Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013277.1 Corchorus capsularis cultivar CVL-1 contig13298, 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: 48093
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:90 original size:50 final size:50
Alignment explanation
Indices: 8--400 Score: 520
Period size: 50 Copynumber: 7.9 Consensus size: 50
1 TTTTGTT
*
8 AAACAAAGGAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAAC
1 AAACAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAAC
* * * ** * *
58 AAACGAAGAGAACAGTGACCTTTTGACTGGGAAGGGGCATTTGGGGAAAC
1 AAACAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAAC
108 AAA-ATAGAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAAC
1 AAACA-A-AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAAC
* *
159 AAACAAAGAGAACAGGGACCTTCCGACCGGGAAGGGGAATTTTGGGAAAC
1 AAACAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAAC
* * * * *
209 AAATAGAGAAAATAGGGACCTTCCAACCAGGAAGGGGCATTTT-GGAAAC
1 AAACAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAAC
*
258 AAACAAAGAAAATAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAAC
1 AAACAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAAC
* * * * * * * *
308 AAATATAGAAAACGGGGACCTTTCAACCAGGAAGGGGTATTTTAGGAAAC
1 AAACAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAAC
* *
358 AAACAAAGAAAACAGGGACCTTACGACCAGGAAGGGGCATTTT
1 AAACAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTT
401 TTGAAAACCT
Statistics
Matches: 296, Mismatches: 43, Indels: 8
0.85 0.12 0.02
Matches are distributed among these distances:
49 45 0.15
50 208 0.70
51 42 0.14
52 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.15
Consensus pattern (50 bp):
AAACAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAAC
Found at i:341 original size:149 final size:150
Alignment explanation
Indices: 8--400 Score: 493
Period size: 149 Copynumber: 2.6 Consensus size: 150
1 TTTTGTT
* * * * * * *
8 AAACAAAGGAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACGAAGAGAACAG
1 AAACAAAGAAAACAGGGACCTTCCAACCAGGAAGGGGAATTTTAGGAAACAAACAAAGAAAACAG
* *** ** *
73 TGACCTTTTGACTGGGAAGGGGCATTTGGGGAAACAAAATAGAGAAAACAGGGACCTTCCGACCG
66 GGACCTTACAACCAGGAAGGGGCATTT-TGGAAACAAAATAGAGAAAACAGGGACCTTCCGACCG
138 GGAAGGGGCATTTTGGGAAAC
130 GGAAGGGGCATTTTGGGAAAC
* * * * * * *
159 AAACAAAGAGAACAGGGACCTTCCGACCGGGAAGGGGAATTTTGGGAAACAAATAGAGAAAATAG
1 AAACAAAGAAAACAGGGACCTTCCAACCAGGAAGGGGAATTTTAGGAAACAAACAAAGAAAACAG
* *
224 GGACCTTCCAACCAGGAAGGGGCATTTTGGAAACAAACA-A-AGAAAATAGGGACCTTCCGACCG
66 GGACCTTACAACCAGGAAGGGGCATTTTGGAAACAAA-ATAGAGAAAACAGGGACCTTCCGACCG
287 GGAAGGGGCATTTTGGGAAAC
130 GGAAGGGGCATTTTGGGAAAC
* * * * *
308 AAATATAGAAAACGGGGACCTTTCAACCAGGAAGGGGTATTTTAGGAAACAAACAAAGAAAACAG
1 AAACAAAGAAAACAGGGACCTTCCAACCAGGAAGGGGAATTTTAGGAAACAAACAAAGAAAACAG
*
373 GGACCTTACGACCAGGAAGGGGCATTTT
66 GGACCTTACAACCAGGAAGGGGCATTTT
401 TTGAAAACCT
Statistics
Matches: 211, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
149 122 0.58
150 10 0.05
151 79 0.37
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.15
Consensus pattern (150 bp):
AAACAAAGAAAACAGGGACCTTCCAACCAGGAAGGGGAATTTTAGGAAACAAACAAAGAAAACAG
GGACCTTACAACCAGGAAGGGGCATTTTGGAAACAAAATAGAGAAAACAGGGACCTTCCGACCGG
GAAGGGGCATTTTGGGAAAC
Found at i:411 original size:32 final size:32
Alignment explanation
Indices: 375--438 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
365 GAAAACAGGG
375 ACCTTACGACCAGGAAGGGGCATTTTTTGAAA
1 ACCTTACGACCAGGAAGGGGCATTTTTTGAAA
* * *
407 ACCTTCCGACCATGATGGGGCATTTTTTGAAA
1 ACCTTACGACCAGGAAGGGGCATTTTTTGAAA
439 CAAACAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (32 bp):
ACCTTACGACCAGGAAGGGGCATTTTTTGAAA
Found at i:621 original size:40 final size:40
Alignment explanation
Indices: 545--621 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
535 TAAAAAAGTA
*
545 AACAACACCTTACGATGGGGAAGGGCAGACTAGGAAACTG
1 AACAACACCTTACGATGGGGAAGGGCAGAATAGGAAACTG
* * *
585 AACAACACCTTCCGGTGGGGAAGGGCAGAATGGGAAA
1 AACAACACCTTACGATGGGGAAGGGCAGAATAGGAAA
622 TGGGAAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.36, C:0.19, G:0.32, T:0.12
Consensus pattern (40 bp):
AACAACACCTTACGATGGGGAAGGGCAGAATAGGAAACTG
Found at i:1277 original size:50 final size:51
Alignment explanation
Indices: 1220--1419 Score: 139
Period size: 51 Copynumber: 4.0 Consensus size: 51
1210 TATTCAAGAG
* * *
1220 TTCATCTTTTAG-CTTAAAGGTTACATCT-TTA-TCACAAATTAATCAAAAGT
1 TTCATCTTTTAGTC-AAAAGATTACAT-TGTTATTCACAAATTAATCAAAACT
* * *
1270 TTGATCTTTTAGTCAAAAGATTTCATTGTTATTTACAAATTAATCAAAACT
1 TTCATCTTTTAGTCAAAAGATTACATTGTTATTCACAAATTAATCAAAACT
* * * * * *
1321 TTCATCTTTTAGTTC-AAAGATCT-CTTTTTTATTTAAAAATTAATCACAA-G
1 TTCATCTTTTAG-TCAAAAGAT-TACATTGTTATTCACAAATTAATCAAAACT
* * *
1371 TTCAATCCTTTAGTCCAAAGATCT-CATTTTTTATT--CAAATTAATCAAAA
1 TTC-ATCTTTTAGTCAAAAGAT-TACA-TTGTTATTCACAAATTAATCAAAA
1420 ATTCAATTTT
Statistics
Matches: 126, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
49 1 0.01
50 40 0.32
51 74 0.59
52 11 0.09
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (51 bp):
TTCATCTTTTAGTCAAAAGATTACATTGTTATTCACAAATTAATCAAAACT
Found at i:1383 original size:102 final size:101
Alignment explanation
Indices: 1255--1440 Score: 250
Period size: 102 Copynumber: 1.8 Consensus size: 101
1245 TCTTTATCAC
** * *
1255 AAATTAATCAAAAGTTTGATCTTTTAGTCAAAAGATTTCATTGTTATT-TACAAATTAATCAAAA
1 AAATTAATCAAAAGTTCAATCCTTTAGTCAAAAGATCTCATT-TT-TTATACAAATTAATCAAAA
*
1319 CTTTC-ATCTTTTAGTTCAAAGATCTCTTTTTTATTTAA
64 -ATTCAATCTTTTAGTTCAAAGATCTCTTTTTTATTTAA
* * *
1357 AAATTAATCACAAGTTCAATCCTTTAGTCCAAAGATCTCATTTTTTATTCAAATTAATCAAAAAT
1 AAATTAATCAAAAGTTCAATCCTTTAGTCAAAAGATCTCATTTTTTATACAAATTAATCAAAAAT
*
1422 TCAATTTTTTAGTTCAAAG
66 TCAATCTTTTAGTTCAAAG
1441 GTTTCATTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
100 5 0.07
101 32 0.44
102 36 0.49
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.42
Consensus pattern (101 bp):
AAATTAATCAAAAGTTCAATCCTTTAGTCAAAAGATCTCATTTTTTATACAAATTAATCAAAAAT
TCAATCTTTTAGTTCAAAGATCTCTTTTTTATTTAA
Found at i:1433 original size:50 final size:50
Alignment explanation
Indices: 1254--1450 Score: 193
Period size: 51 Copynumber: 3.9 Consensus size: 50
1244 ATCTTTATCA
** * * *
1254 CAAATTAATCAAAAGTTTGATCTTTTAGTCAAAAGATTTCATTGTTATT-TA
1 CAAATTAATCAAAAGTTCAATCTTTTAGTCCAAAGATCTCATT-TT-TTATT
* *
1305 CAAATTAATCAAAACTTTC-ATCTTTTAGTTCAAAGATCTC-TTTTTTATTT
1 CAAATTAATCAAAA-GTTCAATCTTTTAGTCCAAAGATCTCATTTTTTA-TT
* * *
1355 AAAAATTAATCACAAGTTCAATCCTTTAGTCCAAAGATCTCATTTTTTATT
1 -CAAATTAATCAAAAGTTCAATCTTTTAGTCCAAAGATCTCATTTTTTATT
* * * * *
1406 CAAATTAATCAAAAATTCAATTTTTTAGTTCAAAGGTTTCATTTT
1 CAAATTAATCAAAAGTTCAATCTTTTAGTCCAAAGATCTCATTTT
1451 GTCATCAACT
Statistics
Matches: 121, Mismatches: 19, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
48 2 0.02
49 2 0.02
50 43 0.36
51 65 0.54
52 9 0.07
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.44
Consensus pattern (50 bp):
CAAATTAATCAAAAGTTCAATCTTTTAGTCCAAAGATCTCATTTTTTATT
Found at i:12418 original size:46 final size:46
Alignment explanation
Indices: 12351--12439 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
12341 ATGGCTGCAA
12351 CCCGACTCCCCCTGGGAACCCATGTAGATGGCTTGTGCGCCCACGG
1 CCCGACTCCCCCTGGGAACCCATGTAGATGGCTTGTGCGCCCACGG
12397 CCCGACTCCCCCTGGGAACCCATGTAGATGGCTTGTGCGCCCA
1 CCCGACTCCCCCTGGGAACCCATGTAGATGGCTTGTGCGCCCA
12440 GGGCATTGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.16, C:0.39, G:0.27, T:0.18
Consensus pattern (46 bp):
CCCGACTCCCCCTGGGAACCCATGTAGATGGCTTGTGCGCCCACGG
Found at i:12535 original size:20 final size:21
Alignment explanation
Indices: 12510--12562 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
12500 ACTAGCGCTG
*
12510 GGCG-CCCATGTGGTTTGCTT
1 GGCGACCCATGTGGTTTGCCT
*
12530 GGCGCCCCATGTGGTTTGCCT
1 GGCGACCCATGTGGTTTGCCT
*
12551 CGCGACCCATGT
1 GGCGACCCATGT
12563 ACTCCAGTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.08, C:0.32, G:0.32, T:0.28
Consensus pattern (21 bp):
GGCGACCCATGTGGTTTGCCT
Found at i:21104 original size:20 final size:21
Alignment explanation
Indices: 21079--21131 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
21069 ACTACCGCTG
*
21079 GGCG-CCCATGTGGTTTGCTT
1 GGCGACCCATGTGGTTTGCCT
*
21099 GGCGCCCCATGTGGTTTGCCT
1 GGCGACCCATGTGGTTTGCCT
*
21120 CGCGACCCATGT
1 GGCGACCCATGT
21132 ACTCCAGTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.08, C:0.32, G:0.32, T:0.28
Consensus pattern (21 bp):
GGCGACCCATGTGGTTTGCCT
Found at i:23617 original size:22 final size:22
Alignment explanation
Indices: 23589--23631 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
23579 TTCTTGCCGA
23589 TAACCTCCCTATGAAATTTTGT
1 TAACCTCCCTATGAAATTTTGT
*
23611 TAACCTCTCTATGAAATTTTG
1 TAACCTCCCTATGAAATTTTG
23632 ATAAACTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (22 bp):
TAACCTCCCTATGAAATTTTGT
Found at i:23647 original size:22 final size:22
Alignment explanation
Indices: 23587--23653 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
23577 CTTTCTTGCC
* *
23587 GATAACCTCCCTATGAAATTTT
1 GATAAACTCTCTATGAAATTTT
* *
23609 GTTAACCTCTCTATGAAATTTT
1 GATAAACTCTCTATGAAATTTT
*
23631 GATAAACT-TCATTTGAAATTTT
1 GATAAACTCTC-TATGAAATTTT
23653 G
1 G
23654 GCAACCGCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 2 0.05
22 37 0.95
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.42
Consensus pattern (22 bp):
GATAAACTCTCTATGAAATTTT
Found at i:23791 original size:29 final size:29
Alignment explanation
Indices: 23732--23795 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
23722 AATTTGCACC
* * **
23732 CCCAAACTTTAATTTTGGCCAATGTGGTA
1 CCCAAACTTCAATTTTGGACAATGTAATA
23761 CCCAAACTATCAATTTTGGACAATG-AATA
1 CCCAAACT-TCAATTTTGGACAATGTAATA
23790 CCCAAA
1 CCCAAA
23796 ATTGGTAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.28
Consensus pattern (29 bp):
CCCAAACTTCAATTTTGGACAATGTAATA
Found at i:24101 original size:22 final size:22
Alignment explanation
Indices: 24076--25002 Score: 200
Period size: 22 Copynumber: 40.3 Consensus size: 22
24066 TCACACTGCT
*
24076 AAATTTTAATAACCTCCTTATG
1 AAATTTTGATAACCTCCTTATG
* * *
24098 AAATTTCGATAACCTCCCTATA
1 AAATTTTGATAACCTCCTTATG
* * *
24120 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCTTATG
* *
24142 AAATTTTGA-CA-C-AC-TATG
1 AAATTTTGATAACCTCCTTATG
* * * * *
24160 AAAATTTAATCACCTTCATATG
1 AAATTTTGATAACCTCCTTATG
*
24182 AAATTTTGACAACCATACAC-TATG
1 AAATTTTGATAACC-T-C-CTTATG
* * * *
24206 AAAATTTAATCACCTCCATATG
1 AAATTTTGATAACCTCCTTATG
*
24228 AAATTTTGACAACCATACAC-TATG
1 AAATTTTGATAACC-T-C-CTTATG
** * * *
24252 AAAACTTAATCACCTCCATATG
1 AAATTTTGATAACCTCCTTATG
* *
24274 AAATTTTGATAACCATAC-TGTG
1 AAATTTTGATAACC-TCCTTATG
* * *
24296 AAATTTTGATAGCCGCCCTATG
1 AAATTTTGATAACCTCCTTATG
* * *
24318 AAATTTTGACAATCGCAT-TTCTACG
1 AAATTTTGATAA-C-C-TCCT-TATG
24343 AAATTTTGATAACCT-CTCTATG
1 AAATTTTGATAACCTCCT-TATG
* * *
24365 AGATTTTGATAACCTCATTATT
1 AAATTTTGATAACCTCCTTATG
*
24387 AAATTTTGATAACCGCAC-TAT-
1 AAATTTTGATAACCTC-CTTATG
* *
24408 ATAATTTTGATAATTAACCTCCCTATT
1 A-AATTTTG---A-TAACCTCCTTATG
*
24435 AAATTTTGATAACCTCTTTATG
1 AAATTTTGATAACCTCCTTATG
* *
24457 AAATTGAGATTTTTATAACATTCC-TATG
1 --A---A-ATTTTGATAAC-CTCCTTATG
* * *
24485 AAATTTTGGTAATCACAC-TATG
1 AAATTTTGATAACCTC-CTTATG
* *
24507 GAATTTTGATAACCACATTCTTACTATG
1 AAATTTTGATAA-C-C--TCCT--TATG
** * *
24535 AAATTTT-ATAATTTTCGTATG
1 AAATTTTGATAACCTCCTTATG
* ****
24556 AAATTTTGACAATCAGAAATCTATG
1 AAATTTTGATAA-C-CTCCT-TATG
24581 AAATTTTGATAAACCACTCC--ATG
1 AAATTTTGAT-AA-C-CTCCTTATG
* *
24604 AGAA-TTTGATAACCTCTTTATA
1 A-AATTTTGATAACCTCCTTATG
* *
24626 AAATTTTGATAACCATAC-TATA
1 AAATTTTGATAACC-TCCTTATG
24648 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCCTTATG
* *
24670 AAATTGAGATTTTTATAACATTCC-TATG
1 --A---A-ATTTTGATAAC-CTCCTTATG
*
24698 AAATTTTGATAACCACACTCTCACTATG
1 AAATTTTGAT-A--AC-CTC-C-TTATG
* *
24726 AAATTTTGAT-A-CTCACACTAAG
1 AAATTTTGATAACCTC-C-TTATG
** * *
24748 AAATTTTGATAATTTTCATATG
1 AAATTTTGATAACCTCCTTATG
* ****
24770 AAATTTTGACAATCAGAAATCTATG
1 AAATTTTGATAA-C-CTCCT-TATG
*
24795 AAATTTTGATAACCATTC-TATG
1 AAATTTTGATAACC-TCCTTATG
* * *
24817 AGAA-TTTAATAACCTCTTTATA
1 A-AATTTTGATAACCTCCTTATG
*
24839 AAATTTTGATAATCTCCTTATG
1 AAATTTTGATAACCTCCTTATG
* *
24861 AAATTGAGATTTTTATAATCTTCC-TATG
1 --A---A-ATTTTGATAA-CCTCCTTATG
* * *
24889 AAGTTTTGGTAACCACAC-TATG
1 AAATTTTGATAACCTC-CTTATG
* *
24911 AAATTTTGATAACCTCCCTACG
1 AAATTTTGATAACCTCCTTATG
* *
24933 AAA-TTTG-GAACCACAC-TATG
1 AAATTTTGATAACCTC-CTTATG
* *
24953 AAAATTTGATAACCTTCTTATG
1 AAATTTTGATAACCTCCTTATG
* * *
24975 AAATTGTGATAACCTCCCTATA
1 AAATTTTGATAACCTCCTTATG
24997 AAATTT
1 AAATTT
25003 AATAACTAGA
Statistics
Matches: 664, Mismatches: 153, Indels: 176
0.67 0.15 0.18
Matches are distributed among these distances:
18 11 0.02
19 3 0.00
20 16 0.02
21 39 0.06
22 369 0.56
23 30 0.05
24 39 0.06
25 51 0.08
26 25 0.04
27 8 0.01
28 65 0.10
29 8 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTCCTTATG
Found at i:24219 original size:46 final size:46
Alignment explanation
Indices: 24152--24329 Score: 254
Period size: 46 Copynumber: 3.9 Consensus size: 46
24142 AAATTTTGAC
*
24152 ACACTATGAAAATTTAATCACCTTCATATGAAATTTTGACAACCAT
1 ACACTATGAAAATTTAATCACCTCCATATGAAATTTTGACAACCAT
24198 ACACTATGAAAATTTAATCACCTCCATATGAAATTTTGACAACCAT
1 ACACTATGAAAATTTAATCACCTCCATATGAAATTTTGACAACCAT
* *
24244 ACACTATGAAAACTTAATCACCTCCATATGAAATTTTGATAACCAT
1 ACACTATGAAAATTTAATCACCTCCATATGAAATTTTGACAACCAT
* * * * *
24290 --ACTGTGAAATTTTGAT-AGCCGCCCTATGAAATTTTGACAA
1 ACACTATGAAAATTTAATCA-CCTCCATATGAAATTTTGACAA
24330 TCGCATTTCT
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
43 1 0.01
44 31 0.26
46 89 0.74
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (46 bp):
ACACTATGAAAATTTAATCACCTCCATATGAAATTTTGACAACCAT
Found at i:24671 original size:213 final size:210
Alignment explanation
Indices: 24430--24850 Score: 627
Period size: 213 Copynumber: 2.0 Consensus size: 210
24420 ATTAACCTCC
* * *
24430 CTATTAAATTTTGATAACCTCTTTATGAAATTGAGATTTTTATAACATTCCTATGAAATTTTGGT
1 CTATAAAATTTTGATAACCTCCTTATGAAATTGAGATTTTTATAACATTCCTATGAAATTTTGAT
* *
24495 -A-A-TCACACTATGGAATTTTGATAAC-CACATTCTTACTATGAAATTTT-ATAATTTTCGTAT
66 AACACTCACACTATGAAATTTTGAT-ACTCACA--C-TA--A-GAAATTTTGATAATTTTCATAT
*
24555 GAAATTTTGACAATCAGAAATCTATGAAATTTTGATAAACCACTCCATGAGAATTTGATAACCTC
124 GAAATTTTGACAATCAGAAATCTATGAAATTTTGAT-AACCACTCCATGAGAATTTAATAACCTC
24620 TTTATAAAATTTTGATAACCATA
188 TTTATAAAATTTTGATAACCATA
24643 CTATAAAATTTTGATAACCTCCTTATGAAATTGAGATTTTTATAACATTCCTATGAAATTTTGAT
1 CTATAAAATTTTGATAACCTCCTTATGAAATTGAGATTTTTATAACATTCCTATGAAATTTTGAT
*
24708 AACCACACTCTCACTATGAAATTTTGATACTCACACTAAGAAATTTTGATAATTTTCATATGAAA
66 -A--ACACTCACACTATGAAATTTTGATACTCACACTAAGAAATTTTGATAATTTTCATATGAAA
* *
24773 TTTTGACAATCAGAAATCTATGAAATTTTGATAACCATTCTATGAGAATTTAATAACCTCTTTAT
128 TTTTGACAATCAGAAATCTATGAAATTTTGATAACCACTCCATGAGAATTTAATAACCTCTTTAT
24838 AAAATTTTGATAA
193 AAAATTTTGATAA
24851 TCTCCTTATG
Statistics
Matches: 191, Mismatches: 9, Indels: 16
0.88 0.04 0.07
Matches are distributed among these distances:
213 113 0.59
214 49 0.26
216 2 0.01
217 2 0.01
218 3 0.02
219 22 0.12
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (210 bp):
CTATAAAATTTTGATAACCTCCTTATGAAATTGAGATTTTTATAACATTCCTATGAAATTTTGAT
AACACTCACACTATGAAATTTTGATACTCACACTAAGAAATTTTGATAATTTTCATATGAAATTT
TGACAATCAGAAATCTATGAAATTTTGATAACCACTCCATGAGAATTTAATAACCTCTTTATAAA
ATTTTGATAACCATA
Found at i:24978 original size:42 final size:43
Alignment explanation
Indices: 24875--25008 Score: 146
Period size: 42 Copynumber: 3.1 Consensus size: 43
24865 TGAGATTTTT
* * *
24875 ATAATCTTCCTATGAAGTTTTGGTAACCACACTATGAAATTTTG
1 ATAACCTTCCTATGAA-ATTTGGTAACCACACTATGAAAATTTG
* *
24919 ATAACCTCCCTACGAAATTTGG-AACCACACTATGAAAATTTG
1 ATAACCTTCCTATGAAATTTGGTAACCACACTATGAAAATTTG
* * * * *
24961 ATAACCTTCTTATGAAATTGTGATAACCTCCCTAT-AAAATTTA
1 ATAACCTTCCTATGAAATT-TGGTAACCACACTATGAAAATTTG
25004 ATAAC
1 ATAAC
25009 TAGACAAAGA
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
42 35 0.46
43 19 0.25
44 22 0.29
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (43 bp):
ATAACCTTCCTATGAAATTTGGTAACCACACTATGAAAATTTG
Found at i:26312 original size:29 final size:29
Alignment explanation
Indices: 26235--26304 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
26225 GGTTTATGGT
26235 TTATTTTAAAATTAACTTTTGAAGTACTA
1 TTATTTTAAAATTAACTTTTGAAGTACTA
26264 TTATTTTAAAATTAACTTTTGAAGTACTA
1 TTATTTTAAAATTAACTTTTGAAGTACTA
26293 TTATTTTAAAAT
1 TTATTTTAAAAT
26305 GTGCTTTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (29 bp):
TTATTTTAAAATTAACTTTTGAAGTACTA
Found at i:30499 original size:18 final size:18
Alignment explanation
Indices: 30455--30509 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
30445 GGTTTTCTTA
30455 ATTTTAATTTAGATTAATT
1 ATTTTAA-TTAGATTAATT
*
30474 ATTGTTAATTAGGTT-ATT
1 ATT-TTAATTAGATTAATT
30492 AGTTTTAATTAG-TTAATT
1 A-TTTTAATTAGATTAATT
30510 TATGAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 2 0.06
18 15 0.47
19 11 0.34
20 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (18 bp):
ATTTTAATTAGATTAATT
Found at i:30539 original size:14 final size:14
Alignment explanation
Indices: 30522--30563 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
30512 TGAATAATCT
30522 ATTTTGAATTTTAA
1 ATTTTGAATTTTAA
*
30536 ATTTTAAATTTGT-A
1 ATTTTGAATTT-TAA
*
30550 ATTTTGAAATTTAA
1 ATTTTGAATTTTAA
30564 TTAACATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
ATTTTGAATTTTAA
Found at i:30601 original size:18 final size:18
Alignment explanation
Indices: 30580--30629 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
30570 TTAATTATTG
*
30580 TTAAATAGTTTATTAGGA
1 TTAATTAGTTTATTAGGA
* * **
30598 TTAATTATTTTGTTAGTT
1 TTAATTAGTTTATTAGGA
30616 TTAATTAGTTTATT
1 TTAATTAGTTTATT
30630 TACGAGTAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (18 bp):
TTAATTAGTTTATTAGGA
Found at i:30798 original size:18 final size:18
Alignment explanation
Indices: 30777--30820 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
30767 CTAAGTTGAC
30777 GAGGGAGAGAGAGGCTT-A
1 GAGGGAGAGAGA-GCTTCA
30795 GAGGGAGAGAGAGCTTCA
1 GAGGGAGAGAGAGCTTCA
*
30813 GAGAGAGA
1 GAGGGAGA
30821 TGAGGGAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.36, C:0.07, G:0.48, T:0.09
Consensus pattern (18 bp):
GAGGGAGAGAGAGCTTCA
Found at i:30804 original size:16 final size:17
Alignment explanation
Indices: 30781--30825 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
30771 GTTGACGAGG
30781 GAGAGAGAGGCTT-AGA
1 GAGAGAGAGGCTTCAGA
*
30797 GGGAGAGAGAGCTTCAGA
1 GAGAGAGAG-GCTTCAGA
30815 GAGAGATGAGG
1 GAGAGA-GAGG
30826 GAGAGAGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 8 0.33
17 4 0.17
18 9 0.38
19 3 0.12
ACGTcount: A:0.36, C:0.07, G:0.47, T:0.11
Consensus pattern (17 bp):
GAGAGAGAGGCTTCAGA
Found at i:30829 original size:27 final size:27
Alignment explanation
Indices: 30795--30847 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
30785 GAGAGGCTTA
30795 GAGGGAGAGAGA-GCTTCAGAGAGAGAT
1 GAGGGAGAGAGAGGC-TCAGAGAGAGAT
*
30822 GAGGGAGAGAGAGGCTCAGAGGGAGA
1 GAGGGAGAGAGAGGCTCAGAGAGAGA
30848 GGCAGCTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.36, C:0.08, G:0.49, T:0.08
Consensus pattern (27 bp):
GAGGGAGAGAGAGGCTCAGAGAGAGAT
Found at i:30829 original size:45 final size:45
Alignment explanation
Indices: 30777--30864 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
30767 CTAAGTTGAC
* *
30777 GAGGGAGAGAGAGGCTTAGAGGGAGAGAG-AGCTTCAGAGAGAGAT
1 GAGGGAGAGAGAGGCTCAGAGGGAGAG-GCAGCTTCAGACAGAGAT
30822 GAGGGAGAGAGAGGCTCAGAGGGAGAGGCAGCTTCAGACAGAG
1 GAGGGAGAGAGAGGCTCAGAGGGAGAGGCAGCTTCAGACAGAG
30865 CCGGTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 1 0.03
45 39 0.98
ACGTcount: A:0.34, C:0.10, G:0.47, T:0.09
Consensus pattern (45 bp):
GAGGGAGAGAGAGGCTCAGAGGGAGAGGCAGCTTCAGACAGAGAT
Found at i:31032 original size:12 final size:12
Alignment explanation
Indices: 31017--31084 Score: 57
Period size: 12 Copynumber: 5.4 Consensus size: 12
31007 ATTTGTTACA
31017 AATTTAGTTATT
1 AATTTAGTTATT
*
31029 AATTTTATATTATT
1 AA-TTTA-GTTATT
*
31043 -ATATTAGTAAATT
1 AAT-TTAGT-TATT
31056 AATTTAGTTATT
1 AATTTAGTTATT
* *
31068 AATTAATTTATT
1 AATTTAGTTATT
31080 AATTT
1 AATTT
31085 TAGGGAGTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
12 21 0.48
13 16 0.36
14 7 0.16
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (12 bp):
AATTTAGTTATT
Found at i:33485 original size:14 final size:14
Alignment explanation
Indices: 33468--33498 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
33458 TCAAAATTTA
33468 AATTAATAATAATT
1 AATTAATAATAATT
33482 AATTAATAATAATT
1 AATTAATAATAATT
33496 AAT
1 AAT
33499 AACTAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTAATAATAATT
Found at i:36304 original size:29 final size:30
Alignment explanation
Indices: 36266--36341 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
36256 AACATTTATG
36266 AAAATGCTCAAATCAGGACAC-AAAG-AAAA
1 AAAATGCTCAAATCAGGAC-CTAAAGAAAAA
*
36295 AAAATACTCAAAGT-AGGACCTAAAGAAAAA
1 AAAATGCTCAAA-TCAGGACCTAAAGAAAAA
36325 AAAATGCTCAAATCAGG
1 AAAATGCTCAAATCAGG
36342 GCCCAACGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 1 0.02
29 21 0.51
30 19 0.46
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.13
Consensus pattern (30 bp):
AAAATGCTCAAATCAGGACCTAAAGAAAAA
Found at i:36745 original size:22 final size:22
Alignment explanation
Indices: 36702--36746 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
36692 TTGATTGTAA
36702 TGAGATTTTCATTTATTATATT
1 TGAGATTTTCATTTATTATATT
*
36724 TGAGATTTTCGTTTATTATATT
1 TGAGATTTTCATTTATTATATT
36746 T
1 T
36747 CCTAAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.04, G:0.11, T:0.60
Consensus pattern (22 bp):
TGAGATTTTCATTTATTATATT
Found at i:40885 original size:57 final size:57
Alignment explanation
Indices: 40816--40931 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
40806 AAGTACCTTA
40816 TAAGGAACTGGTCAACTGAGTAATGAAGGTGTATTCTTTAATTGAGTTTATTTATCT
1 TAAGGAACTGGTCAACTGAGTAATGAAGGTGTATTCTTTAATTGAGTTTATTTATCT
40873 TAAGGAACTGGTCAACTGAGTAATGAAGGTGTATTCTTTAATTGAGTTTATTTATCT
1 TAAGGAACTGGTCAACTGAGTAATGAAGGTGTATTCTTTAATTGAGTTTATTTATCT
40930 TA
1 TA
40932 TAATGACCTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.41
Consensus pattern (57 bp):
TAAGGAACTGGTCAACTGAGTAATGAAGGTGTATTCTTTAATTGAGTTTATTTATCT
Found at i:42128 original size:30 final size:30
Alignment explanation
Indices: 42094--42152 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
42084 AGTATAGACC
42094 GCAGGGACAAACCAAGGAAAAGAACTGATG
1 GCAGGGACAAACCAAGGAAAAGAACTGATG
* *
42124 GCAGGGACAAACCACGGAAAAGCACTGAT
1 GCAGGGACAAACCAAGGAAAAGAACTGAT
42153 AGTAGGCCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.44, C:0.20, G:0.29, T:0.07
Consensus pattern (30 bp):
GCAGGGACAAACCAAGGAAAAGAACTGATG
Found at i:45215 original size:16 final size:16
Alignment explanation
Indices: 45179--45233 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
45169 GGCGGGTTCG
*
45179 GGTTCGGGTA-CTTCA
1 GGTTCGGGTATTTTCA
*
45194 GGTTCGGGTATTTTCC
1 GGTTCGGGTATTTTCA
*
45210 GGTTCGGGTATTTTCG
1 GGTTCGGGTATTTTCA
45226 GGTTCGGG
1 GGTTCGGG
45234 CTCGGATCGG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
15 10 0.28
16 26 0.72
ACGTcount: A:0.07, C:0.16, G:0.38, T:0.38
Consensus pattern (16 bp):
GGTTCGGGTATTTTCA
Found at i:45254 original size:11 final size:10
Alignment explanation
Indices: 45223--45266 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
45213 TCGGGTATTT
45223 TCGGGTTCGGG
1 TCGGG-TCGGG
*
45234 CTCGGATCGGG
1 -TCGGGTCGGG
45245 TCCGGGTCGGG
1 T-CGGGTCGGG
45256 TCGGGTCGGG
1 TCGGGTCGGG
45266 T
1 T
45267 TCACTTTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 11 0.38
11 14 0.48
12 4 0.14
ACGTcount: A:0.02, C:0.23, G:0.52, T:0.23
Consensus pattern (10 bp):
TCGGGTCGGG
Found at i:45255 original size:5 final size:5
Alignment explanation
Indices: 45223--45266 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
45213 TCGGGTATTT
*
45223 TCGGG TTCGGG CTCGGA TCGGG TCCGGG TCGGG TCGGG TCGGG T
1 TCGGG -TCGGG -TCGGG TCGGG T-CGGG TCGGG TCGGG TCGGG T
45267 TCACTTTCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
5 20 0.59
6 14 0.41
ACGTcount: A:0.02, C:0.23, G:0.52, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:46050 original size:16 final size:15
Alignment explanation
Indices: 46029--46089 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
46019 CGGGCTCGGG
*
46029 TCGGGTTCGGGTTGTC
1 TCGGGTTCGGGTT-TT
46045 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGT-TTT
* *
46061 TCGGGTTCGAGTAATT
1 TCGGGTTCGGGT-TTT
46077 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
46090 CGGGCGGGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 38 0.97
17 1 0.03
ACGTcount: A:0.07, C:0.15, G:0.39, T:0.39
Consensus pattern (15 bp):
TCGGGTTCGGGTTTT
Found at i:46418 original size:57 final size:57
Alignment explanation
Indices: 46283--46730 Score: 666
Period size: 57 Copynumber: 7.8 Consensus size: 57
46273 CCCAATAATT
* * * *
46283 AAAGTTCTCAAACACCTGGGCATGCATAAGTCCCTAAACATAGAGACATCTTTCTATCA
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATC--TCTATCA
* * *
46342 AAAGTCCTCAAACATCTGGGCATTCATAAGTCTCTAAACACAGAGGTATCTCTATCA
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCA
*
46399 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTTTCTACCA
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATC--TCTATCA
*
46458 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATTTCTATCA
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCA
*
46515 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGATGCATCTCTATCA
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCA
* * *
46572 AAAGTCCTCAAACACATGGGCATTCATAAGTCTCTAAACACAGAGGCATTTCTATCAA
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATC-A
* *
46630 AAAGTCCTCAAACACATAGGCATTCATAAGTCCCTAAACACAGAGGCATCTC--TCA
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCA
* **
46685 AAAGTCCTCAAATACAAGGGCAATTCATAAGTCCCTAAACACAGAG
1 AAAGTCCTCAAACACCTGGGC-ATTCATAAGTCCCTAAACACAGAG
46731 ACAATTTTCT
Statistics
Matches: 360, Mismatches: 25, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
55 19 0.05
56 26 0.07
57 167 0.46
58 50 0.14
59 98 0.27
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.23
Consensus pattern (57 bp):
AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCA
Found at i:46487 original size:116 final size:114
Alignment explanation
Indices: 46283--46730 Score: 677
Period size: 116 Copynumber: 3.9 Consensus size: 114
46273 CCCAATAATT
* * * *
46283 AAAGTTCTCAAACACCTGGGCATGCATAAGTCCCTAAACATAGAGACATCTTTCTATCAAAAGTC
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATC--TCTATCAAAAGTC
* * *
46348 CTCAAACATC-TGGGCATTCATAAGTCTCTAAACACAGAGGTATCTCTATCA
64 CTCAAACA-CATGGGCATTCATAAGTCCCTAAACACAGAGGCATTTCTATCA
*
46399 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTTTCTACCAAAAGTC
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATC--TCTATCAAAAGTC
*
46464 CTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATTTCTATCA
64 CTCAAACACATGGGCATTCATAAGTCCCTAAACACAGAGGCATTTCTATCA
*
46515 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGATGCATCTCTATCAAAAGTCCT
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAAAAGTCCT
*
46580 CAAACACATGGGCATTCATAAGTCTCTAAACACAGAGGCATTTCTATCAA
66 CAAACACATGGGCATTCATAAGTCCCTAAACACAGAGGCATTTCTATC-A
* *
46630 AAAGTCCTCAAACACATAGGCATTCATAAGTCCCTAAACACAGAGGCATCTC--TCAAAAGTCCT
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAAAAGTCCT
* *
46693 CAAATACAAGGGCAATTCATAAGTCCCTAAACACAGAG
66 CAAACACATGGGC-ATTCATAAGTCCCTAAACACAGAG
46731 ACAATTTTCT
Statistics
Matches: 311, Mismatches: 18, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
113 22 0.07
114 83 0.27
115 51 0.16
116 155 0.50
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.23
Consensus pattern (114 bp):
AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAAAAGTCCT
CAAACACATGGGCATTCATAAGTCCCTAAACACAGAGGCATTTCTATCA
Found at i:46536 original size:173 final size:172
Alignment explanation
Indices: 46283--46730 Score: 677
Period size: 173 Copynumber: 2.6 Consensus size: 172
46273 CCCAATAATT
* * * *
46283 AAAGTTCTCAAACACCTGGGCATGCATAAGTCCCTAAACATAGAGACATCTTTCTATCAAAAGTC
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCA--TTTCTATCAAAAGTC
* * *
46348 CTCAAACATCTGGGCATTCATAAGTCTCTAAACACAGAGGTATCTCTATCAAAAGTCCTCAAACA
64 CTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAAAAGTCCTCAAACA
* *
46413 CCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTTTCTA-CCA
129 CATGGGCATTCATAAGTCCCTAAACACAGAGGCA--TTTCTATCAA
46458 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATTTCTATCAAAAGTCCT
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATTTCTATCAAAAGTCCT
*
46523 CAAACACCTGGGCATTCATAAGTCCCTAAACACAGATGCATCTCTATCAAAAGTCCTCAAACACA
66 CAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAAAAGTCCTCAAACACA
*
46588 TGGGCATTCATAAGTCTCTAAACACAGAGGCATTTCTATCAA
131 TGGGCATTCATAAGTCCCTAAACACAGAGGCATTTCTATCAA
* * *
46630 AAAGTCCTCAAACACATAGGCATTCATAAGTCCCTAAACACAGAGGCA--TCTCTCAAAAGTCCT
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATTTCTATCAAAAGTCCT
* **
46693 CAAATACAAGGGCAATTCATAAGTCCCTAAACACAGAG
66 CAAACACCTGGGC-ATTCATAAGTCCCTAAACACAGAG
46731 ACAATTTTCT
Statistics
Matches: 253, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
170 24 0.09
171 29 0.11
172 48 0.19
173 108 0.43
175 44 0.17
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.23
Consensus pattern (172 bp):
AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATTTCTATCAAAAGTCCT
CAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAAAAGTCCTCAAACACA
TGGGCATTCATAAGTCCCTAAACACAGAGGCATTTCTATCAA
Found at i:46612 original size:26 final size:25
Alignment explanation
Indices: 46459--46728 Score: 145
Period size: 26 Copynumber: 9.6 Consensus size: 25
46449 TTTCTACCAA
*
46459 AAGTCCTCAAACACCTGGGCATTCAT
1 AAGTCCTCAAACA-CAGGGCATTCAT
46485 AAGTCC-CTAAACACAGAGGCATTTCTAT
1 AAGTCCTC-AAACACAG-GGCA-TTC-AT
*
46513 CAAAAGTCCTCAAACACCTGGGCATTCAT
1 ---AAGTCCTCAAACA-CAGGGCATTCAT
*
46542 AAGTCC-CTAAACACAGATGCATCTCTAT
1 AAGTCCTC-AAACACAG-GGCAT-TC-AT
46570 CAAAAGTCCTCAAACACATGGGCATTCAT
1 ---AAGTCCTCAAACACA-GGGCATTCAT
46599 AAGT-CTCTAAACACAGAGGCATTTCTAT
1 AAGTCCTC-AAACACAG-GGCA-TTC-AT
*
46627 CAAAAAGTCCTCAAACACATAGGCATTCAT
1 ----AAGTCCTCAAACACA-GGGCATTCAT
*
46657 AAGTCC-CTAAACACAGAGGCATCTCTCAA
1 AAGTCCTC-AAACACAG-GGCA--T-TCAT
*
46686 AAGTCCTCAAATACAAGGGCAATTCAT
1 AAGTCCTCAAACAC-AGGGC-ATTCAT
46713 AAGTCC-CTAAACACAG
1 AAGTCCTC-AAACACAG
46729 AGACAATTTT
Statistics
Matches: 196, Mismatches: 11, Indels: 74
0.70 0.04 0.26
Matches are distributed among these distances:
25 11 0.06
26 65 0.33
27 22 0.11
28 8 0.04
29 21 0.11
30 11 0.06
31 35 0.18
32 20 0.10
33 3 0.02
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.22
Consensus pattern (25 bp):
AAGTCCTCAAACACAGGGCATTCAT
Found at i:47267 original size:11 final size:12
Alignment explanation
Indices: 47240--47268 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
47230 CAAACTCTAT
47240 CAAAAATTTGAA
1 CAAAAATTTGAA
47252 CAAAAATTTGAA
1 CAAAAATTTGAA
47264 -AAAAA
1 CAAAAA
47269 AAAAATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (12 bp):
CAAAAATTTGAA
Done.