Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011760.1 Corchorus capsularis cultivar CVL-1 contig11781, 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: 9553
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Found at i:345 original size:19 final size:20
Alignment explanation
Indices: 318--355 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
308 TACTATTATT
318 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
338 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
356 AATGTCAATA
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:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:549 original size:22 final size:21
Alignment explanation
Indices: 521--672 Score: 117
Period size: 22 Copynumber: 7.0 Consensus size: 21
511 TGTCTCTATG
*
521 TGGTTATCAAAATTTCATAAGA
1 TGGTTACCAAAATTTCAT-AGA
** *
543 TGGTTATTATAATTTCATGAGGA
1 TGGTTACCAAAATTTCAT-A-GA
* * *
566 -GGTCAGCAAAATTCCATAGA
1 TGGTTACCAAAATTTCATAGA
*
586 GTGGTTACCAAAATTTCATATA
1 -TGGTTACCAAAATTTCATAGA
* * *
608 TAAGTTATCAAAATTTCATAGTG
1 T-GGTTACCAAAATTTCATAG-A
*
631 TGGTTACCAAAATTTCATAGCG
1 TGGTTACCAAAATTTCATAG-A
*
653 TGGTTACCAAAATTTTATAG
1 TGGTTACCAAAATTTCATAG
673 GATCAGATTA
Statistics
Matches: 105, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.02
21 2 0.02
22 98 0.93
23 3 0.03
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (21 bp):
TGGTTACCAAAATTTCATAGA
Found at i:664 original size:44 final size:42
Alignment explanation
Indices: 520--673 Score: 137
Period size: 44 Copynumber: 3.5 Consensus size: 42
510 TTGTCTCTAT
* ** *
520 GTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAG
1 GTGGTTATCAAAATTTCAT-AGGTGGTTACCAAAATTTCAT-AG
* * * * *
564 GAGGTCAGCAAAATTCCATAGAGTGGTTACCAAAATTTCATAT
1 GTGGTTATCAAAATTTCATAG-GTGGTTACCAAAATTTCATAG
* *
607 ATAAGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAG
1 GT-GGTTATCAAAATTTCATAG-GTGGTTACCAAAATTTCATAG
* *
651 CGTGGTTACCAAAATTTTATAGG
1 -GTGGTTATCAAAATTTCATAGG
674 ATCAGATTAT
Statistics
Matches: 86, Mismatches: 21, Indels: 7
0.75 0.18 0.06
Matches are distributed among these distances:
43 4 0.05
44 81 0.94
45 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.35
Consensus pattern (42 bp):
GTGGTTATCAAAATTTCATAGGTGGTTACCAAAATTTCATAG
Found at i:711 original size:22 final size:22
Alignment explanation
Indices: 611--726 Score: 81
Period size: 22 Copynumber: 5.2 Consensus size: 22
601 TCATATATAA
* * *
611 GTTATCAAAATTTCATAGTGTG
1 GTTATTAAAATTTCTTAGGGTG
** * *
633 GTTACCAAAATTTCATAGCGTG
1 GTTATTAAAATTTCTTAGGGTG
** *
655 GTTACCAAAATTT-TATAGGATCAG
1 GTTATTAAAATTTCT-TAGGGT--G
* *
679 ATTATTAAAATTTCTTAGGTTG
1 GTTATTAAAATTTCTTAGGGTG
*
701 GTTATTGAAATTTCTTAGGGTG
1 GTTATTAAAATTTCTTAGGGTG
723 GTTA
1 GTTA
727 GTTATCACAA
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
22 61 0.78
24 16 0.21
25 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (22 bp):
GTTATTAAAATTTCTTAGGGTG
Found at i:726 original size:68 final size:66
Alignment explanation
Indices: 520--692 Score: 179
Period size: 66 Copynumber: 2.6 Consensus size: 66
510 TTGTCTCTAT
* * * * * * * *
520 GTGGTTATCAAAATTTCATAAGAT-GGTTATTATAATTTCATGAG-GAGGTCAGCAAAATTCCAT
1 GTGGTTACCAAAATTTCAT-AGATAAGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCAT
*
583 AGA
64 AGC
*
586 GTGGTTACCAAAATTTCATATATAAGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAG
1 GTGGTTACCAAAATTTCATAGATAAGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAG
651 C
66 C
* * *
652 GTGGTTACCAAAATTTTATAGGATCAGATTATTAAAATTTC
1 GTGGTTACCAAAATTTCATA-GATAAG-TTATCAAAATTTC
693 TTAGGTTGGT
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
65 5 0.06
66 68 0.76
67 4 0.04
68 12 0.13
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (66 bp):
GTGGTTACCAAAATTTCATAGATAAGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAG
C
Found at i:787 original size:22 final size:21
Alignment explanation
Indices: 762--1132 Score: 90
Period size: 22 Copynumber: 16.7 Consensus size: 21
752 ATCGAAGAGA
*
762 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* *
784 TTAT-AAGAATTTCATAATGTGG
1 TTATCAA-AATTTCAT-AGGAGG
*
806 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* *
828 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* * * *
850 TTAGCAAAATTTTATAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
*
872 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
*
894 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * *
919 CGTACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
*
941 TTATC-AAATCTCATA-GA-G
1 TTATCAAAATTTCATAGGAGG
* **
959 TCATAATCGAAATTTCATAGAGATCAAA
1 T--T-ATCAAAATTTCATAG-G---AGG
***
987 TTATCAAAATTTCATAGTGTTA
1 TTATCAAAATTTCATAG-GAGG
* * *
1009 TTATCAAAAATTCAAACCGAGG
1 TTATCAAAATTTCATA-GGAGG
* * *
1031 TTATCAAAATTACATAATGAGA
1 TTATCAAAATTTCAT-AGGAGG
* * *
1053 TTATCAGAATCTCATAGAAGGG
1 TTATCAAAATTTCATAGGA-GG
* * * *
1075 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
1097 TTATCAAATTTTCATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
1119 TTATCAAATTTTCA
1 TTATCAAAATTTCA
1133 AAATATGATT
Statistics
Matches: 255, Mismatches: 62, Indels: 64
0.67 0.16 0.17
Matches are distributed among these distances:
18 2 0.01
19 1 0.00
20 17 0.07
21 13 0.05
22 176 0.69
23 11 0.04
24 1 0.00
25 20 0.08
26 3 0.01
27 1 0.00
28 10 0.04
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:1107 original size:21 final size:22
Alignment explanation
Indices: 1027--1132 Score: 101
Period size: 22 Copynumber: 4.8 Consensus size: 22
1017 AATTCAAACC
* * *
1027 GAGGTTATCAAAATTACATAAT
1 GAGGTTATCAAATTTTCATAAA
* *
1049 GAGATTATCAGAA-TCTCATAGAA
1 GAGGTTATCA-AATTTTCATA-AA
* *
1072 G-GGTCAACAAAATTTT-ATAAA
1 GAGGTTATC-AAATTTTCATAAA
1093 GAGGTTATCAAATTTTCATAAA
1 GAGGTTATCAAATTTTCATAAA
1115 GAGGTTATCAAATTTTCA
1 GAGGTTATCAAATTTTCA
1133 AAATATGATT
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
21 10 0.15
22 51 0.75
23 7 0.10
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (22 bp):
GAGGTTATCAAATTTTCATAAA
Found at i:1356 original size:66 final size:67
Alignment explanation
Indices: 1281--1581 Score: 220
Period size: 66 Copynumber: 4.5 Consensus size: 67
1271 AGTTTAATTT
*
1281 TCAAAATTTCATAAGAG-GGTTATCAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGGT
1 TCAAAATTTCATAAGAGTGGTTATCAAAATTTCATAATGAGGTTATCAAAATATCATAGGGAGGT
1345 TA
66 TA
* ** * ** * * *
1347 TCAAGATTTCATAAGA-AAGTTATCAAAATTTTATACGGAGGTTTATCAAAATTTTATAGGAAGA
1 TCAAAATTTCATAAGAGTGGTTATCAAAATTTCATAATGAGG-TTATCAAAATATCATAGGGAG-
*
1411 TTTA
64 GTTA
* * * * * * * * * *
1415 TCAAAATTTCAT-AGCGTGGTTATCACAATTTCATAGTGTGATTATCAAAATTTCAGAGTGTGAT
1 TCAAAATTTCATAAGAGTGGTTATCAAAATTTCATAATGAGGTTATCAAAATATCATAGGGAGGT
1479 TA
66 TA
* * * * * * * * *
1481 -CTAACAA-TTCATATG-GAGGTTTTTAAATTTTCATAACGTGGTTATCAATATATCATATGGAG
1 TC-AA-AATTTCATAAGAGTGGTTATCAAAATTTCATAATGAGGTTATCAAAATATCATAGGGAG
1543 GTTA
64 GTTA
* *
1547 TCAACATTTCAT-AGTGTTGGTTATCAAAATTTCAT
1 TCAAAATTTCATAAGAG-TGGTTATCAAAATTTCAT
1582 TGGGAAGTTA
Statistics
Matches: 176, Mismatches: 48, Indels: 21
0.72 0.20 0.09
Matches are distributed among these distances:
65 3 0.02
66 89 0.51
67 53 0.30
68 31 0.18
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (67 bp):
TCAAAATTTCATAAGAGTGGTTATCAAAATTTCATAATGAGGTTATCAAAATATCATAGGGAGGT
TA
Found at i:1730 original size:22 final size:22
Alignment explanation
Indices: 1238--1737 Score: 185
Period size: 22 Copynumber: 22.6 Consensus size: 22
1228 TTATGGAGTA
* *
1238 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGAAGGTT
*
1258 ATCAAAATTTCATAGTTTAA--TT
1 ATCAAAATTTCATAG--GAAGGTT
* * *
1280 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATAGGAAGGTT
*
1302 ATCAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-AGGAAGGTT
** *
1324 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGAAGGTT
* * *
1346 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATAGGAAGGTT
*
1368 ATCAAAATTTTATACGG-AGGTTT
1 ATCAAAATTTCATA-GGAAGG-TT
* *
1391 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGAAG-GTT
*
1414 ATCAAAATTTCATAGCG-TGGTT
1 ATCAAAATTTCATAG-GAAGGTT
* * *
1436 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATAG-GAAGGTT
* * *
1458 ATCAAAATTTCAGAGTG-TGATT
1 ATCAAAATTTCATAG-GAAGGTT
1480 A-CTAACAA-TTCATATGG-AGGTT
1 ATC-AA-AATTTCATA-GGAAGGTT
* * * * *
1502 TTTAAATTTTCATAACG-TGGTT
1 ATCAAAATTTCAT-AGGAAGGTT
* *
1524 ATCAATATATCATATGG-AGGTT
1 ATCAAAATTTCATA-GGAAGGTT
* **
1546 ATCAACATTTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GAAGGTT
*
1569 ATCAAAATTTCATTGGGAA-GTT
1 ATCAAAATTTCA-TAGGAAGGTT
* *
1591 ACCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-GGAAGGT-T
* * *
1614 -TCAAAATTCCTTA-GAGAGGTG
1 ATCAAAATTTCATAGGA-AGGTT
* * *
1635 AACAAAA-TTCATAAGAAAGTT
1 ATCAAAATTTCATAGGAAGGTT
** **
1656 AAAAAAAATTT-ATAAAAAGGTT
1 -ATCAAAATTTCATAGGAAGGTT
* * * ***
1678 CTCGAAATTCCATAGTGTATCATT
1 ATCAAAATTTCATAG-G-AAGGTT
*
1702 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATAGGAAGGTT
1724 ATCAAAATTTCATA
1 ATCAAAATTTCATA
1738 ATGGGATCAT
Statistics
Matches: 358, Mismatches: 87, Indels: 68
0.70 0.17 0.13
Matches are distributed among these distances:
20 13 0.04
21 20 0.06
22 245 0.68
23 62 0.17
24 18 0.05
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGGAAGGTT
Found at i:1935 original size:31 final size:31
Alignment explanation
Indices: 1900--1959 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1890 ATGTTTTTCG
*
1900 ATTGTACCCTTATTTT-TAAAACATATTTCCA
1 ATTGTACCCTT-TTTTAAAAAACATATTTCCA
*
1931 ATTGTACTCTTTTTTAAAAAACATATTTC
1 ATTGTACCCTTTTTTAAAAAACATATTTC
1960 TAAATTGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTGTACCCTTTTTTAAAAAACATATTTCCA
Found at i:2833 original size:19 final size:20
Alignment explanation
Indices: 2806--2843 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2796 TACTATTATT
2806 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
2826 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
2844 AATGTCAATA
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:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:3153 original size:24 final size:23
Alignment explanation
Indices: 3009--3183 Score: 96
Period size: 22 Copynumber: 7.9 Consensus size: 23
2999 TGTCTCTATG
** * *
3009 TGGTTATCGAAATTTCATA-AGA
1 TGGTTATTAAAATTTCATAGTGT
*
3031 TGGTTATTATAATTTCATGAG-G-
1 TGGTTATTAAAATTTCAT-AGTGT
* * *
3053 AGGTTATCAAAATTCCATAGTG-
1 TGGTTATTAAAATTTCATAGTGT
** * *
3075 TGGTTACCAAAATTTAATA-TGA
1 TGGTTATTAAAATTTCATAGTGT
** *
3097 AAG-TATCAAAATTTCATAGTGT
1 TGGTTATTAAAATTTCATAGTGT
**
3119 T-GTTACCAAAATTTCATAGTGT
1 TGGTTATTAAAATTTCATAGTGT
*
3141 TAGGTTATTAAAATTTCTTAG-GT
1 T-GGTTATTAAAATTTCATAGTGT
* *
3164 TGATTATTGAAATTTCATAG
1 TGGTTATTAAAATTTCATAG
3184 GGTAGTTAAT
Statistics
Matches: 121, Mismatches: 24, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
21 18 0.15
22 83 0.69
23 5 0.04
24 15 0.12
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.40
Consensus pattern (23 bp):
TGGTTATTAAAATTTCATAGTGT
Found at i:3252 original size:22 final size:22
Alignment explanation
Indices: 3227--4188 Score: 243
Period size: 22 Copynumber: 43.7 Consensus size: 22
3217 ATCAAAGAGA
* *
3227 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
3249 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* *
3271 CTAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGAGG
* * *
3293 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* *
3315 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
3337 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
3359 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * *
3384 AGTA-CTAAAATTTGATAG-AAGG
1 -TTATC-AAAATTTCATAGTGAGG
* * * *
3406 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
3427 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCAT--AG-TGAGG
*
3452 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGTG-AGG
**
3473 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* *
3495 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
3517 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
3539 TTATCAGAATTTCATAGAG-GAG
1 TTATCAAAATTTCATAGTGAG-G
* * * **
3561 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
**
3583 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * ***
3605 TTATCAAATTTTCAAAATGTTA
1 TTATCAAAATTTCATAGTGAGG
3627 TTA-CAAAAATTTCATAGT--GG
1 TTATC-AAAATTTCATAGTGAGG
* * ** *
3647 TATTTCTGGGGAGGTTATCA-A---A-A
1 T-TATC----AAAATT-TCATAGTGAGG
**
3670 TT-TCAGTATGGTTACCAAATTAG-GAAGG
1 TTATCAAAAT--TT--C--A-TAGTG-AGG
* * *
3698 TTATTAAACTTTTATTA-TG-GAG
1 TTATCAAAATTTCA-TAGTGAG-G
*
3720 TAATCAAAATTTC--AGTGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
3740 ATATCAAAATTT-A-AGGGAGG
1 TTATCAAAATTTCATAGTGAGG
*
3760 ATATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
*
3782 TTATCAAAATTTCATA-AGAGGG
1 TTATCAAAATTTCATAGTGA-GG
**
3804 TTATCAAAATTTCATAGT-ATA
1 TTATCAAAATTTCATAGTGAGG
* * *
3825 TAGATCAAAATTTCATAGGGAGA
1 T-TATCAAAATTTCATAGTGAGG
* *
3848 TTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
*
3870 TTATCAGAA-TT--T-GT-A-G
1 TTATCAAAATTTCATAGTGAGG
* * *
3886 TTATCAAGATTTCATAAG-AAAG
1 TTATCAAAATTTCAT-AGTGAGG
* *
3908 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
3930 TTTATCAAAATTTTATAG-GAAGAT
1 -TTATCAAAATTTCATAGTG-AG-G
**
3954 TTATCAAAATTTCATAACGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
3976 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
3998 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
*
4020 TTA-CTAGCAA-TTCATA-TGGAGG
1 TTATC-A-AAATTTCATAGT-GAGG
* * * * * *
4042 TTTTTAAATTTTCATAATGTGT
1 TTATCAAAATTTCATAGTGAGG
* *
4064 TTATCAATATATCATA-TGGAGG
1 TTATCAAAATTTCATAGT-GAGG
* * *
4086 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAGTG-AGG
* * *
4109 TTATCAAAATTTCATTGGGAAG
1 TTATCAAAATTTCATAGTGAGG
* *
4131 TTATC-AAATTTCATATTGAGA
1 TTATCAAAATTTCATAGTGAGG
* * *
4152 TCT-TCAAAATTCCTTAG-GAAG
1 T-TATCAAAATTTCATAGTGAGG
*
4173 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
4189 AAAAGGTTAA
Statistics
Matches: 690, Mismatches: 166, Indels: 169
0.67 0.16 0.16
Matches are distributed among these distances:
16 8 0.01
17 4 0.01
18 2 0.00
19 4 0.01
20 43 0.06
21 82 0.12
22 422 0.61
23 76 0.11
24 6 0.01
25 22 0.03
26 9 0.01
27 7 0.01
28 2 0.00
29 3 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:3903 original size:104 final size:106
Alignment explanation
Indices: 3781--3987 Score: 274
Period size: 104 Copynumber: 2.0 Consensus size: 106
3771 TCATATGAAG
** * * *
3781 GTTATCAAAATTTCATAAGAGGGTTATCAAAATTTCATA-GTATATAGATCAAAATTTCATAGGG
1 GTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGGAGATAGATCAAAATTTCATAGGA
* *
3845 AGA-TTAACAAAATTTCATAATGAGGTTATCAGAATTTGTA
66 AGATTTAACAAAATTTCATAACGAGGTTATCACAATTTGTA
* * * ** *
3885 GTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGA
1 GTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGGAGATAGATCAAAATTTCATAGGA
*
3950 AGATTTATCAAAATTTCATAACGAGGTTATCACAATTT
66 AGATTTAACAAAATTTCATAACGAGGTTATCACAATTT
3988 CATAGTGTGA
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
104 35 0.40
105 21 0.24
106 31 0.36
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.36
Consensus pattern (106 bp):
GTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGGGAGATAGATCAAAATTTCATAGGA
AGATTTAACAAAATTTCATAACGAGGTTATCACAATTTGTA
Found at i:4460 original size:31 final size:31
Alignment explanation
Indices: 4406--4470 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
4396 TACGAATAAG
* *
4406 TTCCGATTGTACCCTTATTTTTAAAACATAT
1 TTCCAATTATACCCTTATTTTTAAAACATAT
4437 TTCCAATTATACCCTT-TTCTTTAAAACATAT
1 TTCCAATTATACCCTTATT-TTTAAAACATAT
4468 TTC
1 TTC
4471 TACATTGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.29, C:0.22, G:0.03, T:0.46
Consensus pattern (31 bp):
TTCCAATTATACCCTTATTTTTAAAACATAT
Found at i:5689 original size:19 final size:21
Alignment explanation
Indices: 5657--5699 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
5647 TTCTTTACTA
5657 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
5678 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
5697 TTA
1 TTA
5700 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:5893 original size:22 final size:22
Alignment explanation
Indices: 5865--6004 Score: 95
Period size: 22 Copynumber: 6.3 Consensus size: 22
5855 TGTCTCTATG
5865 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* *
5887 TGGTTATTATAATTTCATAAGGA
1 TGGTTATCAAAATTTCATAA-GA
* *
5910 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
5931 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * * *
5953 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
5977 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
5999 TGGTTA
1 TGGTTA
6005 ATTATCACAA
Statistics
Matches: 93, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 71 0.76
23 3 0.03
24 17 0.18
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:5945 original size:44 final size:44
Alignment explanation
Indices: 5866--5949 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
5856 GTCTCTATGT
* ** *
5866 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATAAGGA
1 GGTTATCAAAATTCCATAAGATGGTTACCAAAATTTCATAAGGA
*
5910 GGTTATCAAAATTCCAT-AGTGTGGTTACCAAAATTTCATA
1 GGTTATCAAAATTCCATAAG-ATGGTTACCAAAATTTCATA
5950 GGATCAGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.06
44 32 0.94
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (44 bp):
GGTTATCAAAATTCCATAAGATGGTTACCAAAATTTCATAAGGA
Found at i:6002 original size:68 final size:66
Alignment explanation
Indices: 5864--6004 Score: 158
Period size: 68 Copynumber: 2.1 Consensus size: 66
5854 TTGTCTCTAT
* * *
5864 GTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATAAGGAGGTTATCAAAATTCCATAG
1 GTGGTTACCAAAATTTCATAAGATGGTTATTAAAATCTCATAAGGAGGTTATCAAAATTCCATAG
*
5929 T
66 G
* * * ** *
5930 GTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATCTC-TTAGGTTGGTTATTGAAATTTCA
1 GTGGTTACCAAAATTTCATAAGAT--GGTTATTAAAATCTCATAAGG-AGGTTATCAAAATTCCA
5994 TAGG
63 TAGG
5998 GTGGTTA
1 GTGGTTA
6005 ATTATCACAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
66 22 0.35
67 4 0.06
68 36 0.58
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (66 bp):
GTGGTTACCAAAATTTCATAAGATGGTTATTAAAATCTCATAAGGAGGTTATCAAAATTCCATAG
G
Found at i:6163 original size:22 final size:22
Alignment explanation
Indices: 6117--6169 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
6107 TCATGGGGAA
* *
6117 GTTATCAAAATTTTATAGTGTG
1 GTTATCAAAATTTCATAGTGAG
6139 GTTATCAAAATTTCATA-TGAAG
1 GTTATCAAAATTTCATAGTG-AG
6161 GTTAT-AAAA
1 GTTATCAAAA
6170 GTCTCAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGAG
Found at i:6278 original size:21 final size:21
Alignment explanation
Indices: 6192--6288 Score: 72
Period size: 21 Copynumber: 4.4 Consensus size: 21
6182 TAAGGAGAAC
*
6192 CAAAATTTGATA-AAAGGTTAT
1 CAAAATTT-ATAGAAAGATTAT
* **
6213 C-AAATCTCATAGAGTGATTAT
1 CAAAAT-TTATAGAAAGATTAT
* *
6234 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTT-ATAGA-A--AGATTAT
6259 CAAAATTTATAGAAAGATTAT
1 CAAAATTTATAGAAAGATTAT
6280 CAAAATTTA
1 CAAAATTTA
6289 ATAATGTTGT
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
20 7 0.12
21 25 0.42
22 9 0.15
23 1 0.02
24 5 0.08
25 13 0.22
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.33
Consensus pattern (21 bp):
CAAAATTTATAGAAAGATTAT
Found at i:6393 original size:22 final size:22
Alignment explanation
Indices: 6192--6399 Score: 120
Period size: 22 Copynumber: 9.5 Consensus size: 22
6182 TAAGGAGAAC
*
6192 CAAAATTTGATAAA-AGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
* * * *
6213 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAAAGAGGTTAT
* *
6234 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAAAGA--GG-TTAT
*
6259 CAAAATTT-ATAGAA-AGATTAT
1 CAAAATTTCATA-AAGAGGTTAT
* * **
6280 CAAAATTTAATAATGTTGTTAT
1 CAAAATTTCATAAAGAGGTTAT
* *
6302 CAAATTTTCA-AAGCGAGGTTAT
1 CAAAATTTCATAA-AGAGGTTAT
* * * *
6324 CAAAATTACATAATGTGATTAT
1 CAAAATTTCATAAAGAGGTTAT
* * * *
6346 CAAAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAAAGAGGTTAT
*
6368 CAAAATTTTATAAAGAGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
*
6390 CAAATTTTCA
1 CAAAATTTCA
6400 AAATGTGATT
Statistics
Matches: 138, Mismatches: 39, Indels: 19
0.70 0.20 0.10
Matches are distributed among these distances:
20 9 0.07
21 22 0.16
22 88 0.64
23 2 0.01
24 5 0.04
25 12 0.09
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAAAGAGGTTAT
Found at i:6530 original size:20 final size:20
Alignment explanation
Indices: 6505--6555 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
6495 TTATGGAGTA
6505 ATTAAAATTTCAAGGAGGAT
1 ATTAAAATTTCAAGGAGGAT
*
6525 ATTAAAA-TTCAGGGAGGAT
1 ATTAAAATTTCAAGGAGGAT
*
6544 ATCAAAATTTCA
1 ATTAAAATTTCA
6556 TATGAAGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (20 bp):
ATTAAAATTTCAAGGAGGAT
Found at i:6570 original size:22 final size:22
Alignment explanation
Indices: 6543--7104 Score: 230
Period size: 22 Copynumber: 25.7 Consensus size: 22
6533 TCAGGGAGGA
6543 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
6565 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
6587 TTTCAAAATTTCACATGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
6609 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * * *
6630 AGATCAAAATTTGATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
6653 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* ** *
6675 TATAAAAAAATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
6697 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
6713 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
6735 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * * *
6758 TGTCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
6781 TATCAAAATTTCATCATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
6803 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
6825 TATAAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
6847 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * *
6869 TTTTAAATTTTCATAATG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
6891 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
6913 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
6936 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
*
6958 TATCAAAATTTTATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
6980 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * *
7002 TAACCAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** **
7024 TAAAAAAAATTT-ATAAAAAGGT
1 T-ATCAAAATTTCATATGAAGGT
* * **
7046 TCTCAAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* *
7068 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
7090 TATCAAAATTTCATA
1 TATCAAAATTTCATA
7105 ATGGGATCAT
Statistics
Matches: 406, Mismatches: 98, Indels: 72
0.70 0.17 0.12
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 2 0.00
20 2 0.00
21 26 0.06
22 287 0.71
23 74 0.18
24 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:6763 original size:23 final size:23
Alignment explanation
Indices: 6712--6791 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
6702 AAATTTGTAG
* * * *
6712 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* *
6734 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGAT
*
6757 TTGTCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
6780 TTATCAAAATTT
1 TTATCAAAATTT
6792 CATCATGAGG
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 16 0.34
23 31 0.66
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:6960 original size:45 final size:44
Alignment explanation
Indices: 6879--6963 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 44
6869 TTTTAAATTT
* *
6879 TCATAATGTGGTTATCAATATATCATATGGAGGTTATCAACATC
1 TCATAATGTGGTTATCAAAATATCATATGGAAGTTATCAACATC
* *
6923 TCATAGTGTTGGTTATCAAAATTTCAT-TGGGAAGTTATCAA
1 TCATAATG-TGGTTATCAAAATATCATAT-GGAAGTTATCAA
6964 AATTTTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
44 8 0.23
45 27 0.77
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.38
Consensus pattern (44 bp):
TCATAATGTGGTTATCAAAATATCATATGGAAGTTATCAACATC
Found at i:7230 original size:2 final size:2
Alignment explanation
Indices: 7223--7257 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
7213 CCTAAACTAG
7223 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7258 ATTATGATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:8472 original size:21 final size:21
Alignment explanation
Indices: 8446--8485 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
8436 CACTGCTCTA
*
8446 ATAATCTCATCTGTACAGTAC
1 ATAATCTAATCTGTACAGTAC
8467 ATAATCTAATCTGTACAGT
1 ATAATCTAATCTGTACAGT
8486 GTATTCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (21 bp):
ATAATCTAATCTGTACAGTAC
Found at i:8691 original size:21 final size:19
Alignment explanation
Indices: 8667--8729 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 19
8657 TTATTAGTAT
8667 ATTATAACTAATAAAGTAATA
1 ATTATAACTAATAAA-T-ATA
8688 ATTAT-A-TATATAAATATA
1 ATTATAACTA-ATAAATATA
*
8706 ATTATAAACTAA-AACTAT-
1 ATTAT-AACTAATAAATATA
8724 ATTATA
1 ATTATA
8730 TTTCTTATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 1 0.03
18 13 0.35
19 8 0.22
20 8 0.22
21 7 0.19
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTATAACTAATAAATATA
Found at i:9506 original size:2 final size:2
Alignment explanation
Indices: 9501--9550 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
9491 ACACACCCGC
*
9501 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
9543 AT AC AT AT
1 AT AT AT AT
9551 TAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Done.