Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015965.1 Corchorus capsularis cultivar CVL-1 contig15986, 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: 26331
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Found at i:258 original size:32 final size:32
Alignment explanation
Indices: 217--305 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
207 ACTCGTGAAA
***
217 ATATGCGAAGATAAAATATTTTTTTAGGGTAT
1 ATATGCGAAGATAAAATATTTTTTTAAAATAT
249 ATATGCGAAGATAAAATA-TTTTTTAAAATAT
1 ATATGCGAAGATAAAATATTTTTTTAAAATAT
*
280 ATATGCGAAGATAAAAAAATTTTTTT
1 ATATGCGAAGAT-AAAATATTTTTTT
306 GTGAAAGAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 22 0.43
32 23 0.45
33 6 0.12
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.39
Consensus pattern (32 bp):
ATATGCGAAGATAAAATATTTTTTTAAAATAT
Found at i:975 original size:3 final size:3
Alignment explanation
Indices: 967--1007 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
957 ATACAATATG
967 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1008 CACCATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:995 original size:20 final size:20
Alignment explanation
Indices: 970--1007 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
960 CAATATGTAT
970 TATTATTATTATTATTATTA
1 TATTATTATTATTATTATTA
990 TATTATTATTATTATTAT
1 TATTATTATTATTATTAT
1008 CACCATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTATTATTATTATTATTA
Found at i:2345 original size:73 final size:70
Alignment explanation
Indices: 2268--2420 Score: 164
Period size: 73 Copynumber: 2.1 Consensus size: 70
2258 TAATATATCA
* * * *
2268 AGTTTTTTAATTAAAATAGTAAAATGGTAAAATA-TAAGTAATAAGGATATTAGATTTAATTATA
1 AGTTTTTTAAGTAAAATAGTAAAA---TAAAATAGTAACT-ATAAAGATATTAGATTTAATTAAA
2332 TAAAAATAG
62 TAAAAATAG
* * * *
2341 AGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTACTTTAAAGATATTATATTTAATTAAAT
1 AG-TTTT--TTAAGTAAAATAGTAAAATAAAATAGTAACTATAAAGATATTAGATTTAATTAAAT
2406 AAAAATAG
63 AAAAATAG
2414 AGTTTTT
1 AGTTTTT
2421 AGTTAAATAA
Statistics
Matches: 68, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
70 1 0.01
72 4 0.06
73 40 0.59
74 7 0.10
76 16 0.24
ACGTcount: A:0.48, C:0.01, G:0.12, T:0.39
Consensus pattern (70 bp):
AGTTTTTTAAGTAAAATAGTAAAATAAAATAGTAACTATAAAGATATTAGATTTAATTAAATAAA
AATAG
Found at i:2366 original size:68 final size:70
Alignment explanation
Indices: 2285--2446 Score: 186
Period size: 73 Copynumber: 2.3 Consensus size: 70
2275 TAATTAAAAT
* * *
2285 AGTAAAATGGTAAAATATAAG-TA-ATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATATAAGTTACATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
*
2348 AGTTG
66 AGTTA
* * *
2353 AGTAAAATAGTAAAATAAAATAGTTACTTTAAAGATATTATATTTAATTAAATAAAAATAGAGTT
1 AGTAAAATAGTAAAAT-ATA-AGTTAC-ATAAAGATATTAGATTTAATTAAATAAAAATAGAGTT
2418 TTTAGTTA
63 TTTAGTTA
*
2426 AATAAAACTA-TAAAAATATAA
1 AGTAAAA-TAGT-AAAATATAA
2447 AATAGAGTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
68 15 0.19
69 2 0.03
70 2 0.03
71 2 0.03
72 1 0.01
73 49 0.63
74 7 0.09
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.36
Consensus pattern (70 bp):
AGTAAAATAGTAAAATATAAGTTACATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTA
Found at i:2470 original size:38 final size:37
Alignment explanation
Indices: 2402--2767 Score: 200
Period size: 39 Copynumber: 10.1 Consensus size: 37
2392 ATATTTAATT
2402 AAATAAAAATAGAGTTTTTAGTTAAATAAAACTA-TAA
1 AAATAAAAATAGAGTTTTTAGTTAAATAAAA-TAGTAA
* *
2439 AAATATAAAATAGAGTTTTTAGTTGAGTAAAATAGT-A
1 AAATA-AAAATAGAGTTTTTAGTTAAATAAAATAGTAA
* ** * * * *
2476 AAAT-AAAAT--AG-TTATAAATATATTATAT-TTAA
1 AAATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAA
2508 TTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTA-TAAA
1 --AAATAAAAATAGAGTTTTTAGTTAAATAAAA-TAGT-AA
* *
2548 AATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGT-A
1 AA-ATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAA
* ** * * * *
2585 AAAT-AAAAT--AG-TTATAAATATATTATAT-TTAA
1 AAATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAA
2617 TTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTA-TAAA
1 --AAATAAAAATAGAGTTTTTAGTTAAATAAAA-TAGT-AA
* *
2657 AATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGT-A
1 AA-ATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAA
* ** * * * *
2694 AAAT-AAAAT--AG-TTATAAATATATTATAT-TTAA
1 AAATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAA
2726 TTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTA-TAA
1 --AAATAAAAATAGAGTTTTTAGTTAAATAAAA-TAGTAA
2765 AAA
1 AAA
2768 CTTAAACAAT
Statistics
Matches: 243, Mismatches: 51, Indels: 70
0.67 0.14 0.19
Matches are distributed among these distances:
31 3 0.01
32 30 0.12
33 6 0.02
34 12 0.05
35 30 0.12
36 4 0.02
37 27 0.11
38 63 0.26
39 64 0.26
40 4 0.02
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (37 bp):
AAATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAA
Found at i:2787 original size:109 final size:109
Alignment explanation
Indices: 2329--2767 Score: 835
Period size: 109 Copynumber: 4.0 Consensus size: 109
2319 AGATTTAATT
*
2329 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTACTTTAAAGATATTAT
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTA---TAAATATATTAT
2394 ATTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
63 ATTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
2441 ATAT-AAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATAAATATATTATATT
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATAAATATATTATATT
2505 TAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
66 TAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
2549 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATAAATATATTATATT
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATAAATATATTATATT
2614 TAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
66 TAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
2658 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATAAATATATTATATT
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATAAATATATTATATT
2723 TAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
66 TAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
2767 A
1 A
2768 CTTAAACAAT
Statistics
Matches: 325, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
108 62 0.19
109 214 0.66
111 45 0.14
112 4 0.01
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (109 bp):
ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATAAATATATTATATT
TAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
Found at i:6452 original size:2 final size:2
Alignment explanation
Indices: 6445--6480 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6435 AGGTAATTTC
6445 AT AT AT AT AT 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
6481 CTATGTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6683 original size:21 final size:21
Alignment explanation
Indices: 6648--6706 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
6638 GATACTATGG
** *
6648 AATTTTGAGAACCTTTTTAT-
1 AATTTTGTTAACCTTCTTATA
*
6668 AATTTTCTTTAACCTTCTTATGA
1 AATTTT-GTTAACCTTCTTAT-A
6691 AATTTTGTTAACCTTC
1 AATTTTGTTAACCTTC
6707 CTAAGGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 6 0.19
21 10 0.32
22 9 0.29
23 6 0.19
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (21 bp):
AATTTTGTTAACCTTCTTATA
Found at i:6704 original size:22 final size:22
Alignment explanation
Indices: 6599--7234 Score: 282
Period size: 22 Copynumber: 29.4 Consensus size: 22
6589 ATAATCCTAT
**
6599 TATGAAATTTTGATAATGTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
6621 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * **
6643 TATGGAATTTTGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
6665 TAT--AATTTTCTTTAACCTTCT
1 TATGAAATTTT-GATAACCTTCC
*
6686 TATGAAATTTTGTTAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * * *
6708 TAAGGAATTTTGAAAACC-TCAG
1 TATGAAATTTTGATAACCTTC-C
6730 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
6752 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
6775 TATGAGATGTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * * *
6797 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
6820 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
6841 ATATG-AATTGTT-AGTAATCATAC
1 -TATGAAATT-TTGA-TAACCTTCC
* * *
6864 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
6886 TATGAAATTTTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
* *
6908 TATGAAATTTTGATAAATCTTCA
1 TATGAAATTTTGAT-AACCTTCC
* *
6931 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
6954 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
6976 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
6993 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
7014 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
7036 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
*** * *
7058 TATGAAATTTTGATCTGCATAC
1 TATGAAATTTTGATAACCTTCC
* *
7080 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
7102 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
7124 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
7145 -CTGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
7165 ATGATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* * *
7189 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
7206 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
7228 TA-GAAAT
1 TATGAAAT
7235 ACCACTATGA
Statistics
Matches: 460, Mismatches: 116, Indels: 77
0.70 0.18 0.12
Matches are distributed among these distances:
16 11 0.02
17 12 0.03
18 2 0.00
19 1 0.00
20 26 0.06
21 32 0.07
22 272 0.59
23 99 0.22
24 5 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:6824 original size:45 final size:45
Alignment explanation
Indices: 6730--6816 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 45
6720 AAAACCTCAG
* *
6730 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACTTCCCAATGAAATATTGATAACCAACAC
* *
6775 TATGAGATGTTGATAACCTT-CCATATGATATATTGATAACCA
1 TATGAAATGTTGATAA-CTTCCCA-ATGAAATATTGATAACCA
6817 CGTTATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 17 0.47
46 19 0.53
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACTTCCCAATGAAATATTGATAACCAACAC
Found at i:6942 original size:23 final size:23
Alignment explanation
Indices: 6912--6991 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
6902 CCTCGCTATG
6912 AAATTTTGATAAATCTTCATATA
1 AAATTTTGATAAATCTTCATATA
* * *
6935 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCATATA
* * *
6958 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCATATA
*
6980 AAATCTTGATAA
1 AAATTTTGATAA
6992 CTACAAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
22 16 0.33
23 32 0.67
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCATATA
Found at i:6989 original size:45 final size:46
Alignment explanation
Indices: 6868--6991 Score: 148
Period size: 45 Copynumber: 2.8 Consensus size: 46
6858 TCATACTCTG
* * *
6868 AAATTTTGAT-AATC-ACACTATGAAATTTTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTCA-TATGAAATTTTGATAAACCTCCCTATA
*
6912 AAATTTTGATAAATCTTCATATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCATATGAAATTTTGATAAACCTCCCTATA
* * *
6958 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCATATGAAATTTTGATAA
6992 CTACAAATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
44 10 0.14
45 34 0.49
46 25 0.36
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.40
Consensus pattern (46 bp):
AAATTTTGATAAATCTTCATATGAAATTTTGATAAACCTCCCTATA
Found at i:7087 original size:104 final size:106
Alignment explanation
Indices: 6890--7096 Score: 251
Period size: 104 Copynumber: 2.0 Consensus size: 106
6880 TCACACTATG
* *
6890 AAATTTTGATAACCTCGCTATGAAATTTTGATAAATCTTCATATAAAATTTTGATAAACCTCCCT
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAAATCCTCATATAAAATTTTGATAAACCTCCCT
* *
6955 ATAAAATTTTGATAACTTTCTTATGAAATCTTGATAACTAC
66 ATAAAATTTTGATAACATACTTATGAAATCTTGATAACTAC
** * * *
6996 AAATTTTGATAACCTCCCTATGATTTTTTGAT-AA-CCTCATTATGAAATTTTG-TTAATCTCCC
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAAATCCTCA-TATAAAATTTTGATAAACCTCCC
* ** *
7058 TATGAAATTTTGATCTGCATAC-TATGAAATTTTGATAAC
65 TATAAAATTTTGAT-AACATACTTATGAAATCTTGATAAC
7097 CCTCTTATGA
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
104 41 0.48
105 16 0.19
106 29 0.34
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (106 bp):
AAATTTTGATAACCTCCCTATGAAATTTTGATAAATCCTCATATAAAATTTTGATAAACCTCCCT
ATAAAATTTTGATAACATACTTATGAAATCTTGATAACTAC
Found at i:7151 original size:20 final size:20
Alignment explanation
Indices: 7126--7164 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
7116 AACTAAACTA
7126 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
7146 TGAAATTTTGATATCCTCC
1 TGAAATTTTGATATCCTCC
7165 ATGATAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:7402 original size:88 final size:88
Alignment explanation
Indices: 7239--7405 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 88
7229 AGAAATACCA
* * * * ***
7239 CTATGAAATTTTTGTAATCACATTCTGAAAATTTGATAACCTCTTTCTGAAATTTTGATAACCTT
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTCTAAAATTTTGATAACAAC
*
7304 TTTATAAAATTTTGTTGACCCCT
66 ATTATAAAATTTTGTTGACCCCT
* *
7327 CTATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TAAAATTTTGATAACA
1 CTATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCTC-CTTCTAAAATTTTGATAACA
*
7390 ACATTATGAAATTTTG
64 ACATTATAAAATTTTG
7406 ATAATCTTCC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
87 4 0.06
88 60 0.91
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.43
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTCTAAAATTTTGATAACAAC
ATTATAAAATTTTGTTGACCCCT
Found at i:7580 original size:22 final size:22
Alignment explanation
Indices: 7264--7871 Score: 166
Period size: 22 Copynumber: 27.7 Consensus size: 22
7254 AATCACATTC
* ** *
7264 TGAAAATTTGATAACCTCTTTC
1 TGAAATTTTGATAACCTCCCTA
***
7286 TGAAATTTTGATAACCTTTTTA
1 TGAAATTTTGATAACCTCCCTA
* * *
7308 TAAAATTTTGTTGACC-CCTCTA
1 TGAAATTTTGATAACCTCC-CTA
* * * **
7330 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCCCTA
* * *
7352 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTCCCTA
* ** **
7374 TAAAATTTTGATAACAACATTA
1 TGAAATTTTGATAACCTCCCTA
* *
7396 TGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAACCTCCCTA
* **
7418 T-AAATTTTGATAATCTGATATCTA
1 TGAAATTTTGATAA-C--CTCCCTA
* * * * *
7442 TGGAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCCCTA
* *
7464 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCCCTA
* * * *
7484 TCAAATTTTGGT-A-TTCCTTA
1 TGAAATTTTGATAACCTCCCTA
* * *
7504 TGAAATTGAGACTTTATAACCTTCATA
1 TGAAATT-----TTGATAACCTCCCTA
* * *
7531 TGAAATTTTGATTACCACGCTA
1 TGAAATTTTGATAACCTCCCTA
* *
7553 TAAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCCCTA
*
7575 TGAAATATT-AGTAACCT-CCTAA
1 TGAAATTTTGA-TAACCTCCCT-A
* * *
7597 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCCCTA
*
7619 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCCCTA
* *
7641 T-AACATTTTGATAA--TCTCTT
1 TGAA-ATTTTGATAACCTCCCTA
** *
7661 TGATAACCTTTCT-ATAAAAT---TG
1 TGA-AA--TTT-TGATAACCTCCCTA
* *
7683 TGAAA--AT--TAACCACCCTA
1 TGAAATTTTGATAACCTCCCTA
** **
7701 TGAAATTTCAATAACCAACCTA
1 TGAAATTTTGATAACCTCCCTA
* *
7723 AGAAATTTTAATAACCTGACCCTA
1 TGAAATTTTGATAACCT--CCCTA
* * * *
7747 TGAAATTTTGGTAATCACACTA
1 TGAAATTTTGATAACCTCCCTA
* *
7769 TGAAATTTTGATAACTTCCATA
1 TGAAATTTTGATAACCTCCCTA
* * *
7791 TGAAATTTTGGTAACCACGCTA
1 TGAAATTTTGATAACCTCCCTA
7813 TG-AATTTTGATAACCT-CCTCA
1 TGAAATTTTGATAACCTCCCT-A
* *
7834 TGAAATTAT-AGTAACCAT-CTTA
1 TGAAATTTTGA-TAACC-TCCCTA
7856 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
7872 ACATAGAGAC
Statistics
Matches: 420, Mismatches: 123, Indels: 86
0.67 0.20 0.14
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
18 6 0.01
19 1 0.00
20 23 0.05
21 52 0.12
22 270 0.64
23 16 0.04
24 22 0.05
25 14 0.03
26 1 0.00
27 11 0.03
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCCCTA
Found at i:8223 original size:15 final size:15
Alignment explanation
Indices: 8203--8251 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
8193 ATAGTCTAAT
8203 ATAATTAATAATGGA
1 ATAATTAATAATGGA
* *
8218 ATAATTTATAAT-TA
1 ATAATTAATAATGGA
8232 A-AA--AATAATGGA
1 ATAATTAATAATGGA
8244 ATAATTAA
1 ATAATTAA
8252 AATTTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
11 5 0.19
12 2 0.08
13 4 0.15
14 2 0.08
15 13 0.50
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (15 bp):
ATAATTAATAATGGA
Found at i:8709 original size:2 final size:2
Alignment explanation
Indices: 8702--8726 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8692 GCGCACCTGC
8702 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 A
8727 GTAAGGTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10067 original size:12 final size:12
Alignment explanation
Indices: 10047--10078 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
10037 TGTTTGGTGC
10047 CAAGGAAAATAT
1 CAAGGAAAATAT
*
10059 CATGGAAAATAT
1 CAAGGAAAATAT
10071 CAAGGAAA
1 CAAGGAAA
10079 GTATTTTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.19, T:0.16
Consensus pattern (12 bp):
CAAGGAAAATAT
Found at i:10410 original size:15 final size:15
Alignment explanation
Indices: 10390--10419 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10380 GGAAGATCAT
10390 CTTGTTGTGAAGCAC
1 CTTGTTGTGAAGCAC
10405 CTTGTTGTGAAGCAC
1 CTTGTTGTGAAGCAC
10420 TTTTCTGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (15 bp):
CTTGTTGTGAAGCAC
Found at i:14463 original size:15 final size:16
Alignment explanation
Indices: 14428--14466 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
14418 ACTCAAAACC
**
14428 AAAATCAATCATGGTT
1 AAAATCAATCATGCAT
14444 AAAATCAAT-ATGCAT
1 AAAATCAATCATGCAT
14459 AAAATCAA
1 AAAATCAA
14467 ATCCTCACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.54, C:0.13, G:0.08, T:0.26
Consensus pattern (16 bp):
AAAATCAATCATGCAT
Found at i:17872 original size:18 final size:18
Alignment explanation
Indices: 17851--17887 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
17841 AGCATTACTC
17851 AACATTCAACAATTACAA
1 AACATTCAACAATTACAA
17869 AACATTCAACAATTACAA
1 AACATTCAACAATTACAA
17887 A
1 A
17888 GTAGAGTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.22, G:0.00, T:0.22
Consensus pattern (18 bp):
AACATTCAACAATTACAA
Found at i:18196 original size:2 final size:2
Alignment explanation
Indices: 18150--18180 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18140 TGTGTGTGTG
18150 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 T
18181 TCTAGAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.