Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009865.1 Corchorus capsularis cultivar CVL-1 contig09886, 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: 57772
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:58 original size:22 final size:22
Alignment explanation
Indices: 33--171 Score: 113
Period size: 22 Copynumber: 6.3 Consensus size: 22
23 TGTCTCTAAG
*
33 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
55 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
78 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
99 TGGTTACCAAAA-TTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
120 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
144 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
166 TGGTTA
1 TGGTTA
172 ATTATCACAA
Statistics
Matches: 93, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
20 1 0.01
21 9 0.10
22 64 0.69
23 12 0.13
24 7 0.08
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:287 original size:22 final size:22
Alignment explanation
Indices: 262--327 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
252 TTCATTAAAT
*
262 ATTTAATGGGGAGGTTATCAAA
1 ATTTAATAGGGAGGTTATCAAA
* * *
284 ATTTTATAGTGTGGTTATCAAA
1 ATTTAATAGGGAGGTTATCAAA
* * *
306 ATTTCATATGAAGGTTAT-AAA
1 ATTTAATAGGGAGGTTATCAAA
327 A
1 A
328 GTCTCAATTT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (22 bp):
ATTTAATAGGGAGGTTATCAAA
Found at i:289 original size:23 final size:22
Alignment explanation
Indices: 270--577 Score: 67
Period size: 22 Copynumber: 13.9 Consensus size: 22
260 ATATTTAATG
270 GGGAGGTTATCAAAATTTTATA
1 GGGAGGTTATCAAAATTTTATA
* * *
292 GTGTGGTTATCAAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
* *
314 TGAAGGTTAT-AAAAGTCTCAATTTCATA
1 GGGAGGTTATCAAAA---T---TTT-ATA
* *
342 GGGA-G-TACCAAAATTTGATA
1 GGGAGGTTATCAAAATTTTATA
* * *
362 -GAAGGTTATC-AAATCTCATA
1 GGGAGGTTATCAAAATTTTATA
* * * * *
382 GAGTGATTATCGAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
*
404 GAGATCGGATTATCAAAA-TTTATA
1 GGGA--GG-TTATCAAAATTTTATA
** *
428 GAAAGATTATC-AAATTTTCATA
1 GGGAGGTTATCAAAATTTT-ATA
* ** * *
450 GTGTTGTTATCAAAATTTCAAA
1 GGGAGGTTATCAAAATTTTATA
** **
472 ACGAGGTTATCAAAATTACATA
1 GGGAGGTTATCAAAATTTTATA
** * * * *
494 ATGTGATTATCAGAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
* *
516 GAGGA-GTCAACAAAATTTTATA
1 G-GGAGGTTATCAAAATTTTATA
** * *
538 AAGAGGCTATCAAAATTTCATA
1 GGGAGGTTATCAAAATTTTATA
**
560 AAGAGGTTATC-AAATTTT
1 GGGAGGTTATCAAAATTTT
578 CAAAATGTGA
Statistics
Matches: 205, Mismatches: 61, Indels: 41
0.67 0.20 0.13
Matches are distributed among these distances:
19 2 0.01
20 15 0.07
21 31 0.15
22 117 0.57
23 7 0.03
24 11 0.05
25 8 0.04
26 2 0.01
27 7 0.03
28 5 0.02
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
GGGAGGTTATCAAAATTTTATA
Found at i:402 original size:22 final size:21
Alignment explanation
Indices: 367--518 Score: 98
Period size: 22 Copynumber: 6.9 Consensus size: 21
357 TGATAGAAGG
*
367 TTATCAAATCTCATAGAGTGA
1 TTATCAAATTTCATAGAGTGA
388 TTATCGAAATTTCATAGAGATCGGA
1 TTATC-AAATTTCATAGAG-T--GA
**
413 TTATCAAAATTT-ATAGAAAGA
1 TTATC-AAATTTCATAGAGTGA
*
434 TTATCAAATTTTCATAGTGTTG-
1 TTATCAAA-TTTCATAGAG-TGA
*
456 TTATCAAAATTTCAAAACGAG-G-
1 TTATC-AAATTTC-ATA-GAGTGA
*
478 TTATCAAAATTACATA-ATGTGA
1 TTATC-AAATTTCATAGA-GTGA
500 TTATCAGAATTTCATAGAG
1 TTATCA-AATTTCATAGAG
519 GAGTCAACAA
Statistics
Matches: 104, Mismatches: 12, Indels: 29
0.72 0.08 0.20
Matches are distributed among these distances:
19 1 0.01
20 4 0.04
21 19 0.18
22 52 0.50
23 8 0.08
24 7 0.07
25 13 0.12
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (21 bp):
TTATCAAATTTCATAGAGTGA
Found at i:504 original size:44 final size:44
Alignment explanation
Indices: 411--603 Score: 164
Period size: 44 Copynumber: 4.4 Consensus size: 44
401 ATAGAGATCG
* * *
411 GATTATCAAAATTT-ATAGAA-AGATTATCAAATTTTCATAGTGTT
1 GATTATCAAAATTTCATA-AAGAGGTTATCAAAATTTCATAATG-T
*
455 G-TTATCAAAATTTCA-AAACGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAAA-GAGGTTATCAAAATTTCATAATGT
* * * * * * *
498 GATTATCAGAATTTCATAGAG-GAGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCATAAAGAG-GTTATCAAAATTTCATAATGT
** * *
542 GGCTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATGT
586 GATTA-CAAAAATTTCATA
1 GATTATC-AAAATTTCATA
604 GTGGTATTTC
Statistics
Matches: 116, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
42 2 0.02
43 17 0.15
44 94 0.81
45 3 0.03
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATGT
Found at i:579 original size:66 final size:66
Alignment explanation
Indices: 414--579 Score: 178
Period size: 66 Copynumber: 2.5 Consensus size: 66
404 GAGATCGGAT
* ** * *
414 TATCAAAATTT-ATAGAA-AGATTATCAAATTTTCATAGTGTTGTTATCAAAATTTCAAAACGAG
1 TATCAAAATTTCATA-AAGAGATTATCAAATTTTCATAGAGGAGTCAACAAAATTTCAAAACGAG
*
477 GT
65 GC
* * * *
479 TATCAAAATTACATAATGTGATTATCAGAA-TTTCATAGAGGAGTCAACAAAATTTTATAAA-GA
1 TATCAAAATTTCATAAAGAGATTATCA-AATTTTCATAGAGGAGTCAACAAAATTTCA-AAACGA
542 GGC
64 GGC
*
545 TATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
1 TATCAAAATTTCATAAAGAGATTATCAAATTTTCA
580 AAATGTGATT
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
65 13 0.16
66 64 0.78
67 5 0.06
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (66 bp):
TATCAAAATTTCATAAAGAGATTATCAAATTTTCATAGAGGAGTCAACAAAATTTCAAAACGAGG
C
Found at i:723 original size:19 final size:20
Alignment explanation
Indices: 685--733 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
675 TTATGGAGTA
685 ATCAAAATTTCAAAGGAGGAT
1 ATCAAAA-TTCAAAGGAGGAT
*
706 ATCAAAATTC-AGGGAGGAT
1 ATCAAAATTCAAAGGAGGAT
725 ATCAAAATT
1 ATCAAAATT
734 TCATATGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 17 0.63
20 3 0.11
21 7 0.26
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCAAAATTCAAAGGAGGAT
Found at i:752 original size:22 final size:22
Alignment explanation
Indices: 724--1281 Score: 157
Period size: 22 Copynumber: 25.7 Consensus size: 22
714 TCAGGGAGGA
*
724 TATCAAAATTTCATATGAATGT
1 TATCAAAATTTCATATGAAGGT
**
746 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
768 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
790 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
811 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
* *
834 TAACAAAATTTCATAATG-AGAT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
856 TATCAAAAAATCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
878 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
894 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
916 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* *
939 TATCAAAATTTTATAGGAAGAGT
1 TATCAAAATTTCATATGAAG-GT
*
962 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* *
984 TATCACAATTTCATAGTG-TGTGAT
1 TATCAAAATTTCATA-TGAAG-G-T
* * *
1008 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
1030 TA-CTAAGAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
1052 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
**
1074 TATC--AA--T-ATATGTTGGT
1 TATCAAAATTTCATATGAAGGT
* * * **
1091 CATCAACATCTCATAATGTTGGT
1 TATCAAAATTTCAT-ATGAAGGT
*
1114 CATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
1136 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
1158 CT-TTAAAA-TTCCTTTGGGAA-GT
1 -TATCAAAATTTCATAT--GAAGGT
*
1180 TAATC-AAATTTCATATGAAAGT
1 T-ATCAAAATTTCATATGAAGGT
** **
1202 TAGAAAAATTT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
1223 TCTCGAAATTTCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* *
1245 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
1267 TATCAAAATTTCATA
1 TATCAAAATTTCATA
1282 ATGGGATCAT
Statistics
Matches: 401, Mismatches: 86, Indels: 98
0.69 0.15 0.17
Matches are distributed among these distances:
16 11 0.03
17 11 0.03
18 3 0.01
19 1 0.00
20 4 0.01
21 37 0.09
22 233 0.58
23 79 0.20
24 22 0.05
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:779 original size:44 final size:43
Alignment explanation
Indices: 724--998 Score: 195
Period size: 44 Copynumber: 6.3 Consensus size: 43
714 TCAGGGAGGA
* *
724 TATCAAAATTTCATATGAATGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAG-TTAGT
* * **
768 TTTCAAAATTTCACAAGAGGGTTATCAAAATTTCATAG-TATGT
1 TATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTTA-GT
* ** * * *
811 AGATCAAAATTTCAT-AGGGAGATTAACAAAATTTCATAATGAGAT
1 -TATCAAAATTTCATAAGAAAG-TTATCAAAATTTCATAGTTAG-T
** * *
856 TATCAAAAAATCATAAGGAGGTTATCAAAA-TT--T-G-TAGT
1 TATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTTAGT
* * **
894 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTTA-G-T
* * **
939 TATCAAAATTTTATAGGAAGAGTTATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAAGAA-AGTTATCAAAATTTCATAGTTA-GT
*
984 TATCACAATTTCATA
1 TATCAAAATTTCATA
999 GTGTGTGATT
Statistics
Matches: 183, Mismatches: 34, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
38 26 0.14
39 4 0.02
41 2 0.01
42 3 0.02
43 9 0.05
44 80 0.44
45 37 0.20
46 22 0.12
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (43 bp):
TATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTTAGT
Found at i:943 original size:23 final size:23
Alignment explanation
Indices: 891--1020 Score: 124
Period size: 23 Copynumber: 5.7 Consensus size: 23
881 CAAAATTTGT
* * *
891 AGTTATCAAGATTTCATA-AGAA
1 AGTTATCAAAATTTCATAGGGAG
*
913 AGTTATCAAAATTTTATAGGGAG
1 AGTTATCAAAATTTCATAGGGAG
* *
936 -GTTTATCAAAATTTTATAGGAAG
1 AG-TTATCAAAATTTCATAGGGAG
*
959 AGTTATCAAAATTTCATAGCGAG
1 AGTTATCAAAATTTCATAGGGAG
* *
982 -GTTATCACAATTTCATAGTGTGTG
1 AGTTATCAAAATTTCATAG-G-GAG
1006 A-TTATCAAAATTTCA
1 AGTTATCAAAATTTCA
1021 GAGTGTGATT
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
22 34 0.38
23 40 0.44
24 16 0.18
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (23 bp):
AGTTATCAAAATTTCATAGGGAG
Found at i:1020 original size:46 final size:46
Alignment explanation
Indices: 893--999 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 46
883 AAATTTGTAG
* * * *
893 TTATCAAGATTTCATAAGAA-AGTTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGAAGAGTTATCAAAATTTCATAGCGAGGT
*
938 TTATCAAAATTTTATAGGAAGAGTTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTCATAGGAAGAGTTATCAAAATTTCATAGCGAGGT
*
983 TTATCACAATTTCATAG
1 TTATCAAAATTTCATAG
1000 TGTGTGATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 32 0.59
46 22 0.41
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (46 bp):
TTATCAAAATTTCATAGGAAGAGTTATCAAAATTTCATAGCGAGGT
Found at i:1127 original size:23 final size:23
Alignment explanation
Indices: 1083--1127 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1073 TTATCAATAT
*
1083 ATGTTGGTCATCAACATCTCATA
1 ATGTTGGTCATCAAAATCTCATA
*
1106 ATGTTGGTCATCAAAATTTCAT
1 ATGTTGGTCATCAAAATCTCAT
1128 TGGGAAGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (23 bp):
ATGTTGGTCATCAAAATCTCATA
Found at i:10384 original size:49 final size:49
Alignment explanation
Indices: 10312--10410 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
10302 TATTTTGGGA
*
10312 CAAATAAAGTTTTTAGAAGAGAACTTATAATATGGGACAGAGGGAGTAT
1 CAAATAAAGTTTTTAGAAGAGAACTTATAATATGGGACAGAAGGAGTAT
10361 CAAATAAAGTTTTTAGAAGAGAACTTATAATATGGGACAGAAGGAGTAT
1 CAAATAAAGTTTTTAGAAGAGAACTTATAATATGGGACAGAAGGAGTAT
10410 C
1 C
10411 TAAGTTCCCC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.26
Consensus pattern (49 bp):
CAAATAAAGTTTTTAGAAGAGAACTTATAATATGGGACAGAAGGAGTAT
Found at i:11976 original size:32 final size:32
Alignment explanation
Indices: 11922--12050 Score: 136
Period size: 32 Copynumber: 4.0 Consensus size: 32
11912 TACCGTGGCG
* * *
11922 AAGCCGCCTCACTTGGGAGGCTTCGCCACGGC
1 AAGCCGCCCCACTGGGGCGGCTTCGCCACGGC
*
11954 AAGCCGCCCTCA-TGGGGCGGCTTCACCACGGC
1 AAGCCGCCC-CACTGGGGCGGCTTCGCCACGGC
* * **
11986 AAGCCGCCCCA-TGAGGGCGGCTTCCCCATGAA
1 AAGCCGCCCCACTG-GGGCGGCTTCGCCACGGC
*
12018 AAGGCCGCCCCACTGGGGCGGCTTAGCCACGGC
1 AA-GCCGCCCCACTGGGGCGGCTTCGCCACGGC
12051 TCGGCTATTT
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
31 4 0.05
32 50 0.62
33 24 0.30
34 2 0.03
ACGTcount: A:0.17, C:0.39, G:0.32, T:0.12
Consensus pattern (32 bp):
AAGCCGCCCCACTGGGGCGGCTTCGCCACGGC
Found at i:13256 original size:34 final size:34
Alignment explanation
Indices: 13192--13257 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
13182 TGGTTAATTA
** * **
13192 AGTTCCTAAGGTTGTAAAATCGGCTTAAATCATC
1 AGTTCCTAACATTGCAAAATCGGCACAAATCATC
13226 AGTTCCTAACATTGCAAAATCGGCACAAATCA
1 AGTTCCTAACATTGCAAAATCGGCACAAATCA
13258 GTCCCTAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (34 bp):
AGTTCCTAACATTGCAAAATCGGCACAAATCATC
Found at i:14230 original size:29 final size:31
Alignment explanation
Indices: 14151--14231 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 31
14141 TTCCATCCAA
14151 AAGGGCTAATTTGTCCATTTTAAACACATTC
1 AAGGGCTAATTTGTCCATTTTAAACACATTC
* * * *
14182 AAGTGTG-TAA-TTGGCAATTTTGAA-A-GTTC
1 AAG-G-GCTAATTTGTCCATTTTAAACACATTC
14211 AAGGGCTAATTTGTCCATTTT
1 AAGGGCTAATTTGTCCATTTT
14232 TTAAAAGTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
27 1 0.03
28 4 0.10
29 15 0.38
30 1 0.03
31 14 0.35
32 4 0.10
33 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (31 bp):
AAGGGCTAATTTGTCCATTTTAAACACATTC
Found at i:14444 original size:64 final size:63
Alignment explanation
Indices: 14278--14472 Score: 207
Period size: 63 Copynumber: 3.1 Consensus size: 63
14268 TGATATTAAT
* * * * * * *
14278 TTGATTCAAGCGTA-TTGACTATTTGATCTTGAATTGATAACTTGAAAACCTGAATTTCATAAC
1 TTGATTCAAG-GGACTTGACGACTTGATCTTGAATTGATAACTTGGAATCTTGAATTTGATAAC
* * * *
14341 TTGATTCGAGGGTCTTGACGACTTAAACTTGAATTGATAACTTGGAATCTTGAATTTGATAAC
1 TTGATTCAAGGGACTTGACGACTTGATCTTGAATTGATAACTTGGAATCTTGAATTTGATAAC
* * *
14404 TTAGATTCAAGGGACATT-TCGACTTGATCTTGAATCGATAACTT-GAGATCTTGAATTCGATAA
1 TT-GATTCAAGGGAC-TTGACGACTTGATCTTGAATTGATAACTTGGA-ATCTTGAATTTGATAA
14467 C
63 C
14468 TTGAT
1 TTGAT
14473 ATTTTGATAA
Statistics
Matches: 110, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.01
63 57 0.52
64 50 0.45
65 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (63 bp):
TTGATTCAAGGGACTTGACGACTTGATCTTGAATTGATAACTTGGAATCTTGAATTTGATAAC
Found at i:14455 original size:21 final size:22
Alignment explanation
Indices: 14429--14471 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
14419 ATTTCGACTT
14429 GATCTTGAA-TCGATAACTTGA
1 GATCTTGAATTCGATAACTTGA
14450 GATCTTGAATTCGATAACTTGA
1 GATCTTGAATTCGATAACTTGA
14472 TATTTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (22 bp):
GATCTTGAATTCGATAACTTGA
Found at i:16954 original size:38 final size:36
Alignment explanation
Indices: 16863--16993 Score: 119
Period size: 35 Copynumber: 3.6 Consensus size: 36
16853 ATTGATTTAC
16863 TTAATTTACCAGTTTACTTAATTGCACCGAATTAAA
1 TTAATTTACCAGTTTACTTAATTGCACCGAATTAAA
* * *
16899 TTAA-TTACCAAACTACTTAACCTAATT--ACCGAATT-AT
1 TTAATTTACC--AGT--TT-ACTTAATTGCACCGAATTAAA
*
16936 TTAATTTACCAGTTTACTTAATTGCACCGAATTAAG
1 TTAATTTACCAGTTTACTTAATTGCACCGAATTAAA
* * *
16972 TTGA-TTATCAGGTTACTTAATT
1 TTAATTTACCAGTTTACTTAATT
16994 TAATTACCAC
Statistics
Matches: 77, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
33 7 0.09
34 2 0.03
35 29 0.38
36 10 0.13
37 7 0.09
38 13 0.17
39 2 0.03
40 7 0.09
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (36 bp):
TTAATTTACCAGTTTACTTAATTGCACCGAATTAAA
Found at i:16998 original size:57 final size:57
Alignment explanation
Indices: 16934--17050 Score: 182
Period size: 57 Copynumber: 2.1 Consensus size: 57
16924 TTACCGAATT
* * **
16934 ATTTAATTTACCAGTTTAC-TTAATTGCACCGAATTAAGTTGATTATCAGGTTACTTA
1 ATTTAA-TTACCACTTTACTTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTA
16991 ATTTAATTACCACTTTACTTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTA
1 ATTTAATTACCACTTTACTTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTA
17048 ATT
1 ATT
17051 ACACCGAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 11 0.20
57 44 0.80
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (57 bp):
ATTTAATTACCACTTTACTTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTA
Found at i:17056 original size:35 final size:35
Alignment explanation
Indices: 16996--17273 Score: 296
Period size: 35 Copynumber: 7.9 Consensus size: 35
16986 ACTTAATTTA
** *
16996 ATTACCACTTTACTTTAATTGCACCGAATTAAGTTG
1 ATTACCAAATTAC-TTAATTACACCGAATTAAGTTG
17032 ATTACCAAATTACTTAATTACACCGAATTAAGTTG
1 ATTACCAAATTACTTAATTACACCGAATTAAGTTG
*
17067 ATTACCAAATTACTTAATTGCACCGAATTAAGTTG
1 ATTACCAAATTACTTAATTACACCGAATTAAGTTG
* * * *
17102 ATTACCAAATTACTTAATTTAATTACCAAATT-ACTTA
1 ATTACCAAATTACTTAA-TT-A-CACCGAATTAAGTTG
* * * * *
17139 ACTGCACCAAATTAAGTTGATT--ACCAAATT-ACTT-
1 A-T-TACCAAATT-ACTTAATTACACCGAATTAAGTTG
17173 ATTTACCAAATTACTTAATTACACCGAATTAAGTTG
1 A-TTACCAAATTACTTAATTACACCGAATTAAGTTG
* * *
17209 TTTACTAAATTACTTAATTACACTGAATTAAGTTG
1 ATTACCAAATTACTTAATTACACCGAATTAAGTTG
*
17244 ATTACCAAATTACTTACTTACACCGAATTA
1 ATTACCAAATTACTTAATTACACCGAATTA
17274 CTTAATTACA
Statistics
Matches: 207, Mismatches: 25, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
32 6 0.03
33 8 0.04
34 9 0.04
35 145 0.70
36 13 0.06
37 4 0.02
38 8 0.04
39 10 0.05
40 4 0.02
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.37
Consensus pattern (35 bp):
ATTACCAAATTACTTAATTACACCGAATTAAGTTG
Found at i:17130 original size:56 final size:55
Alignment explanation
Indices: 17067--17227 Score: 240
Period size: 56 Copynumber: 3.0 Consensus size: 55
17057 AATTAAGTTG
17067 ATTACCAAATTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTT
1 ATTACCAAATTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTT
* *
17122 AATTACCAAATTACTTAACTGCACCAAATTAAGTTGATTACCAAATTACTT-A--T
1 -ATTACCAAATTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTT
* * *
17175 -TTACCAAATTACTTAATTACACCGAATTAAGTTGTTTACTAAATTACTTAATT
1 ATTACCAAATTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATT
17228 ACACTGAATT
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
51 44 0.46
52 1 0.01
53 1 0.01
55 1 0.01
56 48 0.51
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (55 bp):
ATTACCAAATTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTT
Found at i:17273 original size:53 final size:53
Alignment explanation
Indices: 17216--17326 Score: 195
Period size: 53 Copynumber: 2.1 Consensus size: 53
17206 TTGTTTACTA
* *
17216 AATTACTTAATTACACTGAATTAAGTTGATTACCAAATTACTTACTTACACCG
1 AATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCG
*
17269 AATTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATTACACCG
1 AATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCG
17322 AATTA
1 AATTA
17327 AGTTGATTAC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (53 bp):
AATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCG
Found at i:17274 original size:18 final size:18
Alignment explanation
Indices: 17039--17379 Score: 167
Period size: 18 Copynumber: 19.3 Consensus size: 18
17029 TTGATTACCA
17039 AATTACTTAATTACACCG
1 AATTACTTAATTACACCG
* * *
17057 AATTAAGTTGATT--ACCA
1 AATT-ACTTAATTACACCG
*
17074 AATTACTTAATTGCACCG
1 AATTACTTAATTACACCG
* * *
17092 AATTAAGTTGATT--ACCA
1 AATT-ACTTAATTACACCG
* *
17109 AATTACTTAATTTAATTACCA
1 AATTACTTAA-TT-A-CACCG
* * *
17130 AATTACTTAACTGCACCA
1 AATTACTTAATTACACCG
* * *
17148 AATTAAGTTGATT--ACCA
1 AATT-ACTTAATTACACCG
* *
17165 AATTACTT-ATT-TACCA
1 AATTACTTAATTACACCG
17181 AATTACTTAATTACACCG
1 AATTACTTAATTACACCG
* **
17199 AATTAAGTTGTTTACTA---
1 AATT-ACTTAATTAC-ACCG
*
17216 AATTACTTAATTACACTG
1 AATTACTTAATTACACCG
* * *
17234 AATTAAGTTGATT--ACCA
1 AATT-ACTTAATTACACCG
*
17251 AATTACTTACTTACACCG
1 AATTACTTAATTACACCG
17269 AATTACTTAATTACACCG
1 AATTACTTAATTACACCG
* * * *
17287 AATTAAGTT-GTT-TACCA
1 AATT-ACTTAATTACACCG
17304 AATTACTTAATTACACCG
1 AATTACTTAATTACACCG
* * *
17322 AATTAAGTTGATT--ACCA
1 AATT-ACTTAATTACACCG
*
17339 AATTACTTACTTACACCG
1 AATTACTTAATTACACCG
17357 AATTACTTAATTACACCG
1 AATTACTTAATTACACCG
17375 AATTA
1 AATTA
17380 AGTTGTTTAC
Statistics
Matches: 245, Mismatches: 51, Indels: 54
0.70 0.15 0.15
Matches are distributed among these distances:
15 4 0.02
16 45 0.18
17 53 0.22
18 88 0.36
19 39 0.16
20 2 0.01
21 14 0.06
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (18 bp):
AATTACTTAATTACACCG
Found at i:17307 original size:88 final size:88
Alignment explanation
Indices: 16940--17401 Score: 554
Period size: 88 Copynumber: 5.2 Consensus size: 88
16930 AATTATTTAA
** * * ** * *
16940 TTTACCAGTTTACTTAATTGCACCGAATTAAGTTGATTATCAGGTTACTTAATTTAATTACC-AC
1 TTTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTT-ACTT-A-CACCGA-
* *
17004 TTTACTTTAATTGCACCGAATTAAGTTG
62 ATTAC-TTAATTACACCGAATTAAGTTG
* * *
17032 ATTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTGCACCGAATTA
1 TTTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTACTTACACCGAATT-
* * ** * *
17097 AGTTGATTAC-CAAATTACTTAATTTA
65 ACTTAATTACACCGA--A-TTAAGTTG
* * * * * *
17123 ATTACCAAATTACTTAACTGCACCAAATTAAGTTGATTACCAAATTACTTA-TT-TACCAAATTA
1 TTTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTACTTACACCGAATTA
17186 CTTAATTACACCGAATTAAGTTG
66 CTTAATTACACCGAATTAAGTTG
* *
17209 TTTACTAAATTACTTAATTACACTGAATTAAGTTGATTACCAAATTACTTACTTACACCGAATTA
1 TTTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTACTTACACCGAATTA
17274 CTTAATTACACCGAATTAAGTTG
66 CTTAATTACACCGAATTAAGTTG
17297 TTTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTACTTACACCGAATTA
1 TTTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTACTTACACCGAATTA
17362 CTTAATTACACCGAATTAAGTTG
66 CTTAATTACACCGAATTAAGTTG
* *
17385 TTTACCAACTTATTTAA
1 TTTACCAAATTACTTAA
17402 CTTAATTACC
Statistics
Matches: 321, Mismatches: 41, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
86 51 0.16
87 3 0.01
88 142 0.44
89 20 0.06
90 5 0.02
91 57 0.18
92 43 0.13
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (88 bp):
TTTACCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTACTTACACCGAATTA
CTTAATTACACCGAATTAAGTTG
Found at i:17308 original size:35 final size:35
Alignment explanation
Indices: 17269--17361 Score: 168
Period size: 35 Copynumber: 2.7 Consensus size: 35
17259 ACTTACACCG
*
17269 AATTACTTAATTACACCGAATTAAGTTGTTTACCA
1 AATTACTTAATTACACCGAATTAAGTTGATTACCA
17304 AATTACTTAATTACACCGAATTAAGTTGATTACCA
1 AATTACTTAATTACACCGAATTAAGTTGATTACCA
*
17339 AATTACTTACTTACACCGAATTA
1 AATTACTTAATTACACCGAATTA
17362 CTTAATTACA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (35 bp):
AATTACTTAATTACACCGAATTAAGTTGATTACCA
Found at i:18260 original size:51 final size:50
Alignment explanation
Indices: 18171--18460 Score: 305
Period size: 51 Copynumber: 5.7 Consensus size: 50
18161 AACTAATCAA
** * * * * *
18171 TTTATTTACTAATGGCCTAAAAGTTCAAACTTTAATTCAAATGTGACAT-
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGACATC
* *
18220 TTTATTTACCAATTACTTAAAAAAATTCAATCTTTTATTCAAAGG-GTATATC
1 TTTATTTACTAATTACTT--AAAAATTCAATCTTTTATTCAAAGGTG-ACATC
* ** *
18272 CTTATTTACTAATTACTTAAAAATTCAATCTTTTGCTCAAAGGTGACATT
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGACATC
* * * *
18322 TTTACTTACTAATTACTAAAAAAAATTCAATCTTTTAGTCAAAAGGTTACATC
1 TTTATTTACTAATTACT--TAAAAATTCAATCTTTTATTC-AAAGGTGACATC
** * *
18375 TTTATAAACTAATTACTTAAAAGTTCAATCTTTTATTCAAAAGGTTACATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTC-AAAGGTGACATC
*
18426 TTTATTTACTAATTACTTAAATATTCAATCTTTTA
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTA
18461 ACATAAAGAT
Statistics
Matches: 201, Mismatches: 32, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
49 14 0.07
50 42 0.21
51 87 0.43
52 34 0.17
53 24 0.12
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (50 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGACATC
Found at i:21718 original size:38 final size:38
Alignment explanation
Indices: 21667--21746 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
21657 GCTGAGTTGA
21667 TCTTTACTTGAGCTTGTGCTTGGATGTTGAAAAGCAAG
1 TCTTTACTTGAGCTTGTGCTTGGATGTTGAAAAGCAAG
21705 TCTTTACTTGAGCTTGTGCTTGGATGTTGAAAAGCAAG
1 TCTTTACTTGAGCTTGTGCTTGGATGTTGAAAAGCAAG
21743 TCTT
1 TCTT
21747 GTTTGACCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.39
Consensus pattern (38 bp):
TCTTTACTTGAGCTTGTGCTTGGATGTTGAAAAGCAAG
Found at i:23002 original size:29 final size:29
Alignment explanation
Indices: 22927--23013 Score: 126
Period size: 27 Copynumber: 3.1 Consensus size: 29
22917 ACCCAAGACA
*
22927 CCCCTAAATGCA-AAAATGACCTAAATG-
1 CCCCTAAATGCAGAAAATGACCAAAATGC
* *
22954 CCCCTATATG-TGAAAATGACCAAAATGC
1 CCCCTAAATGCAGAAAATGACCAAAATGC
22982 CCCCTAAATGCAGAAAATGACCAAAATGC
1 CCCCTAAATGCAGAAAATGACCAAAATGC
23011 CCC
1 CCC
23014 TGGACGACCC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
27 23 0.44
28 9 0.17
29 20 0.38
ACGTcount: A:0.41, C:0.29, G:0.13, T:0.17
Consensus pattern (29 bp):
CCCCTAAATGCAGAAAATGACCAAAATGC
Found at i:23955 original size:23 final size:24
Alignment explanation
Indices: 23912--23957 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
23902 TTTAGAGAAA
* *
23912 GAAAGAAGAAGAAGAAGAAAATAG
1 GAAAAAAGAAGAAGAAAAAAATAG
23936 GAAAAAAGAA-AAGAAAAAAATA
1 GAAAAAAGAAGAAGAAAAAAATA
23958 AAATAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (24 bp):
GAAAAAAGAAGAAGAAAAAAATAG
Found at i:23965 original size:23 final size:24
Alignment explanation
Indices: 23917--23965 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
23907 AGAAAGAAAG
* *
23917 AAGAAGAAGAAGAAAATAGGAAAA
1 AAGAAGAAGAAAAAAATAGAAAAA
23941 AAGAA-AAGAAAAAAATA-AAATAA
1 AAGAAGAAGAAAAAAATAGAAA-AA
23964 AA
1 AA
23966 TACTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 2 0.09
23 15 0.68
24 5 0.23
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (24 bp):
AAGAAGAAGAAAAAAATAGAAAAA
Found at i:26240 original size:12 final size:12
Alignment explanation
Indices: 26208--26246 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
26198 ATGGAATTAA
26208 ATATCCGTCG--
1 ATATCCGTCGAT
26218 ATAT-C-TCGAT
1 ATATCCGTCGAT
26228 ATATCCGTCGAT
1 ATATCCGTCGAT
26240 ATATCCG
1 ATATCCG
26247 ATATCTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 1 0.04
10 8 0.32
11 1 0.04
12 12 0.48
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:26370 original size:10 final size:10
Alignment explanation
Indices: 26357--26392 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
26347 ACATCTCGAT
26357 ATATCCGTAA
1 ATATCCGTAA
*
26367 ATATCCATAA
1 ATATCCGTAA
26377 ATATCCGTAA
1 ATATCCGTAA
26387 ATATCC
1 ATATCC
26393 ATATTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:26380 original size:20 final size:20
Alignment explanation
Indices: 26357--26395 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
26347 ACATCTCGAT
26357 ATATCCGTAAATATCCATAA
1 ATATCCGTAAATATCCATAA
26377 ATATCCGTAAATATCCATA
1 ATATCCGTAAATATCCATA
26396 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
ATATCCGTAAATATCCATAA
Found at i:27430 original size:13 final size:12
Alignment explanation
Indices: 27396--27438 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
27386 CATCGATATC
*
27396 TCGATATATTCG
1 TCGATATATCCG
27408 TCGATATATCCG
1 TCGATATATCCG
*
27420 TTCGATGTATCCG
1 -TCGATATATCCG
27433 TCGATA
1 TCGATA
27439 CCTGAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:31500 original size:15 final size:16
Alignment explanation
Indices: 31477--31512 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
31467 TTGGAAATGG
*
31477 TAATTATAAGAAAT-A
1 TAATAATAAGAAATAA
31492 TAATAATAAGAAATAA
1 TAATAATAAGAAATAA
31508 TAATA
1 TAATA
31513 GGAGAAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
TAATAATAAGAAATAA
Found at i:32832 original size:475 final size:464
Alignment explanation
Indices: 31935--32832 Score: 1173
Period size: 475 Copynumber: 1.9 Consensus size: 464
31925 AATGCTTTCG
* * * * *
31935 AAATTTTGTGGTTTTGATTGCCAGTCAATTTAATATCGTATAATTTTTTGTCCACATATCCGATT
1 AAATTTTGTCGTTTCGATTGCCAGTCAATTTAATACCATATAATTTTTTGTCCACATATCCAATT
* * * * * *
32000 GAAGTTATTGAAGTGTCAGTTAAAAGGTTATTGCATGATTTACGACTTTCATGAAGGACCCGAAA
66 AAAGTTATTCAAGTGTCAGTTAAAAGGATACTGCATGATCTACGACTTTCATGAAGAACCCGAAA
* * * *
32065 GTTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATCTCCA
131 ATTAAATTTGATCCACGAGTTTCATAAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATATCCA
* ** *
32130 TTAACAAACATTTTCTTATTTGAATTATTTATCAAATGACCTTCATATTTTTCTCTACTTAGTTC
196 TTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCCCCATATTTTTATCTACTTAGTTC
* * *
32195 TTTACAAATTCTATCTTAATCTAACGGTTTAGATTTATTTTTTTATTCTCTGTTCTATTTGTCCG
261 TTTACAAATTCTATCTTAATCTAACGGCTTACATTTATTTTTTTATTCTCTGTTCTATTTGTCCA
* * * *
32260 ATTAAGTTGATTTATGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTCCATGAAGGATTCA
326 ATTAAGGTAATTTATGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTCCATGAAAGACTCA
* *
32325 AAAGCAAATTTTTATGTTTTAATTCAAAAAAATACTTCCTAAATTTGGTCGTTTCGAACTGCCAA
391 AAAGCAAATTTTCATGTTTCAATTCAAAAAAATACTTCCTAAATTTGGTCGTTTCGAACTGCCAA
32390 AAGAAAAAA
456 AAGAAAAAA
** * *
32399 AAATTTTGGTCGTTTCGATTGTTAGTCTATTTAATACCATATAA-TTTTTGATCCACATGTCCAA
1 AAATTTT-GTCGTTTCGATTGCCAGTCAATTTAATACCATATAATTTTTTG-TCCACATATCCAA
* *
32463 TTAAAGTTATTCAAGTGTCAGTTAAAAGGATACTGTATGATCTACGACTTTCATGAAGAAGCCGA
64 TTAAAGTTATTCAAGTGTCAGTTAAAAGGATACTGCATGATCTACGACTTTCATGAAGAACCCGA
*
32528 AAATT-AATTTGATCCACGAGTTTCATAAAGGGTTCAAAAGGGAA-TTTTATGTTTCAAGATATC
129 AAATTAAATTTGATCCACGAGTTTCATAAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATATC
* *
32591 CATTAAGAAATATTTTCTTATTTGAATTAGTTATCAAATGACCCCCATACTTTTCTATTTTATGC
194 CATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCCCCATA------T-TTTTAT-C
* *
32656 TACTTAG-TCATTTACAAATTTTATCTTATTCGATTTAAC-GCTT-CATTT-TTTTTTTAATTTT
251 TACTTAGTTC-TTTACAAATTCTATCTTA----ATCTAACGGCTTACATTTATTTTTTT-A--TT
* *
32717 CTTTGTTCTATTTGTCCAATTAAGGTAATTTA-GATGTCTATTAAAAGGTAATTTTATGATCTAC
308 CTCTGTTCTATTTGTCCAATTAAGGTAATTTATG-TGTCTATTAAAAGGTAATTTCATGATCTAC
* * *
32781 AACTTTCATGAAAGACTCAAAAGCTAATTTTCATGTTTCAATTCTAAAAAAT
372 AACTTCCATGAAAGACTCAAAAGCAAATTTTCATGTTTCAATTCAAAAAAAT
32833 GTTTTGAAAT
Statistics
Matches: 371, Mismatches: 44, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
463 61 0.16
464 50 0.13
465 101 0.27
469 1 0.00
470 7 0.02
471 25 0.07
472 7 0.02
473 5 0.01
474 4 0.01
475 110 0.30
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (464 bp):
AAATTTTGTCGTTTCGATTGCCAGTCAATTTAATACCATATAATTTTTTGTCCACATATCCAATT
AAAGTTATTCAAGTGTCAGTTAAAAGGATACTGCATGATCTACGACTTTCATGAAGAACCCGAAA
ATTAAATTTGATCCACGAGTTTCATAAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATATCCA
TTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACCCCCATATTTTTATCTACTTAGTTC
TTTACAAATTCTATCTTAATCTAACGGCTTACATTTATTTTTTTATTCTCTGTTCTATTTGTCCA
ATTAAGGTAATTTATGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTCCATGAAAGACTCA
AAAGCAAATTTTCATGTTTCAATTCAAAAAAATACTTCCTAAATTTGGTCGTTTCGAACTGCCAA
AAGAAAAAA
Found at i:36878 original size:21 final size:22
Alignment explanation
Indices: 36838--36878 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
36828 TAACAGCCAT
* *
36838 GGCAGAGATATCTGAAGCAGGA
1 GGCAGAGATAACTAAAGCAGGA
36860 GGCAGAG-TAACTAAAGCAG
1 GGCAGAGATAACTAAAGCAG
36879 AACGCTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.15, G:0.34, T:0.12
Consensus pattern (22 bp):
GGCAGAGATAACTAAAGCAGGA
Found at i:41702 original size:114 final size:114
Alignment explanation
Indices: 41502--41731 Score: 460
Period size: 114 Copynumber: 2.0 Consensus size: 114
41492 AGAGGCCACC
41502 ATTCTAGGCATGGAAATCAATTAAACTAGGAAAAAACAGAATCTCTTCTCAATCCAAATCGAGTT
1 ATTCTAGGCATGGAAATCAATTAAACTAGGAAAAAACAGAATCTCTTCTCAATCCAAATCGAGTT
41567 AGTAGGGGAACATAATTCAATCGCGAAGTCTTGAAATAGAACAAACTCA
66 AGTAGGGGAACATAATTCAATCGCGAAGTCTTGAAATAGAACAAACTCA
41616 ATTCTAGGCATGGAAATCAATTAAACTAGGAAAAAACAGAATCTCTTCTCAATCCAAATCGAGTT
1 ATTCTAGGCATGGAAATCAATTAAACTAGGAAAAAACAGAATCTCTTCTCAATCCAAATCGAGTT
41681 AGTAGGGGAACATAATTCAATCGCGAAGTCTTGAAATAGAACAAACTCA
66 AGTAGGGGAACATAATTCAATCGCGAAGTCTTGAAATAGAACAAACTCA
41730 AT
1 AT
41732 GAACAATCTC
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 116 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (114 bp):
ATTCTAGGCATGGAAATCAATTAAACTAGGAAAAAACAGAATCTCTTCTCAATCCAAATCGAGTT
AGTAGGGGAACATAATTCAATCGCGAAGTCTTGAAATAGAACAAACTCA
Found at i:43287 original size:26 final size:26
Alignment explanation
Indices: 43258--43310 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
43248 AGGATTGAAT
* *
43258 TCACCTATTCAATTTTGGGGAAAATA
1 TCACCCATTCAATTTTGGGAAAAATA
43284 TCACCCATTCAATTTTGGGAAAAATA
1 TCACCCATTCAATTTTGGGAAAAATA
43310 T
1 T
43311 GTGTTTATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (26 bp):
TCACCCATTCAATTTTGGGAAAAATA
Found at i:46279 original size:16 final size:16
Alignment explanation
Indices: 46258--46290 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
46248 CTCTACAAAG
*
46258 GCAGAAAAGCTCTGAA
1 GCAGAAAAGCCCTGAA
46274 GCAGAAAAGCCCTGAA
1 GCAGAAAAGCCCTGAA
46290 G
1 G
46291 AATCAAGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.27, T:0.09
Consensus pattern (16 bp):
GCAGAAAAGCCCTGAA
Found at i:49230 original size:39 final size:39
Alignment explanation
Indices: 49173--49313 Score: 158
Period size: 39 Copynumber: 3.6 Consensus size: 39
49163 CGCTAGGACG
* * *
49173 AGCGAATAATAAATTTTGATCGCTTGAGCCTTGGTCAAA
1 AGCGAATAATAAAATTTGATCGCTTGGGTCTTGGTCAAA
* **
49212 AGCGAATGATAAAATTTGATCGCTTGGGTCTTGGTCCCA
1 AGCGAATAATAAAATTTGATCGCTTGGGTCTTGGTCAAA
* * ** *
49251 AGCGAATGATAAAATTTGGTCATTTGGGTCTTGATCAAA
1 AGCGAATAATAAAATTTGATCGCTTGGGTCTTGGTCAAA
* *
49290 ACCGAATAAT-AAATTTGGTCGCTT
1 AGCGAATAATAAAATTTGATCGCTT
49314 TGTTATGAGC
Statistics
Matches: 86, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
38 12 0.14
39 74 0.86
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (39 bp):
AGCGAATAATAAAATTTGATCGCTTGGGTCTTGGTCAAA
Found at i:51163 original size:62 final size:58
Alignment explanation
Indices: 51065--51184 Score: 177
Period size: 62 Copynumber: 2.0 Consensus size: 58
51055 CCCTCGAATG
* * *
51065 AAATCAAACTCTCAAGTCATCAATTCAAGATCAAGTCATTCGACTCTTGAATCAAATC
1 AAATCAAACTCTCAAATCATCAATTCAAGATCAAGTCATTCGACCCTTGAAGCAAATC
51123 AAATCAAACTCTCACATTATCATCAAGTTCAAGATCAAGTCATTCGACCCTTGAAGCAAATC
1 AAATCAAACTCTCA-A--ATCATCAA-TTCAAGATCAAGTCATTCGACCCTTGAAGCAAATC
51185 TTGAAGCATA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
58 14 0.25
59 1 0.02
61 7 0.13
62 33 0.60
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (58 bp):
AAATCAAACTCTCAAATCATCAATTCAAGATCAAGTCATTCGACCCTTGAAGCAAATC
Done.