Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010556.1 Corchorus capsularis cultivar CVL-1 contig10577, 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: 48525
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:3565 original size:13 final size:14
Alignment explanation
Indices: 3547--3588 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
3537 AAAAAAAATA
3547 AAAAT-AATACAAT
1 AAAATAAATACAAT
3560 AAAATAAATA-AAT
1 AAAATAAATACAAT
3573 -AAATAAATACAA-
1 AAAATAAATACAAT
3585 AAAA
1 AAAA
3589 AATGAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 9 0.35
13 13 0.50
14 4 0.15
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAATAAATACAAT
Found at i:3723 original size:14 final size:14
Alignment explanation
Indices: 3704--3732 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3694 CCCAGACTTA
3704 TTGTAAGCTCTGTT
1 TTGTAAGCTCTGTT
3718 TTGTAAGCTCTGTT
1 TTGTAAGCTCTGTT
3732 T
1 T
3733 AATTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.52
Consensus pattern (14 bp):
TTGTAAGCTCTGTT
Found at i:6477 original size:6 final size:6
Alignment explanation
Indices: 6466--6490 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6456 AGAATGGGGC
6466 GGAGAT GGAGAT GGAGAT GGAGAT G
1 GGAGAT GGAGAT GGAGAT GGAGAT G
6491 AATTAGAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (6 bp):
GGAGAT
Found at i:7651 original size:109 final size:109
Alignment explanation
Indices: 7480--7769 Score: 446
Period size: 109 Copynumber: 2.7 Consensus size: 109
7470 ACTATTATAG
* * *
7480 TTTTATTCTACTAGAAACTTTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
7545 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
7594 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
7659 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
*
7703 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTAT-A-TAATTT-TT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATAATTACTTTATT
7763 TTTACCA
65 TTTACCA
7770 TTTAATTTAA
Statistics
Matches: 170, Mismatches: 5, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
105 9 0.05
106 5 0.03
107 1 0.01
108 6 0.04
109 124 0.73
110 3 0.02
111 2 0.01
114 20 0.12
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:8160 original size:15 final size:17
Alignment explanation
Indices: 8128--8173 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
8118 TGTCGGGTCA
*
8128 TTTGGATTTAGGTCGTT
1 TTTGGATTTGGGTCGTT
8145 TTTGG-TTTGGGT-GTT
1 TTTGGATTTGGGTCGTT
* *
8160 TTCGGTTTTGGGTC
1 TTTGGATTTGGGTC
8174 ATATGGTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 7 0.28
16 13 0.52
17 5 0.20
ACGTcount: A:0.04, C:0.07, G:0.35, T:0.54
Consensus pattern (17 bp):
TTTGGATTTGGGTCGTT
Found at i:13766 original size:13 final size:13
Alignment explanation
Indices: 13748--13773 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13738 TTGCATATGT
13748 GGTATCGGTAATC
1 GGTATCGGTAATC
13761 GGTATCGGTAATC
1 GGTATCGGTAATC
13774 ACATTAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
GGTATCGGTAATC
Found at i:17786 original size:7 final size:7
Alignment explanation
Indices: 17774--17798 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17764 TTTCAAGCTC
17774 AAGACCG
1 AAGACCG
17781 AAGACCG
1 AAGACCG
17788 AAGACCG
1 AAGACCG
17795 AAGA
1 AAGA
17799 ATCAAGCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.24, G:0.28, T:0.00
Consensus pattern (7 bp):
AAGACCG
Found at i:24549 original size:1 final size:1
Alignment explanation
Indices: 24543--24574 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
24533 CGCTCATCAT
24543 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24575 TCATATAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:25812 original size:6 final size:6
Alignment explanation
Indices: 25801--25829 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
25791 GGCTGCTGCT
25801 CCTCTG CCTCTG CCTCTG CCTCTG CCTCT
1 CCTCTG CCTCTG CCTCTG CCTCTG CCTCT
25830 TTAAGGTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.14, T:0.34
Consensus pattern (6 bp):
CCTCTG
Found at i:26304 original size:22 final size:23
Alignment explanation
Indices: 26278--26320 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
26268 AAGAAGGATT
26278 AGGTTTTAC-TTTCCTACCAGAA
1 AGGTTTTACTTTTCCTACCAGAA
26300 AGGTTTTACTTTTCCTACCAG
1 AGGTTTTACTTTTCCTACCAG
26321 GATTAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (23 bp):
AGGTTTTACTTTTCCTACCAGAA
Found at i:30236 original size:213 final size:213
Alignment explanation
Indices: 29869--30300 Score: 756
Period size: 213 Copynumber: 2.0 Consensus size: 213
29859 CAGTAAGATT
*
29869 TTCTGAAACAGCAGCAACTTGACCTTCAGAAGTCTCTGCTGGGGGATCTGAACCCTTAGACTTCT
1 TTCTGAAACAGCAGCAACTTGACCTTCAGAAGTCTCTGCTGGGGAATCTGAACCCTTAGACTTCT
* ** *
29934 TGAGCAGTGGCTCAGCCACATCAGTGCTCGTCTCACCCGGAACAGGTGAATTTTCGTGCAACTCA
66 TGAGCAGTGGCTCAGCCACATCAGCGCTCGTCTCACCCGGAACAGGTGAATCCTCATGCAACTCA
* *
29999 GAAGTGGTAGAAGCAAGACGCTTGCGAACTGGTTCATTCTGTTGAGTTTGAGTTCCTTGAGCATC
131 GAAGTGGTAGAAGCAAGACGCTTGCGAACTGGTTCATTCTGCTGAGTGTGAGTTCCTTGAGCATC
30064 AGCATCATGGGATGTAGC
196 AGCATCATGGGATGTAGC
* *
30082 TTCTGAAACAGCAGCAACTTGACCTTCAGAAGTCTCTGGTGGGGAATCTGAACCCTTGGACTTCT
1 TTCTGAAACAGCAGCAACTTGACCTTCAGAAGTCTCTGCTGGGGAATCTGAACCCTTAGACTTCT
** *
30147 TGAGCAGTGGCTCAGTGACATCAGCGCTCGTCTCACCCGGAACTGGTGAATCCTCATGCAACTCA
66 TGAGCAGTGGCTCAGCCACATCAGCGCTCGTCTCACCCGGAACAGGTGAATCCTCATGCAACTCA
30212 GAAGTGGTAGAAGCAAGACGCTTGCGAACTGGTTCATTCTGCTGAGTGTGAGTTCCTTGAGCATC
131 GAAGTGGTAGAAGCAAGACGCTTGCGAACTGGTTCATTCTGCTGAGTGTGAGTTCCTTGAGCATC
30277 AGCATCATGGGATGTAGC
196 AGCATCATGGGATGTAGC
30295 TTCTGA
1 TTCTGA
30301 CATATCCACA
Statistics
Matches: 207, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
213 207 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (213 bp):
TTCTGAAACAGCAGCAACTTGACCTTCAGAAGTCTCTGCTGGGGAATCTGAACCCTTAGACTTCT
TGAGCAGTGGCTCAGCCACATCAGCGCTCGTCTCACCCGGAACAGGTGAATCCTCATGCAACTCA
GAAGTGGTAGAAGCAAGACGCTTGCGAACTGGTTCATTCTGCTGAGTGTGAGTTCCTTGAGCATC
AGCATCATGGGATGTAGC
Found at i:34198 original size:2 final size:2
Alignment explanation
Indices: 34191--34215 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34181 AAAGAATTAA
34191 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
34216 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34242 original size:10 final size:10
Alignment explanation
Indices: 34211--34245 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
34201 ATATATATAT
34211 ATATACACAC
1 ATATACACAC
* *
34221 ACACACACAC
1 ATATACACAC
34231 ATATACACAC
1 ATATACACAC
34241 ATATA
1 ATATA
34246 AAGACCTGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.17
Consensus pattern (10 bp):
ATATACACAC
Found at i:35035 original size:2 final size:2
Alignment explanation
Indices: 34996--35027 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34986 AAAATAAATG
34996 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35028 ATGAGAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:36450 original size:2 final size:2
Alignment explanation
Indices: 36443--36514 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
36433 GGAGGAGGAA
36443 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
36485 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
36515 GCAAATGGGG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38801 original size:30 final size:31
Alignment explanation
Indices: 38742--38806 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
38732 AACTTTATGC
* * *
38742 TTTCCGATTGTACCCTTATTTTTAAAACATG
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
38773 TTTCCAATTGTACCCTT-TTTTAAAAACATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
38803 TTTC
1 TTTC
38807 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTAAAAACATA
Found at i:38813 original size:31 final size:31
Alignment explanation
Indices: 38748--38813 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
38738 ATGCTTTCCG
* * *
38748 ATTGTACCCTTATTTTTAAAACATGTTTCCA
1 ATTGTACCCTTATTTTAAAAACATATTTCAA
38779 ATTGTACCCTT-TTTTAAAAACATATTTCTAA
1 ATTGTACCCTTATTTTAAAAACATATTTC-AA
38810 ATTG
1 ATTG
38814 CCATTACTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (31 bp):
ATTGTACCCTTATTTTAAAAACATATTTCAA
Found at i:39025 original size:37 final size:37
Alignment explanation
Indices: 38939--39025 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 37
38929 TTTTGTTTCA
* *
38939 AACGTCCTATTTAATTTTGCCTTTTGTCTTTGTTTCC
1 AACGTCCTATTTAATTTTGCCTTTTGTCTTCGTCTCC
** *
38976 AATCGTTGTATTTAATTTTGCTTTTTGTCTTCGTCTCC
1 AA-CGTCCTATTTAATTTTGCCTTTTGTCTTCGTCTCC
39014 AACGTCCTATTT
1 AACGTCCTATTT
39026 GGACTTAGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
37 10 0.24
38 32 0.76
ACGTcount: A:0.15, C:0.21, G:0.11, T:0.53
Consensus pattern (37 bp):
AACGTCCTATTTAATTTTGCCTTTTGTCTTCGTCTCC
Found at i:39111 original size:22 final size:22
Alignment explanation
Indices: 39083--39205 Score: 88
Period size: 22 Copynumber: 5.6 Consensus size: 22
39073 TGGTCCAATT
*
39083 TCAAAATTTCAAAGCGACGTTA
1 TCAAAATTTCAAAGAGACGTTA
* *
39105 TCAAAATTACATAATGTGA--TTA
1 TCAAAATTTCA-AA-GAGACGTTA
* * *
39127 TCAAAATTTCATAGAGGCGTCA
1 TCAAAATTTCAAAGAGACGTTA
* * * *
39149 ACAAAATTTTATAGAGAGGTTA
1 TCAAAATTTCAAAGAGACGTTA
* * *
39171 TCAAAATTTCAAAAAAAGGTTA
1 TCAAAATTTCAAAGAGACGTTA
*
39193 TCAAATTTTCAAA
1 TCAAAATTTCAAA
39206 ATGTGATTAC
Statistics
Matches: 79, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.03
21 1 0.01
22 71 0.90
23 2 0.03
24 3 0.04
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (22 bp):
TCAAAATTTCAAAGAGACGTTA
Found at i:39378 original size:22 final size:22
Alignment explanation
Indices: 39327--39601 Score: 92
Period size: 22 Copynumber: 12.6 Consensus size: 22
39317 TCAGGGAGCA
*
39327 TATCAAAATTTCATATATGAAGGT
1 TATCAAAATTTCATA-A-GAGGGT
*
39351 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATAAGAGGGT
* *
39373 TATCAAAATTTTAT-AGTA-TGT
1 TATCAAAATTTCATAAG-AGGGT
* *
39394 AGATCAAAATTTCATAAG-GAGAT
1 -TATCAAAATTTCATAAGAG-GGT
*
39417 TAACAAAATTTCATAATGA-GGT
1 TATCAAAATTTCATAA-GAGGGT
* * ** *
39439 AATAAAAAAATCAT-AGAGAGAT
1 TATCAAAATTTCATAAGAG-GGT
*
39461 TATCAAAATTT-GT---A--GT
1 TATCAAAATTTCATAAGAGGGT
* **
39477 CATCAGGATTTCATAAG-GAGGT
1 TATCAAAATTTCATAAGAG-GGT
* * **
39499 TATCAAAATTTTATAGGGAGATT
1 TATCAAAATTTCATA-AGAGGGT
* * * *
39522 TATCAAAATTTTACAGGAAGGTT
1 TATCAAAATTTCATAAG-AGGGT
*
39545 TATCAAAATTTCAT-AGCGAGGT
1 TATCAAAATTTCATAAGAG-GGT
* * *
39567 TATCACAATTTCAT-AGTGTGAT
1 TATCAAAATTTCATAAGAG-GGT
39589 TATCAAAATTTCA
1 TATCAAAATTTCA
39602 GAGTGTGATT
Statistics
Matches: 184, Mismatches: 47, Indels: 42
0.67 0.17 0.15
Matches are distributed among these distances:
16 9 0.05
17 1 0.01
19 1 0.01
20 2 0.01
21 7 0.04
22 112 0.61
23 37 0.20
24 15 0.08
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATAAGAGGGT
Found at i:39528 original size:23 final size:23
Alignment explanation
Indices: 39484--39601 Score: 107
Period size: 22 Copynumber: 5.3 Consensus size: 23
39474 AGTCATCAGG
* *
39484 ATTTCATAAGGAG-GTTATCAAA
1 ATTTCATAGGGAGATTTATCAAA
*
39506 ATTTTATAGGGAGATTTATCAAA
1 ATTTCATAGGGAGATTTATCAAA
* * * *
39529 ATTTTACAGGAAGGTTTATCAAA
1 ATTTCATAGGGAGATTTATCAAA
* * *
39552 ATTTCATAGCGAG-GTTATCACA
1 ATTTCATAGGGAGATTTATCAAA
* *
39574 ATTTCATAGTGTGA-TTATCAAA
1 ATTTCATAGGGAGATTTATCAAA
39596 ATTTCA
1 ATTTCA
39602 GAGTGTGATT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
22 42 0.53
23 37 0.47
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (23 bp):
ATTTCATAGGGAGATTTATCAAA
Found at i:39606 original size:22 final size:22
Alignment explanation
Indices: 39544--39612 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
39534 ACAGGAAGGT
* * *
39544 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAGTGTGA
*
39566 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
*
39588 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
39610 TTA
1 TTA
39613 CTGACAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:39772 original size:22 final size:22
Alignment explanation
Indices: 39747--39849 Score: 61
Period size: 22 Copynumber: 4.7 Consensus size: 22
39737 CTTAGGGAGA
39747 TTAACAAAATTTCATA-AGAAGG
1 TTAACAAAATTTCATAGA-AAGG
*
39769 TTAAAAAAAATTT-ATAGAAAGG
1 TT-AACAAAATTTCATAGAAAGG
* **
39791 TT--CTAGAAATTTCATAGTATCG
1 TTAAC-A-AAATTTCATAGAAAGG
*** *
39813 TTATTGAAATTTCATAGGAAGG
1 TTAACAAAATTTCATAGAAAGG
*
39835 TTATCAAAATTTCAT
1 TTAACAAAATTTCAT
39850 GAGGACATCA
Statistics
Matches: 62, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
20 1 0.02
21 6 0.10
22 45 0.73
23 10 0.16
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.35
Consensus pattern (22 bp):
TTAACAAAATTTCATAGAAAGG
Found at i:39894 original size:62 final size:62
Alignment explanation
Indices: 39820--39948 Score: 215
Period size: 62 Copynumber: 2.1 Consensus size: 62
39810 TCGTTATTGA
*
39820 AATTTCATAGGAAGGTTATCAAAATTTCATGA-GGACATCATAAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCAT-ATGGACATCATAAAAAATAGTGCAATTATCAT
* *
39882 AATTTCATAGGAATGTTATCAAAATTTCATATGGACGTCATAAAAAATAGTGCAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATATGGACATCATAAAAAATAGTGCAATTATCAT
39944 AATTT
1 AATTT
39949 AATATATATG
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
61 1 0.02
62 62 0.98
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (62 bp):
AATTTCATAGGAAGGTTATCAAAATTTCATATGGACATCATAAAAAATAGTGCAATTATCAT
Found at i:40044 original size:2 final size:2
Alignment explanation
Indices: 40037--40067 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40027 CTAAAACTAG
40037 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 T
40068 GTCGAGATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41249 original size:1 final size:1
Alignment explanation
Indices: 41243--41275 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
41233 TGCCAAACAG
41243 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
41276 GGCATCAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:45584 original size:32 final size:31
Alignment explanation
Indices: 45505--45585 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 31
45495 TTCAAATTGC
* * *
45505 GACAACTTGCCCCCTGAATTTCCAAATTCAG
1 GACAACTTACCCCCTGAATTCCCAAATTCAA
*
45536 GAC-AGTTAGCCCCCTGAACTTCCCAAATTCAA
1 GACAACTTA-CCCCCTGAA-TTCCCAAATTCAA
*
45568 GACAACTTACCACCTGAA
1 GACAACTTACCCCCTGAA
45586 GGAGGGGGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
30 3 0.07
31 12 0.29
32 22 0.54
33 4 0.10
ACGTcount: A:0.32, C:0.33, G:0.12, T:0.22
Consensus pattern (31 bp):
GACAACTTACCCCCTGAATTCCCAAATTCAA
Found at i:46342 original size:5 final size:5
Alignment explanation
Indices: 46325--46394 Score: 83
Period size: 5 Copynumber: 14.2 Consensus size: 5
46315 AAAAACCATA
*
46325 AAAAG AAAA- AAAAC AAAAC AAAAAAC AAAAC AAAAC AAAAC AAAAC -AAA-
1 AAAAC AAAAC AAAAC AAAAC --AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
*
46374 AAAAC AAAAT AAAAC AAAAC A
1 AAAAC AAAAC AAAAC AAAAC A
46395 TGAAGATACG
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
4 10 0.17
5 43 0.74
7 5 0.09
ACGTcount: A:0.83, C:0.14, G:0.01, T:0.01
Consensus pattern (5 bp):
AAAAC
Found at i:46376 original size:28 final size:27
Alignment explanation
Indices: 46325--46394 Score: 106
Period size: 28 Copynumber: 2.6 Consensus size: 27
46315 AAAAACCATA
*
46325 AAAAGAAAA-AAAACAAAACAAAAAAC
1 AAAACAAAACAAAACAAAACAAAAAAC
46351 AAAACAAAACAAAACAAAACAAAAAAAC
1 AAAACAAAACAAAACAAAAC-AAAAAAC
*
46379 AAAATAAAACAAAACA
1 AAAACAAAACAAAACA
46395 TGAAGATACG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 8 0.20
27 10 0.25
28 22 0.55
ACGTcount: A:0.83, C:0.14, G:0.01, T:0.01
Consensus pattern (27 bp):
AAAACAAAACAAAACAAAACAAAAAAC
Found at i:48180 original size:2 final size:2
Alignment explanation
Indices: 48175--48199 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48165 GGGAAAAAAC
48175 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
48200 TCAGTTCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.