignment explanation
Indices: 48411--48458 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
48401 TAACAATTTA
48411 AATT-AATAATAATTAAT
1 AATTAAATAATAA-TAAT
48428 AATTAAATAATTAATAAT
1 AATTAAATAA-TAATAAT
*
48446 AATTAAAAAATAA
1 AATTAAATAATAA
48459 AAAAAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 7 0.25
18 18 0.64
19 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTAAATAATAATAAT
Found at i:48459 original size:25 final size:25
Alignment explanation
Indices: 48411--48459 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
48401 TAACAATTTA
* *
48411 AATTAATAATAATTAATAATTAAAT
1 AATTAATAATAATTAAAAAATAAAT
48436 AATTAATAATAATTAAAAAATAAA
1 AATTAATAATAATTAAAAAATAAA
48460 AAAAAAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AATTAATAATAATTAAAAAATAAAT
Found at i:48541 original size:13 final size:13
Alignment explanation
Indices: 48525--48549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48515 TGACAGAATT
48525 TTAGATCTACAAC
1 TTAGATCTACAAC
48538 TTAGATCTACAA
1 TTAGATCTACAA
48550 AATCCGACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TTAGATCTACAAC
Found at i:48571 original size:12 final size:12
Alignment explanation
Indices: 48554--48578 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48544 CTACAAAATC
48554 CGACATGATTTT
1 CGACATGATTTT
48566 CGACATGATTTT
1 CGACATGATTTT
48578 C
1 C
48579 TTCAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (12 bp):
CGACATGATTTT
Found at i:49689 original size:25 final size:24
Alignment explanation
Indices: 49650--49696 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
49640 TCGAATTGGA
*
49650 TTTTATTGATGATGATCATGATCT
1 TTTTATTCATGATGATCATGATCT
*
49674 TTTTATTACATGATGATGATGAT
1 TTTTATT-CATGATGATCATGAT
49697 GAGCAGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.49
Consensus pattern (24 bp):
TTTTATTCATGATGATCATGATCT
Found at i:50595 original size:6 final size:6
Alignment explanation
Indices: 50584--50615 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
50574 TTTATTTGAC
50584 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
50616 CATTTTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:51074 original size:28 final size:29
Alignment explanation
Indices: 51030--51090 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
51020 TTTTTTTTTA
** *
51030 AAAAAAGGAAGCTTGAAAC-GAAAAAACG
1 AAAAAAGGAAGAATGAAACACAAAAAACG
51058 AAAAAAGGAAGAATGAAACAACAAAAAACG
1 AAAAAAGGAAGAATGAAAC-ACAAAAAACG
51088 AAA
1 AAA
51091 GGGGAGAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 17 0.61
30 11 0.39
ACGTcount: A:0.67, C:0.10, G:0.18, T:0.05
Consensus pattern (29 bp):
AAAAAAGGAAGAATGAAACACAAAAAACG
Found at i:52064 original size:99 final size:99
Alignment explanation
Indices: 51881--52070 Score: 353
Period size: 99 Copynumber: 1.9 Consensus size: 99
51871 TTGGATCAAA
*
51881 TTTGGTTTCAGGCGGTCGACTCATATACTCGCACTAGGGTCAAATTTTGCTTGCTCTAAATTACT
1 TTTGGTTTCAGGCGGTCGACTCATATACTCACACTAGGGTCAAATTTTGCTTGCTCTAAATTACT
51946 AGGCTTCTTTGGTGAAAAAAAAAATTAAATCAGG
66 AGGCTTCTTTGGTGAAAAAAAAAATTAAATCAGG
*
51980 TTTGGTTTCAGGTGGTCGACTCATATACTCACACTAGGGTCAAATTTTGCTTGCTCTAAAATTAC
1 TTTGGTTTCAGGCGGTCGACTCATATACTCACACTAGGGTCAAATTTTGCTTGCTCT-AAATTAC
52045 TAGGCTTCTTTGGTGAAAAAAAAAAT
65 TAGGCTTCTTTGGTGAAAAAAAAAAT
52071 CCATAGGCTT
Statistics
Matches: 88, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
99 55 0.62
100 33 0.38
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (99 bp):
TTTGGTTTCAGGCGGTCGACTCATATACTCACACTAGGGTCAAATTTTGCTTGCTCTAAATTACT
AGGCTTCTTTGGTGAAAAAAAAAATTAAATCAGG
Found at i:52494 original size:14 final size:14
Alignment explanation
Indices: 52475--52501 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52465 AAGCTTTTTG
52475 TTTTTCTACCACAT
1 TTTTTCTACCACAT
52489 TTTTTCTACCACA
1 TTTTTCTACCACA
52502 ATACCAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTTTCTACCACAT
Found at i:55335 original size:18 final size:19
Alignment explanation
Indices: 55296--55335 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
55286 GTGCTCCCGT
55296 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
55317 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
55335 T
1 T
55336 TCTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:55553 original size:30 final size:32
Alignment explanation
Indices: 55493--55553 Score: 83
Period size: 30 Copynumber: 1.9 Consensus size: 32
55483 GATATCAACT
55493 ACTTTTTTACTTGATTTATTATTTTTTTCTCTA
1 ACTTTTTTACTT-ATTTATTATTTTTTTCTCTA
55526 ACTTTTTTA-TT-TTTATT-TTTTTCTTCTC
1 ACTTTTTTACTTATTTATTATTTTT-TTCTC
55554 CGTTTTCTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 5 0.19
30 11 0.41
32 2 0.07
33 9 0.33
ACGTcount: A:0.15, C:0.13, G:0.02, T:0.70
Consensus pattern (32 bp):
ACTTTTTTACTTATTTATTATTTTTTTCTCTA
Found at i:59387 original size:33 final size:32
Alignment explanation
Indices: 59350--59456 Score: 92
Period size: 33 Copynumber: 3.2 Consensus size: 32
59340 GGAGTTTCCA
59350 GAGTTGATGGGATTGTTGGCGGCAGCAATGGTG
1 GAGTTG-TGGGATTGTTGGCGGCAGCAATGGTG
* * *
59383 GAGTTTGTGGTG-TTGCTGGTGGCAGCAACGGTG
1 GAG-TTGTGG-GATTGTTGGCGGCAGCAATGGTG
*
59416 GGGTT-TGAGGAGTTGTTGGAGGCGGCAGCAATGGTG
1 GAGTTGTG-GGA-TTGTT---GGCGGCAGCAATGGTG
59452 GAGTT
1 GAGTT
59457 TGAGGTGTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
31 3 0.05
32 3 0.05
33 30 0.52
34 4 0.07
36 18 0.31
ACGTcount: A:0.16, C:0.09, G:0.47, T:0.28
Consensus pattern (32 bp):
GAGTTGTGGGATTGTTGGCGGCAGCAATGGTG
Found at i:59476 original size:33 final size:33
Alignment explanation
Indices: 59370--59482 Score: 136
Period size: 33 Copynumber: 3.3 Consensus size: 33
59360 GATTGTTGGC
* * *
59370 GGCAGCAATGGTGGAGTTTGTGGTGTTGCTGGT
1 GGCAGCAATGGTGGAGTTTGAGGTGTTGCGGGG
* * * *
59403 GGCAGCAACGGTGGGGTTTGAGGAGTTGTTGGAGG
1 GGCAGCAATGGTGGAGTTTGAGGTGTTG-CGG-GG
59438 CGGCAGCAATGGTGGAGTTTGAGGTGTTGCGGGG
1 -GGCAGCAATGGTGGAGTTTGAGGTGTTGCGGGG
59472 GGCAGCAATGG
1 GGCAGCAATGG
59483 GGTTGTCGGA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
33 35 0.53
34 3 0.05
35 3 0.05
36 25 0.38
ACGTcount: A:0.16, C:0.11, G:0.49, T:0.25
Consensus pattern (33 bp):
GGCAGCAATGGTGGAGTTTGAGGTGTTGCGGGG
Found at i:62083 original size:31 final size:31
Alignment explanation
Indices: 61956--62094 Score: 161
Period size: 31 Copynumber: 4.5 Consensus size: 31
61946 TCCTTTTGTG
* **
61956 CACGTGGCATGCCATGTGTCACTTTTTGAAA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
61987 TACGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * * ** *
62018 CACATGACGTGATATGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * *
62049 CACGTGTCGTGCCACATGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
62080 CACGTGGCATGCCAC
1 CACGTGGCATGCCAC
62095 CGTCGGACAT
Statistics
Matches: 89, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 89 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:62237 original size:31 final size:31
Alignment explanation
Indices: 62199--62273 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
62189 AAAAAGTTGG
*
62199 GTGCAAAGTGGCAGTTCATACAAACTTAAGA
1 GTGCAAAGTGGCAATTCATACAAACTTAAGA
* *
62230 GTGCAAAGTGACAATTCATACAAACTTAAGG
1 GTGCAAAGTGGCAATTCATACAAACTTAAGA
62261 GTGCAAAGTGGCA
1 GTGCAAAGTGGCA
62274 TTTATGCTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (31 bp):
GTGCAAAGTGGCAATTCATACAAACTTAAGA
Done.