Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012209.1 Corchorus capsularis cultivar CVL-1 contig12230, 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: 7080
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Found at i:438 original size:22 final size:23
Alignment explanation
Indices: 351--443 Score: 104
Period size: 22 Copynumber: 4.2 Consensus size: 23
341 CTTGTCTCTA
351 TGTGGTTATCAAAATTTCATAAG
1 TGTGGTTATCAAAATTTCATAAG
* * *
374 -ATGGTTATTATAATTTCATAAG
1 TGTGGTTATCAAAATTTCATAAG
* *
396 -GAGGTTATCAAAATTCCAT-AG
1 TGTGGTTATCAAAATTTCATAAG
*
417 TGTGGTTACCAAAATTTCAT-AG
1 TGTGGTTATCAAAATTTCATAAG
439 TGTGG
1 TGTGG
444 GGTTATTAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
21 2 0.03
22 56 0.97
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (23 bp):
TGTGGTTATCAAAATTTCATAAG
Found at i:490 original size:22 final size:21
Alignment explanation
Indices: 352--492 Score: 102
Period size: 22 Copynumber: 6.3 Consensus size: 21
342 TTGTCTCTAT
352 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATCAAAATTTCAT-AG
* * *
374 ATGGTTATTATAATTTCATAAG
1 GTGGTTATCAAAATTTCAT-AG
* *
396 GAGGTTATCAAAATTCCATAG
1 GTGGTTATCAAAATTTCATAG
*
417 TGTGGTTACCAAAATTTCATAG
1 -GTGGTTATCAAAATTTCATAG
* ** *
439 TGTGGGGTTATTAAAAACTCTTAG
1 -GT--GGTTATCAAAATTTCATAG
**
463 GTTGGTTATTGAAATTTCATACG
1 G-TGGTTATCAAAATTTCATA-G
486 GTGGTTA
1 GTGGTTA
493 ATTATCACAA
Statistics
Matches: 94, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
21 2 0.02
22 74 0.79
23 3 0.03
24 15 0.16
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (21 bp):
GTGGTTATCAAAATTTCATAG
Found at i:553 original size:22 final size:22
Alignment explanation
Indices: 528--586 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
518 ATCAAAGAGA
*
528 TTATCAAAATGTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
*
550 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
572 TTAACAAAATTTCAT
1 TTATCAAAATTTCAT
587 TAAATATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:651 original size:22 final size:22
Alignment explanation
Indices: 605--975 Score: 96
Period size: 22 Copynumber: 16.7 Consensus size: 22
595 TCATGGGAAA
* *
605 GTTATCAAAATTTTATAGTG-TG
1 GTTATCAAAATTTCATA-TGAAG
627 GTTATCAAAATTTCATATGAAG
1 GTTATCAAAATTTCATATGAAG
*
649 GTTAT-AAAAGTCTCAATTTCAT-AAG
1 GTTATCAAAA-TTTC-A--T-ATGAAG
* * *
674 GAGTACCAAAATTTGATA-GAAG
1 G-TTATCAAAATTTCATATGAAG
* *
696 GTTATC-AAATCTCATA-GACTG
1 GTTATCAAAATTTCATATGA-AG
* *
717 ATTATCGAAATTTCATA-GAGATCG
1 GTTATCAAAATTTCATATGA-A--G
741 GATTATCAAAATTT-ATA-GAAAG
1 G-TTATCAAAATTTCATATG-AAG
* **
763 ATTATCAAAATTTCATAGTG-TT
1 GTTATCAAAATTTCATA-TGAAG
* * *
785 GTTATCAAAATTTTA-AAGCGAG
1 GTTATCAAAATTTCATATG-AAG
* *
807 GTTATCAAAATTACATAATG-TG
1 GTTATCAAAATTTCAT-ATGAAG
* **
829 ATTATCAAAATTTCATAGTG-TT
1 GTTATCAAAATTTCATA-TGAAG
* * *
851 GTTATCAAAATTTTA-AAGCGAG
1 GTTATCAAAATTTCATATG-AAG
* *
873 GTTATCAAAATTACATAATG-TG
1 GTTATCAAAATTTCAT-ATGAAG
* *
895 ATTATCAAAATTTCATA-GAGGG
1 GTTATCAAAATTTCATATGA-AG
* * *
917 GTCAAT-AAAATTTTATA-AAGAG
1 GT-TATCAAAATTTCATATGA-AG
*
939 GTTACCAAAATTTCATAATG-AG
1 GTTATCAAAATTTCAT-ATGAAG
* *
961 GTTATTAAATTTTCA
1 GTTATCAAAATTTCA
976 AAATGTGATT
Statistics
Matches: 259, Mismatches: 57, Indels: 66
0.68 0.15 0.17
Matches are distributed among these distances:
20 13 0.05
21 32 0.12
22 170 0.66
23 5 0.02
24 11 0.04
25 18 0.07
26 6 0.02
27 4 0.02
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATATGAAG
Found at i:834 original size:44 final size:45
Alignment explanation
Indices: 741--841 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 45
731 ATAGAGATCG
* * *
741 GATTATCAAAA-TTTATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTTAAAGAAAGATTATCAAAATTACATAATGTT
** *
785 G-TTATCAAAATTTTAAAGCGAGGTTATCAAAATTACATAATG-T
1 GATTATCAAAATTTTAAAGAAAGATTATCAAAATTACATAATGTT
828 GATTATCAAAATTT
1 GATTATCAAAATTT
842 CATAGTGTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
43 11 0.22
44 38 0.78
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.38
Consensus pattern (45 bp):
GATTATCAAAATTTTAAAGAAAGATTATCAAAATTACATAATGTT
Found at i:855 original size:44 final size:44
Alignment explanation
Indices: 764--862 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
754 TATAGAAAGA
* * *
764 TTATCAAAATTTCATAGTGTTGTTATCAAAATTTTAAAGCGAGG
1 TTATCAAAATTACATAATGTTGTTATCAAAATTTCAAAGCGAGG
* * **
808 TTATCAAAATTACATAATG-TGATTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTACATAATGTTG-TTATCAAAATTTCAAAGCGAGG
852 TTATCAAAATT
1 TTATCAAAATT
863 TTAAAGCGAG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 2 0.04
44 45 0.96
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.40
Consensus pattern (44 bp):
TTATCAAAATTACATAATGTTGTTATCAAAATTTCAAAGCGAGG
Found at i:927 original size:44 final size:44
Alignment explanation
Indices: 879--1000 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 44
869 CGAGGTTATC
* *
879 AAAATTACATAATGTGATTATCAAAATTTCATAGA-GGGGTCAAT
1 AAAATTTCATAATGTGATTA-CAAAATTTCATAGATGAGGTCAAT
* * * * * *
923 AAAATTTTATAAAGAGGTTACCAAAATTTCATA-ATGAGGTTATT
1 AAAATTTCATAATGTGATTA-CAAAATTTCATAGATGAGGTCAAT
* *
967 AAATTTTCAAAATGTGATTACAAAAATTTCATAG
1 AAAATTTCATAATGTGATTAC-AAAATTTCATAG
1001 TGGTATTTCT
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
43 2 0.03
44 58 0.97
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.34
Consensus pattern (44 bp):
AAAATTTCATAATGTGATTACAAAATTTCATAGATGAGGTCAAT
Found at i:958 original size:66 final size:66
Alignment explanation
Indices: 762--912 Score: 302
Period size: 66 Copynumber: 2.3 Consensus size: 66
752 TTTATAGAAA
762 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTTAAAGCGAGGTTATCAAAATTACATAATG
1 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTTAAAGCGAGGTTATCAAAATTACATAATG
827 T
66 T
828 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTTAAAGCGAGGTTATCAAAATTACATAATG
1 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTTAAAGCGAGGTTATCAAAATTACATAATG
893 T
66 T
894 GATTATCAAAATTTCATAG
1 GATTATCAAAATTTCATAG
913 AGGGGTCAAT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 85 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTTAAAGCGAGGTTATCAAAATTACATAATG
T
Found at i:975 original size:66 final size:66
Alignment explanation
Indices: 762--958 Score: 263
Period size: 66 Copynumber: 3.0 Consensus size: 66
752 TTTATAGAAA
* ** *
762 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTTAAAGCGAGGTTATCAAAATTACATAATG
1 GATTATCAAAATTTCATAGAGGGGTAATCAAAATTTTAAAGCGAGGTTATCAAAATTACATAATG
827 T
66 T
* ** *
828 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTTAAAGCGAGGTTATCAAAATTACATAATG
1 GATTATCAAAATTTCATAGAGGGGTAATCAAAATTTTAAAGCGAGGTTATCAAAATTACATAATG
893 T
66 T
* * *
894 GATTATCAAAATTTCATAGAGGGGTCAAT-AAAATTTTATAA-AGAGGTTACCAAAATTTCATAA
1 GATTATCAAAATTTCATAGAGGGGT-AATCAAAATTTTA-AAGCGAGGTTATCAAAATTACATAA
957 TG
64 TG
959 AGGTTATTAA
Statistics
Matches: 122, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
66 118 0.97
67 4 0.03
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTAATCAAAATTTTAAAGCGAGGTTATCAAAATTACATAATG
T
Found at i:1111 original size:19 final size:19
Alignment explanation
Indices: 1081--1128 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
1071 TTATGGAGTA
1081 ATCAAAATTTCAAG-GAGGAT
1 ATCAAAA-TTC-AGTGAGGAT
1101 ATCAAAATTCAGTGAGGAT
1 ATCAAAATTCAGTGAGGAT
1120 ATCAAAATT
1 ATCAAAATT
1129 TCATATGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.07
19 18 0.67
20 7 0.26
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (19 bp):
ATCAAAATTCAGTGAGGAT
Found at i:1147 original size:22 final size:22
Alignment explanation
Indices: 1081--1679 Score: 273
Period size: 22 Copynumber: 27.6 Consensus size: 22
1071 TTATGGAGTA
* *
1081 ATCAAAATTTCA-A-GGAGGAT
1 ATCAAAATTTCATATGAAGGTT
* *
1101 ATCAAAA-TTCA-GTG-AGGAT
1 ATCAAAATTTCATATGAAGGTT
1120 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
1142 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
**
1164 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * * *
1186 TTCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
1208 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * *
1230 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
*
1252 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
** *
1274 ATCAAAAAATCATATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* *
1296 AT-AAAA----ATTTGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * *
1312 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
1334 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
*
1357 ATCAAAATTTCATA-GCGAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
1379 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
1401 ATCAAAATTTCAGAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
*
1423 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * * *
1445 TTTAAATTTTCATAATG-TGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
* * *
1467 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * **
1489 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGAAGGTT
1512 ATCAAAATTTCAT-TGGGAA-GTT
1 ATCAAAATTTCATAT--GAAGGTT
1534 ATCAAAATTTCATATTGAA-GTCT
1 ATCAAAATTTCATA-TGAAGGT-T
* *
1557 -TCAAAATTCCTTA-GAGAGGTT
1 ATCAAAATTTCATATGA-AGGTT
*
1578 AATC-AAATTTCATAAGAAGGTT
1 -ATCAAAATTTCATATGAAGGTT
** **
1600 AAAAAAAATTT-ATAAAAAGGTT
1 -ATCAAAATTTCATATGAAGGTT
* * * **
1622 CTCGAAATTCCATA-GTATCGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
1644 ATTAAAATTTCATAGGAAGATT
1 ATCAAAATTTCATATGAAGGTT
1666 ATCAAAATTTCATA
1 ATCAAAATTTCATA
1680 ATGGGATCAT
Statistics
Matches: 449, Mismatches: 88, Indels: 82
0.73 0.14 0.13
Matches are distributed among these distances:
16 5 0.01
17 8 0.02
19 16 0.04
20 14 0.03
21 31 0.07
22 312 0.69
23 61 0.14
24 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:1208 original size:66 final size:64
Alignment explanation
Indices: 1081--1679 Score: 306
Period size: 66 Copynumber: 9.2 Consensus size: 64
1071 TTATGGAGTA
* * *
1081 ATCAAAATTTCA-A-GGAGGATATCAAAA-TTC--AGTGAGGATATCAAAATTTCATATGAAGGT
1 ATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGT-A-GTTATCAAAATTTCATAAGAAGGT
1141 T
64 T
* * * *
1142 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCACAAGAGGGT
1 ATCAAAATTTCATATGGAGGTTATCAAAATTTCATAG--TAGTTATCAAAATTTCATAAGAAGGT
1207 T
64 T
* * * * *
1208 ATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATG-AG
1 ATCAAAATTTCATATGGAGGT-TATCAAAATTTCATA-GTAG-TTATCAAAATTTCATAA-GAAG
1271 GTT
62 GTT
** * * *
1274 ATCAAAAAATCATATGGAGGTTAT-AAAAATT--T-GTAGTTATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGTAGTTATCAAAATTTCATAAGAAGGTT
* * * * *
1334 ATCAAAATTTTATAGGGAGGTTTATCAAAATTTCATAGCGAGGTTATCACAATTTCAT-AG-TGT
1 ATCAAAATTTCATATGGAGG-TTATCAAAATTTCATAG-TA-GTTATCAAAATTTCATAAGAAG-
1397 GATT
62 G-TT
* * * * *
1401 ATCAAAATTTCAGAGTGTGA--TTA-CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAATG
1 ATCAAAATTTCATA-TG-GAGGTTATC-AA-AATTTCATA-GTA-GTTATCAAAATTTCATAA-G
*
1462 -TGGTT
59 AAGGTT
* * * * * **
1467 ATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTTGGTTATCAAAATTTCATTGGGAA-
1 ATCAAAATTTCATATGGAGGTTATCAAAATTTCATA--G-TAGTTATCAAAATTTCA-TAAGAAG
1531 GTT
62 GTT
* * * * *
1534 ATCAAAATTTCATATTGAAGTCT-TCAAAATTCCTTAGAGAGGTTAATC-AAATTTCATAAGAAG
1 ATCAAAATTTCATATGGAGGT-TATCAAAATTTCATAG-TA-GTT-ATCAAAATTTCATAAGAAG
1597 GTT
62 GTT
** *** * * * * * *
1600 AAAAAAAATTT-ATAAAAAGGTTCTCGAAATTCCATAGTATCGTTATTAAAATTTCATAGGAAGA
1 -ATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGTA--GTTATCAAAATTTCATAAGAAGG
1664 TT
63 TT
1666 ATCAAAATTTCATA
1 ATCAAAATTTCATA
1680 ATGGGATCAT
Statistics
Matches: 409, Mismatches: 83, Indels: 87
0.71 0.14 0.15
Matches are distributed among these distances:
59 1 0.00
60 35 0.09
61 19 0.05
62 7 0.02
63 13 0.03
64 6 0.01
65 34 0.08
66 189 0.46
67 96 0.23
68 7 0.02
69 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (64 bp):
ATCAAAATTTCATATGGAGGTTATCAAAATTTCATAGTAGTTATCAAAATTTCATAAGAAGGTT
Found at i:1380 original size:45 final size:44
Alignment explanation
Indices: 1005--1679 Score: 278
Period size: 44 Copynumber: 15.7 Consensus size: 44
995 TCATAGTGGT
* * *
1005 ATTTC-TAGGGAGGTTATCAAAATTTCATAGTATTGTTA-CCAA
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * * * *
1047 A--T--TAGGAAGGTTATTAAACTTTTATTA-TG-GAGTAATCAAA
1 ATTTCATAGGGAGGTTATCAAAATTTCA-TAGTGTG-GTTATCAAA
* * *
1087 ATTTCA-A-GGAGGATATCAAAA-TTC--AGTGAGGATATCAAA
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * *
1126 ATTTCATATGAAGGTTATCAAAATTTCATA-TGAAGGTTATCAAA
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGTG-TGGTTATCAAA
** * * *
1170 ATTTCATAGTTTA-GTTTTCAAAATTTCACAAGAG-GGTTATCAAA
1 ATTTCATAG-GGAGGTTATCAAAATTTCA-TAGTGTGGTTATCAAA
* * * * * * *
1214 ATTTCATA-GTATGTAGATCAAAATTTCATAGGGAGATTAACAAA
1 ATTTCATAGGGAGGT-TATCAAAATTTCATAGTGTGGTTATCAAA
** ** *
1258 ATTTCATAATGAGGTTATCAAAAAATCATA-TGGAGGTTAT-AAA
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGT-GTGGTTATCAAA
* * * ***
1301 AATT--T--GTA-GTTATCAAGATTTCATAAG-AAAGTTATCAAA
1 ATTTCATAGGGAGGTTATCAAAATTTCAT-AGTGTGGTTATCAAA
* * * *
1340 ATTTTATAGGGAGGTTTATCAAAATTTCATAGCGAGGTTATCACA
1 ATTTCATAGGGAGG-TTATCAAAATTTCATAGTGTGGTTATCAAA
* * * * *
1385 ATTTCATAGTGTGATTATCAAAATTTCAGAGTGTGATTA-CTAACA
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATC-AA-A
* * * * * *
1430 A-TTCATATGGAGGTTTTTAAATTTTCATAATGTGGTTATCAAT
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * * *
1473 ATATCATATGGAGGTTATCAACATCTCATAGTGTTGGTTATCAAA
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGTG-TGGTTATCAAA
* * * **
1518 ATTTCATTGGGAAGTTATCAAAATTTCATATTGAAGTCT-TCAAA
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGT-TATCAAA
* * * ** **
1562 ATTCCTTAGAGAGGTTAATC-AAATTTCATAAG-AAGGTTAAAAAAA
1 ATTTCATAGGGAGGTT-ATCAAAATTTCAT-AGTGTGGTT-ATCAAA
*** * * * * * *
1607 ATTT-ATAAAAAGGTTCTCGAAATTCCATAGTATCGTTATTAAA
1 ATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* *
1650 ATTTCATAGGAAGATTATCAAAATTTCATA
1 ATTTCATAGGGAGGTTATCAAAATTTCATA
1680 ATGGGATCAT
Statistics
Matches: 470, Mismatches: 117, Indels: 90
0.69 0.17 0.13
Matches are distributed among these distances:
38 20 0.04
39 45 0.10
40 9 0.02
41 16 0.03
42 17 0.04
43 31 0.07
44 243 0.52
45 88 0.19
46 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
ATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
Found at i:2767 original size:16 final size:17
Alignment explanation
Indices: 2743--2781 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2733 TAATTAATCA
2743 ATAAA-TTAATAA-AAT
1 ATAAATTTAATAATAAT
*
2758 ATTAATTTAATAATAAT
1 ATAAATTTAATAATAAT
2775 ATAAATT
1 ATAAATT
2782 CGATTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAAATTTAATAATAAT
Found at i:3911 original size:154 final size:153
Alignment explanation
Indices: 3570--3980 Score: 464
Period size: 154 Copynumber: 2.7 Consensus size: 153
3560 TAAGTTTCAT
* *
3570 CTCAAACGGACTTAGAATGAAAAACTTATGCAAGTTTTTTAGTTAAGGACAGTTTGGGGTGAGAA
1 CTCAAACGGACTTAGAATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTTGGGGAGAGAA
* * *
3635 ACCACTTCACCATGATAGG-GAGT---TTTTACTTAGAATTTTTTCCATAAGTTTGTGGAGATAA
66 ACCAGTTCACCATCA-AGGAGAGTCGGTTTTACTTAGAATTTTTTCCATAAGTTTATGGAGATAA
* * *
3696 TCTAAGTCTCTTGGCCAAATTTCAT
130 TCTAAGCCTCTTGG-CAAATATCAC
* *
3721 CTCAAACAGACTTAGAATGAAAAACTTGTGCAAGTTTTTCAGTTAAGGACAGTTTGAGGG-GAGA
1 CTCAAACGGACTTAGAATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTTG-GGGAGAGA
** * *
3785 AGTCGGTTCACTATCAAGGAGAGTTCGGTTTTACTTAGAATTTTTT-CAT-AGTCTTATGGAGAT
65 AACCAGTTCACCATCAAGGAGAG-TCGGTTTTACTTAGAATTTTTTCCATAAGT-TTATGGAGAT
3848 AATCTAAGCCTACTAGTGG-AAA-ATCAGC
128 AATCTAAGCCT-CT--TGGCAAATATCA-C
* ** * * *
3876 CT-TATTGGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAATGACAGTTTGGGGGAGAGA
1 CTCAAACGGACTTAGAATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTT-GGGGAGAGA
3940 AACCAAGTTCACCATCAAGGAGAGCTCGGTTTTACTTAGAA
65 AACC-AGTTCACCATCAAGGAGAG-TCGGTTTTACTTAGAA
3981 GTCTTGTGGC
Statistics
Matches: 220, Mismatches: 26, Indels: 23
0.82 0.10 0.09
Matches are distributed among these distances:
150 3 0.01
151 70 0.32
152 4 0.02
153 3 0.01
154 72 0.33
155 32 0.15
156 33 0.15
157 3 0.01
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (153 bp):
CTCAAACGGACTTAGAATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTTGGGGAGAGAA
ACCAGTTCACCATCAAGGAGAGTCGGTTTTACTTAGAATTTTTTCCATAAGTTTATGGAGATAAT
CTAAGCCTCTTGGCAAATATCAC
Found at i:4573 original size:18 final size:18
Alignment explanation
Indices: 4542--4576 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4532 GGTGAAATGG
*
4542 GTCGGTTGAGTCGGTTTT
1 GTCGGATGAGTCGGTTTT
*
4560 GTCGGATGATTCGGTTT
1 GTCGGATGAGTCGGTTT
4577 GTGAAGTCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.11, G:0.37, T:0.43
Consensus pattern (18 bp):
GTCGGATGAGTCGGTTTT
Found at i:4788 original size:20 final size:21
Alignment explanation
Indices: 4765--4814 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
4755 AATATGTAAA
*
4765 ATATTTTAT-TAAATAAGAAT
1 ATATTATATGTAAATAAGAAT
4785 ATA-TATATGTAAATAAGAAT
1 ATATTATATGTAAATAAGAAT
4805 ATATATATAT
1 ATAT-TATAT
4815 ATGTAAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 4 0.15
20 17 0.65
22 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (21 bp):
ATATTATATGTAAATAAGAAT
Found at i:4821 original size:20 final size:20
Alignment explanation
Indices: 4774--4873 Score: 82
Period size: 20 Copynumber: 5.1 Consensus size: 20
4764 AATATTTTAT
*
4774 TAAATAAGAATATATATATG
1 TAAATAAGAATATATATATA
4794 TAAATAAGAATATATATATA
1 TAAATAAGAATATATATATA
** *
4814 TATGTAAGAAT-T-T-TATT
1 TAAATAAGAATATATATATA
* *
4831 TTAATATATAATATATAT-TA
1 TAAATA-AGAATATATATATA
* *
4851 TTAATATGTAATATATATATA
1 TAAATAAG-AATATATATATA
4872 TA
1 TA
4874 TATGTGTGTG
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
17 6 0.10
18 5 0.08
19 2 0.03
20 45 0.73
21 4 0.06
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (20 bp):
TAAATAAGAATATATATATA
Found at i:4844 original size:7 final size:7
Alignment explanation
Indices: 4832--4875 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
4822 AATTTTATTT
4832 TAATATA
1 TAATATA
4839 TAATATA
1 TAATATA
*
4846 TATTAT-
1 TAATATA
*
4852 TAATATG
1 TAATATA
4859 TAATATA
1 TAATATA
4866 TATATATA
1 TA-ATATA
4874 TA
1 TA
4876 TGTGTGTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
6 5 0.16
7 20 0.62
8 7 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (7 bp):
TAATATA
Found at i:4846 original size:58 final size:57
Alignment explanation
Indices: 4756--4874 Score: 145
Period size: 58 Copynumber: 2.1 Consensus size: 57
4746 TTTTATTTTA
4756 ATATGTAAAATATTTTATTAAATAAGAATATATA-TATGTAAATAAG-AATATATATAT
1 ATATGTAAAATATTTTATTAAATAAGAATATATATTAT-T-AATAAGTAATATATATAT
* * * *
4813 ATATGTAAGA-ATTTTATTTTAATATATAATATATATTATTAATATGTAATATATATAT
1 ATATGTAAAATATTTTA-TTAAATA-AGAATATATATTATTAATAAGTAATATATATAT
4871 ATAT
1 ATAT
4875 ATGTGTGTGT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
56 6 0.11
57 20 0.37
58 25 0.46
59 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (57 bp):
ATATGTAAAATATTTTATTAAATAAGAATATATATTATTAATAAGTAATATATATAT
Found at i:4857 original size:13 final size:14
Alignment explanation
Indices: 4835--4876 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
4825 TTTATTTTAA
4835 TATATAATATATAT
1 TATATAATATATAT
* *
4849 TAT-TAATATGTAA
1 TATATAATATATAT
4862 TATATATATATATAT
1 TATATA-ATATATAT
4877 GTGTGTGTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.50
14 5 0.23
15 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TATATAATATATAT
Done.