Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020322.1 Corchorus olitorius cultivar O-4 contig20355, 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: 68359
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1157 original size:22 final size:21
Alignment explanation
Indices: 1128--1196 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
1118 AAATTGAGAC
*
1128 TTTTATAACCTTCATATGAAA
1 TTTTATAACCTCCATATGAAA
1149 TTTTGATAACCTCCCA-ATGAAA
1 TTTT-ATAACCT-CCATATGAAA
* *
1171 TATTAGTAACCTCCTTATGAAA
1 TTTTA-TAACCTCCATATGAAA
1193 TTTT
1 TTTT
1197 GTTAACCATA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 7 0.17
22 31 0.77
23 2 0.05
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (21 bp):
TTTTATAACCTCCATATGAAA
Found at i:2221 original size:91 final size:91
Alignment explanation
Indices: 2093--2260 Score: 273
Period size: 91 Copynumber: 1.8 Consensus size: 91
2083 AACGTTTTCC
* *
2093 AAAATGCTTAAAAAAGGGTATAATCTTTTAATTTGACCAAATAAGGATCTAACGTTATCGAAAAT
1 AAAATGCTCAAAAAAGGGTATAATCTTTTAATTTGACCAAATAAGGACCTAACGTTATCGAAAAT
2158 GCTCAAATAAGGGCCTAACATTATTG
66 GCTCAAATAAGGGCCTAACATTATTG
* * * * *
2184 AAAATGCTCAAATAAGGGTCTAATCTTTTATTTTGACCAAATAAGGGCCTAACGTTATTGAAAAT
1 AAAATGCTCAAAAAAGGGTATAATCTTTTAATTTGACCAAATAAGGACCTAACGTTATCGAAAAT
2249 GCTCAAATAAGG
66 GCTCAAATAAGG
2261 CATGGCGTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 70 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (91 bp):
AAAATGCTCAAAAAAGGGTATAATCTTTTAATTTGACCAAATAAGGACCTAACGTTATCGAAAAT
GCTCAAATAAGGGCCTAACATTATTG
Found at i:2259 original size:31 final size:31
Alignment explanation
Indices: 2130--2260 Score: 144
Period size: 31 Copynumber: 4.3 Consensus size: 31
2120 TTAATTTGAC
** *
2130 CAAATAAGGATCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATTGAAAATGCT
*
2161 CAAATAAGGGCCTAACATTATTGAAAATGCT
1 CAAATAAGGGCCTAACGTTATTGAAAATGCT
* ***
2192 CAAATAAGGGTCTAATC-TT-TT-ATTTTGAC-
1 CAAATAAGGGCCTAA-CGTTATTGAAAATG-CT
2221 CAAATAAGGGCCTAACGTTATTGAAAATGCT
1 CAAATAAGGGCCTAACGTTATTGAAAATGCT
2252 CAAATAAGG
1 CAAATAAGG
2261 CATGGCGTCA
Statistics
Matches: 82, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
28 1 0.01
29 19 0.23
30 6 0.07
31 55 0.67
32 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATTGAAAATGCT
Found at i:2407 original size:31 final size:31
Alignment explanation
Indices: 2305--2407 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
2295 CGATGTCTGA
*
2305 CCCTTATTTGAACATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
* ** * * *
2336 CTCTTATTTG-GCCACATT---AAAAGACTGGG
1 CCCTTATTTGAG-CATTTTGGCAAACG-TTAGG
2365 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
2396 CCCTTATTTGAG
1 CCCTTATTTGAG
2408 TAATTAGCCA
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
28 4 0.08
29 16 0.30
30 1 0.02
31 28 0.53
32 4 0.08
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAGG
Found at i:10539 original size:41 final size:41
Alignment explanation
Indices: 10471--10558 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 41
10461 CTCCAACTTG
* * *
10471 GCCCTCCTAATAATTAAAGAAATAAATTAAATCCAGGTTTA
1 GCCCCCCTAATAATTAAAGAAAGAAATTAAATCCAAGTTTA
*
10512 GCCCCCCTAATAATT-AAGTTAAGAAATTAAATCCAAGTTTA
1 GCCCCCCTAATAATTAAAG-AAAGAAATTAAATCCAAGTTTA
10553 GCCCCC
1 GCCCCC
10559 AATTATAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 3 0.07
41 39 0.93
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (41 bp):
GCCCCCCTAATAATTAAAGAAAGAAATTAAATCCAAGTTTA
Found at i:12888 original size:38 final size:39
Alignment explanation
Indices: 12819--12908 Score: 130
Period size: 38 Copynumber: 2.3 Consensus size: 39
12809 CCATGGAAAC
* *
12819 TAAACAATGGAAAAGTTTTTTTTACAAAAAAAAAAAAGT
1 TAAACCATGGAAAAGTTATTTTTACAAAAAAAAAAAAGT
*
12858 TAAACCATGGAAAAG-TATTTTTA-AGAAAAAAGAAAAGT
1 TAAACCATGGAAAAGTTATTTTTACA-AAAAAAAAAAAGT
12896 TAAACCATGGAAA
1 TAAACCATGGAAA
12909 TCAAAGGTAC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
37 1 0.02
38 32 0.68
39 14 0.30
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (39 bp):
TAAACCATGGAAAAGTTATTTTTACAAAAAAAAAAAAGT
Found at i:28172 original size:2 final size:2
Alignment explanation
Indices: 28165--28190 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28155 TTAAATAAGA
28165 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
28191 CATGCCTATT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31026 original size:14 final size:13
Alignment explanation
Indices: 31007--31040 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
30997 ACGTTCCCGG
31007 TCTTTTTCTTTTTT
1 TCTTTTT-TTTTTT
31021 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
31034 T-TTTTTT
1 TCTTTTTT
31041 GGCGATCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 7 0.35
14 7 0.35
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (13 bp):
TCTTTTTTTTTTT
Found at i:31310 original size:18 final size:19
Alignment explanation
Indices: 31288--31329 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
31278 TTGCCCTTTG
*
31288 TTCAT-ATTTTTTAA-AAC
1 TTCATCATTTTCTAACAAC
31305 TCTCATCATTTTCTAACAAC
1 T-TCATCATTTTCTAACAAC
31325 TTCAT
1 TTCAT
31330 TTCGTAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 4 0.19
19 12 0.57
20 4 0.19
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (19 bp):
TTCATCATTTTCTAACAAC
Found at i:31986 original size:45 final size:45
Alignment explanation
Indices: 31901--31987 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
31891 TCGGATTTAT
* **
31901 AGGGAGAGGGAGGCTGATGCTGCTGCTCAGAGTTTGAGGGAGCAG
1 AGGGAGAGAGAGGCTGATGCTGCTGCTCAGAGTTACAGGGAGCAG
* *
31946 AGGGAGATAGAGGTTGATGCTGCTGCTCAGA-TTCACAGGGAG
1 AGGGAGAGAGAGGCTGATGCTGCTGCTCAGAGTT-ACAGGGAG
31988 AGGGAGAGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 2 0.06
45 34 0.94
ACGTcount: A:0.24, C:0.14, G:0.43, T:0.20
Consensus pattern (45 bp):
AGGGAGAGAGAGGCTGATGCTGCTGCTCAGAGTTACAGGGAGCAG
Found at i:45123 original size:19 final size:19
Alignment explanation
Indices: 45089--45125 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
45079 TATTATTTAG
* *
45089 GTGCTTTTGCGTTTCAAAC
1 GTGCTTTTGAGCTTCAAAC
45108 GTGCTTTTGAGCTTCAAA
1 GTGCTTTTGAGCTTCAAA
45126 TTACCAAAAA
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:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (19 bp):
GTGCTTTTGAGCTTCAAAC
Found at i:45839 original size:26 final size:28
Alignment explanation
Indices: 45810--45863 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
45800 ATATATTTAC
45810 AATGAAAAT-TTCAAATTG-CCCCCTAA
1 AATGAAAATATTCAAATTGACCCCCTAA
** *
45836 AATGATTATATTCAATTTGACCCCCTAA
1 AATGAAAATATTCAAATTGACCCCCTAA
45864 TCCTCTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 7 0.30
27 8 0.35
28 8 0.35
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.31
Consensus pattern (28 bp):
AATGAAAATATTCAAATTGACCCCCTAA
Found at i:49419 original size:18 final size:18
Alignment explanation
Indices: 49396--49433 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
49386 TTAATGTCCC
49396 TTAAATAATGTTTTAAAT
1 TTAAATAATGTTTTAAAT
*
49414 TTAAATAATGTTTTAGAT
1 TTAAATAATGTTTTAAAT
49432 TT
1 TT
49434 GAGTTTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (18 bp):
TTAAATAATGTTTTAAAT
Found at i:50661 original size:5 final size:6
Alignment explanation
Indices: 50646--50671 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
50636 TATTATTATC
50646 TTTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TT
50672 ATAATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:56423 original size:15 final size:16
Alignment explanation
Indices: 56378--56422 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
56368 AAATTCAACG
56378 AAAAAAATTCAAAATA
1 AAAAAAATTCAAAATA
56394 AAAAAAATTCAAAATA
1 AAAAAAATTCAAAATA
56410 AAAAAAATTCAAA
1 AAAAAAATTCAAA
56423 TGCCAATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAAAATTCAAAATA
Found at i:59524 original size:32 final size:32
Alignment explanation
Indices: 59483--59544 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
59473 TATATCTAAG
*
59483 TTTTTTAATTAAAATAGTAAGATGGTAAAATT
1 TTTTTTAATTAAAATAGTAAAATGGTAAAATT
59515 TTTTTTAATTAAAATAGTAAAATGGTAAAA
1 TTTTTTAATTAAAATAGTAAAATGGTAAAA
59545 ATCAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (32 bp):
TTTTTTAATTAAAATAGTAAAATGGTAAAATT
Found at i:59807 original size:85 final size:86
Alignment explanation
Indices: 59706--59881 Score: 284
Period size: 86 Copynumber: 2.1 Consensus size: 86
59696 AGAAATATAT
* *
59706 TTAAAAAATTCTAATATATCTAA-GTTTTGTAATTAAAATAGTAAACATGGTAAAAAT-AAAATA
1 TTAAAAAATTCCAATATATCTAAGGTTTTGTAATTAAAATAATAAA-ATGGTAAAAATAAAAATA
59769 GTTATAAAGAGATTAGATTTAA
65 GTTATAAAGAGATTAGATTTAA
* *
59791 TTAAAATATTCCAATATATCTAAGGTTTTTTAATTAAAATAATAAAATGGTAAAAATAAAAATAG
1 TTAAAAAATTCCAATATATCTAAGGTTTTGTAATTAAAATAATAAAATGGTAAAAATAAAAATAG
*
59856 TTATAAAGAGATTATATTTAA
66 TTATAAAGAGATTAGATTTAA
59877 TTAAA
1 TTAAA
59882 GAAAAATAGA
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
85 32 0.38
86 52 0.62
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.36
Consensus pattern (86 bp):
TTAAAAAATTCCAATATATCTAAGGTTTTGTAATTAAAATAATAAAATGGTAAAAATAAAAATAG
TTATAAAGAGATTAGATTTAA
Found at i:60166 original size:22 final size:22
Alignment explanation
Indices: 60129--60682 Score: 115
Period size: 22 Copynumber: 25.3 Consensus size: 22
60119 ATGATCTCCG
*
60129 TATGAAATTCTGATAACCTTTC
1 TATGAAATTTTGATAACCTTTC
* ****
60151 TATGAAATTTTAATAACGACAC
1 TATGAAATTTTGATAACCTTTC
* * * *
60173 TATGGAATTTCGAGAACCTTTG
1 TATGAAATTTTGATAACCTTTC
* **
60195 TATAAAATTTTTTTAACC-TTC
1 TATGAAATTTTGATAACCTTTC
* **
60216 TTATGAAATTTTGTTAACCTCCC
1 -TATGAAATTTTGATAACCTTTC
* * **
60239 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCTTTC
60261 TATGAAATTTTGATAA-CTTTCC
1 TATGAAATTTTGATAACCTTT-C
* ***
60283 AATGAAATTTTGATAACCAGCAC
1 TATGAAATTTTGATAACC-TTTC
* * * *
60306 TATGAGATTTTGCTAA-CATCC
1 TATGAAATTTTGATAACCTTTC
* * **
60327 ATATGATATATTGATAACCACGT-
1 -TATGAAATTTTGATAACC-TTTC
* * * *
60350 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTTC
* ***
60371 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTTTC
* ** ***
60394 TCTGAAATTTTGATATTCACAC
1 TATGAAATTTTGATAACCTTTC
* **
60416 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTTTC
* *
60438 TATAAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTTC
* * **
60461 TATAAAATTTTGGTAAACCTCCC
1 TATGAAATTTTGAT-AACCTTTC
* *
60484 TATAAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTTC
*
60505 TTATGAAATCTTGATAA-----C
1 -TATGAAATTTTGATAACCTTTC
* *
60523 TA-CAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-TC
** * *
60544 TATGATTTTTTGATAATCTCAT-
1 TATGAAATTTTGATAACCT-TTC
** * **
60566 TATGAAATTTTTTTAATCTCCC
1 TATGAAATTTTGATAACCTTTC
* * *
60588 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTTC
*
60610 TATGAAATTTTGATAACC-CTC
1 TATGAAATTTTGATAACCTTTC
* **
60631 TTATGAAATTTTGAAAACCAAAT-
1 -TATGAAATTTTGATAACC-TTTC
60654 TATGAAATTTTGATAACC-TTC
1 TATGAAATTTTGATAACCTTTC
60675 ATATGAAA
1 -TATGAAA
60683 ATTCAATATC
Statistics
Matches: 391, Mismatches: 106, Indels: 70
0.69 0.19 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 1 0.00
21 17 0.04
22 291 0.74
23 67 0.17
24 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTTC
Found at i:60292 original size:44 final size:45
Alignment explanation
Indices: 60217--60672 Score: 164
Period size: 44 Copynumber: 10.4 Consensus size: 45
60207 TTAACCTTCT
* * *
60217 TATGAAATTTTGTTAACCTCCCTAAGGAATTTTGA-AGACC-TCAC
1 TATGAAATTTTGATAACCTCCCTAAGAAATTTTGATA-ACCAGCAC
* *
60261 TATGAAATTTTGATAACTTTCC-AATGAAATTTTGATAACCAGCAC
1 TATGAAATTTTGATAACCTCCCTAA-GAAATTTTGATAACCAGCAC
* * * * * * * **
60306 TATGAGATTTTGCTAACATCCATATGATATATTGATAACCA-CGT
1 TATGAAATTTTGATAACCTCCCTAAGAAATTTTGATAACCAGCAC
* * * * * *
60350 TATGAAAATTTAAAAACCTCCATATG-AATTGTT-AGTAATCA-CAC
1 TATGAAATTTTGATAACCTCCCTAAGAAATT-TTGA-TAACCAGCAC
* ** * * * * * *
60394 TCTGAAATTTTGATATTCACACTATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTCCCTAAGAAATTTTGATAACCAGCAC
* * * * *
60438 TATAAAATTTTGATAAACCTTCCTATA-AAATTTTGGTAAACC-TCCC
1 TATGAAATTTTGAT-AACCTCCCTA-AGAAATTTTGAT-AACCAGCAC
* * * *
60484 TATAAAATTTTGATAACCTCCTTATGAAATCTTGAT----A--AC
1 TATGAAATTTTGATAACCTCCCTAAGAAATTTTGATAACCAGCAC
* * * ** * * *
60523 TA-CAAATTTTGATAACTTCCCTATGATTTTTTGATAATC-TCAT
1 TATGAAATTTTGATAACCTCCCTAAGAAATTTTGATAACCAGCAC
** * * * *
60566 TATGAAATTTTTTTAATCTCCCTATGAAATTTTGATCTA-CA-TAC
1 TATGAAATTTTGATAACCTCCCTAAGAAATTTTGAT-AACCAGCAC
* * * * *
60610 TATGAAATTTTGATAACC-CTCTTATGAAATTTTGAAAACCA-AAT
1 TATGAAATTTTGATAACCTC-CCTAAGAAATTTTGATAACCAGCAC
60654 TATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
60673 TCATATGAAA
Statistics
Matches: 306, Mismatches: 80, Indels: 51
0.70 0.18 0.12
Matches are distributed among these distances:
38 27 0.09
39 3 0.01
43 10 0.03
44 174 0.57
45 70 0.23
46 22 0.07
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (45 bp):
TATGAAATTTTGATAACCTCCCTAAGAAATTTTGATAACCAGCAC
Found at i:60840 original size:22 final size:22
Alignment explanation
Indices: 60791--60959 Score: 121
Period size: 22 Copynumber: 7.7 Consensus size: 22
60781 GAAATACCAC
* * *
60791 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAACCTC-TT
*
60814 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
* *
60835 TATGAAATTTTGATAACATCTC
1 TATGAAATTTTGATAACCTCTT
* * * *
60857 TATTAAATTTTGTTGACCCCTT
1 TATGAAATTTTGATAACCTCTT
* * *
60879 TATGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAACCTCTT
* *
60901 TAT-ATAGTTTTGATAACCTCGCT
1 TATGA-AATTTTGATAACCTC-TT
* **
60924 T-TGAAATTTTGATAATCTCCC
1 TATGAAATTTTGATAACCTCTT
60945 TAT-AAATTTTGATAA
1 TATGAAATTTTGATAA
60960 TCTGATCTCT
Statistics
Matches: 115, Mismatches: 26, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
21 18 0.16
22 93 0.81
23 4 0.03
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTT
Found at i:60841 original size:44 final size:43
Alignment explanation
Indices: 60791--60959 Score: 155
Period size: 44 Copynumber: 3.9 Consensus size: 43
60781 GAAATACCAC
* *
60791 TATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACATTTT-AAATTTTGATAACCTCTT
* * *
60835 TATGAAATTTTGATAA-CATC-TCTATTAAATTTTGTTGACCCCTT
1 TATGAAATTTTGATAATCA-CAT-T-TTAAATTTTGATAACCTCTT
* * *
60879 TATGAAATTTTGATAATCACATTATATAGTTTTGATAACCTCGCT
1 TATGAAATTTTGATAATCACATTTTA-AATTTTGATAACCTC-TT
* ** *
60924 T-TGAAATTTTGATAATCTCCCTATAAATTTTGATAA
1 TATGAAATTTTGATAATCACATTTTAAATTTTGATAA
60960 TCTGATCTCT
Statistics
Matches: 103, Mismatches: 15, Indels: 15
0.77 0.11 0.11
Matches are distributed among these distances:
43 15 0.15
44 81 0.79
45 7 0.07
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (43 bp):
TATGAAATTTTGATAATCACATTTTAAATTTTGATAACCTCTT
Found at i:60977 original size:25 final size:22
Alignment explanation
Indices: 60790--60985 Score: 96
Period size: 22 Copynumber: 8.8 Consensus size: 22
60780 AGAAATACCA
* * *
60790 CTATGAAATTTTGGTAATCACA
1 CTATGAAATTTTGATAATCTCC
* * * * *
60812 TTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCTCC
* *
60834 TTATGAAATTTTGATAA-CATCT
1 CTATGAAATTTTGATAATC-TCC
* * *
60856 CTATTAAATTTTGTTGA-C-CC
1 CTATGAAATTTTGATAATCTCC
* *
60876 CTTTATGAAATTTTGATAATCACA
1 C--TATGAAATTTTGATAATCTCC
* * * *
60900 TTAT-ATAGTTTTGATAACCTCG
1 CTATGA-AATTTTGATAATCTCC
*
60922 CTTTGAAATTTTGATAATCTCC
1 CTATGAAATTTTGATAATCTCC
*
60944 CTAT-AAATTTTGATAATCTGATCT
1 CTATGAAATTTTGATAATC---TCC
*
60968 CTATGAAATTTCGATAAT
1 CTATGAAATTTTGATAAT
60986 AACTCTATGA
Statistics
Matches: 132, Mismatches: 31, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
20 2 0.02
21 16 0.12
22 93 0.70
23 2 0.02
24 7 0.05
25 12 0.09
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCTCC
Found at i:61074 original size:22 final size:21
Alignment explanation
Indices: 61045--61376 Score: 105
Period size: 22 Copynumber: 15.5 Consensus size: 21
61035 AAATTGAGAC
61045 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTC-TATGAAA
**
61066 TTTTGATAACCACACTATGAAA
1 TTTTGATAACC-TTCTATGAAA
* * *
61088 TTTTAATAACCTCCCCATGAAA
1 TTTTGATAACCT-TCTATGAAA
** * *
61110 TAGT-AGTAACCTCTTTATGATA
1 TTTTGA-TAACCT-TCTATGAAA
* **
61132 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACC-TTCTATGAAA
*
61154 TTCTT-ATAACCTTGCTATGACA
1 TT-TTGATAACCTT-CTATGAAA
* *
61176 TTTTGATAATC-TCTTTGAAA
1 TTTTGATAACCTTCTATGAAA
*
61196 -----A--ACCTTCTATAAAA
1 TTTTGATAACCTTCTATGAAA
* * *
61210 TTGTGATAAACATACTATGAAA
1 TTTTGAT-AACCTTCTATGAAA
** *
61232 TTTCAATAACCTTCCTAAGAAA
1 TTTTGATAACCTT-CTATGAAA
* *
61254 TTTTAATAACCTGATCCTATGGAA
1 TTTTGATAACCT--T-CTATGAAA
* ** *
61278 TTTTGGTAACCACACTATGCAA
1 TTTTGATAACC-TTCTATGAAA
*
61300 TTTTGATAACCTTCCCATGAAA
1 TTTTGATAACCTT-CTATGAAA
61322 TTTTGATAA-CTTCCATACTG-AA
1 TTTTGATAACCTT-C-TA-TGAAA
* ** *
61344 TTTTGGTAACCACACTATGGAA
1 TTTTGATAACC-TTCTATGAAA
61366 TTTTGATAACC
1 TTTTGATAACC
61377 CCCTCATGAA
Statistics
Matches: 227, Mismatches: 56, Indels: 55
0.67 0.17 0.16
Matches are distributed among these distances:
13 2 0.01
14 7 0.03
15 1 0.00
19 1 0.00
20 6 0.03
21 19 0.08
22 167 0.74
23 7 0.03
24 17 0.07
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCTTCTATGAAA
Found at i:61369 original size:66 final size:67
Alignment explanation
Indices: 61223--61376 Score: 197
Period size: 66 Copynumber: 2.3 Consensus size: 67
61213 TGATAAACAT
** *
61223 ACTATGAAATTTCAATAACCTTCCTAAGAAATTTTAATAACCTGATCCTATGGAATTTTGGTAAC
1 ACTATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAACCT-ATCCTATGGAATTTTGGTAAC
61288 CAC
65 CAC
* * *
61291 ACTATGCAATTTTGATAACCTTCCCATGAAATTTTGATAA-CT-TCCATACT-GAATTTTGGTAA
1 ACTATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAACCTATCC-TA-TGGAATTTTGGTAA
61353 CCAC
64 CCAC
*
61357 ACTATGGAATTTTGATAACC
1 ACTATGAAATTTTGATAACC
61377 CCCTCATGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
65 3 0.04
66 37 0.48
67 3 0.04
68 34 0.44
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.35
Consensus pattern (67 bp):
ACTATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAACCTATCCTATGGAATTTTGGTAACC
AC
Found at i:61618 original size:20 final size:20
Alignment explanation
Indices: 61580--61618 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
61570 TATTGATATT
61580 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
61600 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
61619 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:67697 original size:12 final size:13
Alignment explanation
Indices: 67674--67703 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
67664 ACTAGTAATT
67674 AAAATCAATCAAG
1 AAAATCAATCAAG
67687 AAAAT-AATCAAG
1 AAAATCAATCAAG
67699 AAAAT
1 AAAAT
67704 TAAAGAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (13 bp):
AAAATCAATCAAG
Done.