Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004965.1 Hibiscus syriacus cultivar Beakdansim tig00011157_pilon, 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: 59727
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:774 original size:37 final size:38
Alignment explanation
Indices: 623--991 Score: 250
Period size: 37 Copynumber: 9.7 Consensus size: 38
613 TAGTATATAT
*
623 AATA-ATATA-ATATAGTTTTTGAAAATA--TTTTTGAA
1 AATATATATATATATAG-TTTTGAAAACACGTTTTTGAA
* *
658 AACATATA-ATATATAGTTTTTAGAAAAC-GGTTTTTGAA
1 AATATATATATATATAG-TTTT-GAAAACACGTTTTTGAA
** * *
696 AGCATATA-ATATATAGTTTTTTTTTAAAAAATCAGTTTTTGAA
1 A--ATATATATATATA--TAGTTTTGAAAACA-C-GTTTTTGAA
* *
739 TATATATATA-ATATGGTTTTGAAAACACGTTTTTGAA
1 AATATATATATATATAGTTTTGAAAACACGTTTTTGAA
* *
776 AATGTTTA-ATATATAGTTTTGAAAACACGTTTTTGAA
1 AATATATATATATATAGTTTTGAAAACACGTTTTTGAA
* * ** *
813 AATGTATA-ATATATAGTTTTGAAAATATATTTTCGAA
1 AATATATATATATATAGTTTTGAAAACACGTTTTTGAA
* * *
850 AACATATA-ATATATAGTTTTAAAAAAACGGTTTTTGAA
1 AATATATATATATATAGTTTTGAAAACAC-GTTTTTGAA
** *
888 AACGTATATA-ATATAGTTTTGAAAACA--TATTT-AA
1 AATATATATATATATAGTTTTGAAAACACGTTTTTGAA
* *
922 TATATATATATATATAGGTTTT-TAAA-ACGATTTTTGAAA
1 AATATATATATATATA-GTTTTGAAAACACG-TTTTTG-AA
*
961 ACATATATAATATATATAATTTTGGAAAACA
1 A-ATATAT-ATATATATAGTTTT-GAAAACA
992 TATTTTTTTA
Statistics
Matches: 264, Mismatches: 41, Indels: 50
0.74 0.12 0.14
Matches are distributed among these distances:
34 10 0.04
35 16 0.06
36 20 0.08
37 104 0.39
38 39 0.15
39 14 0.05
40 23 0.09
41 21 0.08
42 7 0.03
43 10 0.04
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (38 bp):
AATATATATATATATAGTTTTGAAAACACGTTTTTGAA
Found at i:910 original size:23 final size:23
Alignment explanation
Indices: 881--925 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
871 AAAAAACGGT
*
881 TTTTGAAAACGTATATAATATAG
1 TTTTGAAAACATATATAATATAG
*
904 TTTTGAAAACATATTTAATATA
1 TTTTGAAAACATATATAATATA
926 TATATATATA
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:0.44, C:0.04, G:0.09, T:0.42
Consensus pattern (23 bp):
TTTTGAAAACATATATAATATAG
Found at i:1037 original size:15 final size:15
Alignment explanation
Indices: 1017--1076 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 15
1007 ATAATATATG
1017 TTATATATTTTTTTA
1 TTATATATTTTTTTA
*
1032 TTATATATTATTTATA
1 TTATATATT-TTTTTA
*
1048 TTAT-TATTTATTTA
1 TTATATATTTTTTTA
1062 TT-TATTAATTTTTTT
1 TTATA-T-ATTTTTTT
1077 CAGGTCCAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 6 0.16
15 14 0.38
16 16 0.43
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATATATTTTTTTA
Found at i:1053 original size:19 final size:20
Alignment explanation
Indices: 1029--1066 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1019 ATATATTTTT
1029 TTATTATATA-TTATTTATA
1 TTATTATATATTTATTTATA
*
1048 TTATTATTTATTTATTTAT
1 TTATTATATATTTATTTAT
1067 TAATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTATATATTTATTTATA
Found at i:1058 original size:4 final size:4
Alignment explanation
Indices: 1017--1072 Score: 51
Period size: 4 Copynumber: 13.5 Consensus size: 4
1007 ATAATATATG
* *
1017 TTAT ATAT TTTT TTAT TATAT ATTAT TTAT ATTA- TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT T-TAT -TTAT TTAT -TTAT TTAT TTAT TTAT TTAT
*
1067 TAAT TT
1 TTAT TT
1073 TTTTCAGGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
3 3 0.07
4 29 0.69
5 9 0.21
6 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:6459 original size:22 final size:22
Alignment explanation
Indices: 6431--6474 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
6421 TGCTACAAAG
6431 TATGGAGAATAAACATAATGAA
1 TATGGAGAATAAACATAATGAA
6453 TATGGAGAATAAACATAATGAA
1 TATGGAGAATAAACATAATGAA
6475 AGCTTCATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.23
Consensus pattern (22 bp):
TATGGAGAATAAACATAATGAA
Found at i:14220 original size:38 final size:37
Alignment explanation
Indices: 14162--14447 Score: 241
Period size: 37 Copynumber: 7.7 Consensus size: 37
14152 AATATAGTAC
14162 AGTTTTTGAAAAT-ATTTTTGAAAACATATAATATAT
1 AGTTTTTGAAAATCATTTTTGAAAACATATAATATAT
* *
14198 AGTTTTTAGAAAATGATTTTTGAAAGCATATAATATAT
1 AGTTTTT-GAAAATCATTTTTGAAAACATATAATATAT
* *
14236 AGTTTTTTAAAAAATCAGTTTTTGAAAATATAT-ATA-AT
1 AG-TTTTT-GAAAATCA-TTTTTGAAAACATATAATATAT
* **
14274 ATGGTTTTGAAAA-CACTTTTTTGAAAATGTATAATATAT
1 A-GTTTTTGAAAATCA--TTTTTGAAAACATATAATATAT
* *
14313 AG-TTTTGAAAACACATTTTTGAAAACATATACTATAT
1 AGTTTTTGAAAA-TCATTTTTGAAAACATATAATATAT
* **
14350 AG-TTTTGAAAACACATTTTTGAAAATGTATAATATAT
1 AGTTTTTGAAAA-TCATTTTTGAAAACATATAATATAT
* * * *
14387 AG-TTTTAAAAAACGGTTTTTGAAAACGTAT-ATAATAT
1 AGTTTTTGAAAATC-ATTTTTGAAAACATATAAT-ATAT
*
14424 AG-TTTTGAAAA-CATATTTTAAAAA
1 AGTTTTTGAAAATCAT-TTTTGAAAA
14448 ACACACACAC
Statistics
Matches: 216, Mismatches: 21, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
35 1 0.00
36 22 0.10
37 124 0.57
38 35 0.16
39 21 0.10
40 13 0.06
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.41
Consensus pattern (37 bp):
AGTTTTTGAAAATCATTTTTGAAAACATATAATATAT
Found at i:14442 original size:74 final size:73
Alignment explanation
Indices: 14176--14442 Score: 317
Period size: 74 Copynumber: 3.6 Consensus size: 73
14166 TTTGAAAATA
* ***
14176 TTTTTGAAAACATATA-ATATATAGTTTTTAGAAA-ATGATTTTTGAAAGCATATAATATATAGT
1 TTTTTGAAAACATATATA-ATATAGTTTTGA-AAACAT-ATTTTTGAAAATGTATAATATATAG-
14239 TTTTTAAAAAATCAG
62 -TTTTAAAAAA-C-G
* *
14254 TTTTTGAAAATATATATAATATGGTTTTGAAAACACT-TTTTTGAAAATGTATAATATATAGTTT
1 TTTTTGAAAACATATATAATATAGTTTTGAAAACA-TATTTTTGAAAATGTATAATATATAGTTT
* *
14318 TGAAAACACA
65 T-AAAAAACG
*
14328 TTTTTGAAAACATATACT-ATATAGTTTTGAAAACACATTTTTGAAAATGTATAATATATAGTTT
1 TTTTTGAAAACATATA-TAATATAGTTTTGAAAACATATTTTTGAAAATGTATAATATATAGTTT
14392 TAAAAAACGG
65 TAAAAAAC-G
*
14402 TTTTTGAAAACGTATATAATATAGTTTTGAAAACATATTTT
1 TTTTTGAAAACATATATAATATAGTTTTGAAAACATATTTT
14443 AAAAAACACA
Statistics
Matches: 166, Mismatches: 15, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
73 7 0.04
74 96 0.58
75 6 0.04
76 5 0.03
77 24 0.14
78 26 0.16
79 2 0.01
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (73 bp):
TTTTTGAAAACATATATAATATAGTTTTGAAAACATATTTTTGAAAATGTATAATATATAGTTTT
AAAAAACG
Found at i:14453 original size:2 final size:2
Alignment explanation
Indices: 14448--14474 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14438 ATTTTAAAAA
14448 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
14475 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:14521 original size:43 final size:42
Alignment explanation
Indices: 14474--14576 Score: 104
Period size: 43 Copynumber: 2.5 Consensus size: 42
14464 ACACACACAC
*
14474 ATATATATATAGTTTTTTAAAA-CGATTTTTGAAAACACATATA
1 ATATATATATAGTTTTTTAAAATAGATTTTTGAAAA-A-ATATA
* * ***
14517 ATATATATA-A-TTTTTGAAAATATATTTTTTTGAAAATATA
1 ATATATATATAGTTTTTTAAAATAGATTTTTGAAAAAATATA
14557 ATATATTATATAGTTTTTTA
1 ATATA-TATATAGTTTTTTA
14577 TTATATATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
40 10 0.20
41 14 0.29
42 10 0.20
43 15 0.31
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (42 bp):
ATATATATATAGTTTTTTAAAATAGATTTTTGAAAAAATATA
Found at i:14545 original size:15 final size:16
Alignment explanation
Indices: 14519--14556 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
14509 CACATATAAT
14519 ATATATAATTTTTGAAA
1 ATATAT-ATTTTTGAAA
*
14536 ATATATTTTTTTGAAA
1 ATATATATTTTTGAAA
14552 ATATA
1 ATATA
14557 ATATATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
ATATATATTTTTGAAA
Found at i:14580 original size:15 final size:15
Alignment explanation
Indices: 14560--14593 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
14550 AAATATAATA
14560 TATTATATAGTT-TTT
1 TATTATATA-TTATTT
14575 TATTATATATTATTT
1 TATTATATATTATTT
14590 TATT
1 TATT
14594 TTATTTTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TATTATATATTATTT
Found at i:14583 original size:43 final size:40
Alignment explanation
Indices: 14512--14590 Score: 95
Period size: 43 Copynumber: 1.9 Consensus size: 40
14502 TTGAAAACAC
*
14512 ATATAATATATATAATTTTTGAAAATATATTTTTTTGAAA
1 ATATAATATATATAATTTTTGAAAATATATTATTTTGAAA
* **
14552 ATATAATATATTATATAGTTTTTTATTATATATTATTTT
1 ATATAATATA-TATA-A-TTTTTGAAAATATATTATTTT
14591 ATTTTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 10 0.31
41 4 0.12
42 1 0.03
43 17 0.53
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (40 bp):
ATATAATATATATAATTTTTGAAAATATATTATTTTGAAA
Found at i:16026 original size:20 final size:21
Alignment explanation
Indices: 16001--16093 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
15991 TTTTCCCAAT
*
16001 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
16021 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
16042 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
16062 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
16083 TCGCAATGCGA
1 TCGCAATGCGA
16094 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:16046 original size:41 final size:41
Alignment explanation
Indices: 16001--16093 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
15991 TTTTCCCAAT
16001 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
16042 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
16083 TCGCAATGCGA
1 TCGCAATGCGA
16094 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:16106 original size:41 final size:41
Alignment explanation
Indices: 16020--16154 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
16010 GAATAAGTAA
** *
16020 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
16061 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * **
16102 ATCGCAATGCGATAAT-ACAAAATCGCAACGATATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
16143 TTCGCAACGCGA
1 ATCGCAACGCGA
16155 TACTGACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 5 0.06
41 73 0.91
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:16107 original size:20 final size:20
Alignment explanation
Indices: 16082--16175 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
16072 AATTGGGAAA
*
16082 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
16102 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
**
16123 ATCGCAACGATATACTTACT
1 ATCGCAACGCGATACTTACT
* *
16143 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
16163 TTCGCAACGCGAT
1 ATCGCAACGCGAT
16176 TTACATAATC
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.05
20 43 0.72
21 11 0.18
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:16391 original size:22 final size:22
Alignment explanation
Indices: 16363--16406 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16353 CACTCTCTCA
16363 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
16385 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
16407 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:17937 original size:18 final size:18
Alignment explanation
Indices: 17916--17960 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
17906 TCCACTTCGG
* *
17916 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
17934 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
17952 GAGCCATCA
1 GAGCCATCA
17961 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:18456 original size:19 final size:20
Alignment explanation
Indices: 18432--18476 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
18422 TAGTTTACTT
18432 TCGCAACAC-GAAATGACTA
1 TCGCAACACGGAAATGACTA
* *
18451 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTA
18471 TCGCAA
1 TCGCAA
18477 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.36, C:0.27, G:0.22, T:0.16
Consensus pattern (20 bp):
TCGCAACACGGAAATGACTA
Found at i:18505 original size:14 final size:14
Alignment explanation
Indices: 18486--18543 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
18476 ATGCGAAATA
18486 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
18500 AAAATCGCAACACGAA
1 AAAATCGC-A-ACGAC
18516 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
18532 AAAATCGCAACG
1 AAAATCGCAACG
18544 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 19 0.50
15 1 0.03
16 10 0.26
17 1 0.03
18 7 0.18
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:18528 original size:32 final size:32
Alignment explanation
Indices: 18487--18553 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
18477 TGCGAAATAA
18487 AAATCGCAACGACAAAATCGCAACACGAAATG
1 AAATCGCAACGACAAAATCGCAACACGAAATG
*
18519 AAATCGCAACGACAAAATCGCAACGCGAAATG
1 AAATCGCAACGACAAAATCGCAACACGAAATG
18551 AAA
1 AAA
18554 ATTGGAATGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.51, C:0.24, G:0.16, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGACAAAATCGCAACACGAAATG
Found at i:18554 original size:19 final size:19
Alignment explanation
Indices: 18432--18555 Score: 63
Period size: 19 Copynumber: 7.1 Consensus size: 19
18422 TAGTTTACTT
* **
18432 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
18451 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
* *
18471 TCGCAATGCGAAATAAAAA
1 TCGCAACGCGAAATGAAAA
*
18490 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
18504 TCGCAACACGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
18522 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
18536 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
18555 T
1 T
18556 TGGAATGCGA
Statistics
Matches: 82, Mismatches: 11, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
14 20 0.24
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.13
19 25 0.30
20 17 0.21
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:18596 original size:14 final size:14
Alignment explanation
Indices: 18577--18634 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
18567 TTGTGTTTCG
18577 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
18591 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
18607 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
18623 CGTTGCGATTTT
1 CGTTGCGATTTT
18635 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:18611 original size:32 final size:33
Alignment explanation
Indices: 18572--18650 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
18562 GCGATTTGTG
18572 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
18604 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
18637 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
18651 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:18649 original size:19 final size:19
Alignment explanation
Indices: 18591--18708 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
18581 GCGATTTTGT
18591 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
18609 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
18623 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
18642 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
18662 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
18681 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
18701 TGTTGCGA
1 CGTTGCGA
18709 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:20596 original size:19 final size:19
Alignment explanation
Indices: 20572--20673 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
20562 AAAACAGACT
* *
20572 ATCGCAACGCGAAATGGAA
1 ATCGCAATGCGAAATGAAA
20591 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
20610 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
20629 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
20648 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
20662 ATCGCAATGCGA
1 ATCGCAATGCGA
20674 TTTTCATTTC
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
14 11 0.14
15 1 0.01
16 2 0.03
17 1 0.01
19 61 0.80
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:20749 original size:20 final size:20
Alignment explanation
Indices: 20692--20749 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
20682 TCGCATTGCG
* *
20692 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
*
20712 ATTTTCGCATTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
20732 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
20750 TCAAATGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:21814 original size:24 final size:24
Alignment explanation
Indices: 21787--21840 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
21777 GTATTCGAAA
* *
21787 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
21811 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
21835 TTTGAT
1 TTTGAT
21841 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:24344 original size:19 final size:19
Alignment explanation
Indices: 24322--24419 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
24312 GGAAATTACT
24322 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
24341 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
24355 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
24374 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
24388 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
24407 ATCGCAACGCGAA
1 ATCGCAATGCGAA
24420 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:24364 original size:33 final size:33
Alignment explanation
Indices: 24322--24415 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
24312 GGAAATTACT
24322 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
24355 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
24388 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
24416 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:24437 original size:19 final size:20
Alignment explanation
Indices: 24415--24457 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
24405 AAATCGCAAC
24415 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
24434 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
24454 GCGA
1 GCGA
24458 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:24442 original size:14 final size:14
Alignment explanation
Indices: 24443--24476 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
24433 TGCGATTTTC
24443 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
24457 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
24471 ATTTTC
1 ATTTTC
24477 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:24618 original size:14 final size:14
Alignment explanation
Indices: 24599--24635 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
24589 CATCAATTAA
24599 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
24613 ACAAATCACCTTTT
1 ACAAATCAACTTTT
24627 ACAAATCAA
1 ACAAATCAA
24636 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:26058 original size:21 final size:21
Alignment explanation
Indices: 25992--26058 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
25982 GTGAATCGGG
*
25992 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
26012 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
26034 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
26055 CTCT
1 CTCT
26059 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:26077 original size:42 final size:41
Alignment explanation
Indices: 25992--26114 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
25982 GTGAATCGGG
* * * * *
25992 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
26034 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
26076 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
26115 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:28143 original size:20 final size:19
Alignment explanation
Indices: 28118--28270 Score: 83
Period size: 20 Copynumber: 8.4 Consensus size: 19
28108 GTTGAAATAA
*
28118 AATCGCAACGAGATAATGAG
1 AATCGCAACGAGA-AATGAC
*
28138 AATCGCAACGCGGAAATGAC
1 AATCGCAACG-AGAAATGAC
*
28158 TATCGCAACGAG--A-G--
1 AATCGCAACGAGAAATGAC
*
28172 AATCGCAACGCGAAATGAC
1 AATCGCAACGAGAAATGAC
* **
28191 TATCG---CGA-CCA-GAC
1 AATCGCAACGAGAAATGAC
* *
28205 AATCGCAACGCGAAATGAA
1 AATCGCAACGAGAAATGAC
* * *
28224 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGAGAAATGAC
* *
28244 AATCGCAACGCGAAATGAA
1 AATCGCAACGAGAAATGAC
28263 AATCGCAA
1 AATCGCAA
28271 TGCGATTTTG
Statistics
Matches: 104, Mismatches: 17, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
14 17 0.16
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 33 0.32
20 42 0.40
21 2 0.02
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGAGAAATGAC
Found at i:28192 original size:33 final size:33
Alignment explanation
Indices: 28135--28233 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
28125 ACGAGATAAT
*
28135 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
28169 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
28202 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
28234 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:28227 original size:19 final size:19
Alignment explanation
Indices: 28111--28275 Score: 127
Period size: 19 Copynumber: 9.1 Consensus size: 19
28101 TCTTTTGGTT
*
28111 GAAAT-AAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
28129 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
28149 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
28167 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
28183 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
28201 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
28216 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
28236 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
28255 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
28274 GA
1 GA
28276 TTTTGGTTTC
Statistics
Matches: 118, Mismatches: 15, Indels: 27
0.74 0.09 0.17
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 6 0.05
19 44 0.37
20 41 0.35
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:28305 original size:20 final size:19
Alignment explanation
Indices: 28271--28338 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
28261 AAAATCGCAA
**
28271 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
28290 TGCGAATTTTTATTTCGCGT
1 TGCG-ATTTTTATTTCGCGT
**
28310 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
28330 TGCGATTTT
1 TGCGATTTT
28339 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.29
20 29 0.71
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:28881 original size:20 final size:20
Alignment explanation
Indices: 28856--28907 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
28846 CGCTATGTAA
28856 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
28876 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
*
28896 ATCTCGTTGCGA
1 ATCGCGTTGCGA
28908 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGT
Found at i:28941 original size:20 final size:20
Alignment explanation
Indices: 28856--28949 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
28846 CGCTATGTAA
*
28856 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
28876 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
28896 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAGT
* *
28917 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
*
28937 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
28950 TTTCCCAATT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.05
20 46 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:28967 original size:21 final size:21
Alignment explanation
Indices: 28938--29030 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
28928 ATAGTAAGTA
28938 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
28959 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
28979 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
29000 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
29020 TCGCATTGCGA
1 TCGCATTGCGA
29031 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:28968 original size:41 final size:41
Alignment explanation
Indices: 28877--29011 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
28867 AAAGTCAGTA
* * * * ** *
28877 TCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
28917 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
28959 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
29000 TCGCGTTGCGAT
1 TCGCGTTGCGAT
29012 TTACTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:29012 original size:41 final size:41
Alignment explanation
Indices: 28938--29030 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
28928 ATAGTAAGTA
28938 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
28979 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
29020 TCGCATTGCGA
1 TCGCATTGCGA
29031 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:29782 original size:24 final size:25
Alignment explanation
Indices: 29730--29783 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
29720 ATAATATCTT
*
29730 ATAACCATCTTGAACTATAAAAAAA
1 ATAACCATCTTAAACTATAAAAAAA
* *
29755 ATAATCATCTTAAACTAT-TAAAAA
1 ATAACCATCTTAAACTATAAAAAAA
29779 ATAAC
1 ATAAC
29784 TTTTTAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.28
Consensus pattern (25 bp):
ATAACCATCTTAAACTATAAAAAAA
Found at i:31258 original size:13 final size:13
Alignment explanation
Indices: 31240--31264 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31230 ATTTTAATCC
31240 AAATTAATATTTG
1 AAATTAATATTTG
31253 AAATTAATATTT
1 AAATTAATATTT
31265 CTTTTCAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
AAATTAATATTTG
Found at i:32285 original size:7 final size:7
Alignment explanation
Indices: 32273--32383 Score: 57
Period size: 7 Copynumber: 15.9 Consensus size: 7
32263 TATGTGATAA
32273 GGTTTAG
1 GGTTTAG
32280 GGTTTAG
1 GGTTTAG
32287 GGTTTAG
1 GGTTTAG
*
32294 AGTTTAG
1 GGTTTAG
*
32301 AGTTTA-
1 GGTTTAG
* *
32307 TGTGATAG
1 GGT-TTAG
* *
32315 GATTTAA
1 GGTTTAG
*
32322 GGTTTAA
1 GGTTTAG
*
32329 AGTTTAG
1 GGTTTAG
*
32336 AGTTTAG
1 GGTTTAG
32343 GGTTTA-
1 GGTTTAG
* *
32349 TGTGTTAA
1 GGT-TTAG
*
32357 AGTTTAG
1 GGTTTAG
32364 GGTTTA-
1 GGTTTAG
*
32370 TGTGTTAG
1 GGT-TTAG
32378 GGTTTA
1 GGTTTA
32384 AGTTATGCCA
Statistics
Matches: 81, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
6 6 0.07
7 70 0.86
8 5 0.06
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (7 bp):
GGTTTAG
Found at i:32300 original size:21 final size:21
Alignment explanation
Indices: 32274--32383 Score: 109
Period size: 21 Copynumber: 5.2 Consensus size: 21
32264 ATGTGATAAG
*
32274 GTTTAGGGTTTA-GGGTTTAGA
1 GTTTAGGGTTTATGTG-TTAGA
* *
32295 GTTTAGAGTTTATGTGATAG-
1 GTTTAGGGTTTATGTGTTAGA
* *
32315 GATTTAAGGTTTAAAGT-TTAGA
1 G-TTTAGGGTTT-ATGTGTTAGA
*
32337 GTTTAGGGTTTATGTGTTAAA
1 GTTTAGGGTTTATGTGTTAGA
*
32358 GTTTAGGGTTTATGTGTTAGG
1 GTTTAGGGTTTATGTGTTAGA
32379 GTTTA
1 GTTTA
32384 AGTTATGCCA
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
20 4 0.06
21 62 0.86
22 6 0.08
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (21 bp):
GTTTAGGGTTTATGTGTTAGA
Found at i:32326 original size:42 final size:42
Alignment explanation
Indices: 32262--32369 Score: 137
Period size: 42 Copynumber: 2.6 Consensus size: 42
32252 TCATAACTAA
* **
32262 TTATGTGATAAGGTTTAGGGTTTAGGGTTTAGAGTTTAGAGT
1 TTATGTGATAAGGTTTAAGGTTTAAAGTTTAGAGTTTAGAGT
*
32304 TTATGTGAT-AGGATTTAAGGTTTAAAGTTTAGAGTTTAGGGT
1 TTATGTGATAAGG-TTTAAGGTTTAAAGTTTAGAGTTTAGAGT
* * *
32346 TTATGTGTTAAAGTTTAGGGTTTA
1 TTATGTGATAAGGTTTAAGGTTTA
32370 TGTGTTAGGG
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 3 0.05
42 52 0.91
43 2 0.04
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (42 bp):
TTATGTGATAAGGTTTAAGGTTTAAAGTTTAGAGTTTAGAGT
Found at i:32343 original size:28 final size:28
Alignment explanation
Indices: 32312--32369 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
32302 GTTTATGTGA
32312 TAGGATTTAAGGT-TTAAAGTTTAGAGTT
1 TAGGATTT-AGGTGTTAAAGTTTAGAGTT
* * *
32340 TAGGGTTTATGTGTTAAAGTTTAGGGTT
1 TAGGATTTAGGTGTTAAAGTTTAGAGTT
32368 TA
1 TA
32370 TGTGTTAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (28 bp):
TAGGATTTAGGTGTTAAAGTTTAGAGTT
Found at i:32383 original size:42 final size:41
Alignment explanation
Indices: 32262--32387 Score: 132
Period size: 42 Copynumber: 3.0 Consensus size: 41
32252 TCATAACTAA
*
32262 TTATGTGATAAGGTTTAGGGTTTAGGGTTTAGAGTTTAGAGT
1 TTATGTGATAAGGTTTAGGGTTTAGTG-TTAGAGTTTAGAGT
* *
32304 TTATGTGAT-AGGATTTAAGGTTTAAAGT-TTAGAGTTTAGGGT
1 TTATGTGATAAGG-TTTAGGGTTT--AGTGTTAGAGTTTAGAGT
* * *
32346 TTATGTGTTAAAGTTTAGGGTTTATGTGTTAGGGTTTA-AGT
1 TTATGTGATAAGGTTTAGGGTTTA-GTGTTAGAGTTTAGAGT
32387 T
1 T
32388 ATGCCATGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
40 1 0.01
41 8 0.11
42 57 0.81
43 2 0.03
44 2 0.03
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (41 bp):
TTATGTGATAAGGTTTAGGGTTTAGTGTTAGAGTTTAGAGT
Found at i:32689 original size:17 final size:17
Alignment explanation
Indices: 32663--32704 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
32653 ATTCGAGTTT
* *
32663 GAGTTCGAGCTTTAATC
1 GAGTTTGAGCTTGAATC
32680 GAGTTTGAGCTTGAATC
1 GAGTTTGAGCTTGAATC
*
32697 GAGCTTGA
1 GAGTTTGA
32705 ATCGAGCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (17 bp):
GAGTTTGAGCTTGAATC
Found at i:32700 original size:11 final size:11
Alignment explanation
Indices: 32686--32759 Score: 67
Period size: 11 Copynumber: 6.5 Consensus size: 11
32676 AATCGAGTTT
32686 GAGCTTGAATC
1 GAGCTTGAATC
32697 GAGCTTGAATC
1 GAGCTTGAATC
**
32708 GAGCTCAAAATC
1 GAGCT-TGAATC
*
32720 GAGCTTCAATC
1 GAGCTTGAATC
* *
32731 GAGCTCGAGTCTC
1 GAGCTTGA--ATC
*
32744 GAGCTTCAATC
1 GAGCTTGAATC
32755 GAGCT
1 GAGCT
32760 CTTGAATTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
11 33 0.66
12 9 0.18
13 8 0.16
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (11 bp):
GAGCTTGAATC
Found at i:32720 original size:23 final size:24
Alignment explanation
Indices: 32693--32760 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 24
32683 TTTGAGCTTG
*
32693 AATCGAGCTTGAATCGAGCTC-AA
1 AATCGAGCTTCAATCGAGCTCGAA
*
32716 AATCGAGCTTCAATCGAGCTCGAG
1 AATCGAGCTTCAATCGAGCTCGAA
**
32740 TCTCGAGCTTCAATCGAGCTC
1 AATCGAGCTTCAATCGAGCTC
32761 TTGAATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 20 0.50
24 20 0.50
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (24 bp):
AATCGAGCTTCAATCGAGCTCGAA
Found at i:36990 original size:21 final size:21
Alignment explanation
Indices: 36964--37020 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
36954 TCGATATACC
*
36964 CGCTATGGCCGCAATAGTGCT
1 CGCTATGGCCGCAATAGCGCT
*
36985 CGCTATGGCTGCAATAGCGCT
1 CGCTATGGCCGCAATAGCGCT
*
37006 CGCTATGGCCACAAT
1 CGCTATGGCCGCAAT
37021 CATGATAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (21 bp):
CGCTATGGCCGCAATAGCGCT
Found at i:42853 original size:37 final size:36
Alignment explanation
Indices: 42754--42872 Score: 161
Period size: 35 Copynumber: 3.3 Consensus size: 36
42744 TGGTAACCAA
42754 CTTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
* * *
42791 CCTTG-AAAATGGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
42826 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
42863 -GTTGAAAAAT
1 CTTTGAAAAAT
42873 GATAATGGGA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
35 32 0.44
36 15 0.21
37 25 0.35
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:42873 original size:72 final size:69
Alignment explanation
Indices: 42727--42870 Score: 193
Period size: 72 Copynumber: 2.1 Consensus size: 69
42717 CCTACATGTT
*
42727 AAAATGGTTTTCAAGTTTGGTAACCAACTTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTTC
1 AAAATGGTTTTCAAGTTTGGTAAACAACTTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTTC
42792 CTTG
66 CTTG
* * *
42796 AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTG-AAAAATAGTTTTTCAAAGTTTGGTAGATG
1 AAAATGGTTTTC-AAGTTTGGTAAACA--ACTTTGAAAAAATAG-TTTTCAAAGTTTGGTAAATG
*
42860 TTT-GTTG
62 TTTCCTTG
42867 AAAA
1 AAAA
42871 ATGATAATGG
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
69 12 0.18
70 12 0.18
71 15 0.23
72 27 0.41
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (69 bp):
AAAATGGTTTTCAAGTTTGGTAAACAACTTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTTC
CTTG
Found at i:47403 original size:35 final size:35
Alignment explanation
Indices: 47364--47475 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 35
47354 CAACTTTGAA
47364 AAAATGGTTTTTAAAGTTTGGTAAATGTTTCCTTG
1 AAAATGGTTTTTAAAGTTTGGTAAATGTTTCCTTG
* * *
47399 AAAATGGTTTTCAAAATTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTTAAAGTTTGGTAAATGTTTCCTTG
* * **
47434 AAAAATAGTTTTTCAAAGTTTGGTAGAT-TTTTGTTG
1 -AAAATGGTTTTT-AAAGTTTGGTAAATGTTTCCTTG
47470 AAAATG
1 AAAATG
47476 ATAATGGGAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
35 37 0.57
36 16 0.25
37 12 0.18
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (35 bp):
AAAATGGTTTTTAAAGTTTGGTAAATGTTTCCTTG
Found at i:50734 original size:14 final size:12
Alignment explanation
Indices: 50718--50779 Score: 70
Period size: 14 Copynumber: 4.7 Consensus size: 12
50708 TGTAAAGAAA
50718 AAATTAAAAATAG
1 AAATTAAAAAT-G
50731 AAAATTAAAGTAATG
1 -AAATTAAA--AATG
50746 AAATTAAAAATG
1 AAATTAAAAATG
50758 AAATTAAAAGACTG
1 AAATTAAAA-A-TG
50772 AAATTAAA
1 AAATTAAA
50780 TTAATAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
12 13 0.30
13 1 0.02
14 26 0.59
15 1 0.02
16 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.24
Consensus pattern (12 bp):
AAATTAAAAATG
Found at i:50734 original size:28 final size:28
Alignment explanation
Indices: 50701--50760 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
50691 TTTAAAGTAT
50701 TGAAAAATGTAAAG-AA-AAAATTAAAAA
1 TGAAAAAT-TAAAGTAATAAAATTAAAAA
*
50728 T-AGAAAATTAAAGTAATGAAATTAAAAA
1 TGA-AAAATTAAAGTAATAAAATTAAAAA
50756 TGAAA
1 TGAAA
50761 TTAAAAGACT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
26 6 0.21
27 8 0.29
28 13 0.46
29 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.22
Consensus pattern (28 bp):
TGAAAAATTAAAGTAATAAAATTAAAAA
Found at i:50740 original size:26 final size:27
Alignment explanation
Indices: 50704--50765 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 27
50694 AAAGTATTGA
50704 AAAATGTAAAG-AA-AAAATTAAAAATAG
1 AAAAT-TAAAGTAATAAAATTAAAAAT-G
*
50731 AAAATTAAAGTAATGAAATTAAAAATG
1 AAAATTAAAGTAATAAAATTAAAAATG
50758 -AAATTAAA
1 AAAATTAAA
50766 AGACTGAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
26 13 0.41
27 8 0.25
28 11 0.34
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (27 bp):
AAAATTAAAGTAATAAAATTAAAAATG
Found at i:50773 original size:26 final size:28
Alignment explanation
Indices: 50718--50779 Score: 85
Period size: 26 Copynumber: 2.3 Consensus size: 28
50708 TGTAAAGAAA
50718 AAATTAAAAATAGAAAATTAAAGTAATG
1 AAATTAAAAATAGAAAATTAAAGTAATG
*
50746 AAATTAAAAAT-G-AAATTAAAAG-ACTG
1 AAATTAAAAATAGAAAATT-AAAGTAATG
50772 AAATTAAA
1 AAATTAAA
50780 TTAATAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 16 0.50
27 5 0.16
28 11 0.34
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.24
Consensus pattern (28 bp):
AAATTAAAAATAGAAAATTAAAGTAATG
Found at i:50789 original size:14 final size:14
Alignment explanation
Indices: 50732--50808 Score: 63
Period size: 14 Copynumber: 5.6 Consensus size: 14
50722 TAAAAATAGA
50732 AAATTAAA-GTAATG
1 AAATTAAATG-AATG
50746 AAATTAAA--AATG
1 AAATTAAATGAATG
* *
50758 AAATTAAAAGACTG
1 AAATTAAATGAATG
* *
50772 AAATTAAATTAATA
1 AAATTAAATGAATG
50786 AAATATAAATGACAT-
1 AAAT-TAAATGA-ATG
50801 AAATTAAA
1 AAATTAAA
50809 ATAAAAGTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
12 12 0.23
14 29 0.55
15 10 0.19
16 2 0.04
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.27
Consensus pattern (14 bp):
AAATTAAATGAATG
Found at i:50827 original size:24 final size:25
Alignment explanation
Indices: 50774--50835 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
50764 AAAGACTGAA
50774 ATTAAATT--AATAAAATATAAATG
1 ATTAAATTAAAATAAAATATAAATG
* *
50797 ACATAAATTAAAATAAAA-GTAAATG
1 A-TTAAATTAAAATAAAATATAAATG
*
50822 ATTAAAATAAAATA
1 ATTAAATTAAAATA
50836 TCAGAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 1 0.03
24 17 0.53
25 7 0.22
26 7 0.22
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (25 bp):
ATTAAATTAAAATAAAATATAAATG
Found at i:52306 original size:14 final size:14
Alignment explanation
Indices: 52284--52317 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
52274 TGAATAAGTT
*
52284 CTTCATATTATGAA
1 CTTCTTATTATGAA
52298 CTTCTTATTATGAA
1 CTTCTTATTATGAA
52312 CTTCTT
1 CTTCTT
52318 CTTCATCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (14 bp):
CTTCTTATTATGAA
Found at i:52415 original size:139 final size:138
Alignment explanation
Indices: 52159--52565 Score: 506
Period size: 123 Copynumber: 3.0 Consensus size: 138
52149 GAACAAGCTA
* * *
52159 TTCTCATTATGAACTTCTTCTTCCTCTTCATTGGATGAGTTCTTCTCATTAT--GAACTCTTTCT
1 TTCTTATTATGAACTTCTTCTT-CTCTTCA---GATGAGTTCTTCTTATTATACGAACTCCTTCT
* * * *
52222 GGAAATCTTGATACTGCTCTATATCCTTATGCAATAGAGTCGAGCAAATGGTTGAATAAGTTCTT
62 GGAAATGTTGATGCTGCTCTATATCCTTCTGCAATAGAGTCGAGCAAAAGGTTGAATAAGTTCTT
*
52287 CATATTATGAAC
127 CAGATTATGAAC
*
52299 TTCTTATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTTATTATACGAGCTCCTTCTGGA
1 TTCTTATTATGAACTTCTTCTTC-TCTTCAGATGAGTTCTTCTTATTATACGAACTCCTTCTGGA
* *
52364 AATGTTGATGCTGCTCTATCTCATTCTGCAATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAG
65 AATGTTGATGCTGCTCTATATCCTTCTGCAATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAG
52429 ATTATG-A-
130 ATTATGAAC
*
52436 -----ATT-T--A-TTCTTC--CTCTTCAGATGAGTTCTTCTTA-T-TACGAACTCCTTTTGGAA
1 TTCTTATTATGAACTTCTTCTTCTCTTCAGATGAGTTCTTCTTATTATACGAACTCCTTCTGGAA
* * * *
52488 ATGTTGATGTTGCTCTATATCCTTCTACGATAGAGTCGAGCAAAAAGTTGAATAAGTTCTTCAGA
66 ATGTTGATGCTGCTCTATATCCTTCTGCAATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGA
52553 TTATGAAC
131 TTATGAAC
52561 TTCTT
1 TTCTT
52566 CTTCCTCTTA
Statistics
Matches: 238, Mismatches: 19, Indels: 30
0.83 0.07 0.10
Matches are distributed among these distances:
123 80 0.34
124 2 0.01
125 21 0.09
126 1 0.00
128 6 0.03
129 1 0.00
131 1 0.00
132 3 0.01
137 18 0.08
138 1 0.00
139 77 0.32
140 27 0.11
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (138 bp):
TTCTTATTATGAACTTCTTCTTCTCTTCAGATGAGTTCTTCTTATTATACGAACTCCTTCTGGAA
ATGTTGATGCTGCTCTATATCCTTCTGCAATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAGA
TTATGAAC
Found at i:52525 original size:123 final size:123
Alignment explanation
Indices: 52304--53248 Score: 1329
Period size: 123 Copynumber: 7.5 Consensus size: 123
52294 TGAACTTCTT
* *
52304 ATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTTATTATACGAGCTCCTTCTGGAAATGT
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTA-T-TACGAACTCCTTCTGGAAATGT
* * *
52369 TGATGCTGCTCTATCTCATTCTGCAATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAG
64 TGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAG
* * *
52429 ATTATGAATTTATTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTTTGGAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
* * *
52494 ATGTTGCTCTATATCCTTCTACGATAGAGTCGAGCAAAAAGTTGAATAAGTTCTTCAG
66 ATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAG
* *
52552 ATTATGAACTTCTTCTTCCTCTTAATATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
* * *
52617 ATGCTGCTCTATCTCCTTCTGCGATTGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAA
66 ATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAG
* *
52675 ATTATAAACTTCTTCAAATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTTATTAC-AAC
1 ATTATGAA------C----T-T---C-T--TCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA-
* * * *
52739 CTCCTTCTGAAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTCGATCAAAAAGTTGAAT
48 CTCCTTCTGGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAAT
*
52804 AAGTTCTTTAG
113 AAGTTCTTCAG
* *
52815 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATCCTTATTACGAACTCCTTCTGGAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
* * * *
52880 ATGCTACTCTATCTCCTTTTGCGATAGAGTTGAGCAAAAGGTTGAATAAGTTCTTCAG
66 ATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAG
*
52938 ATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
* *
53003 ATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGAAAAAAGTTGAATAAGTTCTTCAG
66 ATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAG
* * * *
53061 ATTATGAACATCTTCTTCCTCTTCAGATGAG-T-TTCTTATTATGAACTCCTTCTGGAAATATTA
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
* *
53124 ATATTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCAG
66 ATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAG
* *
53182 ATTATGAACTTCTTATTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGAAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
53247 AT
66 AT
53249 CCCTCGAGTG
Statistics
Matches: 731, Mismatches: 68, Indels: 44
0.87 0.08 0.05
Matches are distributed among these distances:
121 111 0.15
122 2 0.00
123 461 0.63
124 3 0.00
125 38 0.05
126 1 0.00
129 2 0.00
130 1 0.00
133 1 0.00
134 2 0.00
137 1 0.00
138 1 0.00
139 2 0.00
140 105 0.14
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (123 bp):
ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
ATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAG
Found at i:52709 original size:20 final size:17
Alignment explanation
Indices: 52667--52706 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
52657 GTTGAATAAG
52667 TTCTTCAAATTATAAAC
1 TTCTTCAAATTATAAAC
*
52684 TTCTTCAAATTATGAAC
1 TTCTTCAAATTATAAAC
52701 TTCTTC
1 TTCTTC
52707 TTCCTCTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (17 bp):
TTCTTCAAATTATAAAC
Found at i:52709 original size:140 final size:140
Alignment explanation
Indices: 52544--52829 Score: 459
Period size: 140 Copynumber: 2.0 Consensus size: 140
52534 GTTGAATAAG
*
52544 TTCTTCAGATTATGAACTTCTTCTTCCTCTT-AATATGAGTTCTTCTTATTACGAA-CTCCTTCT
1 TTCTTCAAATTATGAACTTCTTCTTCCTCTTCAA-ATGAGTTCTTCTTATTAC-AACCTCCTTCT
* * * *
52607 GGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATTGAGTCGAGCAAAAGGTTGAATAAGTTCTT
64 GAAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAAGTTGAATAAGTTCTT
52672 CAAATTATAAAC
129 CAAATTATAAAC
52684 TTCTTCAAATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTTATTACAACCTCCTTCTGA
1 TTCTTCAAATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTTATTACAACCTCCTTCTGA
* *
52749 AAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTCGATCAAAAAGTTGAATAAGTTCTTTA
66 AAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAAGTTGAATAAGTTCTTCA
* *
52814 GATTATGAAC
131 AATTATAAAC
52824 TTCTTC
1 TTCTTC
52830 TTCCTCTTCA
Statistics
Matches: 135, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
139 2 0.01
140 131 0.97
141 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (140 bp):
TTCTTCAAATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTTATTACAACCTCCTTCTGA
AAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAAGTTGAATAAGTTCTTCA
AATTATAAAC
Found at i:52767 original size:263 final size:260
Alignment explanation
Indices: 52416--53195 Score: 1135
Period size: 263 Copynumber: 3.0 Consensus size: 260
52406 AAAAGGTTGA
* *
52416 ATAAGTTCTTCAGATTATGAATTTATTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCT
1 ATAACTTCTTCAGATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCT
* * *
52481 TTTGGAAATGTTGATGTTGCTCTATATCCTTCTACGATAGAGTCGAGCAAAAAGTTGAATAAGTT
66 TCTGGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAAGTTGAATAAGTT
* *
52546 CTTCAGATTATGAACTTCTTCTTCCTCTTAATATGAGTTCTTCTTATTACGAACTCCTTCTGGAA
131 CTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTT-TTCTTATTACGAACTCCTTCTGGAA
*
52611 ATGTTGATGCTGCTCTATCTCCTTCTGCGATTGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAAA
195 ATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTC-AA
52676 TT
259 TT
* * *
52678 ATAAACTTCTTCAAATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTTATTAC-AACCTC
1 AT-AACTTCTTCAGATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA-CTC
* * *
52742 CTTCTGAAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTCGATCAAAAAGTTGAATAAG
64 CTTCTGGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAAGTTGAATAAG
* *
52807 TTCTTTAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATCCTTATTACGAACTCCTTCTGG
129 TTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTT-TTCTTATTACGAACTCCTTCTGG
* * *
52872 AAATGTTGATGCTACTCTATCTCCTTTTGCGATAGAGTTGAGCAAAAGGTTGAATAAG-------
193 AAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCA
52930 ---
258 ATT
52930 -----TTCTTCAGATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCT
1 ATAACTTCTTCAGATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCT
*
52990 TCTGGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGAAAAAAGTTGAATAAGTT
66 TCTGGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAAGTTGAATAAGTT
* *
53055 CTTCAGATTATGAACATCTTCTTCCTCTTCAGATGAG-TTTCTTATTATGAACTCCTTCTGGAAA
131 CTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTCTTATTACGAACTCCTTCTGGAAA
* * ** *
53119 TATTAATATTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCAGAT
196 TGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCA-AT
53184 T
260 T
53185 ATGAACTTCTT
1 AT-AACTTCTT
53196 ATTCCTCTTC
Statistics
Matches: 459, Mismatches: 39, Indels: 41
0.85 0.07 0.08
Matches are distributed among these distances:
244 71 0.15
245 1 0.00
246 150 0.33
247 2 0.00
261 5 0.01
262 4 0.01
263 226 0.49
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (260 bp):
ATAACTTCTTCAGATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCT
TCTGGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAAGTTGAATAAGTT
CTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTCTTATTACGAACTCCTTCTGGAAA
TGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAATT
Found at i:52843 original size:386 final size:383
Alignment explanation
Indices: 52164--53248 Score: 1490
Period size: 386 Copynumber: 2.9 Consensus size: 383
52154 AGCTATTCTC
* * * * *
52164 ATTATGAACTTCTTCTTCCTCTTCATTGGATGAGTTCTTCTCATTATGAACTCTTTCTGGAAATC
1 ATTATGAACTTCTTCTTCCTCTT-AAT--ATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATG
* * * * * *
52229 TTGATACTGCTCTATATCCTTATGCAATAGAGTCGAGCAAATGGTTGAATAAGTTCTTCATATTA
63 TTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAAATTA
* *
52294 TGAACTTCTT--ATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTTATTATACGAGCTCC
128 T-AACTTCTTCAATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTA-T-TAC-AACTCC
* * *
52357 TTCTGGAAATGTTGATGCTGCTCTATCTCATTCTGCAATAGAGTCGAGCAAAAGGTTGAATAAGT
189 TTCTGGAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGT
* * *
52422 TCTTCAGATTATGAATTTATTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTTTGGA
254 TCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGA
* *
52487 AATGTTGATGTTGCTCTATATCCTTCTACGATAGAGTCGAGCAAAAAGTTGAATAAGTTCTTCAG
319 AATGTTGATGCTACTCTATATCCTTCTACGATAGAGTCGAGCAAAAAGTTGAATAAGTTCTTCAG
52552 ATTATGAACTTCTTCTTCCTCTTAATATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTAATATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
*
52617 ATGCTGCTCTATCTCCTTCTGCGATTGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAAATTATAA
66 ATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAAATTAT-A
*
52682 ACTTCTTCAAATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTTATTACAACCTCCTTCT
130 ACTTCTTC-AATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACAA-CTCCTTCT
* * *
52747 GAAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTCGATCAAAAAGTTGAATAAGTTCTT
193 GGAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTT
* * *
52812 TAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATCCTTATTACGAACTCCTTCTGGAAATG
258 CAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATG
* * * * *
52877 TTGATGCTACTCTATCTCCTTTTGCGATAGAGTTGAGCAAAAGGTTGAATAAGTTCTTCAG
323 TTGATGCTACTCTATATCCTTCTACGATAGAGTCGAGCAAAAAGTTGAATAAGTTCTTCAG
* * *
52938 ATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTAATATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
* * *
53003 ATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGAAAAAAGTTGAATAAGTTCTTC--------A
66 ATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAAATTATAA
* * *
53060 -------GATTATGAACATCTTCTTCCTCTTCAGATGAG-T-TTCTTATTATGAACTCCTTCTGG
131 CTTCTTCAATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTA-CAACTCCTTCTGG
* * *
53116 AAATATTAAT-ATTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTC
195 AAATGTTGATGA-TGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTC
* *
53180 AGATTATGAACTTCTTATTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGAAAATGT
259 AGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGT
53245 TGAT
324 TGAT
53249 CCCTCGAGTG
Statistics
Matches: 634, Mismatches: 57, Indels: 33
0.88 0.08 0.05
Matches are distributed among these distances:
366 1 0.00
367 139 0.22
368 3 0.00
369 29 0.05
377 1 0.00
385 100 0.16
386 297 0.47
387 3 0.00
388 61 0.10
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (383 bp):
ATTATGAACTTCTTCTTCCTCTTAATATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
ATGCTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAAATTATAA
CTTCTTCAATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACAACTCCTTCTGGA
AATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCTTCAG
ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
ATGCTACTCTATATCCTTCTACGATAGAGTCGAGCAAAAAGTTGAATAAGTTCTTCAG
Found at i:56112 original size:12 final size:11
Alignment explanation
Indices: 56109--56190 Score: 66
Period size: 11 Copynumber: 7.6 Consensus size: 11
56099 TTTCCTTCTT
56109 TTTTTCTTTTC
1 TTTTTCTTTTC
56120 TTTTTCTTTTC
1 TTTTTCTTTTC
*
56131 TTTTTCCTTTAC
1 TTTTT-CTTTTC
**
56143 -TTTTC--AGC
1 TTTTTCTTTTC
56151 TTTTTCTTTTC
1 TTTTTCTTTTC
*
56162 TTTTGT-TTTAC
1 TTTT-TCTTTTC
56173 TTTTTTCTTTT-
1 -TTTTTCTTTTC
56184 TTTTTCT
1 TTTTTCT
56191 AATAGATGAG
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
8 1 0.02
9 5 0.09
10 8 0.14
11 30 0.53
12 13 0.23
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:56187 original size:11 final size:11
Alignment explanation
Indices: 56095--56188 Score: 55
Period size: 11 Copynumber: 8.3 Consensus size: 11
56085 CTTGATTCAA
*
56095 TTTTTTTCCTT
1 TTTTTTTTCTT
*
56106 CTTTTTTTCTT
1 TTTTTTTTCTT
*
56117 TTCTTTTTCTT
1 TTTTTTTTCTT
*
56128 TTCTTTTTCCTT
1 TT-TTTTTTCTT
***
56140 TACTTTTCAGCTT
1 T--TTTTTTTCTT
*
56153 TTTCTTTTCTT
1 TTTTTTTTCTT
* *
56164 TTGTTTTACTT
1 TTTTTTTTCTT
56175 TTTTCTTTT-TT
1 TTTT-TTTTCTT
56186 TTT
1 TTT
56189 CTAATAGATG
Statistics
Matches: 61, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
11 42 0.69
12 11 0.18
13 7 0.11
14 1 0.02
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:57749 original size:61 final size:61
Alignment explanation
Indices: 57681--57801 Score: 156
Period size: 61 Copynumber: 2.0 Consensus size: 61
57671 ATGCAGTGGT
**
57681 AGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCAAATGCAATTCATGCATCGATGCATA
1 AGTGCATCGATGCATC-CCATTAATAAT-AAAACATCAAATGCAATTCATGCATCGATGCATA
* * **
57742 AGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGCATCGATGCAT
1 AGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCATGCATCGATGCAT
57802 CCCAGCAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
61 48 0.92
62 4 0.08
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (61 bp):
AGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCATGCATCGATGCATA
Found at i:58186 original size:11 final size:12
Alignment explanation
Indices: 58166--58200 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
58156 CATATATCTT
58166 CATGTGATATGA
1 CATGTGATATGA
*
58178 TAT-TGATATGA
1 CATGTGATATGA
58189 CATGTGATATGA
1 CATGTGATATGA
58201 GAACATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:58218 original size:23 final size:26
Alignment explanation
Indices: 58166--58233 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 26
58156 CATATATCTT
*
58166 CATGTGATAT--GATA-TTGATATGA
1 CATGTGATATGAGATACATGATATGA
58189 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
58214 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
58234 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 21 0.52
24 9 0.22
25 10 0.25
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Done.