Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013186.1 Corchorus capsularis cultivar CVL-1 contig13207, 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: 33197
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:132 original size:22 final size:22
Alignment explanation
Indices: 107--666 Score: 196
Period size: 22 Copynumber: 25.7 Consensus size: 22
97 ATGATCCCAT
107 TATGAAATTTTGATAATCTTAC
1 TATGAAATTTTGATAATCTTAC
* **
129 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAATCTTAC
* * * * **
151 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAATCTTAC
**
173 TAT-AAATTTTTTTTAA-CATT-C
1 TATGAAA-TTTTGATAATC-TTAC
*
194 TTATGAAATTTTGTTAATCTCT-C
1 -TATGAAATTTTGATAATCT-TAC
* * * * * *
217 TAAGGAATTTTGAAAACCTCAA
1 TATGAAATTTTGATAATCTTAC
*
239 TATGAAATTTTGATAA-CTTCC
1 TATGAAATTTTGATAATCTTAC
* * **
260 AAATGAAATTTTGATAACCAACAC
1 -TATGAAATTTTGATAATC-TTAC
* * *
284 TATGAGATGTTGATAACCTT-C
1 TATGAAATTTTGATAATCTTAC
* *
305 ATATGATATATTGATAATC--AC
1 -TATGAAATTTTGATAATCTTAC
* * *
326 GTTATGAAAATTT-AAAAACTTAC
1 --TATGAAATTTTGATAATCTTAC
**
349 ATAT-AAATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAATCTTAC
* **
372 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAATCTTAC
* * **
394 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAATCTTAC
*
416 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AATCTTAC
* * **
439 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AATCTTAC
* *
462 TATAAAATTTTGATAA-CTTTC
1 TATGAAATTTTGATAATCTTAC
*
483 TTATGAAATCTTGATAA-C-TAC
1 -TATGAAATTTTGATAATCTTAC
*
504 ----AAATTTTGATAACCTCT-C
1 TATGAAATTTTGATAATCT-TAC
** * * *
522 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAATCTTAC
* **
544 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAATCTTAC
* *
566 TATGAAATTTTGAT-CTACATAC
1 TATGAAATTTTGATAAT-CTTAC
* *
588 TATGAAATTTTGATAACCCT-C
1 TATGAAATTTTGATAATCTTAC
* *
609 TTATGAAATTTTGA-AAACTAAAC
1 -TATGAAATTTTGATAATCT-TAC
*
632 TATGAAATTTTGAT-ATCCT-C
1 TATGAAATTTTGATAATCTTAC
*
652 CATGAAATTTTGATA
1 TATGAAATTTTGATA
667 TCCTCCCTGA
Statistics
Matches: 402, Mismatches: 100, Indels: 73
0.70 0.17 0.13
Matches are distributed among these distances:
16 11 0.03
17 1 0.00
18 1 0.00
19 1 0.00
20 14 0.03
21 25 0.06
22 273 0.68
23 75 0.19
24 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTTAC
Found at i:270 original size:44 final size:44
Alignment explanation
Indices: 222--712 Score: 274
Period size: 44 Copynumber: 11.3 Consensus size: 44
212 CTCTCTAAGG
* * *
222 AATTTTGAAAACCTCAATATGAAATTTTGATAACTTCCAAATGA
1 AATTTTGATAACCTCACTATGAAATTTTGATAACTTCCATATGA
* * *
266 AATTTTGATAACCAACACTATGAGATGTTGATAACCTT-CATATGA
1 AATTTTGATAACC-TCACTATGAAATTTTGATAA-CTTCCATATGA
* * * * * *
311 TATATTGATAA--TCACGTTATGAAAATTTAAAAACTTACATAT-A
1 AATTTTGATAACCTCAC--TATGAAATTTTGATAACTTCCATATGA
* * *
354 AATTGTT-AGTAATCACACTCTGAAATTTTGATAA--TCACACTATGA
1 AATT-TTGA-TAACCTCACTATGAAATTTTGATAACTTC-CA-TATGA
* * *
399 AATTGTGATAACCTCGCTATGAAATTTTGATAAATCTTCC-TATAA
1 AATTTTGATAACCTCACTATGAAATTTTGAT-AA-CTTCCATATGA
* * * *
444 AATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTATGA
1 AATTTTGAT-AACCTCACTATGAAATTTTGATAACTTCCATATGA
* *
489 AATCTTGATAA-CT-AC----AAATTTTGATAACCTCTC-TATGA
1 AATTTTGATAACCTCACTATGAAATTTTGATAACTTC-CATATGA
** * * *
527 TTTTTTGATAACCTCATTATGAAATTTTGTTAA-TCTCCCTATGA
1 AATTTTGATAACCTCACTATGAAATTTTGATAACT-TCCATATGA
* * * *
571 AATTTTGATCTACAT-ACTATGAAATTTTGATAAC-CCTCTTATGA
1 AATTTTGAT-AACCTCACTATGAAATTTTGATAACTTC-CATATGA
* * * *
615 AATTTTGA-AAACTAAACTATGAAATTTTGATATCCTCC--ATGA
1 AATTTTGATAACCT-CACTATGAAATTTTGATAACTTCCATATGA
* * * *
657 AATTTTGATATCCTC-C-CTGAAATTTTGATTAC-TCCATAATAA
1 AATTTTGATAACCTCACTATGAAATTTTGATAACTTCCAT-ATGA
* *
699 AAGTTTAATAACCT
1 AATTTTGATAACCT
713 TTCTATTTTC
Statistics
Matches: 343, Mismatches: 66, Indels: 78
0.70 0.14 0.16
Matches are distributed among these distances:
38 27 0.08
39 6 0.02
40 14 0.04
41 1 0.00
42 33 0.10
43 16 0.05
44 148 0.43
45 69 0.20
46 26 0.08
47 1 0.00
48 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (44 bp):
AATTTTGATAACCTCACTATGAAATTTTGATAACTTCCATATGA
Found at i:446 original size:23 final size:23
Alignment explanation
Indices: 415--499 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
405 GATAACCTCG
*
415 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
438 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
461 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
483 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
500 CTACAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:447 original size:45 final size:46
Alignment explanation
Indices: 374--477 Score: 133
Period size: 46 Copynumber: 2.3 Consensus size: 46
364 AATCACACTC
* *
374 TGAAATTTTGAT-AATCACACTATGAAATTGTGAT-AACCTCGCTA
1 TGAAATTTTGATAAATCACACTATAAAATTGTGATAAACCTCCCTA
* *
418 TGAAATTTTGATAAATCTTC-CTATAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGATAAATC-ACACTATAAAATTGTGATAAACCTCCCTA
*
464 TAAAATTTTGATAA
1 TGAAATTTTGATAA
478 CTTTCTTATG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 12 0.23
45 17 0.33
46 23 0.44
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (46 bp):
TGAAATTTTGATAAATCACACTATAAAATTGTGATAAACCTCCCTA
Found at i:498 original size:45 final size:45
Alignment explanation
Indices: 376--499 Score: 130
Period size: 45 Copynumber: 2.8 Consensus size: 45
366 TCACACTCTG
* * *
376 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTATA
*
420 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTATA
* *
466 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
500 CTACAAATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
44 11 0.16
45 31 0.46
46 26 0.38
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTATA
Found at i:658 original size:20 final size:20
Alignment explanation
Indices: 633--685 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
623 AAACTAAACT
633 ATGAAATTTTGATATCCTCC
1 ATGAAATTTTGATATCCTCC
653 ATGAAATTTTGATATCCTCC
1 ATGAAATTTTGATATCCTCC
*
673 CTGAAATTTTGAT
1 ATGAAATTTTGAT
686 TACTCCATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGAAATTTTGATATCCTCC
Found at i:816 original size:22 final size:22
Alignment explanation
Indices: 791--842 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
781 AATCACATTT
*
791 TGAAAATTTGATAACCTTTTTA
1 TGAAAATTTGATAACCTCTTTA
* *
813 TGAAATTTTGATAATCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
835 T-AAAATTT
1 TGAAAATTT
843 TATTGACCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.48
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:828 original size:44 final size:44
Alignment explanation
Indices: 770--960 Score: 140
Period size: 44 Copynumber: 4.3 Consensus size: 44
760 ATACCACTAA
* * *
770 GAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTTTTTAT
1 GAAA-TTTTGATAATCACATTTTGAAAATTTGATAACATCTCTAT
* * * **
814 GAAATTTTGATAATCTC-TTTAT-AAAATTTTATTGACCCCTCTAT
1 GAAATTTTGATAATCACATTT-TGAAAATTTGA-TAACATCTCTAT
* * * * *
858 GAAATTCTGATAATCACATTATGTAATTTTGATAACAT-TGCTTT
1 GAAATTTTGATAATCACATTTTGAAAATTTGATAACATCT-CTAT
** * * *
902 GAAATTTTGATAA-CATCGCTTTGAAATTTTGATAACAACACTAT
1 GAAATTTTGATAATCA-CATTTTGAAAATTTGATAACATCTCTAT
946 GAAATTTTGATAATC
1 GAAATTTTGATAATC
961 TTCCTATAAA
Statistics
Matches: 114, Mismatches: 24, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
43 19 0.17
44 86 0.75
45 9 0.08
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (44 bp):
GAAATTTTGATAATCACATTTTGAAAATTTGATAACATCTCTAT
Found at i:927 original size:66 final size:65
Alignment explanation
Indices: 857--979 Score: 160
Period size: 66 Copynumber: 1.9 Consensus size: 65
847 GACCCCTCTA
* * * *
857 TGAAATTCTGATAATC-ACATTATGTAATTTTGATAA-CATTGCTTTGAAATTTTGATAACATCG
1 TGAAATTCTGATAA-CAACACTATGAAATTTTGATAATC-TTCCTAT-AAATTTTGATAACATCG
920 CTT
63 CTT
*
923 TGAAATTTTGATAACAACACTATGAAATTTTGATAATCTTCCTATAAATTTTGATAA
1 TGAAATTCTGATAACAACACTATGAAATTTTGATAATCTTCCTATAAATTTTGATAA
980 TCTGATCTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
65 13 0.26
66 36 0.72
67 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (65 bp):
TGAAATTCTGATAACAACACTATGAAATTTTGATAATCTTCCTATAAATTTTGATAACATCGCTT
Found at i:973 original size:21 final size:22
Alignment explanation
Indices: 854--1204 Score: 124
Period size: 22 Copynumber: 15.8 Consensus size: 22
844 ATTGACCCCT
*
854 CTATGAAATTCTGATAATCA-CA
1 CTATGAAATTTTGATAA-CATCA
* * **
876 TTATGTAATTTTGATAACATTG
1 CTATGAAATTTTGATAACATCA
* *
898 CTTTGAAATTTTGATAACATCG
1 CTATGAAATTTTGATAACATCA
* *
920 CTTTGAAATTTTGATAACAACA
1 CTATGAAATTTTGATAACATCA
*
942 CTATGAAATTTTGATAATCTTC-
1 CTATGAAATTTTGATAA-CATCA
*
964 CTAT-AAATTTTGATAATCTGATCT
1 CTATGAAATTTTGATAA-C--ATCA
* * *
988 CTATGATATTTCGATAATCA-CT
1 CTATGAAATTTTGATAA-CATCA
* * *
1010 CTATGAGA-TTTGATAACCT-T
1 CTATGAAATTTTGATAACATCA
*
1030 CTATCAAATTTT-AGT-AC-TC-
1 CTATGAAATTTTGA-TAACATCA
* *
1049 CTTATGAAATTGAGACTTTTATAACCTTCA
1 C-TATGAAA-T-----TTTGATAA-CATCA
1079 -TATGAAATTTTGATAACCA-CA
1 CTATGAAATTTTGATAA-CATCA
* *
1100 CTATAAAATTTTGATAATC-TCC
1 CTATGAAATTTTGATAA-CATCA
* * * *
1122 CCATGAAATATT-AGTAAC-CCC
1 CTATGAAATTTTGA-TAACATCA
*
1143 CTAATGAAATTTTGTTAACCA-CA
1 CT-ATGAAATTTTGATAA-CATCA
* *
1166 CTATGAAATTCTT-ATAACCTCG
1 CTATGAAATT-TTGATAACATCA
*
1188 CTATGACATTTTGATAA
1 CTATGAAATTTTGATAA
1205 TCACTTTGAT
Statistics
Matches: 257, Mismatches: 40, Indels: 64
0.71 0.11 0.18
Matches are distributed among these distances:
19 2 0.01
20 17 0.07
21 38 0.15
22 156 0.61
23 11 0.04
24 4 0.02
25 12 0.05
26 4 0.02
27 3 0.01
28 8 0.03
29 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
CTATGAAATTTTGATAACATCA
Found at i:1350 original size:44 final size:43
Alignment explanation
Indices: 1292--1391 Score: 146
Period size: 44 Copynumber: 2.3 Consensus size: 43
1282 AATAACCTGA
* *
1292 TCCTATGAAATTTTGGTATCCACACTATGAAATTTCGATAACT
1 TCCTATGAAATTTTGGTAACCACACTATGAAATTTCGATAACC
* *
1335 TCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC
1 TCC-TATGAAATTTTGGTAACCACACTATGAAATTTCGATAACC
1379 TCCTCATGAAATT
1 TCCT-ATGAAATT
1392 ATAATAACCA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
43 4 0.08
44 47 0.92
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (43 bp):
TCCTATGAAATTTTGGTAACCACACTATGAAATTTCGATAACC
Found at i:1377 original size:22 final size:22
Alignment explanation
Indices: 1240--1425 Score: 114
Period size: 22 Copynumber: 8.4 Consensus size: 22
1230 TTGTGATAAT
* * **
1240 TAACCACCCTATGATATTTCAA
1 TAACCACACTATGAAATTTTGA
* *
1262 TAACCA-ACCTAAGAAATTTTAA
1 TAACCACA-CTATGAAATTTTGA
*
1284 TAACCTGATC-CTATGAAATTTTGG
1 TAACC--A-CACTATGAAATTTTGA
* *
1308 TATCCACACTATGAAATTTCGA
1 TAACCACACTATGAAATTTTGA
*
1330 TAACTTC-CA-TATGAAATTTTGG
1 TAAC--CACACTATGAAATTTTGA
*
1352 TAACCACACTATGGAATTTTGA
1 TAACCACACTATGAAATTTTGA
* * *
1374 TAACCTC-CTCATGAAATTATAA
1 TAACCACACT-ATGAAATTTTGA
* *
1396 TAACCATC-TTATGAGATTTTGA
1 TAACCA-CACTATGAAATTTTGA
1418 TAACCACA
1 TAACCACA
1426 TAGAGACAAG
Statistics
Matches: 127, Mismatches: 24, Indels: 26
0.72 0.14 0.15
Matches are distributed among these distances:
20 1 0.01
21 6 0.05
22 99 0.78
23 4 0.03
24 17 0.13
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCACACTATGAAATTTTGA
Found at i:2680 original size:30 final size:30
Alignment explanation
Indices: 2621--2715 Score: 147
Period size: 30 Copynumber: 3.1 Consensus size: 30
2611 TGACAATTTA
2621 GAAATATGTTTTTTAAAA-AAGGGTACAATTG
1 GAAATATG--TTTTAAAATAAGGGTACAATTG
*
2652 GAAATATGTTTTAAAATAAGGGTTCAATTG
1 GAAATATGTTTTAAAATAAGGGTACAATTG
*
2682 GAAATATGTTTTAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAATAAGGGTACAATTG
2712 GAAA
1 GAAA
2716 ACATAAAGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
29 8 0.13
30 44 0.73
31 8 0.13
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (30 bp):
GAAATATGTTTTAAAATAAGGGTACAATTG
Found at i:2905 original size:22 final size:22
Alignment explanation
Indices: 2880--3436 Score: 175
Period size: 22 Copynumber: 25.5 Consensus size: 22
2870 TCCCATTATA
2880 AAATTTTGATAACCTTCCTATG
1 AAATTTTGATAACCTTCCTATG
* ** *
2902 AAATTTTAATAACGATGCTATG
1 AAATTTTGATAACCTTCCTATG
* * * **
2924 GAATTTCGAGAACCTTTTTAT-
1 AAATTTTGATAACCTTCCTATG
* ** **
2945 AATTTTTTTTAACCTTTTTATG
1 AAATTTTGATAACCTTCCTATG
* * * * *
2967 AAGTTTGGTTAACCTCCCTAAG
1 AAATTTTGATAACCTTCCTATG
* *
2989 TAATTTTGA-AGACC-TCAATATG
1 AAATTTTGATA-ACCTTC-CTATG
* *
3011 AAATTTTGATAACTTTCCAATG
1 AAATTTTGATAACCTTCCTATG
**
3033 AAATTTTGATAACCAACACTATG
1 AAATTTTGATAACCTTC-CTATG
* *
3056 AGATGTTGATAACC-TCCATATG
1 AAATTTTGATAACCTTCC-TATG
* * * *
3078 ATATATTGATAACC-ACGTTATG
1 AAATTTTGATAACCTTC-CTATG
* *
3100 AAAATTT-A-AACACCTCCATATG
1 AAATTTTGATAAC-CTTCC-TATG
* * * *
3122 -AATTGTT-AGTAATC-ACACTCTA
1 AAATT-TTGA-TAACCTTC-CTATG
*
3144 AAATTTTGATAATCACAT--TATG
1 AAATTTTGATAA-C-CTTCCTATG
*
3166 AAATTGTGATAACC-TCGCTATG
1 AAATTTTGATAACCTTC-CTATG
* *
3188 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGAT-AACCTTCCTATG
* *
3211 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACCTTCCTATG
* * *
3234 AAATCTTGATAACTTTCTTATG
1 AAATTTTGATAACCTTCCTATG
* *
3256 AAATCTTGATAA-----CTA-C
1 AAATTTTGATAACCTTCCTATG
* *
3272 AAATTTTAATAACCTCCCTATG
1 AAATTTTGATAACCTTCCTATG
** **
3294 ATTTTTTGATAACCTTATTATG
1 AAATTTTGATAACCTTCCTATG
* *
3316 AAATTTTGTTAATC-TCCATATG
1 AAATTTTGATAACCTTCC-TATG
*** * *
3338 AAATTTTGATCTTCATACTATG
1 AAATTTTGATAACCTTCCTATG
* * *
3360 AAATTTTGATAACCCTCTTGTG
1 AAATTTTGATAACCTTCCTATG
* **
3382 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-TCCTATG
* ** *
3404 AAATTTTAATAAGTTTCATATG
1 AAATTTTGATAACCTTCCTATG
3426 AAATTTTGATA
1 AAATTTTGATA
3437 TCCTCCCTGA
Statistics
Matches: 387, Mismatches: 113, Indels: 70
0.68 0.20 0.12
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
19 1 0.00
20 4 0.01
21 31 0.08
22 266 0.69
23 68 0.18
24 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACCTTCCTATG
Found at i:3065 original size:45 final size:45
Alignment explanation
Indices: 3007--3092 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
2997 AAGACCTCAA
* * *
3007 TATGAAATTTTGATAACTTTCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAAC-CTCCATATGAAATATTGATAACCAACAC
* *
3052 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
3093 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 4 0.11
45 31 0.89
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:3214 original size:23 final size:23
Alignment explanation
Indices: 3183--3267 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
3173 GATAACCTCG
* *
3183 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATCTTGATAAATCTTC
* * *
3206 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATCTTGATAAATCTTC
*
3229 CTATAAAATCTTGATAACT-TTC
1 CTATAAAATCTTGATAAATCTTC
* *
3251 TTATGAAATCTTGATAA
1 CTATAAAATCTTGATAA
3268 CTACAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 17 0.32
23 36 0.68
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (23 bp):
CTATAAAATCTTGATAAATCTTC
Found at i:3266 original size:45 final size:45
Alignment explanation
Indices: 3161--3267 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
3151 GATAATCACA
* * *
3161 TTATGAAATTGTGAT-AACCTCGCTATGAAATTTTGATAAATCTTC
1 TTATGAAATT-TGATAAACCTCCCTATAAAATCTTGATAAATCTTC
* * *
3206 CTATAAAATTTTGATAAACCTCCCTATAAAATCTTGATAACT-TTC
1 TTATGAAA-TTTGATAAACCTCCCTATAAAATCTTGATAAATCTTC
3251 TTATGAAATCTTGATAA
1 TTATGAAAT-TTGATAA
3268 CTACAAATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
44 1 0.02
45 26 0.51
46 24 0.47
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (45 bp):
TTATGAAATTTGATAAACCTCCCTATAAAATCTTGATAAATCTTC
Found at i:3469 original size:20 final size:20
Alignment explanation
Indices: 3424--3470 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
3414 AAGTTTCATA
3424 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
* ** *
3444 TG-AATTTTTATATGTTCCT
1 TGAAATTTTGATATCCTCCC
3463 TGAAATTT
1 TGAAATTT
3471 AAATTACTCC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.49
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:3632 original size:22 final size:22
Alignment explanation
Indices: 3580--3827 Score: 150
Period size: 22 Copynumber: 11.3 Consensus size: 22
3570 AATCACATTT
* *
3580 TGAAAATTTGATAACCTATTTA
1 TGAAATTTTGATAACCTCTTTA
3602 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
3624 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
3646 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* * *
3668 TGTAATTTTGATAACTTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
3690 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
*
3712 TGAAATTTTGATAATCT-TTCTA
1 TGAAATTTTGATAACCTCTT-TA
*
3734 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * *
3758 TGAAATTTAGATAAATCACTTTA
1 TGAAATTTTGAT-AACCTCTTTA
*
3781 TGAGA-TTTGATAACCT-TTTA
1 TGAAATTTTGATAACCTCTTTA
* * *
3801 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
3821 TGAAATT
1 TGAAATT
3828 GAGACTTTTA
Statistics
Matches: 169, Mismatches: 46, Indels: 24
0.71 0.19 0.10
Matches are distributed among these distances:
19 2 0.01
20 17 0.10
21 21 0.12
22 102 0.60
23 10 0.06
24 4 0.02
25 11 0.07
26 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:3862 original size:22 final size:22
Alignment explanation
Indices: 3580--3887 Score: 90
Period size: 22 Copynumber: 13.8 Consensus size: 22
3570 AATCACATTT
* *
3580 TGAAAATTTGATAACCTAT-TTA
1 TGAAATTTTGATAACCT-TCATA
*
3602 TGAAATTTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
* * * *
3624 TAAAATTTTGTTGACCCCTC-TA
1 TGAAATTTTGAT-AACCTTCATA
* * *
3646 TGAAATTCTGATAATC-ACATTA
1 TGAAATTTTGATAACCTTCA-TA
* * *
3668 TGTAATTTTGATAA-CTTCGCTT
1 TGAAATTTTGATAACCTTC-ATA
**
3690 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAACCTTCA-TA
*
3712 TGAAATTTTGATAATCTTTC-TA
1 TGAAATTTTGATAA-CCTTCATA
3734 T-AAATTTTGATAATCCGATCTC-TA
1 TGAAATTTTGATAA-CC--T-TCATA
*
3758 TGAAATTTAGATAAATCACTT--TA
1 TGAAATTTTGAT-AA-C-CTTCATA
* *
3781 TGAGA-TTTGATAACCTT-TTA
1 TGAAATTTTGATAACCTTCATA
* * *
3801 TCAAATTTTGGTACTCCTT-ATGAAA
1 TGAAATTTTGATA-ACCTTCAT---A
*
3826 TTGAGACTTTT-ATAACCTTCATA
1 -TGA-AATTTTGATAACCTTCATA
*
3849 TGAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
*
3871 TAAAATTTTGATAACCT
1 TGAAATTTTGATAACCT
3888 CCCCATGAAA
Statistics
Matches: 218, Mismatches: 39, Indels: 57
0.69 0.12 0.18
Matches are distributed among these distances:
19 3 0.01
20 8 0.04
21 32 0.15
22 124 0.57
23 11 0.05
24 9 0.04
25 15 0.07
26 10 0.05
27 6 0.03
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:3898 original size:22 final size:22
Alignment explanation
Indices: 3848--3898 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3838 TAACCTTCAT
*
3848 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
3870 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
3892 ATGAAAT
1 ATGAAAT
3899 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:4023 original size:22 final size:22
Alignment explanation
Indices: 3998--4141 Score: 83
Period size: 22 Copynumber: 6.3 Consensus size: 22
3988 TTGTGATAAT
3998 TAACCACCCTATGAAATTTTAA
1 TAACCACCCTATGAAATTTTAA
* * *
4020 TAACCAACCTAAGAGATTTTAA
1 TAACCACCCTATGAAATTTTAA
* * **
4042 TAACCTGATCCTATAAAATTTTGG
1 TAACC--ACCCTATGAAATTTTAA
* * *
4066 TAACCAGTACACTATGGAATTTTGA
1 TAACC---ACCCTATGAAATTTTAA
* **
4091 TAACC-TCCTCATGAAATCGTAA
1 TAACCACCCT-ATGAAATTTTAA
* * *
4113 TAACCATCTTATGAAATTTTGA
1 TAACCACCCTATGAAATTTTAA
4135 TAACCAC
1 TAACCAC
4142 ATAGAGACAA
Statistics
Matches: 90, Mismatches: 27, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
21 2 0.02
22 52 0.58
23 3 0.03
24 16 0.18
25 17 0.19
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (22 bp):
TAACCACCCTATGAAATTTTAA
Found at i:4062 original size:24 final size:22
Alignment explanation
Indices: 3980--4063 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 22
3970 GATAACCTTT
*
3980 CTATAAAATTGTGATAATTAACCACC
1 CTATAAAATT-T--TAA-TAACCAAC
*
4006 CTATGAAATTTTAATAACCAAC
1 CTATAAAATTTTAATAACCAAC
* *
4028 CTA-AGAGATTTTAATAACCTGATC
1 CTATA-AAATTTTAATAACC--AAC
4052 CTATAAAATTTT
1 CTATAAAATTTT
4064 GGTAACCAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
22 23 0.48
23 3 0.06
24 11 0.23
25 2 0.04
26 9 0.19
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (22 bp):
CTATAAAATTTTAATAACCAAC
Found at i:4337 original size:19 final size:19
Alignment explanation
Indices: 4306--4342 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
4296 TATTGACATT
4306 TAAAAATTGAAATTAAAAG
1 TAAAAATTGAAATTAAAAG
4325 TAAAATATT-AAATTAAAA
1 TAAAA-ATTGAAATTAAAA
4343 AAATAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
TAAAAATTGAAATTAAAAG
Found at i:4691 original size:31 final size:31
Alignment explanation
Indices: 4656--4744 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
4646 TGGCAATTTA
4656 GAAATATGTTTTAAAGAAAAAG-GTACAATTG
1 GAAATATGTTTTAAA-AAAAAGAGTACAATTG
*
4687 GAAATATGTTTTAAAAATAAGAGTACAATTG
1 GAAATATGTTTTAAAAAAAAGAGTACAATTG
* * *
4718 AAAATATGTTTTAAAAATAAGGGTACA
1 GAAATATGTTTTAAAAAAAAGAGTACA
4745 TGAAGTTTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 5 0.09
31 49 0.91
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.30
Consensus pattern (31 bp):
GAAATATGTTTTAAAAAAAAGAGTACAATTG
Found at i:7696 original size:7 final size:7
Alignment explanation
Indices: 7686--7710 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
7676 CTTGAAGATT
7686 GATTGAA
1 GATTGAA
7693 GATTGAA
1 GATTGAA
7700 GATTGAA
1 GATTGAA
7707 GATT
1 GATT
7711 TGATGGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (7 bp):
GATTGAA
Found at i:8060 original size:25 final size:25
Alignment explanation
Indices: 8026--8074 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
8016 GATTGTTTTG
8026 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
* *
8051 TAGAGACCGAGTGAGAGTGTTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
8075 GATTGTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.16, G:0.33, T:0.16
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:10088 original size:2 final size:2
Alignment explanation
Indices: 10081--10151 Score: 60
Period size: 2 Copynumber: 37.5 Consensus size: 2
10071 TTCTTTGAAA
* * *
10081 AT AT AT AT AT AT AT AT AT AT AT A- AT GT A- AT AC AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
10121 AT -T AT TT CT AA AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10152 AAATATAATA
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
1 4 0.07
2 50 0.93
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:10174 original size:52 final size:51
Alignment explanation
Indices: 10079--10177 Score: 137
Period size: 50 Copynumber: 1.9 Consensus size: 51
10069 TTTTCTTTGA
* * *
10079 AAATATATATATATATATATATATAATGTAATACATATCTATATTATTTCT
1 AAATATATATATATATATATATAAAATATAATACAAATCTATATTATTTCT
*
10130 AAATA-ATATATATATATATATAAAATATAATATCACAATTTATATTAT
1 AAATATATATATATATATATATAAAATATAATA-CA-AATCTATATTAT
10178 ACCATATAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
50 25 0.60
51 7 0.17
52 10 0.24
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (51 bp):
AAATATATATATATATATATATAAAATATAATACAAATCTATATTATTTCT
Found at i:11825 original size:31 final size:30
Alignment explanation
Indices: 11772--11930 Score: 118
Period size: 31 Copynumber: 5.4 Consensus size: 30
11762 TTTTGTGCAC
* * **
11772 GTGGCATGCACGTGCCATTTTTTGAAACAT
1 GTGGCATGCACGTGTCACTTTTTGGTACAT
*
11802 GTGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCATG-CACGTGTCACTTTTTGGTACAT
* * *
11833 GTGACGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATG-CACGTGTCACTTTTTGGTACAT
11864 GT-G---GCA--TG--ACTTTTTGGTACAT
1 GTGGCATGCACGTGTCACTTTTTGGTACAT
* * *
11886 GTGGCGTGCCACATGTCACTTTTTGGTACAC
1 GTGGCATG-CACGTGTCACTTTTTGGTACAT
*
11917 GTGGCGTGCCACGT
1 GTGGCATG-CACGT
11931 CGGACACCGT
Statistics
Matches: 106, Mismatches: 13, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
22 16 0.15
23 1 0.01
24 2 0.02
26 3 0.03
27 3 0.03
29 2 0.02
30 8 0.08
31 71 0.67
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (30 bp):
GTGGCATGCACGTGTCACTTTTTGGTACAT
Found at i:11865 original size:19 final size:20
Alignment explanation
Indices: 11841--11888 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
11831 ACGTGACGTG
11841 ACATGTG-TCACTTTTTGGT
1 ACATGTGATCACTTTTTGGT
*
11860 ACATGTGGCATGACTTTTTGGT
1 ACATGT-G-ATCACTTTTTGGT
11882 ACATGTG
1 ACATGTG
11889 GCGTGCCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 6 0.24
20 1 0.04
21 1 0.04
22 17 0.68
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.42
Consensus pattern (20 bp):
ACATGTGATCACTTTTTGGT
Found at i:11877 original size:53 final size:53
Alignment explanation
Indices: 11819--11921 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
11809 GCCACGTGTC
** *
11819 ACTTTTTGGTACACGTGACGTGACATGTGTCACTTTTTGGTACATGTGGCATG
1 ACTTTTTGGTACACGTGACGTGACACATGTCACTTTTTGGTACACGTGGCATG
* * *
11872 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGACGTGACACATGTCACTTTTTGGTACACGTGGC
11922 GTGCCACGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.37
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGACGTGACACATGTCACTTTTTGGTACACGTGGCATG
Found at i:16872 original size:31 final size:31
Alignment explanation
Indices: 16837--16896 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
16827 ATGTTTTTCG
*
16837 ATTGTACCCTTATTTTTAAAATATATTTCCA
1 ATTGTACCCTTATTTTTAAAACATATTTCCA
*
16868 ATTGTACCCTTTTTTTTAAAACATATTTC
1 ATTGTACCCTTATTTTTAAAACATATTTC
16897 TAAATTGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.17, G:0.03, T:0.50
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTCCA
Found at i:17281 original size:22 final size:22
Alignment explanation
Indices: 17188--17317 Score: 118
Period size: 22 Copynumber: 5.9 Consensus size: 22
17178 TTCAAAGCGC
* *
17188 GAGGTTATCAAAATTACATAAT
1 GAGGTTATCAAAATTTCATAAA
* *
17210 GTGATTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCATAAA
* * * * *
17232 GGGGTCAACAAAATTTTATAGA
1 GAGGTTATCAAAATTTCATAAA
17254 GAGGTTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCATAAA
* *
17276 AAGGTTATCAAATTTTCA-AAA
1 GAGGTTATCAAAATTTCATAAA
* * *
17297 TGTGATTACCAAAATTTCATA
1 -GAGGTTATCAAAATTTCATA
17318 GTGGTACTTC
Statistics
Matches: 84, Mismatches: 22, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
21 3 0.04
22 80 0.95
23 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAAA
Found at i:17467 original size:44 final size:43
Alignment explanation
Indices: 17400--17540 Score: 158
Period size: 44 Copynumber: 3.2 Consensus size: 43
17390 TATGGAGTAA
* * ** *
17400 TCAAAATTTCATATGAAGTTTATCAAAATTTCATAGTTTAG-TTT
1 TCAAAATTTCATAAG-AGGTTATCAAAATTTCATAG-GGAGATTG
17444 TCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGGGAGATTG
1 TCAAAATTTCATAAGA-GGTTATCAAAATTTCATAGGGAGATTG
* ** *
17488 ACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGATTA
1 TCAAAATTTCATAA-GAGGTTATCAAAATTTCATAGGGAGATTG
17532 TCAAAATTT
1 TCAAAATTT
17541 GTAGTTATCA
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
43 3 0.04
44 79 0.94
45 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (43 bp):
TCAAAATTTCATAAGAGGTTATCAAAATTTCATAGGGAGATTG
Found at i:17570 original size:22 final size:22
Alignment explanation
Indices: 17399--17930 Score: 141
Period size: 22 Copynumber: 24.8 Consensus size: 22
17389 TTATGGAGTA
* * *
17399 ATCAAAATTTCATATGAAGTTT
1 ATCAAAATTTCATAAGGAGGTT
*
17421 ATCAAAATTTCAT-AGTTTA-GTT
1 ATCAAAATTTCATAAG--GAGGTT
*
17443 TTCAAAATTTCATAA-GAGGGTT
1 ATCAAAATTTCATAAGGA-GGTT
* *
17465 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAAGGAGGTT
*
17487 GA-CAAAATTTCATAATGAGGTT
1 -ATCAAAATTTCATAAGGAGGTT
** * *
17509 ATCAAAAAATCATAGGGAGATT
1 ATCAAAATTTCATAAGGAGGTT
*
17531 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAAGGAGGTT
*
17547 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * * *
17569 ATTAAAATTTTATAGGGAGATT
1 ATCAAAATTTCATAAGGAGGTT
* * *
17591 -T----ATAT-AGGAA-G-GTTT
1 ATCAAAATTTCA-TAAGGAGGTT
*
17606 ATCAAAATTTCAT-AGCGCGGTT
1 ATCAAAATTTCATAAG-GAGGTT
* * * *
17628 ATCACAGTTTCAT-AGTGTGATT
1 ATCAAAATTTCATAAG-GAGGTT
* * *
17650 ATCAAAATTTCA-GAGTGTGATT
1 ATCAAAATTTCATAAG-GAGGTT
* * *
17672 ACTGACAA-TTCATATGGAGGTT
1 A-TCAAAATTTCATAAGGAGGTT
* * * * *
17694 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
17716 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
17738 ATCAACATCTT-AT-AGTGTTGGTT
1 ATCAAAAT-TTCATAAG-G-AGGTT
** * *
17761 ATCAAAA-TTCATTTGAAAGTT
1 ATCAAAATTTCATAAGGAGGTT
*
17782 ATCAAAATTTCATAATGAGGTCT
1 ATCAAAATTTCATAAGGAGGT-T
* * *
17805 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
17826 AACAAAATTTCATAAGAATGTT
1 ATCAAAATTTCATAAGGAGGTT
** ** *
17848 AAAAAAATTT-ATAAAAACGTT
1 ATCAAAATTTCATAAGGAGGTT
* * * * *
17869 CTCGAAATTCCAT-AGTATCGTT
1 ATCAAAATTTCATAAGGA-GGTT
**
17891 ATTGAAATTTCAT-AGGAAGGTT
1 ATCAAAATTTCATAAGG-AGGTT
17913 ATCAAAATTTCATAAGGA
1 ATCAAAATTTCATAAGGA
17931 CGTCATAAAA
Statistics
Matches: 368, Mismatches: 102, Indels: 80
0.67 0.19 0.15
Matches are distributed among these distances:
15 3 0.01
16 11 0.03
17 8 0.02
19 3 0.01
20 4 0.01
21 41 0.11
22 271 0.74
23 27 0.07
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:17615 original size:37 final size:35
Alignment explanation
Indices: 17551--17620 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 35
17541 GTAGTTATCA
* *
17551 AGATTTCATAAGGAGGTTATTAAAATTTTATAGGG
1 AGATTTCATAAGGAGGTTATCAAAATTTCATAGGG
17586 AGATTT-ATATAGGAAGGTTTATCAAAATTTCATAG
1 AGATTTCATA-AGG-AGG-TTATCAAAATTTCATAG
17621 CGCGGTTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 3 0.10
35 9 0.30
36 3 0.10
37 15 0.50
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (35 bp):
AGATTTCATAAGGAGGTTATCAAAATTTCATAGGG
Found at i:17969 original size:62 final size:62
Alignment explanation
Indices: 17896--18047 Score: 243
Period size: 62 Copynumber: 2.5 Consensus size: 62
17886 TCGTTATTGA
17896 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCA-TAAAAGATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATTAAAA-ATAGTGTAATTATCAT
* * *
17958 AATTTCATAGGAAGGTTATCAAAATCTCATAAGTACGTCATTAAAAATAGTGTAATTATTAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATTAAAAATAGTGTAATTATCAT
* *
18020 AATTTAATAGGAAGGTTATCATAATTTC
1 AATTTCATAGGAAGGTTATCAAAATTTC
18048 GTATGAATAT
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
62 78 0.94
63 5 0.06
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (62 bp):
AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATTAAAAATAGTGTAATTATCAT
Found at i:18543 original size:6 final size:6
Alignment explanation
Indices: 18532--18557 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
18522 AAAAGATTAA
18532 ACTAAC ACTAAC ACTAAC ACTAAC AC
1 ACTAAC ACTAAC ACTAAC ACTAAC AC
18558 ATACAATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (6 bp):
ACTAAC
Found at i:18807 original size:22 final size:22
Alignment explanation
Indices: 18688--18827 Score: 113
Period size: 22 Copynumber: 6.3 Consensus size: 22
18678 TGTCTCTATG
* *
18688 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGT
* * *
18710 TAGTTATTATAATTTCATGAGG-
1 TGGTTATCAAAATTTCAT-AGGT
*
18732 AGGTTATCAAAATTTCATA-GT
1 TGGTTATCAAAATTTCATAGGT
*
18753 GTGGTTACCAAAATTTCATAGGAT
1 -TGGTTATCAAAATTTCATAGG-T
* * *
18777 CAGGTTATTAAAATTTCTTAGGT
1 -TGGTTATCAAAATTTCATAGGT
** *
18800 TGGTTATTGAAATTTGATAGGT
1 TGGTTATCAAAATTTCATAGGT
18822 TGGTTA
1 TGGTTA
18828 ATTATCACAA
Statistics
Matches: 94, Mismatches: 19, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 70 0.74
23 4 0.04
24 18 0.19
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGT
Found at i:19063 original size:22 final size:23
Alignment explanation
Indices: 19011--19265 Score: 137
Period size: 22 Copynumber: 11.6 Consensus size: 23
19001 TAAGGAGTAC
* *
19011 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
19032 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
19053 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
**
19078 CAAAATTT-ATAG-GAAAATTAT
1 CAAAATTTCATAGAGATGATTAT
* *
19099 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
19121 CAAAATTTCAAAGCGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
19143 CAAAATTACATA-ATG-TGATTAT
1 CAAAATTTCATAGA-GATGATTAT
* * * * *
19165 CAGAATTTCATAGAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* * *
19187 CAAAATTTTATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
19209 CAAAATTTCATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* *
19231 CAAATTTTCA-AAATG-TGATTA-
1 CAAAATTTCATAGA-GATGATTAT
19252 CAAAAATTTCATAG
1 C-AAAATTTCATAG
19266 TGGTATTTCT
Statistics
Matches: 184, Mismatches: 33, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
20 10 0.05
21 25 0.14
22 126 0.68
23 6 0.03
24 4 0.02
25 13 0.07
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:19165 original size:44 final size:44
Alignment explanation
Indices: 19095--19262 Score: 162
Period size: 44 Copynumber: 3.8 Consensus size: 44
19085 TATAGGAAAA
* *
19095 TTATCAAAATTTCATAGTGTTG-TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAATG-TGATTATCAAAATTTCAAAGAGAGG
* * * *
19139 TTATCAAAATTACATAATGTGATTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGAGAGG
* * * * * *
19183 TCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAA-AGAGG
1 TTATCAAAATTTCATAATGTGATTATCAAAATTTCA-AAGAGAGG
* *
19227 TTATCAAATTTTCAAAATGTGATTA-CAAAAATTTCA
1 TTATCAAAATTTCATAATGTGATTATC-AAAATTTCA
19263 TAGTGGTATT
Statistics
Matches: 97, Mismatches: 24, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
43 3 0.03
44 93 0.96
45 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (44 bp):
TTATCAAAATTTCATAATGTGATTATCAAAATTTCAAAGAGAGG
Found at i:19191 original size:66 final size:66
Alignment explanation
Indices: 19094--19240 Score: 161
Period size: 66 Copynumber: 2.2 Consensus size: 66
19084 TTATAGGAAA
* ** * * *
19094 ATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATG
1 ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAATG
19158 TG
65 TG
* * * * *
19160 ATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAGA
1 ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATGT
19225 G
66 G
* *
19226 GTTATCAAATTTTCA
1 ATTATCAAAATTTCA
19241 AAATGTGATT
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
66 64 0.97
67 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (66 bp):
ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATGT
G
Found at i:19565 original size:23 final size:23
Alignment explanation
Indices: 19539--19642 Score: 104
Period size: 23 Copynumber: 4.6 Consensus size: 23
19529 CATAAGAAAA
*
19539 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
19562 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGGAGGT
* *
19585 TTATCAAAATTACATAGCGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* * * *
19607 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTCATAGGGAGGT
19629 TTATCAAAATTTCA
1 TTATCAAAATTTCA
19643 GAGTGTAATT
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
21 1 0.01
22 29 0.43
23 38 0.56
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGT
Found at i:19639 original size:22 final size:22
Alignment explanation
Indices: 19346--19647 Score: 151
Period size: 22 Copynumber: 13.8 Consensus size: 22
19336 TTATGGAGGA
**
19346 TATCAAAATTTCAGGGTG-GA-
1 TATCAAAATTTCATAGTGAGAT
* *
19366 TATCAAAATTTAATAGTTTAG-T
1 TATCAAAATTTCATAG-TGAGAT
* * *
19388 TTTCAAAATTTTATA-AGAGGAT
1 TATCAAAATTTCATAGTGA-GAT
* *
19410 TATCAAAATTTCATAGTATATAT
1 TATCAAAATTTCATAGT-GAGAT
* *
19433 GTAGATCAAAATATCATAGGGAGAT
1 -T--ATCAAAATTTCATAGTGAGAT
* * *
19458 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCATAGTGAGAT
** *
19480 TATCAAAAAATCATAGGGAGAT
1 TATCAAAATTTCATAGTGAGAT
19502 TATCAAAA-TT--T-GT-AG-T
1 TATCAAAATTTCATAGTGAGAT
* * * *
19518 TACCAAGATTTCATAAG-AAAAT
1 TATCAAAATTTCAT-AGTGAGAT
* * *
19540 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGTGA-GAT
*
19563 TATCAAAATTTTATAG-GAAGATT
1 TATCAAAATTTCATAGTG-AGA-T
* * *
19586 TATCAAAATTACATAGCGAGGT
1 TATCAAAATTTCATAGTGAGAT
* *
19608 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGAGAT
*
19630 TATCAAAATTTCAGAGTG
1 TATCAAAATTTCATAGTG
19648 TAATTGCTAA
Statistics
Matches: 210, Mismatches: 50, Indels: 42
0.70 0.17 0.14
Matches are distributed among these distances:
16 7 0.03
17 4 0.02
18 1 0.00
19 2 0.01
20 14 0.07
21 7 0.03
22 117 0.56
23 37 0.18
24 4 0.02
25 3 0.01
26 14 0.07
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGAGAT
Found at i:19902 original size:22 final size:22
Alignment explanation
Indices: 19742--19904 Score: 94
Period size: 22 Copynumber: 7.3 Consensus size: 22
19732 TTGTCTCTAT
* *
19742 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATTAAAATTTCATAGG
* ** *
19764 ATATTTATTATAATTTCAT-GAG
1 GTGGTTATTAAAATTTCATAG-G
* * * *
19786 GAGGTTATCAAAATTCCATAGT
1 GTGGTTATTAAAATTTCATAGG
** * **
19808 GTGGTTACCAAAATTCCATATT
1 GTGGTTATTAAAATTTCATAGG
**
19830 GTGGTTACCAAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
* * *
19852 ATCATGTTATTAAAATTTCTTAGG
1 GT--GGTTATTAAAATTTCATAGG
* *
19876 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
19898 GTGGTTA
1 GTGGTTA
19905 ATCATCACAA
Statistics
Matches: 107, Mismatches: 30, Indels: 8
0.74 0.21 0.06
Matches are distributed among these distances:
22 89 0.83
23 1 0.01
24 17 0.16
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40
Consensus pattern (22 bp):
GTGGTTATTAAAATTTCATAGG
Found at i:19993 original size:22 final size:22
Alignment explanation
Indices: 19968--20051 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 22
19958 AGGTTATAAG
*
19968 AATTTCATAGTGTGGTTAACAA
1 AATTTCATAGTGAGGTTAACAA
*
19990 AATTTCAT-TTGGAGGTT-ACTAA
1 AATTTCATAGT-GAGGTTAAC-AA
* * * *
20012 TATTTCATGGGGAGGTTATCAA
1 AATTTCATAGTGAGGTTAACAA
* *
20034 AATTTTATAGTGTGGTTA
1 AATTTCATAGTGAGGTTA
20052 TGAAGGTTAT
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
21 3 0.06
22 43 0.91
23 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.40
Consensus pattern (22 bp):
AATTTCATAGTGAGGTTAACAA
Found at i:20160 original size:25 final size:22
Alignment explanation
Indices: 20124--20253 Score: 72
Period size: 22 Copynumber: 5.9 Consensus size: 22
20114 CTCATTGAGT
* *
20124 GATTATCGAAATTTCATAGAGATCC
1 GATTATCAAAATTTCATAG-GA--A
20149 GATTATCAAAATTT-ATAGGAA
1 GATTATCAAAATTTCATAGGAA
* **
20170 AATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAG-GAA
*
20193 G-TTATC-AAATTTCAAAGCG-A
1 GATTATCAAAATTTCATAG-GAA
* * * *
20213 GGTTATCAAAATTACATAATG-T
1 GATTATCAAAATTTCAT-AGGAA
*
20235 GATTATCAGAATTTCATAG
1 GATTATCAAAATTTCATAG
20254 AGGGGTCAAC
Statistics
Matches: 83, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.01
21 30 0.36
22 31 0.37
23 4 0.05
24 4 0.05
25 13 0.16
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (22 bp):
GATTATCAAAATTTCATAGGAA
Found at i:20288 original size:22 final size:22
Alignment explanation
Indices: 20172--20316 Score: 114
Period size: 22 Copynumber: 6.6 Consensus size: 22
20162 TATAGGAAAA
** **
20172 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
*
20194 TTATC-AAATTTCA-AAGCGAGG
1 TTATCAAAATTTCATAA-AGAGG
* * * *
20215 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGG
* * *
20237 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAAAGAGG
* * *
20259 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
*
20281 TTATCAAAATGTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
*
20303 TTATCAAATTTTCA
1 TTATCAAAATTTCA
20317 GAATGTGATT
Statistics
Matches: 94, Mismatches: 26, Indels: 6
0.75 0.21 0.05
Matches are distributed among these distances:
20 1 0.01
21 15 0.16
22 76 0.81
23 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:20603 original size:38 final size:38
Alignment explanation
Indices: 20550--20622 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
20540 TCATAATGAG
* * *
20550 GTTATCAAAAATTCATAGGGAGATTATCAAAATTTGTA
1 GTTATCAAAAATTCATAAGAAAATTATCAAAATTTGTA
* *
20588 GTTATCAAGATTTCATAAGAAAATTATCAAAATTT
1 GTTATCAAAAATTCATAAGAAAATTATCAAAATTT
20623 TATAGGGAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (38 bp):
GTTATCAAAAATTCATAAGAAAATTATCAAAATTTGTA
Found at i:20639 original size:23 final size:23
Alignment explanation
Indices: 20589--20668 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
20579 AAATTTGTAG
* * * *
20589 TTATCAAGATTTCATAAGAA-AA
1 TTATCAAAATTTTATAGGAAGAT
* *
20611 TTATCAAAATTTTATAGGGAGTT
1 TTATCAAAATTTTATAGGAAGAT
20634 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
20657 TTATCAAAATTT
1 TTATCAAAATTT
20669 CATAACGAGA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:20679 original size:23 final size:22
Alignment explanation
Indices: 20466--20714 Score: 144
Period size: 22 Copynumber: 11.5 Consensus size: 22
20456 AGTTTAGTTT
* *
20466 TCAAAATTTTATAA-GAGGGTTA
1 TCAAAATTTCATAAGGA-GATTA
*
20488 TCAAAATTTCAT-AGTATG-TTGA
1 TCAAAATTTCATAAGGA-GATT-A
* *
20510 TCAAAATATCATAGGGAGATT-
1 TCAAAATTTCATAAGGAGATTA
* * * *
20531 TAAAAAAATTCATAATGAGGTTA
1 T-CAAAATTTCATAAGGAGATTA
* *
20554 TCAAAAATTCATAGGGAGATTA
1 TCAAAATTTCATAAGGAGATTA
*
20576 TCAAAA-TT--T--GTAG-TTA
1 TCAAAATTTCATAAGGAGATTA
* * *
20592 TCAAGATTTCATAAGAAAATTA
1 TCAAAATTTCATAAGGAGATTA
* * *
20614 TCAAAATTTTATAGGGAGTTTTA
1 TCAAAATTTCATAAGGAG-ATTA
*
20637 TCAAAATTTTAT-AGGAAGATTTA
1 TCAAAATTTCATAAGG-AGA-TTA
*
20660 TCAAAATTTCATAACGAGATTA
1 TCAAAATTTCATAAGGAGATTA
* *
20682 TCACAATTTCAT-AGTGTGATTA
1 TCAAAATTTCATAAG-GAGATTA
20704 TCAAAATTTCA
1 TCAAAATTTCA
20715 GAGTGTAATT
Statistics
Matches: 176, Mismatches: 34, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
16 8 0.05
17 5 0.03
19 2 0.01
21 9 0.05
22 111 0.63
23 39 0.22
24 2 0.01
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATAAGGAGATTA
Found at i:20683 original size:45 final size:41
Alignment explanation
Indices: 20422--20714 Score: 154
Period size: 44 Copynumber: 6.8 Consensus size: 41
20412 TGATGGAGGA
* *
20422 TATCAAAATTTCA-AGGTGGA-TATCAAAATTTAAT-AGTTTAGT
1 TATCAAAATTTCATAGG-AGATTATCAAAATTTCATAAG---AGT
* * * *
20464 TTTCAAAATTTTATAAGAGGGTTATCAAAATTTCAT-AGTATGT
1 TATCAAAATTTCATAGGA-GATTATCAAAATTTCATAAG-A-GT
* * *
20507 TGATCAAAATATCATAGGGAGATT-TAAAAAAATTCATAATGAGGT
1 T-ATCAAAATTTCATA-GGAGATTAT-CAAAATTTCATAA-GA-GT
* *
20552 TATCAAAAATTCATAGGGAGATTATCAAAATTT-GT---AGT
1 TATCAAAATTTCATA-GGAGATTATCAAAATTTCATAAGAGT
* * * * *
20590 TATCAAGATTTCATAAGAAAATTATCAAAATTTTATAGGGAGTTT
1 TATCAAAATTTCAT-AGGAGATTATCAAAATTTCATA-AGAG--T
*
20635 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAACGAGAT
1 TATCAAAATTTCATAGG-AGA-TTATCAAAATTTCATAA-GAG-T
* *
20680 TATCACAATTTCATAGTGTGATTATCAAAATTTCA
1 TATCAAAATTTCATAG-GAGATTATCAAAATTTCA
20715 GAGTGTAATT
Statistics
Matches: 195, Mismatches: 34, Indels: 42
0.72 0.13 0.15
Matches are distributed among these distances:
38 29 0.15
39 3 0.02
42 13 0.07
43 10 0.05
44 80 0.41
45 40 0.21
46 20 0.10
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.37
Consensus pattern (41 bp):
TATCAAAATTTCATAGGAGATTATCAAAATTTCATAAGAGT
Found at i:20719 original size:22 final size:22
Alignment explanation
Indices: 20422--20720 Score: 106
Period size: 22 Copynumber: 13.9 Consensus size: 22
20412 TGATGGAGGA
20422 TATCAAAATTTCA-AG-GTGGA-
1 TATCAAAATTTCATAGTGT-GAT
* *
20442 TATCAAAATTTAATAGT-TTAGT
1 TATCAAAATTTCATAGTGTGA-T
* * * *
20464 TTTCAAAATTTTATAAGAG-GGT
1 TATCAAAATTTCAT-AGTGTGAT
*
20486 TATCAAAATTTCATAGTATG-T
1 TATCAAAATTTCATAGTGTGAT
* * *
20507 TGATCAAAATATCATAGGGAGAT
1 T-ATCAAAATTTCATAGTGTGAT
* * * * *
20530 T-TAAAAAAATTCATAATGAGGT
1 TAT-CAAAATTTCATAGTGTGAT
* * *
20552 TATCAAAAATTCATAGGGAGAT
1 TATCAAAATTTCATAGTGTGAT
*
20574 TATCAAAA-TT--T-GT-AG-T
1 TATCAAAATTTCATAGTGTGAT
* ***
20590 TATCAAGATTTCATAAG-AAAAT
1 TATCAAAATTTCAT-AGTGTGAT
* * * *
20612 TATCAAAATTTTATAGGGAGTTT
1 TATCAAAATTTCATAGTGTG-AT
* *
20635 TATCAAAATTTTATAG-GAAGATT
1 TATCAAAATTTCATAGTG-TGA-T
** *
20658 TATCAAAATTTCATAACGAGAT
1 TATCAAAATTTCATAGTGTGAT
*
20680 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
*
20702 TATCAAAATTTCAGAGTGT
1 TATCAAAATTTCATAGTGT
20721 AATTGCTAAC
Statistics
Matches: 214, Mismatches: 42, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
16 8 0.04
17 4 0.02
18 1 0.00
19 2 0.01
20 13 0.06
21 14 0.07
22 129 0.60
23 42 0.20
24 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGAT
Found at i:20757 original size:22 final size:21
Alignment explanation
Indices: 20732--20804 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 21
20722 ATTGCTAACA
*
20732 ATTCATATGAAGGTTTTTAAAT
1 ATTCATATG-AGGTTTATAAAT
*
20754 ATTCATAATGAGG-TTATCAAT
1 ATTCAT-ATGAGGTTTATAAAT
*
20775 ATATCATATGGAGG-TTATCAAT
1 AT-TCATAT-GAGGTTTATAAAT
20797 ATCTCATA
1 AT-TCATA
20805 CTGTTGGTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 10 0.22
22 32 0.71
23 3 0.07
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.40
Consensus pattern (21 bp):
ATTCATATGAGGTTTATAAAT
Found at i:20817 original size:23 final size:22
Alignment explanation
Indices: 20751--20850 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
20741 AAGGTTTTTA
20751 AATAT-TCATAAT-GAGGTTATC
1 AATATATCAT-ATGGAGGTTATC
20772 AATATATCATATGGAGGTTATC
1 AATATATCATATGGAGGTTATC
* **
20794 AATATCTCATACTGTTGGTTATC
1 AATATATCATA-TGGAGGTTATC
* * *
20817 AACATTTCAT-TGGGAAGTTATC
1 AATATATCATAT-GGAGGTTATC
* *
20839 AAAATTTCATAT
1 AATATATCATAT
20851 TGAGATCTTC
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
21 8 0.12
22 39 0.60
23 18 0.28
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (22 bp):
AATATATCATATGGAGGTTATC
Found at i:23683 original size:7 final size:7
Alignment explanation
Indices: 23665--23711 Score: 87
Period size: 7 Copynumber: 6.9 Consensus size: 7
23655 TTTCTGATGA
23665 AAGAAA-
1 AAGAAAG
23671 AAGAAAG
1 AAGAAAG
23678 AAGAAAG
1 AAGAAAG
23685 AAGAAAG
1 AAGAAAG
23692 AAGAAAG
1 AAGAAAG
23699 AAGAAAG
1 AAGAAAG
23706 AAGAAA
1 AAGAAA
23712 TCGTACTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 6 0.15
7 34 0.85
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:26558 original size:25 final size:25
Alignment explanation
Indices: 26530--26584 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
26520 ATTTTAATGT
*
26530 TTAAATT-TTATTTTTTATTAAAAAA
1 TTAAATTATTATTTTAT-TTAAAAAA
26555 TT-AATTATTATTTTATTTAAAAAA
1 TTAAATTATTATTTTATTTAAAAAA
*
26579 ATAAAT
1 TTAAAT
26585 ATGGGCGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TTAAATTATTATTTTATTTAAAAAA
Done.