Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012792.1 Corchorus capsularis cultivar CVL-1 contig12813, 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: 34711
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1178 original size:75 final size:75
Alignment explanation
Indices: 1028--1296 Score: 432
Period size: 75 Copynumber: 3.6 Consensus size: 75
1018 TTAATATTTT
* *
1028 CTAAATCTCCCACAATCTGGCAAGATTTAGAGAAATATTCTCATTCTTTATTATT-TATTTATTT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGA-AAATATTCTCA-ACTTTATTATTAT-TTTATTT
1092 CTTAAAATATCTC
63 CTTAAAATATCTC
* * * *
1105 GTAAACCTTCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTCATTATTATTTTATTTCTT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
*
1170 AAAGTATCTC
66 AAAATATCTC
*
1180 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATGCTCAACTTTATTATTATTTTATTTCTT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
1245 AAAATATCTC
66 AAAATATCTC
1255 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCA
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCA
1297 TTAATTATTT
Statistics
Matches: 177, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
75 138 0.78
76 12 0.07
77 27 0.15
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.40
Consensus pattern (75 bp):
CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
AAAATATCTC
Found at i:2615 original size:35 final size:35
Alignment explanation
Indices: 2548--3397 Score: 1183
Period size: 35 Copynumber: 24.3 Consensus size: 35
2538 ACTCCTCTGA
* * * * *
2548 ATCAACTCTGATCATCGGAAATTTCTTG-AAATGAG
1 ATCAACTCTGATCGTTGGAAACTAC-TGAAAATGCG
* * * *
2583 ATCACCTCTAATTGTTGGAAACTACTGAAAATGTG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
2618 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
* *
2653 ATAAACTCTGATCGTTGGAAAATACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
* *
2688 ATCAACTCCGATCATTGGAAACTACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
* * * *
2723 ATCAACTCTGATC-ATGGAAAATATTGAAAATGTG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
*
2757 ATCAACTCTGATCGTTGGAAAATACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
* *
2792 ACCAACTCTGATCGTTGGAAAATACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
* *
2827 ATCAACTCTGATCATTGGAAACTTCTTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTAC-TGAAAATGCG
* *
2863 ATCAACTCCGATCATTGGAAACTACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
* * *
2898 ATCAACTCTGATC-ATGGAAAATACTGAAAATGTG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
*
2932 ATCAACTCTGATCGTTGGAAAATACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
2967 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
* * *
3002 ATCAACTCTGATTGTTGGAAACTTCTGAAAAATGTG
1 ATCAACTCTGATCGTTGGAAACTACTG-AAAATGCG
3038 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
*
3073 ATCAACTCTGATCGTTGGAAAATACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
* *
3108 ATCAACTCCGATCATTGGAAACTACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
* *
3143 ATCAACTCTGATC-ATGGAGAA-TACTGAAAATGTG
1 ATCAACTCTGATCGTTGGA-AACTACTGAAAATGCG
*
3177 ATCAACTCTGATCGTTGGAAAATACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
*
3212 ATCAACTCTGATCGTTGGAAACTTCTTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTAC-TGAAAATGCG
* *
3248 ATCAACTCCGATCATTGGAAACTACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
* *
3283 ATCAACTCTGATAG-TGGAAAATACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
*
3317 ATCAACTCTGATCGTTGGAAAATACTGAAAATGCG
1 ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
* * *
3352 ATCAACTCTGATTGTTGGAAACTTCTTG-AAATGAG
1 ATCAACTCTGATCGTTGGAAACTAC-TGAAAATGCG
3387 ATCAACTCTGA
1 ATCAACTCTGA
3398 CCTCTGAAAA
Statistics
Matches: 735, Mismatches: 69, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
34 126 0.17
35 510 0.69
36 99 0.13
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (35 bp):
ATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
Found at i:3409 original size:35 final size:35
Alignment explanation
Indices: 3370--3801 Score: 740
Period size: 35 Copynumber: 12.4 Consensus size: 35
3360 TGATTGTTGG
3370 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
* * *
3405 AAACTTCTTGATATGAGATCAACTATGACCTCTGG
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
3440 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
*
3475 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
*
3510 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
* *
3545 AAACTTCTTGGAATGATATCAACTCTGACCTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
*
3580 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
*
3615 AAACTTCTTGATATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
* *
3650 AAACTTCTTGATATGAGATCAATTCTGACCTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
3685 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
*
3720 AAACTTCTTGATATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
*
3755 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
3790 AAACTTC-TGAAA
1 AAACTTCTTGAAA
3802 ACGACCGCAC
Statistics
Matches: 379, Mismatches: 18, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
34 4 0.01
35 375 0.99
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (35 bp):
AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
Found at i:3426 original size:70 final size:70
Alignment explanation
Indices: 2576--3782 Score: 975
Period size: 70 Copynumber: 17.3 Consensus size: 70
2566 AAATTTCTTG
* * * * * * *
2576 AAATGAGATCACCTCTAATTGTTGGAAACTACTGAAAATGTGATCAACTCTGATCGTTGGAAACT
1 AAATGCGATCAACTCTGATTGTTGGAAACTTCTGAAAATGCGATCAACTCTGATCCTTGAAAACT
2641 ACTGA
66 ACTGA
* * * * * * *
2646 AAATGCGATAAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTCCGATCATTGGAAACT
1 AAATGCGATCAACTCTGATTGTTGGAAACTTCTGAAAATGCGATCAACTCTGATCCTTGAAAACT
2711 ACTGA
66 ACTGA
** * * *
2716 AAATGCGATCAACTCTGA-TCATGGAAAATAT-TGAAAATGTGATCAACTCTGATCGTTGGAAAA
1 AAATGCGATCAACTCTGATTGTTGGAAACT-TCTGAAAATGCGATCAACTCTGATCCTT-GAAAA
2779 -TACTGA
64 CTACTGA
* * * * * *
2785 AAATGCGACCAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTCTGATCATTGGAAACT
1 AAATGCGATCAACTCTGATTGTTGGAAACTTCTGAAAATGCGATCAACTCTGATCCTTGAAAACT
*
2850 TCTTGA
66 AC-TGA
* ** * * *
2856 AAATGCGATCAACTCCGATCATTGGAAACTACTGAAAATGCGATCAACTCTGATCATGGAAAA-T
1 AAATGCGATCAACTCTGATTGTTGGAAACTTCTGAAAATGCGATCAACTCTGATCCTTGAAAACT
2920 ACTGA
66 ACTGA
* * * * * *
2925 AAATGTGATCAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTCTGATCGTTGGAAACT
1 AAATGCGATCAACTCTGATTGTTGGAAACTTCTGAAAATGCGATCAACTCTGATCCTTGAAAACT
2990 ACTGA
66 ACTGA
* * *
2995 AAATGCGATCAACTCTGATTGTTGGAAACTTCTGAAAAATGTGATCAACTCTGATCGTTGGAAAC
1 AAATGCGATCAACTCTGATTGTTGGAAACTTCTG-AAAATGCGATCAACTCTGATCCTTGAAAAC
3060 TACTGA
65 TACTGA
* * * * * *
3066 AAATGCGATCAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTCCGATCATTGGAAACT
1 AAATGCGATCAACTCTGATTGTTGGAAACTTCTGAAAATGCGATCAACTCTGATCCTTGAAAACT
3131 ACTGA
66 ACTGA
** * * *
3136 AAATGCGATCAACTCTGA-TCATGGAGAA-TACTGAAAATGTGATCAACTCTGATCGTTGGAAAA
1 AAATGCGATCAACTCTGATTGTTGGA-AACTTCTGAAAATGCGATCAACTCTGATCCTT-GAAAA
3199 -TACTGA
64 CTACTGA
* * * *
3205 AAATGCGATCAACTCTGATCGTTGGAAACTTCTTGAAAATGCGATCAACTCCGATCATTGGAAAC
1 AAATGCGATCAACTCTGATTGTTGGAAACTTC-TGAAAATGCGATCAACTCTGATCCTTGAAAAC
3270 TACTGA
65 TACTGA
* * * *
3276 AAATGCGATCAACTCTGATAG-TGGAAAATACTGAAAATGCGATCAACTCTGATCGTTGGAAAA-
1 AAATGCGATCAACTCTGATTGTTGGAAACTTCTGAAAATGCGATCAACTCTGATCCTT-GAAAAC
3339 TACTGA
65 TACTGA
*
3345 AAATGCGATCAACTCTGATTGTTGGAAACTTCTTG-AAATGAGATCAACTCTGA-CCTCTGAAAA
1 AAATGCGATCAACTCTGATTGTTGGAAACTTC-TGAAAATGCGATCAACTCTGATCCT-TGAAAA
*
3408 CTTCTTG-
64 CTAC-TGA
* * * * * *
3415 ATATGAGATCAACTATGACCT-CTGGAAACTTCTTG-AAATGAGATCAACTCTGA-CCTCTGAAA
1 AAATGCGATCAACTCTGA-TTGTTGGAAACTTC-TGAAAATGCGATCAACTCTGATCCT-TGAAA
*
3477 ACTTCTTG-
63 ACTAC-TGA
* * * * * * *
3485 GAATGAGATCAACTCTGACCT-CTGAAAACTTCTTG-GAATGAGATCAACTCTGA-CCTCTGAAA
1 AAATGCGATCAACTCTGA-TTGTTGGAAACTTC-TGAAAATGCGATCAACTCTGATCCT-TGAAA
*
3547 ACTTCTTG-
63 ACTAC-TGA
* ** * * * * *
3555 GAATGATATCAACTCTGACCT-CTGAAAACTTCTTG-GAATGAGATCAACTCTGA-CCTCTGAAA
1 AAATGCGATCAACTCTGA-TTGTTGGAAACTTC-TGAAAATGCGATCAACTCTGATCCT-TGAAA
*
3617 ACTTCTTG-
63 ACTAC-TGA
* * * * * * * *
3625 ATATGAGATCAACTCTGACCT-CTGAAAACTTCTTG-ATATGAGATCAATTCTGA-CCTCTGAAA
1 AAATGCGATCAACTCTGA-TTGTTGGAAACTTC-TGAAAATGCGATCAACTCTGATCCT-TGAAA
*
3687 ACTTCTTG-
63 ACTAC-TGA
* * * * * *
3695 AAATGAGATCAACTCTGACCT-CTGAAAACTTCTTG-ATATGAGATCAACTCTGA-CCTCTGAAA
1 AAATGCGATCAACTCTGA-TTGTTGGAAACTTC-TGAAAATGCGATCAACTCTGATCCT-TGAAA
*
3757 ACTTCTTG-
63 ACTAC-TGA
* *
3765 GAATGAGATCAACTCTGA
1 AAATGCGATCAACTCTGA
3783 CCTCTGAAAA
Statistics
Matches: 1017, Mismatches: 99, Indels: 42
0.88 0.09 0.04
Matches are distributed among these distances:
69 230 0.23
70 607 0.60
71 180 0.18
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (70 bp):
AAATGCGATCAACTCTGATTGTTGGAAACTTCTGAAAATGCGATCAACTCTGATCCTTGAAAACT
ACTGA
Found at i:3497 original size:175 final size:177
Alignment explanation
Indices: 2548--3802 Score: 1145
Period size: 175 Copynumber: 7.2 Consensus size: 177
2538 ACTCCTCTGA
* * * * ** *
2548 ATCAACTCTGATCATC-GGAAATTTCTTG-AAATGAGATCACCTCTAATTGTTGGAAACTACTGA
1 ATCAACTCTGA-CCTCTGGAAACTTC-TGAAAATGAGATCAACTCTGATCCTTGGAAAATACTGA
* * * * *
2611 AAATGTGATCAACTCTGATCGTTGGAAACTACTGAAAATGCGATAAACTCTGATCGTTGGAAAAT
64 AAATGCGATCAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTCTGATTGTTGGAAACT
* * * * *
2676 AC-TGAAAATGCGATCAACTCCGATCATTGGAAACTAC-TGAAAATGCG
129 TCTTGAAAATGAGATCAACTCTGATCCTTGGAAACTTCTTGAAAATGCG
* * *
2723 ATCAACTCTGA--TCATGGAAAATAT-TGAAAATGTGATCAACTCTGATCGTTGGAAAATACTGA
1 ATCAACTCTGACCTC-TGGAAACT-TCTGAAAATGAGATCAACTCTGATCCTTGGAAAATACTGA
* **
2785 AAATGCGACCAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTCTGATCATTGGAAACT
64 AAATGCGATCAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTCTGATTGTTGGAAACT
* * * *
2850 TCTTGAAAATGCGATCAACTCCGATCATTGGAAACTAC-TGAAAATGCG
129 TCTTGAAAATGAGATCAACTCTGATCCTTGGAAACTTCTTGAAAATGCG
* * * *
2898 ATCAACTCTGA--TCATGGAAAATACTGAAAATGTGATCAACTCTGATCGTTGGAAAATACTGAA
1 ATCAACTCTGACCTC-TGGAAACTTCTGAAAATGAGATCAACTCTGATCCTTGGAAAATACTGAA
*
2961 AATGCGATCAACTCTGATCGTTGGAAACTACTGAAAATGCGATCAACTCTGATTGTTGGAAACTT
65 AATGCGATCAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTCTGATTGTTGGAAACTT
* * *
3026 C-TGAAAAATGTGATCAACTCTGATCGTTGGAAACTAC-TGAAAATGCG
130 CTTG-AAAATGAGATCAACTCTGATCCTTGGAAACTTCTTGAAAATGCG
* * * * * * *
3073 ATCAACTCTGATCGT-TGGAAAATACTGAAAATGCGATCAACTCCGATCATTGGAAACTACTGAA
1 ATCAACTCTGA-CCTCTGGAAACTTCTGAAAATGAGATCAACTCTGATCCTTGGAAAATACTGAA
* * * * * *
3137 AATGCGATCAACTCTGATC-ATGGAGAATACTGAAAATGTGATCAACTCTGATCGTTGGAAAATA
65 AATGCGATCAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTCTGATTGTTGGAAACTT
* *
3201 C-TGAAAATGCGATCAACTCTGATCGTTGGAAACTTCTTGAAAATGCG
130 CTTGAAAATGAGATCAACTCTGATCCTTGGAAACTTCTTGAAAATGCG
* * * * **
3248 ATCAACTCCGATCAT-TGGAAACTACTGAAAATGCGATCAACTCTGAT-AGTGGAAAATACTGAA
1 ATCAACTCTGA-CCTCTGGAAACTTCTGAAAATGAGATCAACTCTGATCCTTGGAAAATACTGAA
3311 AATGCGATCAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTCTGATTGTTGGAAACTT
65 AATGCGATCAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTCTGATTGTTGGAAACTT
* * *
3376 CTTG-AAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTG-ATATGAG
130 CTTGAAAATGAGATCAACTCTGATCCT-TGGAAACTTCTTGAAAATGCG
* *
3422 ATCAACTATGACCTCTGGAAACTTCTTG-AAATGAGATCAACTCTGA-CCTCT-GAAAACTTCTT
1 ATCAACTCTGACCTCTGGAAACTTC-TGAAAATGAGATCAACTCTGATCCT-TGGAAAA-TAC-T
* * * * * * * *
3484 G-GAATGAGATCAACTCTGA-CCTCT-GAAAACTTCTTG-GAATGAGATCAACTCTGACCT-CTG
62 GAAAATGCGATCAACTCTGATCGT-TGGAAAA-TAC-TGAAAATGCGATCAACTCTGA-TTGTTG
* * * * * *
3544 AAAACTTCTTG-GAATGATATCAACTCTGA-CCTCTGAAAACTTCTTG-GAATGAG
123 GAAACTTCTTGAAAATGAGATCAACTCTGATCCT-TGGAAACTTCTTGAAAATGCG
* * *
3597 ATCAACTCTGACCTCTGAAAACTTCTTG-ATATGAGATCAACTCTGA-CCTCT-GAAAACTTCTT
1 ATCAACTCTGACCTCTGGAAACTTC-TGAAAATGAGATCAACTCTGATCCT-TGGAAAA-TAC-T
* * * * * * * *
3659 G-ATATGAGATCAATTCTGA-CCTCT-GAAAACTTCTTG-AAATGAGATCAACTCTGACCT-CTG
62 GAAAATGCGATCAACTCTGATCGT-TGGAAAA-TAC-TGAAAATGCGATCAACTCTGA-TTGTTG
* * * * *
3719 AAAACTTCTTG-ATATGAGATCAACTCTGA-CCTCTGAAAACTTCTTG-GAATGAG
123 GAAACTTCTTGAAAATGAGATCAACTCTGATCCT-TGGAAACTTCTTGAAAATGCG
*
3772 ATCAACTCTGACCTCTGAAAACTTCTGAAAA
1 ATCAACTCTGACCTCTGGAAACTTCTGAAAA
3803 CGACCGCACT
Statistics
Matches: 972, Mismatches: 83, Indels: 50
0.88 0.08 0.05
Matches are distributed among these distances:
172 2 0.00
173 4 0.00
174 218 0.22
175 676 0.70
176 71 0.07
178 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (177 bp):
ATCAACTCTGACCTCTGGAAACTTCTGAAAATGAGATCAACTCTGATCCTTGGAAAATACTGAAA
ATGCGATCAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTCTGATTGTTGGAAACTTC
TTGAAAATGAGATCAACTCTGATCCTTGGAAACTTCTTGAAAATGCG
Found at i:6373 original size:6 final size:6
Alignment explanation
Indices: 6364--6390 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6354 TTTTTCTTTT
6364 CCTCAG CCTCAG CCTCAG CCTCAG CCT
1 CCTCAG CCTCAG CCTCAG CCTCAG CCT
6391 AATCTTCTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.52, G:0.15, T:0.19
Consensus pattern (6 bp):
CCTCAG
Found at i:11287 original size:76 final size:75
Alignment explanation
Indices: 11190--11458 Score: 416
Period size: 76 Copynumber: 3.6 Consensus size: 75
11180 TTAATATTTT
* * *
11190 CTAAATCTCCTACAATCTGGCAAGATTTAGAGAAATATTCTCATTCTTTATTATT-TATTTATTT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGA-AAATATTCTCA-ACTTTATTATTAT-TTTATTT
11254 CTTAAAATATCT-
63 CTTAAAATATCTC
* * *
11266 CTAAACCTTCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTCATTATTATTTTATTTCTT
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
*
11331 AAAGTATCTC
66 AAAATATCTC
*
11341 CTAAATCTCCCACAAATTTGGCAAGATTTAGAAAATATGCTCAACTTTATTATTATTTTATTTCT
1 CTAAATCTCCCAC-AATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCT
11406 TAAAATATCTC
65 TAAAATATCTC
11417 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCA
1 CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCA
11459 TTAACTATTT
Statistics
Matches: 177, Mismatches: 13, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
74 27 0.15
75 51 0.29
76 99 0.56
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.41
Consensus pattern (75 bp):
CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCAACTTTATTATTATTTTATTTCTT
AAAATATCTC
Found at i:12225 original size:14 final size:14
Alignment explanation
Indices: 12206--12234 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12196 TACTAGCCGG
12206 AAAAATCTATTCCA
1 AAAAATCTATTCCA
12220 AAAAATCTATTCCA
1 AAAAATCTATTCCA
12234 A
1 A
12235 CGTATGTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAATCTATTCCA
Found at i:17236 original size:16 final size:16
Alignment explanation
Indices: 17215--17249 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
17205 ACAATTCAGA
17215 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
17231 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
17247 AAG
1 AAG
17250 TATTTCAGAT
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:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:27624 original size:20 final size:21
Alignment explanation
Indices: 27587--27628 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
27577 TTACAAAGAA
*
27587 AACTCACAATTTCGTGAGAGT
1 AACTCACAATTCCGTGAGAGT
27608 AACTCAC-ATTCCGTGAGAGT
1 AACTCACAATTCCGTGAGAGT
27628 A
1 A
27629 TAACCCAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (21 bp):
AACTCACAATTCCGTGAGAGT
Found at i:29418 original size:32 final size:32
Alignment explanation
Indices: 29354--29418 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
29344 TTGTGTTTTC
* * * * *
29354 ACCTTGACTATAATTTTTTTTTTTTGGCATTA
1 ACCTTGACTATAAATTTATTTGTTTAGAATTA
*
29386 ACCTTGACTATAAATTTATTTGTTTATAATTA
1 ACCTTGACTATAAATTTATTTGTTTAGAATTA
29418 A
1 A
29419 GCATGAACTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (32 bp):
ACCTTGACTATAAATTTATTTGTTTAGAATTA
Found at i:32513 original size:19 final size:20
Alignment explanation
Indices: 32467--32514 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
32457 TGTGGCACGC
*
32467 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
32489 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
32508 CACATGT
1 CACATGT
32515 CACGCCATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:32565 original size:31 final size:31
Alignment explanation
Indices: 32486--32584 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 31
32476 CAAAAAGTCG
*
32486 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACATGACA
* * *
32517 CGCCATATGTACCAAAAAGTGACACGTGACA
1 TGCCACATGTACCAAAAAGTGACACATGACA
* * * * *
32548 TGCCACATGTTCAAAAAAATGGCACATGGCA
1 TGCCACATGTACCAAAAAGTGACACATGACA
32579 TGCCAC
1 TGCCAC
32585 GTGCACAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACATGACA
Found at i:34302 original size:2 final size:2
Alignment explanation
Indices: 34295--34337 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
34285 ATGAGGATTC
34295 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34337 T
1 T
34338 GAGATATTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.