Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004034.1 Hibiscus syriacus cultivar Beakdansim tig00008813_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: 87627
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:5098 original size:27 final size:27
Alignment explanation
Indices: 5060--5116 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
5050 TCTCTGAAGG
*
5060 TCTCATCTTCACGTTCACATTCTCCCT
1 TCTCATCTTCACCTTCACATTCTCCCT
* * *
5087 TCTCTTCTTCACCTTCACGTTCTCCGT
1 TCTCATCTTCACCTTCACATTCTCCCT
5114 TCT
1 TCT
5117 TCTCACCTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.11, C:0.40, G:0.05, T:0.44
Consensus pattern (27 bp):
TCTCATCTTCACCTTCACATTCTCCCT
Found at i:6494 original size:15 final size:13
Alignment explanation
Indices: 6473--6508 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
6463 CAAAAATAAA
6473 TTATTTTTTATTT
1 TTATTTTTTATTT
6486 ATCTATTTTTTATTT
1 -T-TATTTTTTATTT
6501 TTATTTTT
1 TTATTTTT
6509 ATCATATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.33
14 2 0.10
15 12 0.57
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (13 bp):
TTATTTTTTATTT
Found at i:8650 original size:19 final size:19
Alignment explanation
Indices: 8626--8662 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
8616 ACAAACGTGT
8626 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
8645 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
8663 TCCAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:8913 original size:12 final size:12
Alignment explanation
Indices: 8893--8926 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
8883 GTCCCGTCTC
*
8893 GGGTTGTGGTCG
1 GGGTCGTGGTCG
8905 GGGTCGTGGTCG
1 GGGTCGTGGTCG
*
8917 TGGTCGTGGT
1 GGGTCGTGGT
8927 AATACGTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.12, G:0.56, T:0.32
Consensus pattern (12 bp):
GGGTCGTGGTCG
Found at i:9066 original size:21 final size:21
Alignment explanation
Indices: 9042--9159 Score: 123
Period size: 21 Copynumber: 5.6 Consensus size: 21
9032 AATTTGAAAA
*
9042 ATCGCATTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
* **
9063 ATCGCGTTGCGA--TAGTCAGA
1 ATCGCGTTGCGATTTTGT-ATT
*
9083 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTTTGTATT
* *
9104 ATAGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTTTGTATT
**
9125 ATCGCGTTGCGATTTACATATT
1 ATCGCGTTGCGATTT-TGTATT
9147 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
9160 AGTCAAAATC
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.04
20 13 0.16
21 45 0.56
22 19 0.24
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:9102 original size:41 final size:41
Alignment explanation
Indices: 9039--9180 Score: 169
Period size: 41 Copynumber: 3.4 Consensus size: 41
9029 GTAAATTTGA
* *
9039 AAAATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTC
1 AAAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTC
* *
9080 AGAATCGCGTTGCGATTATGTATTATAGCGTTGCGATTATGT-
1 AAAATCGCGTTGCGATTATGTATTATCGCGTTGCGA-TA-GTC
** **
9122 ATTATCGCGTTGCGATTTACATATTATCGCGTTGCGATAGTC
1 AAAATCGCGTTGCGA-TTATGTATTATCGCGTTGCGATAGTC
*
9164 AAAATCGCGTTGTGATT
1 AAAATCGCGTTGCGATT
9181 TATATATTCA
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
41 36 0.42
42 29 0.34
43 20 0.24
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.37
Consensus pattern (41 bp):
AAAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTC
Found at i:9316 original size:142 final size:142
Alignment explanation
Indices: 9147--9441 Score: 482
Period size: 142 Copynumber: 2.1 Consensus size: 142
9137 TTTACATATT
* *
9147 ATCGCGTTGCGATAGTCAAAATCGCGTTGTGATTTATATATTCACATTGCGACTTTCTAAAATCG
1 ATCGCGTTGCGATAGTCAAAATCGCGTTGCGATTTACATATTCACATTGCGACTTTCTAAAATCG
*
9212 CAACGCGAATTTGGAAAATCGTAATGCGATAGTCAAAATCGCGTTGCGAATCTGAAAACTGATTT
66 CAACGCGAATTTGGAAAATCGCAATGCGATAGTCAAAATCGCGTTGCGAATCTGAAAACTGATTT
*
9277 GTGATACTGGAG
131 GCGATACTGGAG
* * * *
9289 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTACATATTCGCATTTCGATTTTCTAAAATCG
1 ATCGCGTTGCGATAGTCAAAATCGCGTTGCGATTTACATATTCACATTGCGACTTTCTAAAATCG
* * *
9354 CAACGCGAATTTGGAAAATCGCAATGCGATAGTCAAAATCGCGTTGTGAATCTGGAAATTGATTT
66 CAACGCGAATTTGGAAAATCGCAATGCGATAGTCAAAATCGCGTTGCGAATCTGAAAACTGATTT
9419 GCGATACTGGAG
131 GCGATACTGGAG
*
9431 ATCGTGTTGCG
1 ATCGCGTTGCG
9442 GTTTAGAGAT
Statistics
Matches: 141, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (142 bp):
ATCGCGTTGCGATAGTCAAAATCGCGTTGCGATTTACATATTCACATTGCGACTTTCTAAAATCG
CAACGCGAATTTGGAAAATCGCAATGCGATAGTCAAAATCGCGTTGCGAATCTGAAAACTGATTT
GCGATACTGGAG
Found at i:10017 original size:29 final size:29
Alignment explanation
Indices: 9973--10061 Score: 97
Period size: 29 Copynumber: 3.1 Consensus size: 29
9963 ACACCCCTAT
*
9973 ATTAAATCCCCTTCCTGATTCTACATGAG
1 ATTAAATCCCCGTCCTGATTCTACATGAG
* * *
10002 ATTAAATCCCCGTCCTAATTCTATATGGG
1 ATTAAATCCCCGTCCTGATTCTACATGAG
* * * * *
10031 ATTAAATCTCTGTCATGTTTCTGCATGAG
1 ATTAAATCCCCGTCCTGATTCTACATGAG
10060 AT
1 AT
10062 CATATCTCAG
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.37
Consensus pattern (29 bp):
ATTAAATCCCCGTCCTGATTCTACATGAG
Found at i:12607 original size:20 final size:19
Alignment explanation
Indices: 12570--12617 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
12560 TCTAAATCCT
*
12570 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATTCCATTTTG
12589 ATTTTCAAAA-TCCATTTTTG
1 -TTTTCAAAATTCCA-TTTTG
*
12609 CTTTCAAAA
1 TTTTCAAAA
12618 GAAAATCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (19 bp):
TTTTCAAAATTCCATTTTG
Found at i:13116 original size:20 final size:20
Alignment explanation
Indices: 13091--13134 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
13081 ATTGAAGTAT
*
13091 GGAGGCTTGTTGATCGGTTG
1 GGAGGCTTGTTGATCGGTTA
13111 GGAGGCTTGTTGATCGGTTA
1 GGAGGCTTGTTGATCGGTTA
13131 GGAG
1 GGAG
13135 TCTTCCATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.09, G:0.45, T:0.32
Consensus pattern (20 bp):
GGAGGCTTGTTGATCGGTTA
Found at i:17438 original size:20 final size:21
Alignment explanation
Indices: 17397--17597 Score: 105
Period size: 20 Copynumber: 10.0 Consensus size: 21
17387 AAATGACCAA
* *
17397 CAAATTCGCAACGCGAA-CTC
1 CAAATTCGCAACACGAATTTC
* *
17417 CAATTTCGCAGCAC-AATTTC
1 CAAATTCGCAACACGAATTTC
*
17437 CAAATTCGCAACACGATTTTC
1 CAAATTCGCAACACGAATTTC
*
17458 CAAATTCGCAACTCG-ATTTC
1 CAAATTCGCAACACGAATTTC
** *
17478 TGAATTCGCAACGCGAATTT-
1 CAAATTCGCAACACGAATTTC
***
17498 CTTTTTCGCAACAC-AAGTTTC
1 CAAATTCGCAACACGAA-TTTC
** * *
17519 C-TTTTCGCAACAAGATTTTC
1 CAAATTCGCAACACGAATTTC
* *
17539 TAAA-TCGCAACACAAATTT-
1 CAAATTCGCAACACGAATTTC
**** * *
17558 TGTTTTCGCAACTCG-ATTTT
1 CAAATTCGCAACACGAATTTC
*
17578 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
17598 TAATTTCGTA
Statistics
Matches: 137, Mismatches: 34, Indels: 19
0.72 0.18 0.10
Matches are distributed among these distances:
19 9 0.07
20 99 0.72
21 29 0.21
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (21 bp):
CAAATTCGCAACACGAATTTC
Found at i:17477 original size:41 final size:40
Alignment explanation
Indices: 17397--17498 Score: 105
Period size: 41 Copynumber: 2.5 Consensus size: 40
17387 AAATGACCAA
** * *
17397 CAAATTCGCAACGCGAACTCCAATTTCGCAGCACAATTTC
1 CAAATTCGCAACGCGATTTCCAAATTCGCAACACAATTTC
* * *
17437 CAAATTCGCAACACGATTTTCCAAATTCGCAACTCGATTTC
1 CAAATTCGCAACGCGA-TTTCCAAATTCGCAACACAATTTC
**
17478 TGAATTCGCAACGCGAATTTC
1 CAAATTCGCAACGCG-ATTTC
17499 TTTTTCGCAA
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
40 15 0.30
41 34 0.68
42 1 0.02
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.26
Consensus pattern (40 bp):
CAAATTCGCAACGCGATTTCCAAATTCGCAACACAATTTC
Found at i:17507 original size:81 final size:80
Alignment explanation
Indices: 17399--17549 Score: 196
Period size: 81 Copynumber: 1.9 Consensus size: 80
17389 ATGACCAACA
* *
17399 AATTCGCAACGCGAACTCCAATTTCGCAGCACAA-TTTCCAAATTCGCAACACGATTTTCCAAAT
1 AATTCGCAACGCGAACTCCAATTTCGCAACACAAGTTTCC-AATTCGCAACAAGATTTTCCAAA-
17463 TCGCAACTCGATTTCTG
64 TCGCAACTCGATTTCTG
* * ** ** *
17480 AATTCGCAACGCGAATTTCTTTTTCGCAACACAAGTTTCCTTTTCGCAACAAGATTTTCTAAATC
1 AATTCGCAACGCGAACTCCAATTTCGCAACACAAGTTTCCAATTCGCAACAAGATTTTCCAAATC
17545 GCAAC
66 GCAAC
17550 ACAAATTTTG
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
80 7 0.12
81 48 0.80
82 5 0.08
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (80 bp):
AATTCGCAACGCGAACTCCAATTTCGCAACACAAGTTTCCAATTCGCAACAAGATTTTCCAAATC
GCAACTCGATTTCTG
Found at i:17586 original size:60 final size:60
Alignment explanation
Indices: 17441--17590 Score: 151
Period size: 60 Copynumber: 2.5 Consensus size: 60
17431 AATTTCCAAA
** * * *
17441 TTCGCAACACGATTTTCCAAATTCGCAACTCGATTTCTGAATTCGCAACGCGAATTTCTTT
1 TTCGCAACACGATTTT-CAAATTCGCAACAAGATTTCTGAAATCGCAACACAAATTTCTTT
* * ***
17502 TTCGCAACACAAGTTTCCTTTTCGCAACAAGATTTTCT-AAATCGCAACACAAATTT-TGTT
1 TTCGCAACACGATTTTCAAATTCGCAACAAGA-TTTCTGAAATCGCAACACAAATTTCT-TT
* *
17562 TTCGCAACTCGATTTTCGAATTCGCAACA
1 TTCGCAACACGATTTTCAAATTCGCAACA
17591 CGAATTTTAA
Statistics
Matches: 71, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
59 1 0.01
60 51 0.72
61 19 0.27
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (60 bp):
TTCGCAACACGATTTTCAAATTCGCAACAAGATTTCTGAAATCGCAACACAAATTTCTTT
Found at i:17598 original size:40 final size:40
Alignment explanation
Indices: 17441--17598 Score: 140
Period size: 40 Copynumber: 3.9 Consensus size: 40
17431 AATTTCCAAA
* * **
17441 TTCGCAACACGATTTTCCAAATTCGCAACTCG-ATTTCTGAA
1 TTCGCAACACGATTTT-CTAATTCGCAACACGAATTT-TGTT
* * ** **
17482 TTCGCAACGCGAATTTCTTTTTCGCAACAC-AAGTTTCCTT
1 TTCGCAACACGATTTTCTAATTCGCAACACGAA-TTTTGTT
* * *
17522 TTCGCAACAAGATTTTCTAAATCGCAACACAAATTTTGTT
1 TTCGCAACACGATTTTCTAATTCGCAACACGAATTTTGTT
* *
17562 TTCGCAACTCGATTTTCGAATTCGCAACACGAATTTT
1 TTCGCAACACGATTTTCTAATTCGCAACACGAATTTT
17599 AATTTCGTAA
Statistics
Matches: 91, Mismatches: 23, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
40 72 0.79
41 19 0.21
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (40 bp):
TTCGCAACACGATTTTCTAATTCGCAACACGAATTTTGTT
Found at i:17605 original size:20 final size:20
Alignment explanation
Indices: 17418--17629 Score: 77
Period size: 20 Copynumber: 10.7 Consensus size: 20
17408 CGCGAACTCC
* *
17418 AATTTCGCAGCAC-AATTTCC
1 AATTTCGCAACACGAATTT-T
*
17438 AAATTCGCAACACG-ATTTT
1 AATTTCGCAACACGAATTTT
* *
17457 CCAAATTCGCAACTCG-ATTTCT
1 --AATTTCGCAACACGAATTT-T
*
17479 GAA-TTCGCAACGCGAATTTCT
1 -AATTTCGCAACACGAATTT-T
* *
17500 -TTTTCGCAACAC-AAGTTTC
1 AATTTCGCAACACGAA-TTTT
** * *
17519 CTTTTCGCAACAAGATTTTCT
1 AATTTCGCAACACGAATTT-T
* *
17540 AA-ATCGCAACACAAATTTT
1 AATTTCGCAACACGAATTTT
** *
17559 GTTTTCGCAACTCG-ATTTT
1 AATTTCGCAACACGAATTTT
17578 CGAA-TTCGCAACACGAATTTT
1 --AATTTCGCAACACGAATTTT
* *
17599 AATTTCGTAACA-G-CTTTT
1 AATTTCGCAACACGAATTTT
*
17617 ATTTTCGCAACAC
1 AATTTCGCAACAC
17630 AAATATTTTG
Statistics
Matches: 146, Mismatches: 30, Indels: 33
0.70 0.14 0.16
Matches are distributed among these distances:
18 14 0.10
19 11 0.08
20 89 0.61
21 31 0.21
22 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (20 bp):
AATTTCGCAACACGAATTTT
Found at i:17786 original size:14 final size:15
Alignment explanation
Indices: 17767--17804 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
17757 TCCCCATCTC
17767 TAATTTTTTT-TACA
1 TAATTTTTTTATACA
*
17781 TAATTTTATTTATATA
1 TAATTTT-TTTATACA
17797 TAATTTTT
1 TAATTTTT
17805 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTATACA
Found at i:24618 original size:23 final size:23
Alignment explanation
Indices: 24592--24647 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
24582 CACCACAGCT
* *
24592 CGTATAAATGCACCTAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* *
24615 CGTAGAATTGCACCAAAGTGCCG
1 CGTAGAAATGCACCAAAGTGCCA
*
24638 CGTAGGAATG
1 CGTAGAAATG
24648 GACCGTAGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Found at i:24699 original size:22 final size:22
Alignment explanation
Indices: 24674--24715 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
24664 AAAATGTCCA
* *
24674 TAAGGACCATATAGATATTCTT
1 TAAGAACCATATACATATTCTT
*
24696 TAAGAATCATATACATATTC
1 TAAGAACCATATACATATTC
24716 CAAGGACCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (22 bp):
TAAGAACCATATACATATTCTT
Found at i:25008 original size:15 final size:14
Alignment explanation
Indices: 24988--25017 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
24978 ACCTGCTTTC
24988 TGGTATCGATAGCTA
1 TGGTATCGATA-CTA
25003 TGGTATCGATACTA
1 TGGTATCGATACTA
25017 T
1 T
25018 CATTTTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (14 bp):
TGGTATCGATACTA
Found at i:29034 original size:3 final size:3
Alignment explanation
Indices: 29026--29124 Score: 171
Period size: 3 Copynumber: 33.0 Consensus size: 3
29016 CGGAAGGTGA
*
29026 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
29074 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29122 AAT
1 AAT
29125 TGTAAACATT
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29160 original size:3 final size:3
Alignment explanation
Indices: 29152--29208 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
29142 TCATTTCGTT
*
29152 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29200 TTA TTA TTA
1 TTA TTA TTA
29209 AATAAAATAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:31340 original size:20 final size:21
Alignment explanation
Indices: 31317--31368 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
31307 AGAAATTAAA
31317 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
31337 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
31359 -ATT-ATTTATT
1 AATTCATTTATT
31369 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:33489 original size:22 final size:22
Alignment explanation
Indices: 33458--33500 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
33448 TTGAATTGCA
33458 CATTTTGCATTCTT-ATTTTTC
1 CATTTTGCATTCTTCATTTTTC
*
33479 CATTTATGCATTTTTCATTTTT
1 CATTT-TGCATTCTTCATTTTT
33501 TATTTAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.63
Consensus pattern (22 bp):
CATTTTGCATTCTTCATTTTTC
Found at i:37775 original size:114 final size:114
Alignment explanation
Indices: 37575--37803 Score: 350
Period size: 114 Copynumber: 2.0 Consensus size: 114
37565 AGCAAGTGCC
*
37575 ATTTGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATG
1 ATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATG
* * * * *
37640 ATCTGGTTTGATATGAACCCCAAAACCAATCATTGGATTTAAAAGATGA
66 ATCTGATTCGATAGGAACCCCAAAACCAATCATTGAAATTAAAAGATGA
* *
37689 ATTTGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATG
* * * *
37754 ATCTGATTCGGTAGGAACCCCAGAACCGATCATTGAAATTGAAAGATGA
66 ATCTGATTCGATAGGAACCCCAAAACCAATCATTGAAATTAAAAGATGA
37803 A
1 A
37804 ATGCATGATC
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
ATTTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATG
ATCTGATTCGATAGGAACCCCAAAACCAATCATTGAAATTAAAAGATGA
Found at i:40419 original size:22 final size:22
Alignment explanation
Indices: 40389--40443 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
40379 AGATTCTCAC
* *
40389 TTCAGAGATGACAAATTTTCTT
1 TTCAAAGATGACAAATTCTCTT
* * *
40411 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAAATTCTCTT
40433 TTCAAAGATGA
1 TTCAAAGATGA
40444 AAGCTTTATG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGACAAATTCTCTT
Found at i:41223 original size:76 final size:76
Alignment explanation
Indices: 41124--42891 Score: 3131
Period size: 76 Copynumber: 23.6 Consensus size: 76
41114 CTATTTCCCA
*
41124 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCTGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41189 AGCCTTAGGGT
66 AGCCTTAGGGT
41200 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41265 AGCCTTAGGGT
66 AGCCTTAGGGT
41276 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41341 AGCCTTAGGGT
66 AGCCTTAGGGT
41352 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41417 AGCCTTAGGGT
66 AGCCTTAGGGT
41428 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGC----T--T-TTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
41486 AAGCCTTAGGGT
65 AAGCCTTAGGGT
41498 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41563 AGCCTTAGGGT
66 AGCCTTAGGGT
41574 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
41639 AAGCCTTAGGGT
65 AAGCCTTAGGGT
41651 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41716 AGCCTTAGGGT
66 AGCCTTAGGGT
41727 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41792 AGCCTTAGGGT
66 AGCCTTAGGGT
41803 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41868 AGCCTTAGGGT
66 AGCCTTAGGGT
41879 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGC----T--T-TTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
41937 AAGCCTTAGGGT
65 AAGCCTTAGGGT
41949 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42014 AGCCTTAGGGT
66 AGCCTTAGGGT
42025 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42090 AAGCCTTAGGGT
65 AAGCCTTAGGGT
42102 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
42167 AGCCTTAAGGT
66 AGCCTTAGGGT
*
42178 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42243 AAGCCTTAGGGT
65 AAGCCTTAGGGT
42255 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42320 AAGCCTTAGGGT
65 AAGCCTTAGGGT
42332 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAG----TT--T-TTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42390 AAGCCTTAGGGT
65 AAGCCTTAGGGT
42402 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGC----T--T-TTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42460 AAGCCTTAGGGT
65 AAGCCTTAGGGT
*
42472 CATCTGTAAGTCCTTCAGTGCATGATTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42537 AGCCTTAGGGT
66 AGCCTTAGGGT
42548 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42613 AAGCCTTAGGGT
65 AAGCCTTAGGGT
42625 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
42689 AGCCTTAAGGT
66 AGCCTTAGGGT
42700 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAG----TT--T-TTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42758 AAGCCTTAGGGT
65 AAGCCTTAGGGT
* *
42770 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAACCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42835 AGCCTTAGGGT
66 AGCCTTAGGGT
42846 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
42892 TCATATGTAA
Statistics
Matches: 1643, Mismatches: 12, Indels: 74
0.95 0.01 0.04
Matches are distributed among these distances:
69 85 0.05
70 247 0.15
71 4 0.00
73 11 0.01
75 73 0.04
76 764 0.47
77 459 0.28
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:41993 original size:451 final size:452
Alignment explanation
Indices: 41124--42891 Score: 3243
Period size: 451 Copynumber: 3.9 Consensus size: 452
41114 CTATTTCCCA
*
41124 CATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCTGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
41188 AAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
41253 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
131 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
41318 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATG-TTT
196 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
41382 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGT
261 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGT
41447 GCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCT
326 GCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCT
41512 TCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
391 TCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
41574 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
41639 AAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
41704 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
131 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
41769 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATG-TTT
196 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
41833 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGT
261 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGT
41898 GCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCT
326 GCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCT
41963 TCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
391 TCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
42025 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42090 AAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
42155 TGATGTTTTCAAAGCCTTAAGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
131 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCT
*
42220 TCGGGAGTTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
195 TCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
42285 TCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAG
260 TCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAG
*
42350 TGCATGATGTTTTCCAAAAAGCCTTCGGGAGTTTTTTTCAAAGCCTTAGGGTCATCTGTAAGTCC
325 TGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTTCAAAGCCTTAGGGTCATCTGTAAGTCC
42415 TTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGC----T--T-TTTTCAAAGCCTTAGGGT
390 TTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
42472 CATCTGTAAGTCCTTCAGTGCATGAT-TTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
42536 AAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTT
66 AAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTT
42601 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCT
130 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCT
*
42665 TCGGGAGCTTTTTGATGTTTTCAAAGCCTTAAGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
195 TCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
42730 TCCAAAAAGCCTTCGGGAG----TT--T-TTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAG
260 TCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAG
* *
42788 TGCATGATG-TTTCCAAAAAACCTTCGGGAACTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTG
325 TGCATGATGTTTTCCAAAAAGCCTTCGGGAGC----T--T-TTTTCAAAGCCTTAGGGTCATCTG
42852 TAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
383 TAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
42892 TCATATGTAA
Statistics
Matches: 1296, Mismatches: 10, Indels: 31
0.97 0.01 0.02
Matches are distributed among these distances:
437 19 0.01
438 45 0.03
439 1 0.00
441 3 0.00
443 20 0.02
444 45 0.03
445 90 0.07
446 82 0.06
447 119 0.09
448 1 0.00
450 28 0.02
451 601 0.46
452 75 0.06
453 145 0.11
454 22 0.02
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (452 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGT
GCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCT
TCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
Found at i:42887 original size:47 final size:47
Alignment explanation
Indices: 42833--42927 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 47
42823 TGATGTTTTC
* * *
42833 AAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAA
1 AAAGCCTTAGGGTCATATGTAAGCCCTTCAGTACATGATGTTTCCAA
* *
42880 AAAGCCTTCGGGTCATATGTAAGCCCTTCAGTACATGATGTTTTCAA
1 AAAGCCTTAGGGTCATATGTAAGCCCTTCAGTACATGATGTTTCCAA
42927 A
1 A
42928 CATTTCCATC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (47 bp):
AAAGCCTTAGGGTCATATGTAAGCCCTTCAGTACATGATGTTTCCAA
Found at i:43063 original size:3 final size:3
Alignment explanation
Indices: 43055--43132 Score: 147
Period size: 3 Copynumber: 26.0 Consensus size: 3
43045 CATTTCGTTT
43055 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
43103 TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43133 AATAAAATAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:46168 original size:21 final size:21
Alignment explanation
Indices: 46144--46192 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
46134 TATAGTAGCT
46144 GTTGCAGCTCGAGATTCTGTA
1 GTTGCAGCTCGAGATTCTGTA
46165 GTTGCAGCTCGAGATTCTGTA
1 GTTGCAGCTCGAGATTCTGTA
46186 GTTGCAG
1 GTTGCAG
46193 TGCGTATTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.33
Consensus pattern (21 bp):
GTTGCAGCTCGAGATTCTGTA
Found at i:47010 original size:88 final size:88
Alignment explanation
Indices: 46861--47045 Score: 361
Period size: 88 Copynumber: 2.1 Consensus size: 88
46851 TTCATGAAAT
46861 TATTTTGATAAAATTTGTTCCAATTGCTTTGAAATAAGCCATTTTTTATTCCTCCTGTTTGAATA
1 TATTTTGATAAAATTTGTTCCAATTGCTTTGAAATAAGCCATTTTTTATTCCTCCTGTTTGAATA
46926 TTTTTTAAATGAAATGTGTGTAC
66 TTTTTTAAATGAAATGTGTGTAC
46949 TATTTTGATAAAATTTGTTCCAATTGCTTTGAAATAAGCCATTTTTTATTCCTCCTGTTTGAATA
1 TATTTTGATAAAATTTGTTCCAATTGCTTTGAAATAAGCCATTTTTTATTCCTCCTGTTTGAATA
*
47014 TTTTTTTAATGAAATGTGTGTAC
66 TTTTTTAAATGAAATGTGTGTAC
47037 TATTTTGAT
1 TATTTTGAT
47046 CGCTCCCGTT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 96 1.00
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (88 bp):
TATTTTGATAAAATTTGTTCCAATTGCTTTGAAATAAGCCATTTTTTATTCCTCCTGTTTGAATA
TTTTTTAAATGAAATGTGTGTAC
Found at i:49584 original size:19 final size:19
Alignment explanation
Indices: 49557--49626 Score: 58
Period size: 19 Copynumber: 3.9 Consensus size: 19
49547 AATTAAAATT
*
49557 TATACAATAATATTTTAAA
1 TATAAAATAATATTTTAAA
*
49576 TATAAAATAA-AATTT---
1 TATAAAATAATATTTTAAA
**
49591 TATACGATAATATTTTAAA
1 TATAAAATAATATTTTAAA
* *
49610 TAAAAAATAAAATTTTA
1 TATAAAATAATATTTTA
49627 TACGATAAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
15 8 0.21
16 4 0.11
18 4 0.11
19 22 0.58
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (19 bp):
TATAAAATAATATTTTAAA
Found at i:49600 original size:15 final size:15
Alignment explanation
Indices: 49582--49642 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 15
49572 TAAATATAAA
49582 ATAAAATTTTATACG
1 ATAAAATTTTATACG
* **
49597 ATAATATTTTAAATAAAAA
1 ATAAAATTTT--AT--ACG
49616 ATAAAATTTTATACG
1 ATAAAATTTTATACG
49631 ATAAAATTTTAT
1 ATAAAATTTTAT
49643 TTATTAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
15 22 0.61
17 4 0.11
19 10 0.28
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
ATAAAATTTTATACG
Found at i:49653 original size:34 final size:34
Alignment explanation
Indices: 49550--49641 Score: 150
Period size: 34 Copynumber: 2.7 Consensus size: 34
49540 TAAAATTAAT
*
49550 TAAAA-TTTATACAATAATATTTTAAATATAAAA
1 TAAAATTTTATACGATAATATTTTAAATATAAAA
*
49583 TAAAATTTTATACGATAATATTTTAAATAAAAAA
1 TAAAATTTTATACGATAATATTTTAAATATAAAA
*
49617 TAAAATTTTATACGATAAAATTTTA
1 TAAAATTTTATACGATAATATTTTA
49642 TTTATTAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 5 0.09
34 50 0.91
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.40
Consensus pattern (34 bp):
TAAAATTTTATACGATAATATTTTAAATATAAAA
Found at i:57760 original size:46 final size:46
Alignment explanation
Indices: 57685--57811 Score: 182
Period size: 46 Copynumber: 2.8 Consensus size: 46
57675 CCTAGCCATA
* * * *
57685 TATTACCACATAGTCCACCTACTCTATTAAATTGCTAGTTATACAT
1 TATTGCCACATAGTCCACCTACTCCATTAAATTGATAGTCATACAT
*
57731 TATTGCCACATAGTCCACCTACTCCATTAAATTGATAGTCATTCAT
1 TATTGCCACATAGTCCACCTACTCCATTAAATTGATAGTCATACAT
* * *
57777 TATTGCCACCTACTTCACCTACTCCATTAAATTGA
1 TATTGCCACATAGTCCACCTACTCCATTAAATTGA
57812 GAAATTTTCA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (46 bp):
TATTGCCACATAGTCCACCTACTCCATTAAATTGATAGTCATACAT
Found at i:62572 original size:46 final size:46
Alignment explanation
Indices: 62511--62626 Score: 180
Period size: 46 Copynumber: 2.5 Consensus size: 46
62501 TATACATTAT
*
62511 CACCTAC-CCACCTACTCCATTAAATTGTTAGTCATACATTATTGC
1 CACCTACTCCACCTACTCCATTAAATTGATAGTCATACATTATTGC
* *
62556 CACCTACTCCACCTACTCCATTAAATTGATAGTCATTCATTATTGT
1 CACCTACTCCACCTACTCCATTAAATTGATAGTCATACATTATTGC
* *
62602 CACCAACTTCACCTACTCCATTAAA
1 CACCTACTCCACCTACTCCATTAAA
62627 CTGAGAAACT
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
45 7 0.11
46 58 0.89
ACGTcount: A:0.30, C:0.32, G:0.05, T:0.33
Consensus pattern (46 bp):
CACCTACTCCACCTACTCCATTAAATTGATAGTCATACATTATTGC
Found at i:63483 original size:3 final size:3
Alignment explanation
Indices: 63475--63499 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
63465 CAGGCTTTAT
63475 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
63500 CAAAACGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:69131 original size:15 final size:15
Alignment explanation
Indices: 69111--69149 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
69101 TATTCCAACA
69111 ATCCTTCTTCAAGTG
1 ATCCTTCTTCAAGTG
69126 ATCCTTCTTCAAGTG
1 ATCCTTCTTCAAGTG
*
69141 ACCCTTCTT
1 ATCCTTCTT
69150 TCCACAGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.18, C:0.31, G:0.10, T:0.41
Consensus pattern (15 bp):
ATCCTTCTTCAAGTG
Found at i:73579 original size:32 final size:32
Alignment explanation
Indices: 73512--73588 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
73502 TTGGGCGTAG
* * * * *
73512 GAGCCAACCTAAGGGAGTACCTTGGGTCCTTA
1 GAGCCTACCCAAGAGAGTAACTTGGGTCCTAA
73544 GAGCCTACCCAAGAGAGTAACTT-GGTGCCTAA
1 GAGCCTACCCAAGAGAGTAACTTGGGT-CCTAA
*
73576 GAGCCTCCCCAAG
1 GAGCCTACCCAAG
73589 GGTCACCTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 3 0.08
32 35 0.92
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (32 bp):
GAGCCTACCCAAGAGAGTAACTTGGGTCCTAA
Found at i:80526 original size:164 final size:162
Alignment explanation
Indices: 80255--80722 Score: 763
Period size: 164 Copynumber: 2.9 Consensus size: 162
80245 TAGTCATCAT
*
80255 TACTCAAACTGCGTAGTAAGTACAATTATTTTAGAAATTTTCCATGTTATCTTTTAGACCGTATC
1 TACTCAAACTGCGTTGTAAGTACAATTATTTTAGAAATTTT-CAT-TTATCTTTTAGACCGTATC
* * *
80320 AATTATTACGATATCGACTATTGATACTATTTGATATGATCAAGATATTGAATCATTTTAAATTT
64 AGTTATTATGATATCCACTATTGATACTATTTGATATGATCAAGATATTGAATCATTTTAAATTT
*
80385 TATACATCAAATTAATTATAAAAAAATTATTTGA
129 TATACATCAAATTAATTATAAAAAAAATATTTGA
80419 TACTCAAACTGCGTTGTAAGTACAATTATTTTAGAAATTTTCTATATTATCTTTTAGACCGTATC
1 TACTCAAACTGCGTTGTAAGTACAATTATTTTAGAAATTTTC-AT-TTATCTTTTAGACCGTATC
80484 AGTTATTATGATATCCACTATTGATACTATTTGATATGATCAAGATATTGAATCATTTTAAATTT
64 AGTTATTATGATATCCACTATTGATACTATTTGATATGATCAAGATATTGAATCATTTTAAATTT
*
80549 TATACATCAAATAAATTATAAAAAAAATATTTGA
129 TATACATCAAATTAATTATAAAAAAAATATTTGA
*
80583 TACTCAAACTGCGTTGTATGTACAATTATTTTAGAAATTTTC---TA-----TAGACCGTATCAG
1 TACTCAAACTGCGTTGTAAGTACAATTATTTTAGAAATTTTCATTTATCTTTTAGACCGTATCAG
80640 TTATTATGATATCCACTATTGATACTATTTGATATGATCAAGATATTGAATCATTTTAAATTTTA
66 TTATTATGATATCCACTATTGATACTATTTGATATGATCAAGATATTGAATCATTTTAAATTTTA
* *
80705 TTCATCAAGTTAATTATA
131 TACATCAAATTAATTATA
80723 TTAATAAATT
Statistics
Matches: 292, Mismatches: 11, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
154 93 0.32
159 2 0.01
163 1 0.00
164 196 0.67
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (162 bp):
TACTCAAACTGCGTTGTAAGTACAATTATTTTAGAAATTTTCATTTATCTTTTAGACCGTATCAG
TTATTATGATATCCACTATTGATACTATTTGATATGATCAAGATATTGAATCATTTTAAATTTTA
TACATCAAATTAATTATAAAAAAAATATTTGA
Found at i:83336 original size:84 final size:83
Alignment explanation
Indices: 83050--83349 Score: 338
Period size: 84 Copynumber: 3.6 Consensus size: 83
83040 AGAAAATTTC
* * * *
83050 GCTACTGCTTACTTTCACAAAACCTCTAATTCTGAAAACCATTGA-AGAGACGAGGAGGAGATGA
1 GCTACTGCTTACTTCCACAAAACCTCTAATGCTAAAAACC-TTGACAGAGACGA-GAAGAGATGA
*
83114 TGAGTTTGGAAGACAAGTAT
64 AGAGTTTGGAAGACAAGTAT
* ** * * * *
83134 GCTACTGCTTACTTCCACAAAAGCTCTGCTGCTAAAAACCATGGCAAAGAGGAGAAG-G-TGAAG
1 GCTACTGCTTACTTCCACAAAACCTCTAATGCTAAAAACCTTGACAGAGACGAGAAGAGATGAAG
83197 AG-TTGGAAGACAAGTAT
66 AGTTTGGAAGACAAGTAT
* ** * * *
83214 GCTACTGCTTACTTCCACAAAAACTCTGCTGCTAAAAACCTTGACAGGGATGACAAGATGATGAA
1 GCTACTGCTTACTTCCACAAAACCTCTAATGCTAAAAACCTTGACAGAGACGAGAAGA-GATGAA
*
83279 GAGTTTGGAAAACAAGTAT
65 GAGTTTGGAAGACAAGTAT
* * * *
83298 GCTGCAGCTTACTTCCACAAAACCTCTAATTCTGAAAACCTTGACAGAGACG
1 GCTACTGCTTACTTCCACAAAACCTCTAATGCTAAAAACCTTGACAGAGACG
83350 GGGTAGTGAA
Statistics
Matches: 182, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
80 65 0.36
81 6 0.03
82 2 0.01
83 12 0.07
84 97 0.53
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (83 bp):
GCTACTGCTTACTTCCACAAAACCTCTAATGCTAAAAACCTTGACAGAGACGAGAAGAGATGAAG
AGTTTGGAAGACAAGTAT
Done.