Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010931.1 Corchorus capsularis cultivar CVL-1 contig10952, 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: 96091
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:11082 original size:21 final size:21
Alignment explanation
Indices: 11058--11102 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
11048 TTGGCCCACA
**
11058 AAAAGAAAATGCCATGGCATC
1 AAAAGAAAATGCCATAACATC
11079 AAAAGAAAATGCCATAACATC
1 AAAAGAAAATGCCATAACATC
11100 AAA
1 AAA
11103 CAAGCACACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.56, C:0.18, G:0.13, T:0.13
Consensus pattern (21 bp):
AAAAGAAAATGCCATAACATC
Found at i:16879 original size:83 final size:83
Alignment explanation
Indices: 16740--16897 Score: 316
Period size: 83 Copynumber: 1.9 Consensus size: 83
16730 GCGCACCACG
16740 TCAGATTAAGTGGACCCACCTTGACCCAATTTAAAATACCCAACCCACCCGATTCTCATACCCGA
1 TCAGATTAAGTGGACCCACCTTGACCCAATTTAAAATACCCAACCCACCCGATTCTCATACCCGA
16805 CCCGACCCGACCCGATTC
66 CCCGACCCGACCCGATTC
16823 TCAGATTAAGTGGACCCACCTTGACCCAATTTAAAATACCCAACCCACCCGATTCTCATACCCGA
1 TCAGATTAAGTGGACCCACCTTGACCCAATTTAAAATACCCAACCCACCCGATTCTCATACCCGA
16888 CCCGACCCGA
66 CCCGACCCGA
16898 AAAAAACCAC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 75 1.00
ACGTcount: A:0.30, C:0.39, G:0.12, T:0.19
Consensus pattern (83 bp):
TCAGATTAAGTGGACCCACCTTGACCCAATTTAAAATACCCAACCCACCCGATTCTCATACCCGA
CCCGACCCGACCCGATTC
Found at i:18032 original size:22 final size:22
Alignment explanation
Indices: 17957--18031 Score: 141
Period size: 22 Copynumber: 3.4 Consensus size: 22
17947 TTTAAAGATC
17957 GGGTCGGGTATCAGAATCAAGT
1 GGGTCGGGTATCAGAATCAAGT
17979 GGGTCGGGTATCAGAATCAAGT
1 GGGTCGGGTATCAGAATCAAGT
*
18001 GGGTCGGGTCTCAGAATCAAGT
1 GGGTCGGGTATCAGAATCAAGT
18023 GGGTCGGGT
1 GGGTCGGGT
18032 CGGGTATTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.23
Consensus pattern (22 bp):
GGGTCGGGTATCAGAATCAAGT
Found at i:18331 original size:12 final size:12
Alignment explanation
Indices: 18310--18339 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18300 TTTATATCCA
18310 CCTCTACCTCTT
1 CCTCTACCTCTT
*
18322 CCTCTTCCTCTT
1 CCTCTACCTCTT
18334 CCTCTA
1 CCTCTA
18340 GTAAATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.50, G:0.00, T:0.43
Consensus pattern (12 bp):
CCTCTACCTCTT
Found at i:23320 original size:15 final size:15
Alignment explanation
Indices: 23300--23328 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
23290 CAGCAAGGAG
23300 AATCAATAATTCTGT
1 AATCAATAATTCTGT
23315 AATCAATAATTCTG
1 AATCAATAATTCTG
23329 ACAAACACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (15 bp):
AATCAATAATTCTGT
Found at i:24838 original size:21 final size:21
Alignment explanation
Indices: 24812--24852 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
24802 AAGGCGAGGT
*
24812 GATCGATGGAAGATTGAAGAC
1 GATCGATGGAAGAATGAAGAC
24833 GATCGATGGAAGAATGAAGA
1 GATCGATGGAAGAATGAAGA
24853 TTATCAACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.07, G:0.34, T:0.17
Consensus pattern (21 bp):
GATCGATGGAAGAATGAAGAC
Found at i:27188 original size:6 final size:6
Alignment explanation
Indices: 27177--27219 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
27167 CCTTATATCC
* * * *
27177 ACCTCT ACCTCT TCCTCT TCCTCT TCCTCT ACCTCT TCCTCT A
1 ACCTCT ACCTCT ACCTCT ACCTCT ACCTCT ACCTCT ACCTCT A
27220 GTAAATGATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.09, C:0.49, G:0.00, T:0.42
Consensus pattern (6 bp):
ACCTCT
Found at i:27199 original size:12 final size:12
Alignment explanation
Indices: 27178--27219 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
27168 CTTATATCCA
27178 CCTCTACCTCTT
1 CCTCTACCTCTT
*
27190 CCTCTTCCTCTT
1 CCTCTACCTCTT
27202 CCTCTACCTCTT
1 CCTCTACCTCTT
27214 CCTCTA
1 CCTCTA
27220 GTAAATGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.07, C:0.50, G:0.00, T:0.43
Consensus pattern (12 bp):
CCTCTACCTCTT
Found at i:27205 original size:18 final size:18
Alignment explanation
Indices: 27178--27219 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
27168 CTTATATCCA
*
27178 CCTCTACCTCTTCCTCTT
1 CCTCTACCTCTACCTCTT
*
27196 CCTCTTCCTCTACCTCTT
1 CCTCTACCTCTACCTCTT
27214 CCTCTA
1 CCTCTA
27220 GTAAATGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.07, C:0.50, G:0.00, T:0.43
Consensus pattern (18 bp):
CCTCTACCTCTACCTCTT
Found at i:35068 original size:1 final size:1
Alignment explanation
Indices: 35062--35087 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
35052 GTTTAAAAGA
35062 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
35088 AGTGGTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:42883 original size:22 final size:22
Alignment explanation
Indices: 42858--43434 Score: 187
Period size: 22 Copynumber: 26.6 Consensus size: 22
42848 ATGATCCTAT
42858 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
42880 TATGAAATTTTAATAATGATGC
1 TATGAAATTTTGATAACCTTCC
* * * **
42902 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** * *
42924 TAT-AAATTTTTTTAACTTTCT
1 TATGAAATTTTGATAACCTTCC
* *
42945 TGTGAAATTTTGTTAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
42966 GTAAGGAATTTTGA-AGACC-TCAA
1 -TATGAAATTTTGATA-ACCTTC-C
42989 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
43011 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* * * *
43034 TATGAGATGTTGATAACATTCA
1 TATGAAATTTTGATAACCTTCC
* * * * *
43056 TATGATATATTAATAACC-ACGT
1 TATGAAATTTTGATAACCTTC-C
* * * * *
43078 TACGAAAATTTAAAAACC-TCTA
1 TATGAAATTTTGATAACCTTC-C
* *
43100 TATG-AATTGTT-AGTAATC-ACAC
1 TATGAAATT-TTGA-TAACCTTC-C
* * *
43122 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
* *
43144 TATGAAATTGTGATAACC-TCGT
1 TATGAAATTTTGATAACCTTC-C
*
43166 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
43189 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
43212 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
43234 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* * *
43251 TA-CAAATTTGGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** **
43272 TATGATTTTTTGATAACCTTAT
1 TATGAAATTTTGATAACCTTCC
* *
43294 TATGAAA-TTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
43315 TATGAAATTTTGATTTA-CATAC
1 TATGAAATTTTGA-TAACCTTCC
* *
43337 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
43359 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
43381 TATGAAATTGTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
43402 -CTGAAATTTTTATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
43422 T-TGAAATTTTGAT
1 TATGAAATTTTGAT
43435 TACTCCATAA
Statistics
Matches: 405, Mismatches: 122, Indels: 58
0.69 0.21 0.10
Matches are distributed among these distances:
16 10 0.02
17 2 0.00
20 28 0.07
21 48 0.12
22 250 0.62
23 65 0.16
24 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:43198 original size:23 final size:23
Alignment explanation
Indices: 43170--43249 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
43160 CCTCGTTATG
43170 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
* *
43193 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATA
* * *
43216 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCCTATA
*
43238 AAATCTTGATAA
1 AAATTTTGATAA
43250 CTACAAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:43248 original size:45 final size:45
Alignment explanation
Indices: 43126--43249 Score: 121
Period size: 45 Copynumber: 2.8 Consensus size: 45
43116 TCACACTCTG
* ** *
43126 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGTTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTATA
*
43170 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTATA
* *
43216 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
43250 CTACAAATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
44 11 0.16
45 31 0.46
46 25 0.37
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTATA
Found at i:43274 original size:60 final size:60
Alignment explanation
Indices: 43193--43309 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
43183 TCTTCCTATA
* * *
43193 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTATGAAATCTTGATAACTAC
1 AAATTTGGATAAACCTCCCTATAAAATTTTGATAACCTTATTATGAAAT-TTGATAACTAC
* ** *
43254 AAATTTGGAT-AACCTCCCTATGATTTTTTGATAACCTTATTATGAAATTTGTTAAC
1 AAATTTGGATAAACCTCCCTATAAAATTTTGATAACCTTATTATGAAATTTGATAAC
43310 CTCCCTATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
59 7 0.14
60 33 0.67
61 9 0.18
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (60 bp):
AAATTTGGATAAACCTCCCTATAAAATTTTGATAACCTTATTATGAAATTTGATAACTAC
Found at i:43440 original size:19 final size:20
Alignment explanation
Indices: 43383--43434 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
43373 AACTAAACTA
*
43383 TGAAATTGTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
* *
43403 TGAAATTTTTATATCCTCCT
1 TGAAATTTTGATATCCTCCC
43423 TGAAATTTTGAT
1 TGAAATTTTGAT
43435 TACTCCATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:43569 original size:22 final size:22
Alignment explanation
Indices: 43542--43762 Score: 130
Period size: 22 Copynumber: 10.0 Consensus size: 22
43532 ATTTTAAAAA
43542 TTTGATAACCTCTTTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
*
43564 TTTGATAACCTCTTTATAAAAT
1 TTTGATAACCTCTTTATGAAAT
* * * *
43586 TTTGTTCACCCCTCTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
* * * * *
43608 TCTGATAATCACATTATGTAAT
1 TTTGATAACCTCTTTATGAAAT
*
43630 TTTGATAACCTCGCTT-TGAAAT
1 TTTGATAACCTC-TTTATGAAAT
** **
43652 TTTGATAACAACAATATGAAAT
1 TTTGATAACCTCTTTATGAAAT
*
43674 TTTGATAA--TTTTCCTAT-AAAT
1 TTTGATAACCTCTT--TATGAAAT
* *
43695 TTTGATAATCTAATCTCTATGAAAT
1 TTTGATAA-C--CTCTTTATGAAAT
* * * * *
43720 TTCGATAATCACTCTATGAGA-
1 TTTGATAACCTCTTTATGAAAT
*
43741 TTTGATAACCT-TCTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
43762 T
1 T
43763 ATGGTACTTC
Statistics
Matches: 150, Mismatches: 38, Indels: 23
0.71 0.18 0.11
Matches are distributed among these distances:
20 8 0.05
21 22 0.15
22 102 0.68
23 2 0.01
24 3 0.02
25 11 0.07
26 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (22 bp):
TTTGATAACCTCTTTATGAAAT
Found at i:43817 original size:22 final size:21
Alignment explanation
Indices: 43788--43927 Score: 97
Period size: 22 Copynumber: 6.4 Consensus size: 21
43778 AAATTGAGAC
43788 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
43809 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCA-TATGAAA
*
43831 TTTTGATAACCTCCTCATGAAA
1 TTTTGATAACCTCAT-ATGAAA
* *
43853 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
* * *
43875 TCTTGTTAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
43897 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
43919 TTTTGATAA
1 TTTTGATAA
43928 TCTCTTTGAT
Statistics
Matches: 94, Mismatches: 16, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
21 10 0.11
22 81 0.86
23 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:44070 original size:22 final size:21
Alignment explanation
Indices: 44015--44101 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 21
44005 AATAACATGA
*
44015 TCCTATGAAATTTTGGTAACC
1 TCCTATGAAATTTTGATAACC
*
44036 ACACTAT-AGAATTTTGATAACC
1 TC-CTATGA-AATTTTGATAACC
* * *
44058 TCCTCATGAAATTATAATAATCA
1 TCCT-ATGAAATTTTGATAA-CC
*
44081 TCTTATGAAATTTTGATAACC
1 TCCTATGAAATTTTGATAACC
44102 ACATAGAGAC
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
21 5 0.10
22 41 0.80
23 5 0.10
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (21 bp):
TCCTATGAAATTTTGATAACC
Found at i:44300 original size:19 final size:20
Alignment explanation
Indices: 44269--44306 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
44259 TATTGACAGT
44269 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
44288 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
44307 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:44997 original size:30 final size:29
Alignment explanation
Indices: 44935--45004 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
44925 ACCGAACCAT
* ***
44935 CAAATAAGCCCCTGAACTTTTATTCCGGC
1 CAAATAAGCCCCTGAACTTTAAAAACGGC
*
44964 CAAATAAGCCCCTGAACTCTTAAAAATGGC
1 CAAATAAGCCCCTGAACT-TTAAAAACGGC
44994 CAAATAAGCCC
1 CAAATAAGCCC
45005 TGTTGCTAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.36, C:0.30, G:0.13, T:0.21
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTTTAAAAACGGC
Found at i:52984 original size:2 final size:2
Alignment explanation
Indices: 52977--53003 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52967 AAAGGAAAAG
52977 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
53004 ATAATAATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54241 original size:22 final size:22
Alignment explanation
Indices: 54209--54250 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
54199 AATTAATAAA
54209 TTAAATACAGGTTTAGCCCCCC
1 TTAAATACAGGTTTAGCCCCCC
*
54231 TTAAATCCAGGTTTAGCCCC
1 TTAAATACAGGTTTAGCCCC
54251 TAGTTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (22 bp):
TTAAATACAGGTTTAGCCCCCC
Found at i:65342 original size:30 final size:30
Alignment explanation
Indices: 65306--65396 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
65296 TTGCTTCTTG
*
65306 GTTTTCTCAGCAGACTCTGACTCACCAACA
1 GTTTTCTCAGCAGACTCTGACTCATCAACA
*
65336 GTTTTCTCCGCAGACTCTGACTCATCAACA
1 GTTTTCTCAGCAGACTCTGACTCATCAACA
65366 GTTTTCTCAGCAGACTCTGACTCATCAACA
1 GTTTTCTCAGCAGACTCTGACTCATCAACA
65396 G
1 G
65397 GGACTAACTG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (30 bp):
GTTTTCTCAGCAGACTCTGACTCATCAACA
Found at i:67185 original size:126 final size:126
Alignment explanation
Indices: 66960--67335 Score: 698
Period size: 126 Copynumber: 3.0 Consensus size: 126
66950 GCATATGACA
66960 TAGCCTTTTTATCTTCTCTTAACAAATTGAGAAATATAGTTTGCTACCAAATCTCTTTTTCCTTT
1 TAGCCTTTTTATCTTCTCTTAACAAATTGAGAAATATAGTTTGCTACCAAATCTCTTTTTCCTTT
* * *
67025 TTAGCTATGTAGACAGCCAGAGGTTAGACCTAGAGCATCAAATGAGAGAAGCTTTTGAACC
66 TTAGCTAGGTAGACAGCCAGAGGTTAAACCTAGAGCATCAAATGAGAGAAGCATTTGAACC
*
67086 TAGCCTTTTTATCTTCTCTTAACAAATTGAGAAATATAGTTTGCTACGAAATCTCTTTTTCCTTT
1 TAGCCTTTTTATCTTCTCTTAACAAATTGAGAAATATAGTTTGCTACCAAATCTCTTTTTCCTTT
67151 TTAGCTAGGTAGACAGCCAGAGGTTAAACCTAGAGCATCAAATGAGAGAAGCATTTGAACC
66 TTAGCTAGGTAGACAGCCAGAGGTTAAACCTAGAGCATCAAATGAGAGAAGCATTTGAACC
* *
67212 TAGCCTTTTCATCTTCTCTTAACAAATTGAGAAATATAGTTTGCTACCAAATCTCTTTTTCTTTT
1 TAGCCTTTTTATCTTCTCTTAACAAATTGAGAAATATAGTTTGCTACCAAATCTCTTTTTCCTTT
67277 TTAGCTAGGTAGACAGCCAGAGGTTAAACCTAGAGCATCAAATGAGAGAAGCATTTGAA
66 TTAGCTAGGTAGACAGCCAGAGGTTAAACCTAGAGCATCAAATGAGAGAAGCATTTGAA
67336 GTAAGACATG
Statistics
Matches: 243, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 243 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (126 bp):
TAGCCTTTTTATCTTCTCTTAACAAATTGAGAAATATAGTTTGCTACCAAATCTCTTTTTCCTTT
TTAGCTAGGTAGACAGCCAGAGGTTAAACCTAGAGCATCAAATGAGAGAAGCATTTGAACC
Found at i:70106 original size:2 final size:2
Alignment explanation
Indices: 70090--70125 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
70080 TTAATTAAAC
70090 AT AT A- AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70126 TGTATCAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70874 original size:3 final size:3
Alignment explanation
Indices: 70866--70904 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
70856 TCTTTGTTTA
70866 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
70905 CCTTAGCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:90250 original size:20 final size:20
Alignment explanation
Indices: 90225--90271 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
90215 TAAAAGTGAT
90225 ATATAATGGATGATGTGTTC
1 ATATAATGGATGATGTGTTC
90245 ATATAATGGATGATGTGTTC
1 ATATAATGGATGATGTGTTC
90265 ATA-AATG
1 ATATAATG
90272 AGTGGCAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.38
Consensus pattern (20 bp):
ATATAATGGATGATGTGTTC
Found at i:94733 original size:2 final size:2
Alignment explanation
Indices: 94726--94758 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
94716 GCATTTTTGC
94726 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
94759 TAAGATAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.