Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008356.1 Corchorus capsularis cultivar CVL-1 contig08377, 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: 87270
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:1639 original size:24 final size:25
Alignment explanation
Indices: 1597--1643 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1587 GAATAAGTGA
*
1597 ATAATAAAAATAAATAAACAAGAAG
1 ATAATAAAAATAAACAAACAAGAAG
*
1622 ATAAT-AAAATTAACAAACAAGA
1 ATAATAAAAATAAACAAACAAGA
1644 TAAGTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.17
Consensus pattern (25 bp):
ATAATAAAAATAAACAAACAAGAAG
Found at i:7592 original size:36 final size:36
Alignment explanation
Indices: 7550--7700 Score: 214
Period size: 36 Copynumber: 4.2 Consensus size: 36
7540 CTCTTCTTAG
* *
7550 ATTAAG-CTCTTTATTGACTCCACTTAATTACCCTGA
1 ATTAAGCCT-TTTATTGACGCTACTTAATTACCCTGA
** *
7586 ATTAAGCCTTTTATTGACATTACTTAATTACCTTGA
1 ATTAAGCCTTTTATTGACGCTACTTAATTACCCTGA
7622 ATTAAGCCTTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGCCTTTTATTGACGCTACTTAATTACCCTGA
* *
7658 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCCGA
1 ATTAAG-CCTTTTATTGACGCTACTTAATTACCCTGA
7695 ATTAAG
1 ATTAAG
7701 TCCCTAACTT
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
36 68 0.65
37 36 0.35
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (36 bp):
ATTAAGCCTTTTATTGACGCTACTTAATTACCCTGA
Found at i:7735 original size:37 final size:37
Alignment explanation
Indices: 7693--7972 Score: 358
Period size: 37 Copynumber: 7.7 Consensus size: 37
7683 TAATTACCCC
* * * *
7693 GAATTAAGTCCCTAACT-TGACTTGATTTCCTTCCTTG
1 GAATCAAGTCCCTTACTCT-ACTTAATTCCCTTCCTTG
* *
7730 AAATTAAGT-CCTTAACTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCTT-ACTCTACTTAATTCCCTTCCTTG
*
7767 GAATCAAGT--C---CTCTACTTAATTCCTTTCCTTG
1 GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
7799 GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
7836 GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
*
7873 GAATCAAGTCCTTTACTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
* * *
7910 GAATCAAGTCCTTTGCTCTACTTAATTCCCTTCCTTT
1 GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
* * * *
7947 GAACCAAGTCCTTTTCTTTACTTAAT
1 GAATCAAGTCCCTTACTCTACTTAAT
7973 CCCCGGAGGT
Statistics
Matches: 222, Mismatches: 14, Indels: 14
0.89 0.06 0.06
Matches are distributed among these distances:
32 30 0.14
34 1 0.00
36 4 0.02
37 186 0.84
38 1 0.00
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.40
Consensus pattern (37 bp):
GAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTG
Found at i:7830 original size:18 final size:18
Alignment explanation
Indices: 7807--7904 Score: 65
Period size: 18 Copynumber: 5.3 Consensus size: 18
7797 TGGAATCAAG
7807 TCCCTTACTCTACTTAAT
1 TCCCTTACTCTACTTAAT
* * * *
7825 TCCCTTCCT-TGGAATCAAG
1 TCCCTTACTCT--ACTTAAT
7844 TCCCTTACTCTACTTAAT
1 TCCCTTACTCTACTTAAT
* * * *
7862 TCCCTTCCT-TGGAATCAAG
1 TCCCTTACTCT--ACTTAAT
*
7881 TCCTTTACTCTACTTAAT
1 TCCCTTACTCTACTTAAT
7899 TCCCTT
1 TCCCTT
7905 CCTTGGAATC
Statistics
Matches: 56, Mismatches: 18, Indels: 12
0.65 0.21 0.14
Matches are distributed among these distances:
17 2 0.04
18 29 0.52
19 23 0.41
20 2 0.04
ACGTcount: A:0.20, C:0.33, G:0.06, T:0.41
Consensus pattern (18 bp):
TCCCTTACTCTACTTAAT
Found at i:8224 original size:76 final size:76
Alignment explanation
Indices: 8128--8837 Score: 1235
Period size: 76 Copynumber: 9.3 Consensus size: 76
8118 CCTTCCTTGA
* * * *
8128 AATTAAGT-TCATGCTCGTCTTTACCTAATTTCCTTTAC-TGAAATTAAGTTTGTGCTTAGTTTA
1 AATTAAGTCT-ATGCTTGTCTTTACCTAATTTCC-TTCCTTGAAATTAAGTCTGTGCTTACTTTA
* * *
8191 CTCAATTACCCCG
64 CTTAACTACCCTG
8204 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
*
8269 TAACTATCCTG
66 TAACTACCCTG
*
8280 AATTAAGTCTATGCTTGTCTTTACTTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
8345 TAACTACCCTG
66 TAACTACCCTG
8356 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
* *
8421 TAATTACCCCG
66 TAACTACCCTG
8432 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
*
8497 TAACTATCCTG
66 TAACTACCCTG
*
8508 AATTAAGTCTATGCGTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
8573 TAACTACCCTG
66 TAACTACCCTG
*
8584 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTATGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
8649 TAACTACCCTG
66 TAACTACCCTG
8660 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
*
8725 TAATTACCCTG
66 TAACTACCCTG
8736 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
*
8801 TAATTACCCTG
66 TAACTACCCTG
*
8812 AATTAAGTCTATGATTGTCTTTACCT
1 AATTAAGTCTATGCTTGTCTTTACCT
8838 TTTAACTGTT
Statistics
Matches: 609, Mismatches: 23, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
75 3 0.00
76 605 0.99
77 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (76 bp):
AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
TAACTACCCTG
Found at i:8891 original size:37 final size:36
Alignment explanation
Indices: 8839--9542 Score: 617
Period size: 37 Copynumber: 18.9 Consensus size: 36
8829 TCTTTACCTT
*
8839 TTAACTGTTTTTACTTAATTACCCTGAATTAAGTTC
1 TTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
8875 TTCAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
1 TT-AACTGCTTTTACTTAATTACCCTGAATTAAGTTC
** *
8912 TTAACTGCTTTTACTTAATT-GTCTAGAATTAAGCTC
1 TTAACTGCTTTTACTTAATTACCCT-GAATTAAGTTC
* *
8948 TTAATTGTTCTTTACTTAATTACCCTGAATTAAGTTC
1 TTAACTGCT-TTTACTTAATTACCCTGAATTAAGTTC
* * * * *
8985 TTTGACCG-TGTTTATTTAATTTCCCTGAATTAAGCTCC
1 -TTAACTGCT-TTTACTTAATTACCCTGAATTAAG-TTC
* * * *
9023 TTTGACTGTTTTTACCTT-ATTTCCTTGAATTAAGATT-
1 -TTAACTGCTTTTA-CTTAATTACCCTGAATTAAG-TTC
* * *
9060 TTGACTGACTATGTTTACTTTTCTTAATTGCCCTGATTTAAGATT-
1 TTAACTG-C--T-TTTA-----CTTAATTACCCTGAATTAAG-TTC
* * * ** *
9105 TTGACCGTTTTTACTTAATTGTCCTGAATTAAGTTTT
1 TTAACTGCTTTTACTTAATTACCCTGAATTAAG-TTC
* *
9142 TTACCTGCTTTTACTTAATTGCCCTGAATTAAGTTC
1 TTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* *
9178 TCAACCTGTTTTTACTTAATTACCCTGAATTAAGTTC
1 TTAA-CTGCTTTTACTTAATTACCCTGAATTAAGTTC
* * *
9215 TTAACTGCTTTTAGTTATTTACCCTGAATTAAATTC
1 TTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* *
9251 CTAACTGCTCTTACTTAATTACCCTGAATTAAGTTCC
1 TTAACTGCTTTTACTTAATTACCCTGAATTAAGTT-C
* * *
9288 TTAACTACTCTTACTTAATTACCCTAAATTAAGTTC
1 TTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* * * *
9324 TTTGACTGCTTGTACTTAATTTCCATGAATTAAGTTC
1 -TTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
*
9361 TTAACGTGCTTTTACTTAATTATCCTGAATTAAGTTC
1 TTAAC-TGCTTTTACTTAATTACCCTGAATTAAGTTC
* * *
9398 TTTAACTGCTCTTACTTAATTACCCCGAATTAAGTTGT
1 -TTAACTGCTTTTACTTAATTACCCTGAATTAAGTT-C
* *
9436 TTAACTGCTCTTAATTAATTACCCTGAATTAAGTTC
1 TTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* * * **
9472 TTTGATTGCTTTTACTTAATTTCCAAGAATTAAGTTC
1 -TTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* * * *
9509 TTTAACTTCTCTTTTCTTAATCACCCTGGATTAA
1 -TTAACTGCT-TTTACTTAATTACCCTGAATTAA
9543 AACTTTAACT
Statistics
Matches: 553, Mismatches: 89, Indels: 50
0.80 0.13 0.07
Matches are distributed among these distances:
35 2 0.00
36 131 0.24
37 325 0.59
38 57 0.10
39 4 0.01
40 4 0.01
41 4 0.01
42 1 0.00
44 3 0.01
45 22 0.04
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.46
Consensus pattern (36 bp):
TTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
Found at i:9614 original size:41 final size:40
Alignment explanation
Indices: 9521--9664 Score: 225
Period size: 41 Copynumber: 3.5 Consensus size: 40
9511 TAACTTCTCT
* * ** *
9521 TTTCTTAATCACCCTGGATTAAAACTTTAACTAATCTGAC
1 TTTCTTAATCGCCCTGGATTAAAACCTTAACTTGTTTGAC
9561 TTTCTTAATCGCCCTGGATTAAAACCTTAACTGTGTTTGAC
1 TTTCTTAATCGCCCTGGATTAAAACCTTAACT-TGTTTGAC
9602 TTTCTTAATCGCCCTGGATTAAAACCTTAACTATGTTTGAC
1 TTTCTTAATCGCCCTGGATTAAAACCTTAACT-TGTTTGAC
9643 TTTCTTAATCGCCCTGGATTAA
1 TTTCTTAATCGCCCTGGATTAA
9665 GACTTTACTT
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
40 30 0.31
41 67 0.69
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (40 bp):
TTTCTTAATCGCCCTGGATTAAAACCTTAACTTGTTTGAC
Found at i:12873 original size:26 final size:26
Alignment explanation
Indices: 12834--12894 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
12824 TGGACCTAAA
*
12834 GACAAAAATGCCCTTGA-AGTGAAAAT
1 GACAAAAATACCCTTGAGA-TGAAAAT
* *
12860 GACCAAAATACCCTTGGGATGAAAAT
1 GACAAAAATACCCTTGAGATGAAAAT
12886 GACAAAAAT
1 GACAAAAAT
12895 GCCCCTGACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (26 bp):
GACAAAAATACCCTTGAGATGAAAAT
Found at i:15484 original size:13 final size:13
Alignment explanation
Indices: 15466--15490 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15456 TTTATTTACC
15466 AAACTATTAAATA
1 AAACTATTAAATA
15479 AAACTATTAAAT
1 AAACTATTAAAT
15491 CAGATATTAG
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
AAACTATTAAATA
Found at i:18510 original size:15 final size:15
Alignment explanation
Indices: 18490--18523 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
18480 CTTGATTTCC
*
18490 TTTGTATGTAACTCT
1 TTTGTATATAACTCT
18505 TTTGTATATAACTCT
1 TTTGTATATAACTCT
18520 TTTG
1 TTTG
18524 GAATTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.56
Consensus pattern (15 bp):
TTTGTATATAACTCT
Found at i:20076 original size:68 final size:69
Alignment explanation
Indices: 19963--20099 Score: 231
Period size: 68 Copynumber: 2.0 Consensus size: 69
19953 ACCCATATAA
* *
19963 AAAATTCCATACAATTATGTTTTTATATATTAATACAATTACACATTAATATGAGAAAAAGTAGA
1 AAAATTCCATACAATTATGTTTTTATACATTAATACAATTACACATTAATATAAGAAAAAGTAGA
20028 ATTT
66 ATTT
* *
20032 AAAATTCCATACAA-TATGTTTTTATACATTGATACAATTGCACATTAATATAAGAAAAAGTAGA
1 AAAATTCCATACAATTATGTTTTTATACATTAATACAATTACACATTAATATAAGAAAAAGTAGA
20096 ATTT
66 ATTT
20100 GATAATAATA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 50 0.78
69 14 0.22
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.36
Consensus pattern (69 bp):
AAAATTCCATACAATTATGTTTTTATACATTAATACAATTACACATTAATATAAGAAAAAGTAGA
ATTT
Found at i:23149 original size:33 final size:32
Alignment explanation
Indices: 23107--23231 Score: 108
Period size: 33 Copynumber: 3.8 Consensus size: 32
23097 AGCTAAAGAA
*
23107 TCATATGGCCGGTTGTGGCCGGGCATGGCCGA-G
1 TCATGTGGCCGG-TGTGGCCGGGCATGGCC-ATG
*
23140 TCATGTGGCCGAGTGTGGTCGGGCATGGCCATG
1 TCATGTGGCCG-GTGTGGCCGGGCATGGCCATG
** **
23173 TCGCGTGGCCGGTGATGGCCGGGCATCTCCATG
1 TCATGTGGCCGGTG-TGGCCGGGCATGGCCATG
*** *
23206 TCGCATGGCCGGTGTTGCGCGGGCAT
1 TCATGTGGCCGGTGTGGC-CGGGCAT
23232 CTCCAAGTCG
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
32 7 0.09
33 71 0.90
34 1 0.01
ACGTcount: A:0.10, C:0.26, G:0.42, T:0.22
Consensus pattern (32 bp):
TCATGTGGCCGGTGTGGCCGGGCATGGCCATG
Found at i:23232 original size:33 final size:33
Alignment explanation
Indices: 23144--23250 Score: 128
Period size: 33 Copynumber: 3.2 Consensus size: 33
23134 GCCGAGTCAT
* **
23144 GTGGCCGAGTG-TGGTCGGGCATGGCCATGTCGC
1 GTGGCCG-GTGATGGCCGGGCATCTCCATGTCGC
23177 GTGGCCGGTGATGGCCGGGCATCTCCATGTCGC
1 GTGGCCGGTGATGGCCGGGCATCTCCATGTCGC
* * *
23210 ATGGCCGGTG-TTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGATGGC-CGGGCATCTCCATGTCGC
23243 GTGGCCGG
1 GTGGCCGG
23251 ATCTCCAAGT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
32 6 0.09
33 59 0.91
ACGTcount: A:0.09, C:0.28, G:0.42, T:0.21
Consensus pattern (33 bp):
GTGGCCGGTGATGGCCGGGCATCTCCATGTCGC
Found at i:23268 original size:21 final size:21
Alignment explanation
Indices: 23230--23269 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23220 TTGCGCGGGC
* *
23230 ATCTCCAAGTCGCGTGGCCGG
1 ATCTCCAAGTCACATGGCCGG
23251 ATCTCCAAGTCACATGGCC
1 ATCTCCAAGTCACATGGCC
23270 TGTCACTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (21 bp):
ATCTCCAAGTCACATGGCCGG
Found at i:28754 original size:8 final size:8
Alignment explanation
Indices: 28726--28759 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
28716 GAATCGGCTA
28726 TGAATTTT
1 TGAATTTT
*
28734 TGAAGTTTC
1 TGAA-TTTT
28743 TGAATTTT
1 TGAATTTT
28751 TGAATTTT
1 TGAATTTT
28759 T
1 T
28760 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:29699 original size:33 final size:32
Alignment explanation
Indices: 29657--29781 Score: 117
Period size: 33 Copynumber: 3.8 Consensus size: 32
29647 AGCTAAAGGA
*
29657 TCATATGGCCGGTTGTGGCCGGGCATGGCCGA-G
1 TCATGTGGCCGG-TGTGGCCGGGCATGGCC-ATG
29690 TCATGTGGCCGGGTGTGGCCGGGCATGGCCATG
1 TCATGTGGCC-GGTGTGGCCGGGCATGGCCATG
** **
29723 TCGCGTGGCCGGTGATGGCCGGGCATCTCCATG
1 TCATGTGGCCGGTG-TGGCCGGGCATGGCCATG
*** *
29756 TCGCATGGCCGGTGTTGCGCGGGCAT
1 TCATGTGGCCGGTGTGGC-CGGGCAT
29782 CTCCAAGTCG
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
32 8 0.10
33 71 0.88
34 2 0.02
ACGTcount: A:0.10, C:0.26, G:0.42, T:0.22
Consensus pattern (32 bp):
TCATGTGGCCGGTGTGGCCGGGCATGGCCATG
Found at i:29782 original size:33 final size:33
Alignment explanation
Indices: 29695--29800 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 33
29685 CCGAGTCATG
* ** *
29695 TGGCCGGGTGTGGC-CGGGCATGGCCATGTCGCG
1 TGGCC-GGTGTTGCGCGGGCATCTCCATGTCGCA
*
29728 TGGCCGGTGATG-GCCGGGCATCTCCATGTCGCA
1 TGGCCGGTGTTGCG-CGGGCATCTCCATGTCGCA
*
29761 TGGCCGGTGTTGCGCGGGCATCTCCAAGTCGCA
1 TGGCCGGTGTTGCGCGGGCATCTCCATGTCGCA
29794 TGGCCGG
1 TGGCCGG
29801 ATCTCCAAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 5 0.08
33 57 0.90
34 1 0.02
ACGTcount: A:0.09, C:0.29, G:0.42, T:0.20
Consensus pattern (33 bp):
TGGCCGGTGTTGCGCGGGCATCTCCATGTCGCA
Found at i:29806 original size:21 final size:21
Alignment explanation
Indices: 29780--29821 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
29770 TTGCGCGGGC
*
29780 ATCTCCAAGTCGCATGGCCGG
1 ATCTCCAAGTCACATGGCCGG
29801 ATCTCCAAGTCACATGGCCGG
1 ATCTCCAAGTCACATGGCCGG
29822 TCACTTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.19
Consensus pattern (21 bp):
ATCTCCAAGTCACATGGCCGG
Found at i:35323 original size:2 final size:2
Alignment explanation
Indices: 35312--35347 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
35302 TTTCAACTTT
35312 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35348 GAGGGATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41668 original size:62 final size:62
Alignment explanation
Indices: 41592--41709 Score: 209
Period size: 62 Copynumber: 1.9 Consensus size: 62
41582 ATCCCTTGGA
*
41592 AGAATTATTACCATTACACTTCCGATTGCTACCAACAATTAAACTTAAGTTATTAGGGTATT
1 AGAATTATTACCATTACACTTCCAATTGCTACCAACAATTAAACTTAAGTTATTAGGGTATT
* *
41654 AGAATTATTACCATTACACTTCTAATTGCTACCAACGATTAAACTTAAGTTATTAG
1 AGAATTATTACCATTACACTTCCAATTGCTACCAACAATTAAACTTAAGTTATTAG
41710 TGTCGACTCC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (62 bp):
AGAATTATTACCATTACACTTCCAATTGCTACCAACAATTAAACTTAAGTTATTAGGGTATT
Found at i:46257 original size:31 final size:31
Alignment explanation
Indices: 46160--46258 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
46150 TATTTTACTG
* * *
46160 CAATTTGAGGCATGTTCATGTTGATTTGTTT
1 CAATTTGAGGCTTGTTCATGTTAATTTGCTT
* * * * * *
46191 CAACTTAATGCTTGATT-ATGGTAGATCT-CTG
1 CAATTTGAGGCTTG-TTCATGTTA-ATTTGCTT
46222 CAATTTGAGGCTTGTTCATGTTAATTTGCTT
1 CAATTTGAGGCTTGTTCATGTTAATTTGCTT
46253 CAATTT
1 CAATTT
46259 AAGACTGGTT
Statistics
Matches: 49, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
30 5 0.10
31 39 0.80
32 5 0.10
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.45
Consensus pattern (31 bp):
CAATTTGAGGCTTGTTCATGTTAATTTGCTT
Found at i:48002 original size:23 final size:22
Alignment explanation
Indices: 47953--48002 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
47943 AAAATGGAAT
* *
47953 TTTTCAAAGCAAAAATAAAAGA
1 TTTTAAAAACAAAAATAAAAGA
* *
47975 CTTTAAAAACAAAAATAGAAAGG
1 TTTTAAAAACAAAAATA-AAAGA
47998 TTTTA
1 TTTTA
48003 TCACAGCATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (22 bp):
TTTTAAAAACAAAAATAAAAGA
Found at i:55093 original size:84 final size:84
Alignment explanation
Indices: 54952--55122 Score: 333
Period size: 84 Copynumber: 2.0 Consensus size: 84
54942 TTTAAGATTA
54952 TGAAGATTTGGAGCAATTTTGGACCAATTTGGAGAAACTACTGATTTCGGACCATTTTGGCCCAG
1 TGAAGATTTGGAGCAATTTTGGACCAATTTGGAGAAACTACTGATTTCGGACCATTTTGGCCCAG
55017 TAGGCCCATTAGACACGTT
66 TAGGCCCATTAGACACGTT
55036 TGAAGATTTGGAGCAATTTTGGACCAATTTGGAGAAACTACTGATTTCGGACCATTTTGGCCCAG
1 TGAAGATTTGGAGCAATTTTGGACCAATTTGGAGAAACTACTGATTTCGGACCATTTTGGCCCAG
*
55101 TAGGCCCATTAGGCACGTT
66 TAGGCCCATTAGACACGTT
55120 TGA
1 TGA
55123 GCCCATGAAG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (84 bp):
TGAAGATTTGGAGCAATTTTGGACCAATTTGGAGAAACTACTGATTTCGGACCATTTTGGCCCAG
TAGGCCCATTAGACACGTT
Found at i:57115 original size:14 final size:14
Alignment explanation
Indices: 57096--57122 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57086 AATTTTGGGA
57096 ATGAGAGATCATGC
1 ATGAGAGATCATGC
57110 ATGAGAGATCATG
1 ATGAGAGATCATG
57123 TTCCCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (14 bp):
ATGAGAGATCATGC
Found at i:57576 original size:26 final size:26
Alignment explanation
Indices: 57547--57627 Score: 99
Period size: 26 Copynumber: 3.0 Consensus size: 26
57537 TAAGAAATCG
* *
57547 TCAGGGGCATTTTTGTCATTTTCACT
1 TCAGGGGTATTTTCGTCATTTTCACT
* *
57573 TCAGGGGTATTTTGGTCATTTTCACAA
1 TCAGGGGTATTTTCGTCATTTTCAC-T
57600 TCAGGGGTATTTTCGTCATCTTTACACT
1 TCAGGGGTATTTTCGTCAT-TTT-CACT
57628 AAAAGGGGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 23 0.49
27 18 0.38
28 3 0.06
29 3 0.06
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (26 bp):
TCAGGGGTATTTTCGTCATTTTCACT
Found at i:62036 original size:42 final size:40
Alignment explanation
Indices: 61988--62077 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
61978 ATTAAGAGGT
* *
61988 AATTAAGAAAGTCAAGTACAATTAAAAGTCTTAATTCAGGGC
1 AATTAAGAAAATCAAGCACAATT-AAA-TCTTAATTCAGGGC
* * * *
62030 AATTAAGAAAATCAAGCATAGTTAAATCTTAATTCAGTGT
1 AATTAAGAAAATCAAGCACAATTAAATCTTAATTCAGGGC
62070 AATTAAGA
1 AATTAAGA
62078 GGTAATTAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 20 0.48
41 3 0.07
42 19 0.45
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (40 bp):
AATTAAGAAAATCAAGCACAATTAAATCTTAATTCAGGGC
Found at i:62074 original size:40 final size:42
Alignment explanation
Indices: 61976--62077 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
61966 TAATTCAGTG
* * *
61976 TAATTAAGAGGTAATTAAGAAAGTCAAGTACAATTAAAAGTCT
1 TAATTCAG-GGTAATTAAGAAAATCAAGCACAATTAAAAGTCT
* * *
62019 TAATTCAGGGCAATTAAGAAAATCAAGCATAGTT-AAA-TCT
1 TAATTCAGGGTAATTAAGAAAATCAAGCACAATTAAAAGTCT
*
62059 TAATTCAGTGTAATTAAGA
1 TAATTCAGGGTAATTAAGA
62078 GGTAATTAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 20 0.39
41 3 0.06
42 21 0.41
43 7 0.14
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.29
Consensus pattern (42 bp):
TAATTCAGGGTAATTAAGAAAATCAAGCACAATTAAAAGTCT
Found at i:62154 original size:70 final size:67
Alignment explanation
Indices: 62111--62581 Score: 568
Period size: 70 Copynumber: 6.7 Consensus size: 67
62101 GTTAAAGTCC
*
62111 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
1 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAACTCTTAA--
*
62176 CGGGG
64 -AGGG
* * *
62181 TAATTAAGAAAAGTAAGCATAGTTAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAGTT
1 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAACTCTTA---
*
62246 CAGGG
63 AAGGG
* *
62251 TAATTAAGAAAAGTAAGCATAGT-AAGGGTCTTAATTTGGTAATTAAGAAAAGTAAAGTCTTAAT
1 TAATTAAGAAAAGTAAGCATAGTCAA-GGTCTTAATTTGGTAATTAAGAAAAGCAAACTCTTAA-
62315 TCAGGG
64 --AGGG
*
62321 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
1 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAACTCTTAA--
*
62386 CAAGG
64 -AGGG
* *
62391 TAATTAAGAAAAGTAAGCATAGTCAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
1 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAACTCTTAA--
62456 CAGGG
64 -AGGG
* * *
62461 TAATTAAGAAAAGTGAGCATAGTCAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
1 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAACTCTTAA--
62526 CAGGG
64 -AGGG
* * * *
62531 TAATTAAGAAAAGTAAACATAGT-AAAGTATTAATTCAGGGTAATTAAGAAA
1 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATT--TGGTAATTAAGAAA
62582 GTCAAACACA
Statistics
Matches: 373, Mismatches: 18, Indels: 19
0.91 0.04 0.05
Matches are distributed among these distances:
69 10 0.03
70 348 0.93
71 15 0.04
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (67 bp):
TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAACTCTTAAAG
GG
Found at i:62311 original size:29 final size:30
Alignment explanation
Indices: 62278--62336 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
62268 CATAGTAAGG
*
62278 GTCTTAATT-TGGTAATTAAGAAAAGTAAA
1 GTCTTAATTAGGGTAATTAAGAAAAGTAAA
62307 GTCTTAATTCAGGGTAATTAAGAAAAGTAA
1 GTCTTAATT-AGGGTAATTAAGAAAAGTAA
62337 GCATAGTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 9 0.33
31 18 0.67
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (30 bp):
GTCTTAATTAGGGTAATTAAGAAAAGTAAA
Found at i:62330 original size:140 final size:139
Alignment explanation
Indices: 62111--62581 Score: 789
Period size: 140 Copynumber: 3.4 Consensus size: 139
62101 GTTAAAGTCC
62111 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
1 TAATTAAGAAAAGTAAGCATAGT-AAGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
* *
62176 CGGGGTAATTAAGAAAAGTAAGCATAGTTAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCT
65 CAGGGTAATTAAGAAAAGTAAGCATAGTCAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCT
*
62241 TAGTTCAGGG
130 TAATTCAGGG
*
62251 TAATTAAGAAAAGTAAGCATAGTAAGGGTCTTAATTTGGTAATTAAGAAAAGTAAAGTCTTAATT
1 TAATTAAGAAAAGTAAGCATAGTAA-GGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
*
62316 CAGGGTAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCT
65 CAGGGTAATTAAGAAAAGTAAGCATAGTCAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCT
*
62381 TAATTCAAGG
130 TAATTCAGGG
*
62391 TAATTAAGAAAAGTAAGCATAGTCAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
1 TAATTAAGAAAAGTAAGCATAGT-AAGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
*
62456 CAGGGTAATTAAGAAAAGTGAGCATAGTCAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCT
65 CAGGGTAATTAAGAAAAGTAAGCATAGTCAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCT
62521 TAATTCAGGG
130 TAATTCAGGG
* * * *
62531 TAATTAAGAAAAGTAAACATAGTAAAGTATTAATTCAGGGTAATTAAGAAA
1 TAATTAAGAAAAGTAAGCATAGTAAGGTCTTAATT--TGGTAATTAAGAAA
62582 GTCAAACACA
Statistics
Matches: 311, Mismatches: 16, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
139 11 0.04
140 286 0.92
141 14 0.05
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (139 bp):
TAATTAAGAAAAGTAAGCATAGTAAGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATTC
AGGGTAATTAAGAAAAGTAAGCATAGTCAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTT
AATTCAGGG
Found at i:62343 original size:210 final size:210
Alignment explanation
Indices: 62111--62581 Score: 818
Period size: 210 Copynumber: 2.2 Consensus size: 210
62101 GTTAAAGTCC
62111 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
1 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
** *
62176 CGGGGTAATTAAGAAAAGTAAGCATAGTTAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCT
66 CAAGGTAATTAAGAAAAGTAAGCATAGTCAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCT
* *
62241 TAGTTCAGGGTAATTAAGAAAAGTAAGCATAGTAAGGGTCTTAATTTGGTAATTAAGAAAAGTAA
131 TAATTCAGGGTAATTAAGAAAAGTAAGCATAGTAAGGGTCTTAATTTGGTAATTAAGAAAAGCAA
62306 AGTCTTAATTCAGGG
196 AGTCTTAATTCAGGG
62321 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
1 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
62386 CAAGGTAATTAAGAAAAGTAAGCATAGTCAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCT
66 CAAGGTAATTAAGAAAAGTAAGCATAGTCAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCT
* *
62451 TAATTCAGGGTAATTAAGAAAAGTGAGCATAGTCAGGGTCTTAATTTGGTAATTAAGAAAAGCAA
131 TAATTCAGGGTAATTAAGAAAAGTAAGCATAGTAAGGGTCTTAATTTGGTAATTAAGAAAAGCAA
62516 AGTCTTAATTCAGGG
196 AGTCTTAATTCAGGG
* * * *
62531 TAATTAAGAAAAGTAAACATAGT-AAAGTATTAATTCAGGGTAATTAAGAAA
1 TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATT--TGGTAATTAAGAAA
62582 GTCAAACACA
Statistics
Matches: 248, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
209 10 0.04
210 225 0.91
211 13 0.05
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (210 bp):
TAATTAAGAAAAGTAAGCATAGTCAAGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCTTAATT
CAAGGTAATTAAGAAAAGTAAGCATAGTCAGGGTCTTAATTTGGTAATTAAGAAAAGCAAAGTCT
TAATTCAGGGTAATTAAGAAAAGTAAGCATAGTAAGGGTCTTAATTTGGTAATTAAGAAAAGCAA
AGTCTTAATTCAGGG
Found at i:62564 original size:40 final size:41
Alignment explanation
Indices: 62514--62746 Score: 247
Period size: 41 Copynumber: 5.7 Consensus size: 41
62504 TAAGAAAAGC
*
62514 AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACATAG-T
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTT
*
62554 AAAGTATTAATTCAGGGTAATTAAG-AAAGTCAAACACAGTT
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGT-AAACACAGTT
* * *
62595 AAAGTCTTAATTCATGGTGATTAAG-AAAGTGAAACACAGTC
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGT-AAACACAGTT
* * * * * * * *
62636 AGAGTCCTAATTTAGGATAATTAAGAAGAGCATACGCAGTT
1 AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTT
* * *
62677 AAGGTCTTAATTCATGGAAATTAAGGAAAAGTAAACACAGTT
1 AAAGTCTTAATTCAGGGTAATTAA-GAAAAGTAAACACAGTT
* **
62719 AAGGTCTTAATTCACAGTAATTAAGAAA
1 AAAGTCTTAATTCAGGGTAATTAAGAAA
62747 GGTGATCACA
Statistics
Matches: 157, Mismatches: 32, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
39 5 0.03
40 31 0.20
41 84 0.54
42 37 0.24
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.27
Consensus pattern (41 bp):
AAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTT
Found at i:62833 original size:41 final size:41
Alignment explanation
Indices: 62788--62946 Score: 266
Period size: 41 Copynumber: 3.9 Consensus size: 41
62778 AAGTACTAAG
62788 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
62829 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTGA
1 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
62870 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
* * *
62911 AG-ACAGGCACAAACTTAATTTCAGGGAAGGAAATTA
1 AGTA-AAGCACAGACTTAATTTCAAGGAAGGAAATTA
62947 AGTAGAGTCA
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 1 0.01
41 111 0.99
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (41 bp):
AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
Found at i:62968 original size:41 final size:41
Alignment explanation
Indices: 62788--62972 Score: 232
Period size: 41 Copynumber: 4.5 Consensus size: 41
62778 AAGTACTAAG
*
62788 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGTAAAGCAAAGACTTAATTTCAAGGAAGGAAATTAGGTAA
* *
62829 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTGA
1 AGTAAAGCAAAGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
62870 AGTAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGTAAAGCAAAGACTTAATTTCAAGGAAGGAAATTAGGTAA
* * * *
62911 AG-ACAGGCACAA-ACTTAATTTCAGGGAAGGAAATTAAGTAG
1 AGTA-AAGCA-AAGACTTAATTTCAAGGAAGGAAATTAGGTAA
* *
62952 AGTCAA-TAAAGTACTTAATTT
1 AGTAAAGCAAAG-ACTTAATTT
62973 AGGGTAATTA
Statistics
Matches: 129, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 124 0.96
42 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.23
Consensus pattern (41 bp):
AGTAAAGCAAAGACTTAATTTCAAGGAAGGAAATTAGGTAA
Found at i:63000 original size:32 final size:32
Alignment explanation
Indices: 62956--63206 Score: 290
Period size: 32 Copynumber: 7.5 Consensus size: 32
62946 AAGTAGAGTC
* *
62956 AATAAAGTACTTAATTTAGGGTAATTAAGTAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGTAG
62988 AATAAAGAACTTAATTCAGGGTAATTAAGTGGAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGT--AG
** *
63022 TCAATAAA-AGGTTTAACTCAGGGTAATTAAGTAG
1 --AATAAAGA-ACTTAATTCAGGGTAATTAAGTAG
*
63056 AATAAAGAACTTAATTCAGGGTATTTAAGTGGAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGT--AG
63090 TCAATAAA-AGACTTAATTCAGGGTAATTAAGTAG
1 --AATAAAGA-ACTTAATTCAGGGTAATTAAGTAG
*
63124 AATAAAGAACTTAATTCTGGGTAATTAAGTAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGTAG
*
63156 AATAAAGAACTTAATTCCGGGTAATTAAGTGGAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGT--AG
63190 TCAATAAAGAACTTAAT
1 --AATAAAGAACTTAAT
63207 CAAAAAAAGA
Statistics
Matches: 191, Mismatches: 12, Indels: 28
0.83 0.05 0.12
Matches are distributed among these distances:
32 110 0.58
33 2 0.01
34 10 0.05
35 2 0.01
36 67 0.35
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.29
Consensus pattern (32 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTAG
Found at i:63014 original size:68 final size:69
Alignment explanation
Indices: 62942--63206 Score: 359
Period size: 68 Copynumber: 3.9 Consensus size: 69
62932 CAGGGAAGGA
* *
62942 AATTAAGTAGAGTCAAT-AAAGTACTTAATTTAGGGTAATTAAGTAGAATAAAGAACTTAATTCA
1 AATTAAGTGGAGTCAATAAAAGTACTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCA
63006 GGGT
66 GGGT
*
63010 AATTAAGTGGAGTCAATAAAAGGT--TTAACTCAGGGTAATTAAGTAGAATAAAGAACTTAATTC
1 AATTAAGTGGAGTCAATAAAA-GTACTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTC
63073 AGGGT
65 AGGGT
* *
63078 ATTTAAGTGGAGTCAATAAAAG-ACTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCT
1 AATTAAGTGGAGTCAATAAAAGTACTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCA
63142 GGGT
66 GGGT
* *
63146 AATTAAGT--AG--AAT-AAAGAACTTAATTCCGGGTAATTAAGTGGAGTCAATAAAGAACTTAA
1 AATTAAGTGGAGTCAATAAAAGTACTTAATTCAGGGTAATTAAGT--AG--AATAAAGAACTTAA
63206 T
62 T
63207 CAAAAAAAGA
Statistics
Matches: 180, Mismatches: 8, Indels: 18
0.87 0.04 0.09
Matches are distributed among these distances:
63 4 0.02
64 24 0.13
66 4 0.02
67 1 0.01
68 142 0.79
69 3 0.02
70 2 0.01
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.29
Consensus pattern (69 bp):
AATTAAGTGGAGTCAATAAAAGTACTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCA
GGGT
Found at i:63147 original size:100 final size:102
Alignment explanation
Indices: 62956--63206 Score: 338
Period size: 100 Copynumber: 2.5 Consensus size: 102
62946 AAGTAGAGTC
* *
62956 AATAAAGTACTTAATTTAGGGTAATTAAGT--AG--AATAAAGAACTTAATTCAGGGTAATTAAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATTCAGGGTAATTAAG
**
63017 TGGAGTCAATAAAAGGTTTAACTCAGGGTAATTAAGTAG
66 T-GAG-CAATAAAAGACTTAACTCAGGGTAATTAAGTAG
*
63056 AATAAAGAACTTAATTCAGGGTATTTAAGTGGAGTCAATAAA-AGACTTAATTCAGGGTAATTAA
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGA-ACTTAATTCAGGGTAATTAA
* *
63120 GT-AG-AAT-AAAGAACTTAATTCTGGGTAATTAAGTAG
65 GTGAGCAATAAAAG-ACTTAACTCAGGGTAATTAAGTAG
*
63156 AATAAAGAACTTAATTCCGGGTAATTAAGTGGAGTCAATAAAGAACTTAAT
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAAT
63207 CAAAAAAAGA
Statistics
Matches: 135, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
99 4 0.03
100 97 0.72
101 1 0.01
102 4 0.03
103 1 0.01
104 28 0.21
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.29
Consensus pattern (102 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATTCAGGGTAATTAAG
TGAGCAATAAAAGACTTAACTCAGGGTAATTAAGTAG
Found at i:65821 original size:21 final size:21
Alignment explanation
Indices: 65779--65822 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
65769 TCTATCTATC
* *
65779 TTGCATATTTAAATTTCTTGT
1 TTGCATATTTAAATTGCATGT
65800 TTGCATA-TTAAGATTGCATGT
1 TTGCATATTTAA-ATTGCATGT
65821 TT
1 TT
65823 AGATTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (21 bp):
TTGCATATTTAAATTGCATGT
Found at i:65971 original size:30 final size:29
Alignment explanation
Indices: 65898--65975 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
65888 TTGCCTATTC
* * *
65898 TATCTTTCAATTG-TTGATTTGAATTGCCA
1 TATCTTGCTATTGATTGA-TTGAATTGCAA
65927 TATCTTGCTATTGATTGATTGAATTGCAA
1 TATCTTGCTATTGATTGATTGAATTGCAA
*
65956 TTAT-TTGGTAGTTGATTGAT
1 -TATCTTGCTA-TTGATTGAT
65976 AGATTTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 26 0.62
30 16 0.38
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.49
Consensus pattern (29 bp):
TATCTTGCTATTGATTGATTGAATTGCAA
Found at i:73094 original size:25 final size:25
Alignment explanation
Indices: 73061--73128 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
73051 CACTGCTAGG
* *
73061 AACTTGCTGCTAGGAAGCTCGTTGA
1 AACTCGCTGCTAGGAAGCTCGCTGA
*
73086 AGCTCGCTGCTAGGAAGCTCGCTGA
1 AACTCGCTGCTAGGAAGCTCGCTGA
73111 AACTCGCTGCTAGGAAGC
1 AACTCGCTGCTAGGAAGC
73129 CGGCAGAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.22
Consensus pattern (25 bp):
AACTCGCTGCTAGGAAGCTCGCTGA
Found at i:74296 original size:22 final size:23
Alignment explanation
Indices: 74268--74310 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
74258 GGAAGAAAAA
74268 AAAAACTTGCACTA-GGCAAGAC
1 AAAAACTTGCACTAGGGCAAGAC
*
74290 AAAAACTTGCATTAGGGCAAG
1 AAAAACTTGCACTAGGGCAAG
74311 CCGAAAGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (23 bp):
AAAAACTTGCACTAGGGCAAGAC
Found at i:76399 original size:21 final size:21
Alignment explanation
Indices: 76370--76412 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
76360 ATTATCATTC
76370 AATTCATTTTTTAACTAAATT
1 AATTCATTTTTTAACTAAATT
* *
76391 AATTTATTTTTTAACTTAATT
1 AATTCATTTTTTAACTAAATT
76412 A
1 A
76413 TTGTTGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTCATTTTTTAACTAAATT
Found at i:81633 original size:2 final size:2
Alignment explanation
Indices: 81626--81658 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
81616 ACATTGCTGC
81626 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
81659 TAGAGCAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81896 original size:16 final size:16
Alignment explanation
Indices: 81875--81917 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 16
81865 CCTCGGGAAA
81875 TTTTGGTGGCATTTTT
1 TTTTGGTGGCATTTTT
*
81891 TTTTGGT---AATTTT
1 TTTTGGTGGCATTTTT
81904 TTTTGGTGGCATTT
1 TTTTGGTGGCATTT
81918 GGGCACTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
13 12 0.55
16 10 0.45
ACGTcount: A:0.09, C:0.05, G:0.23, T:0.63
Consensus pattern (16 bp):
TTTTGGTGGCATTTTT
Found at i:82314 original size:14 final size:13
Alignment explanation
Indices: 82273--82316 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
82263 CAATCAAATG
82273 TTCTTTTATAGAA
1 TTCTTTTATAGAA
* *
82286 TTTTTTTAGATGAA
1 TTCTTTTATA-GAA
82300 TTGCTTTTATAGAA
1 TT-CTTTTATAGAA
82314 TTC
1 TTC
82317 ATCAAAACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 9 0.36
14 10 0.40
15 6 0.24
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (13 bp):
TTCTTTTATAGAA
Found at i:83318 original size:15 final size:14
Alignment explanation
Indices: 83276--83323 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 14
83266 AATTAGTACT
83276 TATTATTATATA-A
1 TATTATTATATATA
83289 TAATATATTATATATCA
1 T-AT-TATTATATAT-A
83306 TATTATTATATATA
1 TATTATTATATATA
83320 TATT
1 TATT
83324 TTAAAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.03
14 7 0.23
15 19 0.61
16 2 0.06
17 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTATTATATATA
Done.