Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006876.1 Corchorus capsularis cultivar CVL-1 contig06897, 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: 44197
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Found at i:3467 original size:36 final size:36
Alignment explanation
Indices: 3424--3575 Score: 209
Period size: 36 Copynumber: 4.2 Consensus size: 36
3414 CTCTTTTTAG
*
3424 ATTAAGTTCTTTATTGAC-TTCACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACGCT-ACTTAATTACCCTGA
3460 ATTAAGTTCTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACGCTACTTAATTACCCTGA
* * * *
3496 ATTAAG-TCTCTAACTTGACTCGACTTAATTACCCTAA
1 ATTAAGTTCT-TTA-TTGACGCTACTTAATTACCCTGA
*
3533 ATTAAGTTCTTTAGTGACGCTACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACGCTACTTAATTACCCTGA
3569 ATTAAGT
1 ATTAAGT
3576 CTCTAACTTG
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
35 3 0.03
36 67 0.66
37 29 0.28
38 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.40
Consensus pattern (36 bp):
ATTAAGTTCTTTATTGACGCTACTTAATTACCCTGA
Found at i:3514 original size:73 final size:74
Alignment explanation
Indices: 3437--3589 Score: 274
Period size: 73 Copynumber: 2.1 Consensus size: 74
3427 AAGTTCTTTA
* *
3437 TTGACTTC-ACTTAATTACCCTGAATTAAGTTCTTTATTGACGCTACTTAATTACCCTGAATTAA
1 TTGACTTCGACTTAATTACCCTAAATTAAGTTCTTTAGTGACGCTACTTAATTACCCTGAATTAA
3501 GTCTCTAAC
66 GTCTCTAAC
3510 TTGAC-TCGACTTAATTACCCTAAATTAAGTTCTTTAGTGACGCTACTTAATTACCCTGAATTAA
1 TTGACTTCGACTTAATTACCCTAAATTAAGTTCTTTAGTGACGCTACTTAATTACCCTGAATTAA
3574 GTCTCTAAC
66 GTCTCTAAC
3583 TTGACTT
1 TTGACTT
3590 GATTCCCTTC
Statistics
Matches: 76, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
72 2 0.03
73 73 0.96
74 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (74 bp):
TTGACTTCGACTTAATTACCCTAAATTAAGTTCTTTAGTGACGCTACTTAATTACCCTGAATTAA
GTCTCTAAC
Found at i:3632 original size:32 final size:32
Alignment explanation
Indices: 3586--3652 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
3576 CTCTAACTTG
*
3586 ACTTGATTCCCTTCCTTGGAATCAA-GTCTCTA
1 ACTTAATTCCCTTCCTTGGAATCAAGGTCT-TA
*
3618 ACTTAATTCCCTTCCTTGGAATTAAGGTCTTA
1 ACTTAATTCCCTTCCTTGGAATCAAGGTCTTA
3650 ACT
1 ACT
3653 CTACTTAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 28 0.88
33 4 0.12
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (32 bp):
ACTTAATTCCCTTCCTTGGAATCAAGGTCTTA
Found at i:3734 original size:37 final size:35
Alignment explanation
Indices: 3666--3770 Score: 95
Period size: 35 Copynumber: 2.9 Consensus size: 35
3656 CTTAATCCCC
* * * *
3666 TTGGGTTAAGTTTTTAACTGATCTTACTTAATCATCTT
1 TTGGATTAAGTCTTTGA-TGATTTTACTTAAT--TCTT
3704 TTGGATTAAGTCTTTGATGATTTTACTTAATTCTT
1 TTGGATTAAGTCTTTGATGATTTTACTTAATTCTT
* * * *
3739 GTGAAATTAAGTCTTTGCT-AATTTACTTAATT
1 TTG-GATTAAGTCTTTGATGATTTTACTTAATT
3771 ACCTTGAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
35 18 0.31
36 13 0.22
37 13 0.22
38 14 0.24
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.50
Consensus pattern (35 bp):
TTGGATTAAGTCTTTGATGATTTTACTTAATTCTT
Found at i:3786 original size:34 final size:36
Alignment explanation
Indices: 3708--3791 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
3698 CATCTTTTGG
* * *
3708 ATTAAGTCTTTGATGATTTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTGAATTTACTTAATTCCTGTGAA
3744 ATTAAGTCTTTGCT-AATTTACTTAATTACCT-TG-A
1 ATTAAGTCTTTGCTGAATTTACTTAATT-CCTGTGAA
*
3778 ATTAAGTCTGTGCT
1 ATTAAGTCTTTGCT
3792 TGTCTTTAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 14 0.33
35 14 0.33
36 15 0.35
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (36 bp):
ATTAAGTCTTTGCTGAATTTACTTAATTCCTGTGAA
Found at i:3856 original size:77 final size:77
Alignment explanation
Indices: 3760--3918 Score: 239
Period size: 77 Copynumber: 2.1 Consensus size: 77
3750 TCTTTGCTAA
* * *
3760 TTTACTTAATTACCTTGAATTAAGTCTGTGCTTGTCTTTAACTAATTTCCT-TCATTGAAATTAA
1 TTTACTTAATTACCCTGAATTAAGTCTGTGCTAGTCCTTAACTAATTTCCTCTC-TTGAAATTAA
*
3824 GTCTGTGCTTTTC
65 GTCTGTGCTTGTC
* *
3837 TTTACTTAATTGCCCTGAATTAAGTCTGTGCTAGTCCTTACCTAATTTCCTCTCTTGAAATTAAG
1 TTTACTTAATTACCCTGAATTAAGTCTGTGCTAGTCCTTAACTAATTTCCTCTCTTGAAATTAAG
*
3902 TTTGTGCTTGTC
66 TCTGTGCTTGTC
3914 TTTAC
1 TTTAC
3919 CTTCTTTTAC
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
77 72 0.97
78 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.47
Consensus pattern (77 bp):
TTTACTTAATTACCCTGAATTAAGTCTGTGCTAGTCCTTAACTAATTTCCTCTCTTGAAATTAAG
TCTGTGCTTGTC
Found at i:3919 original size:41 final size:40
Alignment explanation
Indices: 3773--3920 Score: 171
Period size: 41 Copynumber: 3.8 Consensus size: 40
3763 ACTTAATTAC
*
3773 CTTGAATTAAGTCTGTGCTTGTCTTTAACTAATTTCCT-T
1 CTTGAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTCT
* * *
3812 CATTGAAATTAAGTCTGTGCTTTTCTTTACTTAA-TTGC-C-
1 C-TTG-AATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTCT
* *
3851 C-TGAATTAAGTCTGTGCTAGTCCTTACCTAATTTCCTCT
1 CTTGAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTCT
*
3890 CTTGAAATTAAGTTTGTGCTTGTCTTTACCT
1 CTTG-AATTAAGTCTGTGCTTGTCTTTACCT
3921 TCTTTTACTT
Statistics
Matches: 89, Mismatches: 12, Indels: 14
0.77 0.10 0.12
Matches are distributed among these distances:
36 24 0.27
37 5 0.06
38 1 0.01
39 3 0.03
40 8 0.09
41 48 0.54
ACGTcount: A:0.21, C:0.20, G:0.14, T:0.46
Consensus pattern (40 bp):
CTTGAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTCT
Found at i:3951 original size:36 final size:39
Alignment explanation
Indices: 3911--3994 Score: 93
Period size: 42 Copynumber: 2.2 Consensus size: 39
3901 GTTTGTGCTT
3911 GTCTTT-AC-CTT-CTTTTACTTAATTACCCTGAATTAA
1 GTCTTTAACGCTTCCTTTTACTTAATTACCCTGAATTAA
* *
3947 GTCTTTAACTGTGTTTCCTTTTTCTTAATTACCCTGAATTAA
1 GTCTTTAAC---GCTTCCTTTTACTTAATTACCCTGAATTAA
*
3989 GACTTT
1 GTCTTT
3995 GACTGACCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
36 6 0.15
37 2 0.05
41 2 0.05
42 29 0.74
ACGTcount: A:0.23, C:0.20, G:0.08, T:0.49
Consensus pattern (39 bp):
GTCTTTAACGCTTCCTTTTACTTAATTACCCTGAATTAA
Found at i:4030 original size:45 final size:43
Alignment explanation
Indices: 3922--4153 Score: 263
Period size: 45 Copynumber: 5.2 Consensus size: 43
3912 TCTTTACCTT
* *
3922 CTTTTACTTAATTACCCTGAATTAAG-TCTTTAACTG--TGTTTC
1 CTTTT-CTTAATTACCCTGAATTAAGAT-TTTGACTGACTGTTTA
* *
3964 CTTTTTCTTAATTACCCTGAATTAAGACTTTGACTGACCATGTTTG
1 C-TTTTCTTAATTACCCTGAATTAAGATTTTGACTGA-C-TGTTTA
4010 CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGACTGGTTTTA
1 CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGACT-G-TTTA
* *
4055 CTTTTCTTAATTACTCTGAATTAAGATTTTGACTGACTATGTTTG
1 CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGAC--TGTTTA
* * *
4100 CTTTTCTTAATTATCCTGAATTAAGATTTTTACTGATTGTGTTTA
1 CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGA--CTGTTTA
4145 CTTTTCTTA
1 CTTTTCTTA
4154 CTTTGAATTA
Statistics
Matches: 166, Mismatches: 12, Indels: 21
0.83 0.06 0.11
Matches are distributed among these distances:
42 28 0.17
43 5 0.03
44 2 0.01
45 123 0.74
46 7 0.04
47 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.49
Consensus pattern (43 bp):
CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGACTGTTTA
Found at i:4076 original size:90 final size:88
Alignment explanation
Indices: 3922--4153 Score: 317
Period size: 90 Copynumber: 2.6 Consensus size: 88
3912 TCTTTACCTT
*
3922 CTTTTACTTAATTACCCTGAATTAAG-TCTTTAACTG-TG-TTTCCTTTTTCTTAATTACCCTGA
1 CTTTT-CTTAATTACCCTGAATTAAGAT-TTTAACTGATGTTTTAC-TTTTCTTAATTACCCTGA
3984 ATTAAGACTTTGACTGACCATGTTTG
63 ATTAAGACTTTGACTGACCATGTTTG
* *
4010 CTTTTCTTAATTACCCTGAATTAAGATTTTGACTGACTGGTTTTACTTTTCTTAATTACTCTGAA
1 CTTTTCTTAATTACCCTGAATTAAGATTTTAACTGA-T-GTTTTACTTTTCTTAATTACCCTGAA
* *
4075 TTAAGATTTTGACTGACTATGTTTG
64 TTAAGACTTTGACTGACCATGTTTG
* *
4100 CTTTTCTTAATTATCCTGAATTAAGATTTTTACTGATTGTGTTTACTTTTCTTA
1 CTTTTCTTAATTACCCTGAATTAAGATTTTAACTGA-TGT-TTTACTTTTCTTA
4154 CTTTGAATTA
Statistics
Matches: 130, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
87 27 0.21
88 6 0.05
89 3 0.02
90 90 0.69
91 4 0.03
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.49
Consensus pattern (88 bp):
CTTTTCTTAATTACCCTGAATTAAGATTTTAACTGATGTTTTACTTTTCTTAATTACCCTGAATT
AAGACTTTGACTGACCATGTTTG
Found at i:4259 original size:37 final size:37
Alignment explanation
Indices: 4179--4506 Score: 482
Period size: 37 Copynumber: 8.9 Consensus size: 37
4169 TTGAGATTTC
* * *
4179 TACTTAATTTCCTTGAATTAAG-CCCTT-ACTTGCTTT
1 TACTTAATTACCCTGAATTAAGTCCTTTAAC-TGCTTT
4215 TACTTAATTACCCTGAATTAAG-CTCTTTAACTGCTTT
1 TACTTAATTACCCTGAATTAAGTC-CTTTAACTGCTTT
*
4252 TACTTAATTACCTTGAATTAAGTCCTTTAACTGCTTT
1 TACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTT
* *
4289 TACTTAATTACCCTGAATTAAATCCTTTAACTGATTT
1 TACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTT
*
4326 TACTTAATTACCCTGAATTAAGTTCTTTAACTGCTTT
1 TACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTT
* * *
4363 TACTTAAATACCCTGAATTAAGTCTTTTAACTGTTTT
1 TACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTT
*
4400 TACTTAATTACCTTGAATTAAGTCCTTTAACTGCTTT
1 TACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTT
* * *
4437 TACTTAATTACCCTTAATTAAGTCCTTTTACCGCTTT
1 TACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTT
*
4474 TACTTAATTATCCTGAATTAAGTCCTTTAACTG
1 TACTTAATTACCCTGAATTAAGTCCTTTAACTG
4507 TACTCACCTT
Statistics
Matches: 263, Mismatches: 26, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
36 21 0.08
37 239 0.91
38 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (37 bp):
TACTTAATTACCCTGAATTAAGTCCTTTAACTGCTTT
Found at i:9675 original size:24 final size:24
Alignment explanation
Indices: 9630--9675 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
9620 TGTTGCTTAT
**
9630 TCTTTTTCTTCAGCTGTTGCTCAC
1 TCTTTTTCTTCAGCTGCAGCTCAC
**
9654 TCTTTTTCTTCTTCTGCAGCTC
1 TCTTTTTCTTCAGCTGCAGCTC
9676 TTTTGCTTTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.07, C:0.30, G:0.11, T:0.52
Consensus pattern (24 bp):
TCTTTTTCTTCAGCTGCAGCTCAC
Found at i:17166 original size:2 final size:2
Alignment explanation
Indices: 17159--17249 Score: 68
Period size: 2 Copynumber: 47.5 Consensus size: 2
17149 TTACTATGTA
17159 AT AT AT AT -T AT AT AT AT AT GAT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
17200 CAT GT A- AT AC AT AT CT AT AT -T AT TT CT AA AT A- AT AT AT AT
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17240 AT AT A- AT AT A
1 AT AT AT AT AT A
17250 AAATCACAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
1 6 0.09
2 60 0.86
3 4 0.06
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17213 original size:22 final size:21
Alignment explanation
Indices: 17153--17244 Score: 78
Period size: 22 Copynumber: 4.1 Consensus size: 21
17143 CCCGAATTAC
17153 TATGTAATATATATTATATATA
1 TATGTAATATATA-TATATATA
17175 TATGATATTATATATATATATATA
1 TATG-TA--ATATATATATATATA
* *
17199 TCATGTAATACATATCTATATTA
1 T-ATGTAATATATATATATA-TA
* *
17222 TTTCTAA-ATAATATATATATA
1 TATGTAATAT-ATATATATATA
17243 TA
1 TA
17245 ATATAAAATC
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
21 4 0.07
22 27 0.47
23 5 0.09
24 11 0.19
25 10 0.18
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (21 bp):
TATGTAATATATATATATATA
Found at i:19281 original size:21 final size:21
Alignment explanation
Indices: 19256--19295 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19246 CTTTAGTAAT
19256 TTAATGCAT-ATGGTTTATTTA
1 TTAAT-CATAATGGTTTATTTA
*
19277 TTAATCTTAATGGTTTATT
1 TTAATCATAATGGTTTATT
19296 GATTGCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.55
Consensus pattern (21 bp):
TTAATCATAATGGTTTATTTA
Found at i:19476 original size:20 final size:21
Alignment explanation
Indices: 19453--19491 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19443 TCTATGATTT
19453 ATGATCTAT-TGTTTTGATAA
1 ATGATCTATGTGTTTTGATAA
*
19473 ATGATTTATGTGTTTTGAT
1 ATGATCTATGTGTTTTGAT
19492 CCGTGATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.54
Consensus pattern (21 bp):
ATGATCTATGTGTTTTGATAA
Found at i:21880 original size:54 final size:54
Alignment explanation
Indices: 21838--22324 Score: 658
Period size: 54 Copynumber: 9.0 Consensus size: 54
21828 TTCAGAAGAA
* * *
21838 TAAGTTTATATTCAAGTGA-CCTAGTGCGGTCAATCAA-AGAAGTATCCAGTGGTAT
1 TAAGTTTATCTTCAAGTGATCC-AGTGCGGTCAATCAAGA-AAGTTTCCAATGGT-T
* * *
21893 TAAGTTTATCTTCAAGTGATCCAGTGTGCTCAATCAAGAAAGTTTCCAATTGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
* *
21947 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTGCAGTGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
* * *
22001 TAAGTTTATCTTCAAGTGATCCAATGCGGTCAGTCAAGAAAGTTTCCAATGGTC
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
*
22055 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATTGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
* * * * *
22109 TAAATTTATCTTCAATTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGATAT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGT-T
*
22164 TGAG-TTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTT-CAACTGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAA-TGGTT
** *
22217 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCGGTGCTAT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGT-T
* * ** *
22272 TTAGTTTATCTTCAAGTAAAGCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGT
22325 ATCTTTAAGT
Statistics
Matches: 384, Mismatches: 41, Indels: 14
0.87 0.09 0.03
Matches are distributed among these distances:
53 6 0.02
54 281 0.73
55 94 0.24
56 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (54 bp):
TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
Found at i:22348 original size:46 final size:46
Alignment explanation
Indices: 22278--22368 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
22268 CTATTTAGTT
* *
22278 TATCTTCAAGTAAAGCAGTGCGGTCAATCAAGAAAGTTTCCAGTGG
1 TATCTTCAAGTAAACCAATGCGGTCAATCAAGAAAGTTTCCAGTGG
* * * * *
22324 TATCTTTAAGTGAACCAATGCGGTCAGTCAAGGAAGTTTCTAGTG
1 TATCTTCAAGTAAACCAATGCGGTCAATCAAGAAAGTTTCCAGTG
22369 ATTTGGGTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (46 bp):
TATCTTCAAGTAAACCAATGCGGTCAATCAAGAAAGTTTCCAGTGG
Found at i:22468 original size:35 final size:35
Alignment explanation
Indices: 22422--22500 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 35
22412 GTGTAGCAAA
* *
22422 TTCAAAGTTGGAATCAGATAACTCGGTGGAGCATT
1 TTCAAAGTTGGAATCAGATAACTCGGTGCAACATT
* *
22457 TTCAAAGTTGGATTCAGATGACTCGGTGCAACATT
1 TTCAAAGTTGGAATCAGATAACTCGGTGCAACATT
*
22492 TTTAAAGTT
1 TTCAAAGTT
22501 TGATACGGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (35 bp):
TTCAAAGTTGGAATCAGATAACTCGGTGCAACATT
Found at i:22565 original size:35 final size:35
Alignment explanation
Indices: 22517--22584 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
22507 GGTGGATCAG
* * *
22517 ATGACTCGGTGTAGCATTTTCAAAGTTAGATTCAA
1 ATGACTCGATGTAGCATCTTCAAAATTAGATTCAA
*
22552 ATGACTCGATGTAGCATCTTCAAAATTGGATTC
1 ATGACTCGATGTAGCATCTTCAAAATTAGATTC
22585 GGTGAACCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (35 bp):
ATGACTCGATGTAGCATCTTCAAAATTAGATTCAA
Found at i:22588 original size:78 final size:78
Alignment explanation
Indices: 22432--22606 Score: 206
Period size: 78 Copynumber: 2.2 Consensus size: 78
22422 TTCAAAGTTG
* * * * * *
22432 GAATCAGATAACTCGGTGGAGCATTTTCAAAGTTGGATTCAGATGACTCGGTGCAACATTTTTAA
1 GAATCAGATGACTCGGTGGAGCATTTTCAAAGTTAGATTCAAATGACTCGATGCAACATCTTCAA
* *
22497 AGTTTGATACGGT
66 AATTGGATACGGT
* * * *
22510 GGATCAGATGACTCGGTGTAGCATTTTCAAAGTTAGATTCAAATGACTCGATGTAGCATCTTCAA
1 GAATCAGATGACTCGGTGGAGCATTTTCAAAGTTAGATTCAAATGACTCGATGCAACATCTTCAA
*
22575 AATTGGATTCGGT
66 AATTGGATACGGT
* *
22588 GAACCAGGTGAGCTCGGTG
1 GAATCAGATGA-CTCGGTG
22607 CAGTAAATTT
Statistics
Matches: 80, Mismatches: 16, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
78 73 0.91
79 7 0.09
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (78 bp):
GAATCAGATGACTCGGTGGAGCATTTTCAAAGTTAGATTCAAATGACTCGATGCAACATCTTCAA
AATTGGATACGGT
Found at i:22695 original size:81 final size:81
Alignment explanation
Indices: 22594--22748 Score: 274
Period size: 81 Copynumber: 1.9 Consensus size: 81
22584 CGGTGAACCA
*
22594 GGTGAGCTCGGTGCAGTAAATTTTCAAACAAATCATGGTGATTCGGTGAATCAAGTTAATGCGCT
1 GGTGAGCTCGGTGAAGTAAATTTTCAAACAAATCATGGTGATTCGGTGAATCAAGTTAATGCGCT
22659 GCATCTATTGGAATTC
66 GCATCTATTGGAATTC
* *
22675 GGTGAGCTCGGTGAAGTAAATTTTCAAACAGATCATGGTGATTCGGTGAATCAAGTTAATGCGGT
1 GGTGAGCTCGGTGAAGTAAATTTTCAAACAAATCATGGTGATTCGGTGAATCAAGTTAATGCGCT
*
22740 GCATTTATT
66 GCATCTATT
22749 CAAAAATTGG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (81 bp):
GGTGAGCTCGGTGAAGTAAATTTTCAAACAAATCATGGTGATTCGGTGAATCAAGTTAATGCGCT
GCATCTATTGGAATTC
Found at i:22816 original size:98 final size:91
Alignment explanation
Indices: 22671--23543 Score: 590
Period size: 90 Copynumber: 9.6 Consensus size: 91
22661 ATCTATTGGA
* * * * *
22671 ATTCGGTGAGCTCGGTGAAGTAAATTTTCAAACAGATCATGGTGATTCGGTGAATCAAGTTAATG
1 ATTCGGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCAAGATGATTCGGTGAATCAAGTTAATG
22736 CGGTGCATTTATTCAAAAATTGGAATTCGTCGG
66 CGGTGCATTTATTCAAAAA---GAA----TCGG
* * *
22769 ATTCGGTGAGCTCGGTGCAGCAGATTTTTAAACGGTTCAAGATGATTCGGTGAATCAAGTTAAT-
1 ATTCGGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCAAGATGATTCGGTGAATCAAGTTAATG
*
22833 CGGTGCTTTTATTC-AAAAG-ATCGG
66 CGGTGCATTTATTCAAAAAGAATCGG
* * *
22857 AATCGGTGAGCTCGGTGCAGCAAATTTTCAAATAGTT-AAGGATGATTCGGTGAATCAAGATTGA
1 ATTCGGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCAA-GATGATTCGGTGAATCAAG-TTAA
* * ***
22921 GGCGGTGCCATAT-TTCTTCAAGAAT-GG
64 TGCGGTG-CATTTATTCAAAAAGAATCGG
* ** * * *
22948 ATTCGGTGAGCTCGGTGCAGCAGATTTTCGGACAGTTCAGGATAATTCGATGAATCAAGTTAATG
1 ATTCGGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCAAGATGATTCGGTGAATCAAGTTAATG
23013 CGGTGCATTTATTC--AAAG-ATCGG
66 CGGTGCATTTATTCAAAAAGAATCGG
* * * * * *
23036 AATCGGTAAGCTCGGTGCAGCAAATTATCAAATAGTT-AAGGATGATTCGGTGAAACAAGATTGA
1 ATTCGGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCAA-GATGATTCGGTGAATCAAG-TTAA
* * *** *
23100 GGCGGTG-ACTTATTTCTTCAAG-ATTGG
64 TGCGGTGCATTTA-TTCAAAAAGAATCGG
* * * * **
23127 ACTCGGTGAGCTCGGTGCAGCAGACTTTCAAATAGTT-AAGGATGATTCGGTGAATCAAGATTGC
1 ATTCGGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCAA-GATGATTCGGTGAATCAAG-TTAA
* * *** *
23191 GGCGGTGC-CTTATTTCTTCAAG-ATTGG
64 TGCGGTGCATTTA-TTCAAAAAGAATCGG
* * * * * * *
23218 ATTCGGTGAGCTCGGTGCAGCAGATTTTCAGACAGTTCAGGATAAATCGGTGAATCAAGTTGAGG
1 ATTCGGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCAAGATGATTCGGTGAATCAAGTTAATG
* *** *
23283 C-GT-TATCTTATTTCTTCAAG-ATTGG
66 CGGTGCAT-TTA-TTCAAAAAGAATCGG
* * * * *
23308 ATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTCAGGATGATTCGGTGAATCAAGTTGAGG
1 ATTCGGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCAAGATGATTCGGTGAATCAAGTTAATG
* *** * *
23373 CGGTGC-CTTATTTCTTCAA-TATTGG
66 CGGTGCATTTA-TTCAAAAAGAATCGG
* * * * * * *
23398 ATTCGGTGAGCTCGGTGTAGCACATTTTCAAATAGTTCAGGATAATTCAGTGAATCAAGTTGATG
1 ATTCGGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCAAGATGATTCGGTGAATCAAGTTAATG
* * * * *
23463 TAGTGTAGTATTTCTTC---AAG-ATTGA
66 -CG-GT-GCATTTATTCAAAAAGAATCGG
* * * *
23488 ATTCGGTGAGCTCGGTGCAACACATTTTCAGACAATTC-AGATTGATTCGGTGAATC
1 ATTCGGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCAAGA-TGATTCGGTGAATC
23544 GATTAGTTTT
Statistics
Matches: 659, Mismatches: 89, Indels: 62
0.81 0.11 0.08
Matches are distributed among these distances:
87 5 0.01
88 110 0.17
89 23 0.03
90 234 0.36
91 200 0.30
92 7 0.01
93 5 0.01
94 2 0.00
96 4 0.01
97 13 0.02
98 56 0.08
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.31
Consensus pattern (91 bp):
ATTCGGTGAGCTCGGTGCAGCAAATTTTCAAACAGTTCAAGATGATTCGGTGAATCAAGTTAATG
CGGTGCATTTATTCAAAAAGAATCGG
Found at i:22952 original size:179 final size:179
Alignment explanation
Indices: 22767--23543 Score: 899
Period size: 179 Copynumber: 4.3 Consensus size: 179
22757 GGAATTCGTC
* *
22767 GGATTCGGTGAGCTCGGTGCAGCAGATTTTTAAACGGTTCAAGATGATTCGGTGAATCAAGTT-A
1 GGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAAGATGATTCGGTGAATCAAGTTGA
*
22831 ATCGGTG-C-T-TTTATTCAAAAGATCGGAATCGGTGAGCTCGGTGCAGCAAATTTTCAAATAGT
66 AGCGGTGCCTTATTTATTC--AAGATCGGAATCGGTGAGCTCGGTGCAGCAAATTTTCAAATAGT
* *
22893 TAAGGATGATTCGGTGAATCAAGATTGAGGCGGTGCCATATTTCTTCAAGAAT
129 TAAGGATAATTCGGTGAATCAAG-TTGAGGCGGTG-CATATTTCTTCAAGATT
** * * *
22946 GGATTCGGTGAGCTCGGTGCAGCAGATTTTCGGACAGTTCAGGATAATTCGATGAATCAAGTT-A
1 GGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAAGATGATTCGGTGAATCAAGTTGA
* *
23010 ATGCGGTG-C--ATTTATTCAAAGATCGGAATCGGTAAGCTCGGTGCAGCAAATTATCAAATAGT
66 A-GCGGTGCCTTATTTATTC-AAGATCGGAATCGGTGAGCTCGGTGCAGCAAATTTTCAAATAGT
* * *
23072 TAAGGATGATTCGGTGAAACAAGATTGAGGCGGTGACTTATTTCTTCAAGATT
129 TAAGGATAATTCGGTGAATCAAG-TTGAGGCGGTG-CATATTTCTTCAAGATT
* * *
23125 GGACTCGGTGAGCTCGGTGCAGCAGACTTTCAAATAGTT-AAGGATGATTCGGTGAATCAAGATT
1 GGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAA-GATGATTCGGTGAATCAAG-TT
** * * * * * *
23189 GCGGCGGTGCCTTATTTCTTCAAGATTGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAGACAGT
64 GAAGCGGTGCCTTATTTATTCAAGATCGGAATCGGTGAGCTCGGTGCAGCAAATTTTCAAATAGT
* * * * *
23254 TCAGGATAAATCGGTGAATCAAGTTGAGGCGTTATCTTATTTCTTCAAGATT
129 TAAGGATAATTCGGTGAATCAAGTTGAGGCGGT-GCATATTTCTTCAAGATT
* * *
23306 GGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTCAGGATGATTCGGTGAATCAAGTTGA
1 GGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAAGATGATTCGGTGAATCAAGTTGA
* * * * * * * *
23371 GGCGGTGCCTTATTTCTTCAATATTGGATTCGGTGAGCTCGGTGTAGCACATTTTCAAATAGTTC
66 AGCGGTGCCTTATTTATTCAAGATCGGAATCGGTGAGCTCGGTGCAGCAAATTTTCAAATAGTTA
* * ** *
23436 AGGATAATTCAGTGAATCAAGTTGATGTAGTGTAGTATTTCTTCAAGATT
131 AGGATAATTCGGTGAATCAAGTTGAGGCGGTGCA-TATTTCTTCAAGATT
* * * * *
23486 GAATTCGGTGAGCTCGGTGCAACACATTTTCAGACAATTC-AGATTGATTCGGTGAATC
1 GGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAAGA-TGATTCGGTGAATC
23544 GATTAGTTTT
Statistics
Matches: 523, Mismatches: 63, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
178 1 0.00
179 203 0.39
180 173 0.33
181 82 0.16
182 57 0.11
183 7 0.01
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (179 bp):
GGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAAGATGATTCGGTGAATCAAGTTGA
AGCGGTGCCTTATTTATTCAAGATCGGAATCGGTGAGCTCGGTGCAGCAAATTTTCAAATAGTTA
AGGATAATTCGGTGAATCAAGTTGAGGCGGTGCATATTTCTTCAAGATT
Found at i:23180 original size:270 final size:268
Alignment explanation
Indices: 22665--23543 Score: 1029
Period size: 270 Copynumber: 3.2 Consensus size: 268
22655 CGCTGCATCT
* * * * * *
22665 ATTGGAATTCGGTGAGCTCGGTGAAGTAAATTTTCAAACAGATCATGG-TGATTCGGTGAATCAA
1 ATTGG-ATTCGGTGAGCTCGGTGCAGCAGATTTTCAGACAGTTCA-GGATAATTCGGTGAATCAA
*
22729 GTTAATGCGGTGCATTTATTCAAAAATTGGAATTCGTCGGATTCGGTGAGCTCGGTGCAGCAGAT
64 GTTAATGCGGTGCATTTATTC--AAA---G-A----TCGGATTCGGTGAGCTCGGTGCAGCAAAT
* ** ** * *
22794 TTTTAAACGGTTCAA-GATGATTCGGTGAATCAAGTT-AATCGGTGC-T-TTTATTCAAAAGATC
119 TTTCAAATAGTT-AAGGATGATTCGGTGAATCAAGTTGAGGCGGTGCTTATTTCTTC--AAGATT
22855 GGAATCGGTGAGCTCGGTGCAGCAAATTTTCAAATAGTTAAGGATGATTCGGTGAATCAAGATTG
181 GGAATCGGTGAGCTCGGTGCAGCAAATTTTCAAATAGTTAAGGATGATTCGGTGAATCAAGATTG
22920 AGGCGGTGCCATATTTCTTCAAG
246 AGGCGGTGCCATATTTCTTCAAG
* * *
22943 AATGGATTCGGTGAGCTCGGTGCAGCAGATTTTCGGACAGTTCAGGATAATTCGATGAATCAAGT
1 ATTGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAGACAGTTCAGGATAATTCGGTGAATCAAGT
* * *
23008 TAATGCGGTGCATTTATTCAAAGATCGGAATCGGTAAGCTCGGTGCAGCAAATTATCAAATAGTT
66 TAATGCGGTGCATTTATTCAAAGATCGGATTCGGTGAGCTCGGTGCAGCAAATTTTCAAATAGTT
* *
23073 AAGGATGATTCGGTGAAACAAGATTGAGGCGGTGACTTATTTCTTCAAGATTGGACTCGGTGAGC
131 AAGGATGATTCGGTGAATCAAG-TTGAGGCGGTG-CTTATTTCTTCAAGATTGGAATCGGTGAGC
* * * *
23138 TCGGTGCAGCAGACTTTCAAATAGTTAAGGATGATTCGGTGAATCAAGATTGCGGCGGTGCCTTA
194 TCGGTGCAGCAAATTTTCAAATAGTTAAGGATGATTCGGTGAATCAAGATTGAGGCGGTGCCATA
23203 TTTCTTCAAG
259 TTTCTTCAAG
*
23213 ATTGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAGACAGTTCAGGATAAATCGGTGAATCAAGT
1 ATTGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAGACAGTTCAGGATAATTCGGTGAATCAAGT
* * * * * * *
23278 TGAGGCGTTATCTTATTTCTTC-AAGATTGGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATA
66 TAATGCGGT-GC--ATTTATTCAAAGATCGGATTCGGTGAGCTCGGTGCAGCAAATTTTCAAATA
* * *
23342 GTTCAGGATGATTCGGTGAATCAAGTTGAGGCGGTGCCTTATTTCTTCAATATTGGATTCGGTGA
128 GTTAAGGATGATTCGGTGAATCAAGTTGAGGCGGTG-CTTATTTCTTCAAGATTGGAATCGGTGA
* * * * * * ** *
23407 GCTCGGTGTAGCACATTTTCAAATAGTTCAGGATAATTCAGTGAATCAAG-TTGATGTAGTG-TA
192 GCTCGGTGCAGCAAATTTTCAAATAGTTAAGGATGATTCGGTGAATCAAGATTGAGGCGGTGCCA
23470 GTATTTCTTCAAG
257 -TATTTCTTCAAG
* * * * *
23483 ATTGAATTCGGTGAGCTCGGTGCAACACATTTTCAGACAATTCA-GATTGATTCGGTGAATC
1 ATTGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAGACAGTTCAGGA-TAATTCGGTGAATC
23544 GATTAGTTTT
Statistics
Matches: 526, Mismatches: 63, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
266 2 0.00
267 52 0.10
268 2 0.00
269 8 0.02
270 227 0.43
271 84 0.16
272 67 0.13
273 7 0.01
275 3 0.01
276 2 0.00
277 68 0.13
278 4 0.01
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (268 bp):
ATTGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAGACAGTTCAGGATAATTCGGTGAATCAAGT
TAATGCGGTGCATTTATTCAAAGATCGGATTCGGTGAGCTCGGTGCAGCAAATTTTCAAATAGTT
AAGGATGATTCGGTGAATCAAGTTGAGGCGGTGCTTATTTCTTCAAGATTGGAATCGGTGAGCTC
GGTGCAGCAAATTTTCAAATAGTTAAGGATGATTCGGTGAATCAAGATTGAGGCGGTGCCATATT
TCTTCAAG
Found at i:23358 original size:90 final size:89
Alignment explanation
Indices: 22767--23543 Score: 812
Period size: 90 Copynumber: 8.7 Consensus size: 89
22757 GGAATTCGTC
* * ** *
22767 GGATTCGGTGAGCTCGGTGCAGCAGATTTTTAAACGGTTCAAGATGATTCGGTGAATCAAGTT-A
1 GGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTCAGGATGATTCGGTGAATCAAGTTGA
** * * * *
22831 ATCGGTGC-T-TTTATTCAAAAGATC
66 GGCGTTACTTATTTCTTC--AAGATT
* * *
22855 GGAATCGGTGAGCTCGGTGCAGCAAATTTTCAAATAGTTAAGGATGATTCGGTGAATCAAGATTG
1 GGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTCAGGATGATTCGGTGAATCAAG-TTG
** * *
22920 AGGCGGTGCCATATTTCTTCAAGAAT
65 AGGC-GTTACTTATTTCTTCAAGATT
* ** * * * *
22946 GGATTCGGTGAGCTCGGTGCAGCAGATTTTCGGACAGTTCAGGATAATTCGATGAATCAAGTTAA
1 GGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTCAGGATGATTCGGTGAATCAAGTTGA
* * * * *
23011 TGCGGTGC--ATTTATTCAAAGATC
66 GGCGTTACTTATTTCTTC-AAGATT
* * * * * *
23034 GGAATCGGTAAGCTCGGTGCAGCAAATTATCAAATAGTTAAGGATGATTCGGTGAAACAAGATTG
1 GGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTCAGGATGATTCGGTGAATCAAG-TTG
*
23099 AGGCGGTGACTTATTTCTTCAAGATT
65 AGGC-GTTACTTATTTCTTCAAGATT
* * * *
23125 GGACTCGGTGAGCTCGGTGCAGCAGACTTTCAAATAGTTAAGGATGATTCGGTGAATCAAGATTG
1 GGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTCAGGATGATTCGGTGAATCAAG-TTG
* **
23190 CGGCGGTGCCTTATTTCTTCAAGATT
65 AGGC-GTTACTTATTTCTTCAAGATT
* * * * *
23216 GGATTCGGTGAGCTCGGTGCAGCAGATTTTCAGACAGTTCAGGATAAATCGGTGAATCAAGTTGA
1 GGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTCAGGATGATTCGGTGAATCAAGTTGA
23281 GGCGTTATCTTATTTCTTCAAGATT
66 GGCGTTA-CTTATTTCTTCAAGATT
23306 GGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTCAGGATGATTCGGTGAATCAAGTTGA
1 GGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTCAGGATGATTCGGTGAATCAAGTTGA
** *
23371 GGCGGTGCCTTATTTCTTCAATATT
66 GGC-GTTACTTATTTCTTCAAGATT
* * *
23396 GGATTCGGTGAGCTCGGTGTAGCACATTTTCAAATAGTTCAGGATAATTCAGTGAATCAAGTTGA
1 GGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTCAGGATGATTCGGTGAATCAAGTTGA
** *
23461 TGTAGTGTA-GTATTTCTTCAAGATT
66 -GGCGT-TACTTATTTCTTCAAGATT
* * * * *
23486 GAATTCGGTGAGCTCGGTGCAACACATTTTCAGACAATTCA-GATTGATTCGGTGAATC
1 GGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTCAGGA-TGATTCGGTGAATC
23544 GATTAGTTTT
Statistics
Matches: 582, Mismatches: 92, Indels: 28
0.83 0.13 0.04
Matches are distributed among these distances:
87 7 0.01
88 108 0.19
89 13 0.02
90 236 0.41
91 204 0.35
92 8 0.01
93 6 0.01
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (89 bp):
GGATTCGGTGAGCTCGGTGCAGCACATTTTCAAATAGTTCAGGATGATTCGGTGAATCAAGTTGA
GGCGTTACTTATTTCTTCAAGATT
Found at i:25604 original size:5 final size:5
Alignment explanation
Indices: 25583--25643 Score: 79
Period size: 5 Copynumber: 12.4 Consensus size: 5
25573 CAGTCTTTTC
* * * *
25583 TTTAT TTT-T GTTCT TTTAT TTTAT TTTAT TTTAT TGTAT TTTAT TTAAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
25632 TTTAT TTTAT TT
1 TTTAT TTTAT TT
25644 CAATTTTCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
4 3 0.06
5 45 0.94
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:30537 original size:2 final size:2
Alignment explanation
Indices: 30530--30557 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30520 TATTGTATTG
30530 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30558 GTGAGTATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31624 original size:18 final size:17
Alignment explanation
Indices: 31591--31629 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
31581 ATTATTTAAT
31591 TAAAAAATAATATTTTC
1 TAAAAAATAATATTTTC
31608 ATAAAAAA-AATATTTTTC
1 -TAAAAAATAATA-TTTTC
31626 TAAA
1 TAAA
31630 GTTATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAAATAATATTTTC
Found at i:32465 original size:17 final size:17
Alignment explanation
Indices: 32443--32477 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
32433 ATAAGGCTAG
32443 AGTTTACTAGTGATTGT
1 AGTTTACTAGTGATTGT
32460 AGTTTACTAGTGATTGT
1 AGTTTACTAGTGATTGT
32477 A
1 A
32478 CTTCTATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.46
Consensus pattern (17 bp):
AGTTTACTAGTGATTGT
Found at i:42383 original size:20 final size:20
Alignment explanation
Indices: 42345--42382 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
42335 AAAAAATTCA
42345 TGTGTTCATGGGCCATTTTG
1 TGTGTTCATGGGCCATTTTG
*
42365 TGTGTTCA-GGGTCATTTT
1 TGTGTTCATGGGCCATTTT
42383 TCCCATTTTT
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:0.11, C:0.13, G:0.29, T:0.47
Consensus pattern (20 bp):
TGTGTTCATGGGCCATTTTG
Done.