Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011424.1 Corchorus capsularis cultivar CVL-1 contig11445, 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: 52066
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--43 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1 AT AT AT 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 AT AT AT
43 A
1 A
44 CCTATAAATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:264 original size:32 final size:31
Alignment explanation
Indices: 200--266 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 31
190 AACTTTATGT
*
200 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
231 TTTCCAATTGTACCCTT-TTTTTAAAAAACATA
1 TTTCCAATTGTACCCTTATTTTT--AAAACATA
263 TTTC
1 TTTC
267 TAAATTGTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 5 0.15
31 16 0.48
32 12 0.36
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.46
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:325 original size:18 final size:19
Alignment explanation
Indices: 276--328 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
266 CTAAATTGTC
*
276 ATTACTAAATAATATTTTTA
1 ATTACTAAATTAT-TTTTTA
* **
296 ATTATTCCATTATTTTTTA
1 ATTACTAAATTATTTTTTA
315 ATTA-TAAATTATTT
1 ATTACTAAATTATTT
329 CATTATATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 8 0.30
19 10 0.37
20 9 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTACTAAATTATTTTTTA
Found at i:426 original size:44 final size:44
Alignment explanation
Indices: 378--484 Score: 178
Period size: 44 Copynumber: 2.4 Consensus size: 44
368 TCCATGAGGA
* * *
378 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCACAGTGT
1 GGTTACCAAAATTTCATAGTGTAGTTACCAAAATTTCACAGAGT
*
422 GGTTACCAAAATTTCATAGTGTAGTTACCAAAATTTCATAGAGT
1 GGTTACCAAAATTTCATAGTGTAGTTACCAAAATTTCACAGAGT
466 GGTTACCAAAATTTCATAG
1 GGTTACCAAAATTTCATAG
485 GATCAAGTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (44 bp):
GGTTACCAAAATTTCATAGTGTAGTTACCAAAATTTCACAGAGT
Found at i:523 original size:22 final size:22
Alignment explanation
Indices: 355--538 Score: 127
Period size: 22 Copynumber: 8.3 Consensus size: 22
345 TATTTTACTT
* *
355 TGGTTATTATAATTCCAT-GAGG
1 TGGTTATTAAAATTTCATAG-GG
* * *
377 AGGTTATCAAAATTTCATAGTG
1 TGGTTATTAAAATTTCATAGGG
** * *
399 TGGTTACCAAAATTTCACAGTG
1 TGGTTATTAAAATTTCATAGGG
** *
421 TGGTTACCAAAATTTCATAGTG
1 TGGTTATTAAAATTTCATAGGG
* ** *
443 TAGTTACCAAAATTTCATAGAG
1 TGGTTATTAAAATTTCATAGGG
** *
465 TGGTTACCAAAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGG
* * *
487 TCAAGTTATTAAAATTTCTTAGGT
1 T--GGTTATTAAAATTTCATAGGG
*
511 TGGTTATTGAAATTTCATAGGG
1 TGGTTATTAAAATTTCATAGGG
533 TGGTTA
1 TGGTTA
539 ATTATCACAA
Statistics
Matches: 136, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
22 118 0.87
23 1 0.01
24 17 0.12
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.38
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGG
Found at i:627 original size:22 final size:22
Alignment explanation
Indices: 577--698 Score: 79
Period size: 22 Copynumber: 5.5 Consensus size: 22
567 AAAAAGATTT
* *
577 CAAAATGTCATAGCGAGGTTATA
1 CAAAATTTCATAGTGAGGTTA-A
* *
600 C-GAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAGTGAGGTTAA
*
621 CAAAATTTCATTAG-AAGGTT-A
1 CAAAATTTCA-TAGTGAGGTTAA
* ** * *
642 CTAATATTTCACCGGGAGGTTAT
1 C-AAAATTTCATAGTGAGGTTAA
* * *
665 CAAAATTTTATAGTGCGGTTAT
1 CAAAATTTCATAGTGAGGTTAA
687 CAAAATTTCATA
1 CAAAATTTCATA
699 TGAAAGTTAT
Statistics
Matches: 75, Mismatches: 19, Indels: 11
0.71 0.18 0.10
Matches are distributed among these distances:
21 5 0.07
22 65 0.87
23 5 0.07
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:707 original size:22 final size:21
Alignment explanation
Indices: 660--960 Score: 89
Period size: 22 Copynumber: 13.7 Consensus size: 21
650 TCACCGGGAG
* **
660 GTTATCAAAATTTTATAGTGCG
1 GTTATCAAAATTTCATA-TGAA
682 GTTATCAAAATTTCATATGAAA
1 GTTATCAAAATTTCATATG-AA
* *
704 GTTAT-AAAAGTCTCAATTTGATAA
1 GTTATCAAAA-TTTC-ATATG--AA
* * *
728 GGAGTACCAAAATTTGATA-GAA
1 -G-TTATCAAAATTTCATATGAA
*
750 GGTTATC-AAATCTCATA-G-A
1 -GTTATCAAAATTTCATATGAA
* *
769 G-TATCGAAATTTCATAAAGATA
1 GTTATCAAAATTTCAT-ATGA-A
791 TGATTATCAAAATTT-ATATGAA
1 -G-TTATCAAAATTTCATATGAA
* **
813 GATTATCAAAATTCCATAGTGTT
1 G-TTATCAAAATTTCATA-TGAA
* * *
836 GTTATCAAAATTTCAAAGCGAG
1 GTTATCAAAATTTCATA-TGAA
* *
858 GTTATCAAAATTACATAATG-T
1 GTTATCAAAATTTCAT-ATGAA
*
879 GATTATCAAAATTTCATA-GAGGG
1 G-TTATCAAAATTTCATATGA--A
* * * * *
902 GTCAACAAAATTTTATAAAGAT
1 GTTATCAAAATTTCAT-ATGAA
* *
924 GTTATCAAAATTTCATAAAGAG
1 GTTATCAAAATTTCAT-ATGAA
*
946 GTTATCAAATTTTCA
1 GTTATCAAAATTTCA
961 AAATCTGATT
Statistics
Matches: 214, Mismatches: 41, Indels: 48
0.71 0.14 0.16
Matches are distributed among these distances:
17 4 0.02
18 9 0.04
19 2 0.01
20 11 0.05
21 24 0.11
22 122 0.57
23 14 0.07
24 7 0.03
25 13 0.06
26 4 0.02
27 4 0.02
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (21 bp):
GTTATCAAAATTTCATATGAA
Found at i:811 original size:18 final size:19
Alignment explanation
Indices: 788--825 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
778 TTTCATAAAG
788 ATAT-GATTATCAAAATTT
1 ATATAGATTATCAAAATTT
806 ATATGAAGATTATCAAAATT
1 ATAT--AGATTATCAAAATT
826 CCATAGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
21 13 0.76
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (19 bp):
ATATAGATTATCAAAATTT
Found at i:885 original size:44 final size:44
Alignment explanation
Indices: 770--960 Score: 156
Period size: 44 Copynumber: 4.3 Consensus size: 44
760 TCTCATAGAG
* * * *
770 TATCGAAATTTCATAAAGATATGATTATCAAAATTT-ATATGA-AGAT
1 TATCAAAATTTCATAATG--ATG-TTATCAAAATTTCA-AAGAGAGGT
* * * *
816 TATCAAAATTCCATAGTGTTGTTATCAAAATTTCAAAGCGAGGT
1 TATCAAAATTTCATAATGATGTTATCAAAATTTCAAAGAGAGGT
* * *
860 TATCAAAATTACATAATG-TGATTATCAAAATTTCATAGAGGGGT
1 TATCAAAATTTCATAATGATG-TTATCAAAATTTCAAAGAGAGGT
* * * *
904 CAACAAAATTTTATAAAGATGTTATCAAAATTTCATAA-AGAGGT
1 TATCAAAATTTCATAATGATGTTATCAAAATTTCA-AAGAGAGGT
*
948 TATCAAATTTTCA
1 TATCAAAATTTCA
961 AAATCTGATT
Statistics
Matches: 116, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
43 16 0.14
44 83 0.72
45 3 0.03
46 14 0.12
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (44 bp):
TATCAAAATTTCATAATGATGTTATCAAAATTTCAAAGAGAGGT
Found at i:911 original size:66 final size:66
Alignment explanation
Indices: 812--960 Score: 156
Period size: 66 Copynumber: 2.3 Consensus size: 66
802 ATTTATATGA
* * ** * * *
812 AGATTATCAAAATTCCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAA
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAA
*
876 TG
65 AG
* * * *
878 TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAAAGATGTTATCAAAATTTCATAAA
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAAA
943 G
66 G
* *
944 AGGTTATCAAATTTTCA
1 AGATTATCAAAATTTCA
961 AAATCTGATT
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
66 65 0.97
67 2 0.03
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (66 bp):
AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAAA
G
Found at i:1091 original size:20 final size:20
Alignment explanation
Indices: 1066--1116 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1056 TGATGGAGTA
*
1066 ATCAAAATTTTAGGGAGGAT
1 ATCAAAATTTCAGGGAGGAT
*
1086 ATCAAAA-TTCAGTGAGGAT
1 ATCAAAATTTCAGGGAGGAT
1105 ATCAAAATTTCA
1 ATCAAAATTTCA
1117 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:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (20 bp):
ATCAAAATTTCAGGGAGGAT
Found at i:1132 original size:22 final size:22
Alignment explanation
Indices: 1104--1661 Score: 132
Period size: 22 Copynumber: 25.6 Consensus size: 22
1094 TCAGTGAGGA
1104 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
1126 TATCAAATTTTCAAAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* *
1148 TTTCAAAATTTCATAAG-AGTGT
1 TATCAAAATTTCATATGAAG-GT
* *
1170 TATCAAAATTTCATA-GCATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
1191 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
1214 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * * *
1236 TATCAAAAAATCATAAGGAGCT
1 TATCAAAATTTCATATGAAGGT
*
1258 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * * *
1274 TATTAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
1296 TATCAAAATTTTATAAGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
1319 TATTAAAATTTTATA-GAAAGATT
1 TATCAAAATTTCATATG-AAG-GT
* *
1342 TATTAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
1364 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
1386 TATCAAAATTT--T-T-AAGTGT
1 TATCAAAATTTCATATGAAG-GT
* *
1405 GATTACTAACAA-TTCATATGGAGGT
1 TA-T-C-AA-AATTTCATATGAAGGT
** *
1430 T-TTTAAATTT-TTATGAAGTGGT
1 TATCAAAATTTCATATGAA--GGT
* * *
1452 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
1474 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
1497 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
*
1519 TATCAAAATTTTATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* *
1541 CT-TCAAAATTT-ATTAGGGAGGT
1 -TATCAAAATTTCA-TATGAAGGT
* * *
1563 TAACAAAATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* *
1585 T-TAAAAAATTT-ATA-AAAGGAT
1 TAT-CAAAATTTCATATGAAGG-T
* ** * **
1606 TCTTGAAATTCCATA-GTACCGT
1 TATCAAAATTTCATATG-AAGGT
*
1628 TATCAAAATTTCATA-GGAGGT
1 TATCAAAATTTCATATGAAGGT
1649 TATCAAAATTTCA
1 TATCAAAATTTCA
1662 GAATGAGATC
Statistics
Matches: 392, Mismatches: 94, Indels: 101
0.67 0.16 0.17
Matches are distributed among these distances:
16 7 0.02
17 2 0.01
18 4 0.01
19 2 0.01
20 15 0.04
21 41 0.10
22 236 0.60
23 72 0.18
24 8 0.02
25 3 0.01
26 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:1197 original size:66 final size:66
Alignment explanation
Indices: 1098--1243 Score: 154
Period size: 66 Copynumber: 2.2 Consensus size: 66
1088 CAAAATTCAG
* * * ** **
1098 TGAGGATATCAAAATTTCATATGAAGGTTATCAAATTTTCAAAGTTTAG-TTTTCAAAATTTCAT
1 TGAGGTTATCAAAATTTCATATGAAGGTGATCAAAATTTCAAAG-GGAGATTAACAAAATTTCAT
1162 AA
65 AA
* * *
1164 -GAGTGTTATCAAAATTTCATA-GCATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCA
1 TGAG-GTTATCAAAATTTCATATGAAGGT-GATCAAAATTTCAAAGGGAGATTAACAAAATTTCA
1227 TAA
64 TAA
1230 TGAGGTTATCAAAA
1 TGAGGTTATCAAAA
1244 AATCATAAGG
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
65 9 0.14
66 54 0.82
67 3 0.05
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (66 bp):
TGAGGTTATCAAAATTTCATATGAAGGTGATCAAAATTTCAAAGGGAGATTAACAAAATTTCATA
A
Found at i:1241 original size:44 final size:44
Alignment explanation
Indices: 1066--1578 Score: 187
Period size: 44 Copynumber: 11.8 Consensus size: 44
1056 TGATGGAGTA
* *
1066 ATCAAAATTT--TAGGGAGGA-TATCAAAA-TTC--AGTGAGGAT
1 ATCAAAATTTCATAGGGA-GATTATCAAAATTTCATAATGAGGTT
* * * * *
1105 ATCAAAATTTCATATGAAGGTTATCAAATTTTCA-AAGTTTA-GTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAA--TGAGGTT
* * *
1149 TTCAAAATTTCATA-AGAGTGTTATCAAAATTTCATAGCATGTA-G--
1 ATCAAAATTTCATAGGGAG-ATTATCAAAATTTCATA--ATG-AGGTT
*
1193 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
** * * *
1237 ATCAAAAAATCATAAGGAGCTTATCAAAA-TT--T-GT-A-GTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
* * * * * *
1275 ATTAAGATTTCATA-AGAAAGTTATCAAAATTTTATAAGGAGGTTT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAATGAGG-TT
* * ** * **
1320 ATTAAAATTTTATAGAAAGATTTATTAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAATGAGGTT
* * * * * *
1365 ATCACAATTTCATAGTGTGATTATCAAAATTT-TTAAGTGTGATT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAA-TGAGGTT
* * * * * * *
1409 A-CTAACAA-TTCATATGGAGGTTTTTAAATTTTTATGAA-GTGGTT
1 ATC-AA-AATTTCATAGGGAGATTATCAAAATTTCAT-AATGAGGTT
* * * * * * * *
1453 ATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATG-AGGTT
* * *
1498 ATCAAAATTTCATTGGGA-AGTTATCAAAATTTTATATTGAGGTCT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAATGAGGT-T
* *
1543 -TCAAAATTT-ATTAGGGAGGTTAACAAAATTTCATAA
1 ATCAAAATTTCA-TAGGGAGATTATCAAAATTTCATAA
1579 GAAAGTTTAA
Statistics
Matches: 350, Mismatches: 86, Indels: 71
0.69 0.17 0.14
Matches are distributed among these distances:
37 2 0.01
38 22 0.06
39 13 0.04
40 2 0.01
41 14 0.04
42 7 0.02
43 12 0.03
44 176 0.50
45 76 0.22
46 25 0.07
47 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (44 bp):
ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
Found at i:1326 original size:23 final size:23
Alignment explanation
Indices: 1273--1352 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
1263 AAATTTGTAG
* * *
1273 TTATTAAGATTTCATAAGAAAG-
1 TTATTAAAATTTTATAAGAAGGT
* *
1295 TTATCAAAATTTTATAAGGAGGT
1 TTATTAAAATTTTATAAGAAGGT
*
1318 TTATTAAAATTTTAT-AGAAAGAT
1 TTATTAAAATTTTATAAG-AAGGT
1341 TTATTAAAATTT
1 TTATTAAAATTT
1353 CATAGCGAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 19 0.40
23 29 0.60
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (23 bp):
TTATTAAAATTTTATAAGAAGGT
Found at i:1363 original size:46 final size:45
Alignment explanation
Indices: 1273--1378 Score: 110
Period size: 45 Copynumber: 2.4 Consensus size: 45
1263 AAATTTGTAG
* *
1273 TTATTAAGATTTCATAAGAAAGTTATCAAAATTTTATAAGGAGGT
1 TTATTAAAATTTCATAAGAAAGTTATCAAAATTTCATAAGGAGGT
* *
1318 TTATTAAAATTTTAT-AGAAAGATTTATTAAAATTTCAT-AGCGAGG-
1 TTATTAAAATTTCATAAGAAAG--TTATCAAAATTTCATAAG-GAGGT
* *
1363 TTATCACAATTTCATA
1 TTATTAAAATTTCATA
1379 GTGTGATTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
44 6 0.12
45 27 0.54
46 17 0.34
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (45 bp):
TTATTAAAATTTCATAAGAAAGTTATCAAAATTTCATAAGGAGGT
Found at i:2692 original size:2 final size:2
Alignment explanation
Indices: 2687--2712 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2677 TGTTTTGAAG
2687 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
2713 CATTTTAAAT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3290 original size:49 final size:50
Alignment explanation
Indices: 3217--3315 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 50
3207 TGGTATCAAT
*
3217 ATGAACCTTTTTTTAATGTATGTTTAGAAGAAGTTATGCCCACCCTAAAA
1 ATGAACCTTTTTTTAATCTATGTTTAGAAGAAGTTATGCCCACCCTAAAA
3267 ATGAACC-TTTTTTAATCTATGTTTAGAAGAAGTTATGCCCACCCTAAAA
1 ATGAACCTTTTTTTAATCTATGTTTAGAAGAAGTTATGCCCACCCTAAAA
3316 GTAATTCCTG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 41 0.85
50 7 0.15
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (50 bp):
ATGAACCTTTTTTTAATCTATGTTTAGAAGAAGTTATGCCCACCCTAAAA
Found at i:4870 original size:21 final size:21
Alignment explanation
Indices: 4844--4949 Score: 122
Period size: 21 Copynumber: 5.0 Consensus size: 21
4834 GACCGAGCTT
*
4844 GCTGTTGTACCAGTTCGGATC
1 GCTGTTGTACGAGTTCGGATC
** *
4865 GCTGTTGTACGACATCGGATA
1 GCTGTTGTACGAGTTCGGATC
* * * *
4886 GGTCTCGTGCGAGTTCGGATC
1 GCTGTTGTACGAGTTCGGATC
4907 GCTGTTGTACGAGTTCGGATC
1 GCTGTTGTACGAGTTCGGATC
* *
4928 GCTGTCGTGCGAGTTCGGATC
1 GCTGTTGTACGAGTTCGGATC
4949 G
1 G
4950 TTGTCGTGCG
Statistics
Matches: 68, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 68 1.00
ACGTcount: A:0.14, C:0.22, G:0.34, T:0.30
Consensus pattern (21 bp):
GCTGTTGTACGAGTTCGGATC
Found at i:4914 original size:42 final size:42
Alignment explanation
Indices: 4855--4985 Score: 172
Period size: 42 Copynumber: 3.1 Consensus size: 42
4845 CTGTTGTACC
*
4855 AGTTCGGATCGCTGTTGTACGACATCGGATAGGTCTCGTGCG
1 AGTTCGGATCGCTGTTGTACGACTTCGGATAGGTCTCGTGCG
* * * *
4897 AGTTCGGATCGCTGTTGTACGAGTTCGGATCGCTGTCGTGCG
1 AGTTCGGATCGCTGTTGTACGACTTCGGATAGGTCTCGTGCG
* * * * *
4939 AGTTCGGATCGTTGTCGTGCGATTTCCGATAGGTCTCGTGCG
1 AGTTCGGATCGCTGTTGTACGACTTCGGATAGGTCTCGTGCG
4981 AGTTC
1 AGTTC
4986 CGATAGCTCT
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.14, C:0.21, G:0.34, T:0.31
Consensus pattern (42 bp):
AGTTCGGATCGCTGTTGTACGACTTCGGATAGGTCTCGTGCG
Found at i:4954 original size:21 final size:21
Alignment explanation
Indices: 4855--5165 Score: 135
Period size: 21 Copynumber: 14.7 Consensus size: 21
4845 CTGTTGTACC
* *
4855 AGTTCGGATCGCTGTTGTACG
1 AGTTCGGATCGCTGTCGTGCG
** * * *
4876 ACATCGGATAGGTCTCGTGCG
1 AGTTCGGATCGCTGTCGTGCG
* *
4897 AGTTCGGATCGCTGTTGTACG
1 AGTTCGGATCGCTGTCGTGCG
4918 AGTTCGGATCGCTGTCGTGCG
1 AGTTCGGATCGCTGTCGTGCG
*
4939 AGTTCGGATCGTTGTCGTGCG
1 AGTTCGGATCGCTGTCGTGCG
* * * * *
4960 ATTTCCGATAGGTCTCGTGCG
1 AGTTCGGATCGCTGTCGTGCG
* * * *
4981 AGTTCCGATAGCTCTAGTGCG
1 AGTTCGGATCGCTGTCGTGCG
* * * *
5002 AGTTCCGATAG-TTTGGCTGGCTG
1 AGTTCGGATCGCTGTCG-T-GC-G
* * ** **
5025 TTGTGCGAGAAAG--GCTCCCGCG
1 -AGTTCG-GATCGCTG-TCGTGCG
* * * *
5047 AGTTTGGCTGGTTGTCGTGCG
1 AGTTCGGATCGCTGTCGTGCG
* * *
5068 AGTTCGGCTCGCTGCCTTGCG
1 AGTTCGGATCGCTGTCGTGCG
*** *
5089 AGTTCCCCTCGCTGTTGTGCG
1 AGTTCGGATCGCTGTCGTGCG
* * *
5110 AGTCCCGATCGCTGTTG-GCG
1 AGTTCGGATCGCTGTCGTGCG
* *
5130 AGTTCCGATCGCTGTTGTGCG
1 AGTTCGGATCGCTGTCGTGCG
5151 AGTTCGGATCGCTGT
1 AGTTCGGATCGCTGT
5166 TGAGTATTTG
Statistics
Matches: 223, Mismatches: 58, Indels: 18
0.75 0.19 0.06
Matches are distributed among these distances:
20 24 0.11
21 184 0.83
22 4 0.02
23 3 0.01
24 3 0.01
25 5 0.02
ACGTcount: A:0.12, C:0.23, G:0.34, T:0.31
Consensus pattern (21 bp):
AGTTCGGATCGCTGTCGTGCG
Found at i:5001 original size:42 final size:42
Alignment explanation
Indices: 4855--5012 Score: 163
Period size: 42 Copynumber: 3.8 Consensus size: 42
4845 CTGTTGTACC
* * ** *
4855 AGTTCGGATCGCTGTTGTACGACATCGGATAGGTCTCGTGCG
1 AGTTCGGATCGCTGTAGTGCGAGTTCCGATAGGTCTCGTGCG
* * * * * *
4897 AGTTCGGATCGCTGTTGTACGAGTTCGGATCGCTGTCGTGCG
1 AGTTCGGATCGCTGTAGTGCGAGTTCCGATAGGTCTCGTGCG
* * *
4939 AGTTCGGATCGTTGTCGTGCGATTTCCGATAGGTCTCGTGCG
1 AGTTCGGATCGCTGTAGTGCGAGTTCCGATAGGTCTCGTGCG
* * *
4981 AGTTCCGATAGCTCTAGTGCGAGTTCCGATAG
1 AGTTCGGATCGCTGTAGTGCGAGTTCCGATAG
5013 TTTGGCTGGC
Statistics
Matches: 97, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 97 1.00
ACGTcount: A:0.15, C:0.22, G:0.33, T:0.30
Consensus pattern (42 bp):
AGTTCGGATCGCTGTAGTGCGAGTTCCGATAGGTCTCGTGCG
Found at i:5142 original size:41 final size:41
Alignment explanation
Indices: 5086--5167 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
5076 TCGCTGCCTT
*
5086 GCGAGTTCCCCTCGCTGTTGTGCGAGTCCCGATCGCTGTTG
1 GCGAGTTCCCATCGCTGTTGTGCGAGTCCCGATCGCTGTTG
* * *
5127 GCGAGTTCCGATCGCTGTTGTGCGAGTTCGGATCGCTGTTG
1 GCGAGTTCCCATCGCTGTTGTGCGAGTCCCGATCGCTGTTG
5168 AGTATTTGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.09, C:0.27, G:0.34, T:0.30
Consensus pattern (41 bp):
GCGAGTTCCCATCGCTGTTGTGCGAGTCCCGATCGCTGTTG
Found at i:5840 original size:2 final size:2
Alignment explanation
Indices: 5833--5866 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5823 ATACCATCAC
5833 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
5867 AAATAATGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7332 original size:31 final size:31
Alignment explanation
Indices: 7294--7353 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
7284 TATGTATCCG
*
7294 ATTGTACCCTTATT-TTTAAAATATATTTCCA
1 ATTGTACCCTT-TTCTTTAAAACATATTTCCA
7325 ATTGTACCCTTTTCTTTAAAACATATTTC
1 ATTGTACCCTTTTCTTTAAAACATATTTC
7354 TAAATTGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTGTACCCTTTTCTTTAAAACATATTTCCA
Found at i:7687 original size:19 final size:20
Alignment explanation
Indices: 7660--7697 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
7650 TACTATTATT
7660 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
7680 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
7698 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:7850 original size:24 final size:22
Alignment explanation
Indices: 7822--7880 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
7812 CGTGGTTACC
7822 AAAATTTCATAGGATCAGATTATT
1 AAAATTTCATAGG-T-AGATTATT
* * * *
7846 AAAATCTCTTAGGTTGGTTATT
1 AAAATTTCATAGGTAGATTATT
*
7868 GAAATTTCATAGG
1 AAAATTTCATAGG
7881 GTGGTTAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
22 16 0.57
23 1 0.04
24 11 0.39
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (22 bp):
AAAATTTCATAGGTAGATTATT
Found at i:7872 original size:22 final size:22
Alignment explanation
Indices: 7841--7887 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
7831 TAGGATCAGA
* *
7841 TTATTAAAATCTCTTAGGTTGG
1 TTATTAAAATCTCATAGGGTGG
* *
7863 TTATTGAAATTTCATAGGGTGG
1 TTATTAAAATCTCATAGGGTGG
7885 TTA
1 TTA
7888 ATTATCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (22 bp):
TTATTAAAATCTCATAGGGTGG
Found at i:7948 original size:22 final size:22
Alignment explanation
Indices: 7923--8062 Score: 128
Period size: 22 Copynumber: 6.4 Consensus size: 22
7913 ATCAAAGAGA
* *
7923 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
7945 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
7967 TTAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGAGG
* * *
7989 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* *
8011 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
8033 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
8055 TTAT-AAAA
1 TTATCAAAA
8063 GTCTCAATTT
Statistics
Matches: 97, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
21 11 0.11
22 80 0.82
23 6 0.06
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:8449 original size:22 final size:22
Alignment explanation
Indices: 8333--8605 Score: 122
Period size: 22 Copynumber: 12.6 Consensus size: 22
8323 TCAGGGAGGA
*
8333 TATCAAAATTTCAT-AGTTTAGT
1 TATCAAAATTTCATAAG-TAAGT
* * *
8355 TTTCAAAATTTCACAAG-AGGGT
1 TATCAAAATTTCATAAGTA-AGT
*
8377 TATCAAAATTTCAT-AGTATGT
1 TATCAAAATTTCATAAGTAAGT
* **
8398 AGATCAAAATTTCAT-AGGGAGAT
1 -TATCAAAATTTCATAAGTAAG-T
* *
8421 TAACAAAATTTCATAATTAAGT
1 TATCAAAATTTCATAAGTAAGT
** * * *
8443 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAAGTAAGT
8465 TATCAAAA-TT--T--GT-AGT
1 TATCAAAATTTCATAAGTAAGT
* * *
8481 TATCAAGATTTCATAAGAAATT
1 TATCAAAATTTCATAAGTAAGT
* * * *
8503 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAAGTAAG-T
* *
8526 TATCAAAATTTTAT-AGGAAGATT
1 TATCAAAATTTCATAAGTAAG--T
*
8549 TATCAAAATTTCAT-AGCGAAGT
1 TATCAAAATTTCATAAG-TAAGT
* **
8571 TATCACAATTTCAT-AGTGTGAT
1 TATCAAAATTTCATAAGTAAG-T
8593 TATCAAAATTTCA
1 TATCAAAATTTCA
8606 GAGTGTGATT
Statistics
Matches: 192, Mismatches: 43, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
16 9 0.05
17 3 0.02
19 2 0.01
21 7 0.04
22 129 0.67
23 38 0.20
24 4 0.02
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAAGTAAGT
Found at i:8574 original size:45 final size:45
Alignment explanation
Indices: 8333--8605 Score: 167
Period size: 44 Copynumber: 6.3 Consensus size: 45
8323 TCAGGGAGGA
*** * * * **
8333 TATCAAAATTTCATAGTTTAGTTTTCAAAATTTCACAAG-AGGGT
1 TATCAAAATTTCATAGCGAAGTTATCAAAATTTCATAGGAAGATT
* * * *
8377 TATCAAAATTTCATAG-TATGTAGATCAAAATTTCATAGGGAGA-T
1 TATCAAAATTTCATAGCGAAGT-TATCAAAATTTCATAGGAAGATT
* *** ** * *
8421 TAACAAAATTTCATAATTAAGTTATCAAAAAATCATAGGGAG-GT
1 TATCAAAATTTCATAGCGAAGTTATCAAAATTTCATAGGAAGATT
* * *
8465 TATCAAAA-TT--T---GTAGTTATCAAGATTTCATAAGAA-ATT
1 TATCAAAATTTCATAGCGAAGTTATCAAAATTTCATAGGAAGATT
* * * *
8503 TATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGCGAAG-TTATCAAAATTTCATAGGAAGATT
* *
8549 TATCAAAATTTCATAGCGAAGTTATCACAATTTCATAGTG-TGA-T
1 TATCAAAATTTCATAGCGAAGTTATCAAAATTTCATAG-GAAGATT
8593 TATCAAAATTTCA
1 TATCAAAATTTCA
8606 GAGTGTGATT
Statistics
Matches: 182, Mismatches: 33, Indels: 28
0.75 0.14 0.12
Matches are distributed among these distances:
38 26 0.14
39 2 0.01
41 2 0.01
43 5 0.03
44 85 0.47
45 40 0.22
46 22 0.12
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (45 bp):
TATCAAAATTTCATAGCGAAGTTATCAAAATTTCATAGGAAGATT
Found at i:8610 original size:22 final size:22
Alignment explanation
Indices: 8333--8740 Score: 118
Period size: 22 Copynumber: 18.7 Consensus size: 22
8323 TCAGGGAGGA
*
8333 TATCAAAATTTCATAGT-TTAGT
1 TATCAAAATTTCATAGTGTGA-T
* * * *
8355 TTTCAAAATTTCACAAGAG-GGT
1 TATCAAAATTTCA-TAGTGTGAT
*
8377 TATCAAAATTTCATAGTATG-T
1 TATCAAAATTTCATAGTGTGAT
* * *
8398 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGTGTGAT
* * *
8421 TAACAAAATTTCATAAT-TAAGT
1 TATCAAAATTTCATAGTGTGA-T
** * * *
8443 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGTGTGAT
*
8465 TATCAAAA-TT--T-GT-AG-T
1 TATCAAAATTTCATAGTGTGAT
* * **
8481 TATCAAGATTTCATA-AGAAATT
1 TATCAAAATTTCATAGTGTGA-T
* * * *
8503 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGTG-TGAT
* *
8526 TATCAAAATTTTATAG-GAAGATT
1 TATCAAAATTTCATAGTG-TGA-T
* *
8549 TATCAAAATTTCATAGCG-AAGT
1 TATCAAAATTTCATAGTGTGA-T
*
8571 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
*
8593 TATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
*
8615 TA-CTAACAA-TTCATA-TGGAGAT
1 TATC-AA-AATTTCATAGT-GTGAT
* * * ** *
8637 TTTTAAATTTTCATAACGTGGT
1 TATCAAAATTTCATAGTGTGAT
* *
8659 TATCAATATATCATA-TG-GAGGT
1 TATCAAAATTTCATAGTGTGA--T
* * *
8681 TATCAATATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGTG-TGAT
*
8704 TATCAAAATTTCAT--TGGGAAGT
1 TATCAAAATTTCATAGTGTG-A-T
8726 TATCAAAATTTCATA
1 TATCAAAATTTCATA
8741 TTGAGGTCTT
Statistics
Matches: 284, Mismatches: 69, Indels: 65
0.68 0.17 0.16
Matches are distributed among these distances:
16 8 0.03
17 4 0.01
18 1 0.00
19 2 0.01
20 3 0.01
21 11 0.04
22 198 0.70
23 55 0.19
24 1 0.00
25 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGAT
Found at i:8728 original size:45 final size:45
Alignment explanation
Indices: 8655--8740 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
8645 TTTCATAACG
* * *
8655 TGGTTATCAATATATCATATGGAGGTTATCAATATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
8700 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
8741 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:25136 original size:15 final size:15
Alignment explanation
Indices: 25116--25147 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
25106 ATCATTTTCT
25116 TTTCTTGGTTTGGGA
1 TTTCTTGGTTTGGGA
25131 TTTCTTGGTTTGGGA
1 TTTCTTGGTTTGGGA
25146 TT
1 TT
25148 ACAAACGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.31, T:0.56
Consensus pattern (15 bp):
TTTCTTGGTTTGGGA
Found at i:25216 original size:28 final size:28
Alignment explanation
Indices: 25176--25231 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
25166 CCGTACACCG
25176 CTACATGATTAGCACATTACTGAAACGT
1 CTACATGATTAGCACATTACTGAAACGT
*
25204 CTACATGATTAGCATATTACTGAAACGT
1 CTACATGATTAGCACATTACTGAAACGT
25232 TAATCTATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (28 bp):
CTACATGATTAGCACATTACTGAAACGT
Found at i:29119 original size:2 final size:2
Alignment explanation
Indices: 29112--29160 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
29102 ATAATAACAT
* *
29112 TA TA TA TA TA TA TA TA TA TT TA GT- TA TA TA GA 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
29154 TA TA TA T
1 TA TA TA T
29161 GTCACCCTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35351 original size:15 final size:15
Alignment explanation
Indices: 35331--35362 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35321 CTCTCCATAT
*
35331 ATGCAAATTTGAAAG
1 ATGCAAACTTGAAAG
35346 ATGCAAACTTGAAAG
1 ATGCAAACTTGAAAG
35361 AT
1 AT
35363 AGGAATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
ATGCAAACTTGAAAG
Found at i:39933 original size:4 final size:4
Alignment explanation
Indices: 39906--39957 Score: 61
Period size: 4 Copynumber: 12.8 Consensus size: 4
39896 AATAAGACTT
* *
39906 ATAA A-AA ATTA ATAA TAAAA ATAA ATAA ATAA ATAA ATAA ATAA AGTAA
1 ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA A-TAA
39955 ATA
1 ATA
39958 CTATAGTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 3 0.07
4 31 0.76
5 7 0.17
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:40864 original size:21 final size:21
Alignment explanation
Indices: 40840--40912 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
40830 TTAGCCTCAC
40840 CGCCACCACCTTCCTTCTTCT
1 CGCCACCACCTTCCTTCTTCT
40861 CGCCACCACCTTCCTTCTTCT
1 CGCCACCACCTTCCTTCTTCT
* * * *
40882 CTCCTCCGCCTTCCTTTTTCT
1 CGCCACCACCTTCCTTCTTCT
*
40903 CTCCACCACC
1 CGCCACCACC
40913 AGCAGCTGCT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.08, C:0.53, G:0.04, T:0.34
Consensus pattern (21 bp):
CGCCACCACCTTCCTTCTTCT
Found at i:40969 original size:18 final size:18
Alignment explanation
Indices: 40948--41005 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
40938 TCACCTCCGG
*
40948 CGTCTTTCTTTTCACCGC
1 CGTCTTTCTTCTCACCGC
* *
40966 CGTCCTTCTTCTCTCCGC
1 CGTCTTTCTTCTCACCGC
40984 CGTCTTTCTTCTCACCGC
1 CGTCTTTCTTCTCACCGC
41002 CGTC
1 CGTC
41006 GTCCTTCTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.03, C:0.45, G:0.12, T:0.40
Consensus pattern (18 bp):
CGTCTTTCTTCTCACCGC
Found at i:41008 original size:21 final size:21
Alignment explanation
Indices: 40935--41014 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 21
40925 TTCTTTTCCT
* *
40935 TTCTCACCTCCGGCGTCTTTC
1 TTCTCACCGCCGTCGTCTTTC
*
40956 TTTTCACCGCCGTC--C-TTC
1 TTCTCACCGCCGTCGTCTTTC
*
40974 TTCTCTCCG-C--CGTCTTTC
1 TTCTCACCGCCGTCGTCTTTC
*
40992 TTCTCACCGCCGTCGTCCTTC
1 TTCTCACCGCCGTCGTCTTTC
41013 TT
1 TT
41015 TGGTGGAACG
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
15 1 0.02
17 2 0.04
18 21 0.46
19 2 0.04
21 20 0.43
ACGTcount: A:0.04, C:0.44, G:0.12, T:0.40
Consensus pattern (21 bp):
TTCTCACCGCCGTCGTCTTTC
Found at i:41013 original size:36 final size:36
Alignment explanation
Indices: 40942--41013 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
40932 CCTTTCTCAC
* * *
40942 CTCCGGCGTCTTTCTTTTCACCGCCGTCCTTCTTCT
1 CTCCGCCGTCTTTCTTCTCACCGCCGTCCTCCTTCT
*
40978 CTCCGCCGTCTTTCTTCTCACCGCCGTCGTCCTTCT
1 CTCCGCCGTCTTTCTTCTCACCGCCGTCCTCCTTCT
41014 TTGGTGGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.03, C:0.44, G:0.14, T:0.39
Consensus pattern (36 bp):
CTCCGCCGTCTTTCTTCTCACCGCCGTCCTCCTTCT
Found at i:42569 original size:19 final size:20
Alignment explanation
Indices: 42543--42595 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
42533 AATGAATGTA
42543 TGTATGTATGTATGATGATG
1 TGTATGTATGTATGATGATG
42563 T-TATGTATGT-T-ATGATG
1 TGTATGTATGTATGATGATG
*
42580 TGGATGTATG-ATGATG
1 TGTATGTATGTATGATG
42596 GATATTTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 7 0.24
18 9 0.31
19 12 0.41
20 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (20 bp):
TGTATGTATGTATGATGATG
Found at i:51821 original size:21 final size:21
Alignment explanation
Indices: 51782--51821 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
51772 TGGGGGTTGT
* *
51782 TAAATACCGCCCTAGTTTTGC
1 TAAATACCGCCCCACTTTTGC
51803 TAAATACCGCCCCACTTTT
1 TAAATACCGCCCCACTTTT
51822 TACACTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.33, G:0.10, T:0.33
Consensus pattern (21 bp):
TAAATACCGCCCCACTTTTGC
Found at i:51840 original size:15 final size:16
Alignment explanation
Indices: 51819--51863 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
51809 CCGCCCCACT
*
51819 TTTTACACTTTTGCCC
1 TTTTACACTTTTACCC
51835 -TTTACA-TTTTACCC
1 TTTTACACTTTTACCC
51849 TTTTTACACTTTTAC
1 -TTTTACACTTTTAC
51864 ACTGAACCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.28
15 6 0.24
16 6 0.24
17 6 0.24
ACGTcount: A:0.18, C:0.27, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTTACACTTTTACCC
Found at i:51912 original size:33 final size:33
Alignment explanation
Indices: 51870--51954 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
51860 TTACACTGAA
*
51870 CCTCCCCACTA-GGACGGCTCAGCCACGGCGGAG
1 CCTCCCCACTAGGGA-GGCTCAACCACGGCGGAG
51903 CCTCCCCACTAGGGAGGCTCAACCACGGCGGAG
1 CCTCCCCACTAGGGAGGCTCAACCACGGCGGAG
* *
51936 CCTCCCCACTGGGGTGGCT
1 CCTCCCCACTAGGGAGGCT
51955 TCACCATGGG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
33 45 0.94
34 3 0.06
ACGTcount: A:0.16, C:0.41, G:0.31, T:0.12
Consensus pattern (33 bp):
CCTCCCCACTAGGGAGGCTCAACCACGGCGGAG
Found at i:52004 original size:32 final size:33
Alignment explanation
Indices: 51939--52019 Score: 137
Period size: 32 Copynumber: 2.5 Consensus size: 33
51929 GGCGGAGCCT
*
51939 CCCCACTGGGGTGGCTTCACCATGGGCAGGCCG
1 CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
51972 CCCCACTGGGGCGGCTTCACCAT-GGCAGGCCG
1 CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
*
52004 CCCCACCGGGGCGGCT
1 CCCCACTGGGGCGGCT
52020 AGACCAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 24 0.52
33 22 0.48
ACGTcount: A:0.11, C:0.41, G:0.36, T:0.12
Consensus pattern (33 bp):
CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
Done.