Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015046.1 Corchorus capsularis cultivar CVL-1 contig15067, 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: 81549
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1909 original size:2 final size:2
Alignment explanation
Indices: 1902--1934 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
1892 GCCACCATAC
1902 AT AT AT AT AT AT AT AT AT AT AT -T ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
1935 AAGTACGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1997 original size:31 final size:31
Alignment explanation
Indices: 1962--2058 Score: 151
Period size: 31 Copynumber: 3.1 Consensus size: 31
1952 AACTTTATGT
* *
1962 TTTCCGATTGTACCCTTATTTTTAAAGCATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
*
1993 TTTCCAATTATACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
2024 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
1 TTTCCAATTGTACCCTTATT-TTTAAAACATA
2055 TTTC
1 TTTC
2059 TAAATTGACA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
30 2 0.03
31 59 0.97
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:2394 original size:19 final size:20
Alignment explanation
Indices: 2367--2404 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2357 TACTATTATT
2367 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
2387 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
2405 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:2598 original size:22 final size:22
Alignment explanation
Indices: 2570--2734 Score: 127
Period size: 22 Copynumber: 7.3 Consensus size: 22
2560 TGTCTCTATG
*
2570 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* **
2592 TGGTTATTACGATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
2615 -GGTTATCAAAATTCCATAGTGTA
1 TGGTTATCAAAATTTCATAG-G-A
*
2638 CTGGTTACCAAAATTTCATAGTG-
1 -TGGTTATCAAAATTTCATAG-GA
*
2661 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
2683 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
2707 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
2729 TGGTTA
1 TGGTTA
2735 ATTATCACAA
Statistics
Matches: 116, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
21 3 0.03
22 73 0.63
23 4 0.03
24 17 0.15
25 19 0.16
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:2892 original size:22 final size:21
Alignment explanation
Indices: 2844--3151 Score: 135
Period size: 22 Copynumber: 13.8 Consensus size: 21
2834 TTTCATGGGG
* *
2844 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAG-A
*
2866 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
2888 AGGTTAT-AAAAGTCTCAATTTTATA
1 AGGTTATCAAAA-TTTC-A---TAGA
* * *
2913 AGGAGTATCAAAATTTGATAAA
1 AGG-TTATCAAAATTTCATAGA
*
2935 AGGTTATC-AAATCTCATA-A
1 AGGTTATCAAAATTTCATAGA
*
2954 AGTGATTTATCTAAATTTCATAGA
1 AG-G--TTATCAAAATTTCATAGA
2978 GATCGGATTATCAAAATTT-ATAGAA
1 -A--GG-TTATCAAAATTTCATAG-A
*
3003 AGATTATCAAAATTTCATAG-
1 AGGTTATCAAAATTTCATAGA
* * *
3023 TGTTGTTATCAAAATTTCAAAGCG
1 AG--GTTATCAAAATTTCATAG-A
*
3047 AGGTTATCAAAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
* *
3067 TGTGATTATCAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * *
3090 GGGGTCAACAAAATTTTAT-GAA
1 -AGGTTATCAAAATTTCATAG-A
*
3112 GAGGTTATCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
3134 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
3152 AAATGTGATT
Statistics
Matches: 220, Mismatches: 38, Indels: 56
0.70 0.12 0.18
Matches are distributed among these distances:
19 3 0.01
20 11 0.05
21 22 0.10
22 132 0.60
23 13 0.06
24 8 0.04
25 18 0.08
26 8 0.04
27 5 0.02
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:3076 original size:44 final size:44
Alignment explanation
Indices: 2983--3173 Score: 167
Period size: 44 Copynumber: 4.4 Consensus size: 44
2973 ATAGAGATCG
* * * *
2983 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG-T
* *
3027 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * * *
3070 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATGAA-GA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCAT-AATGT
* * *
3114 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
3158 GATTA-CAAAAATTTCA
1 GATTATC-AAAATTTCA
3174 TAGTGGTATT
Statistics
Matches: 115, Mismatches: 26, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
43 17 0.15
44 95 0.83
45 3 0.03
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:3102 original size:66 final size:65
Alignment explanation
Indices: 3004--3151 Score: 154
Period size: 66 Copynumber: 2.2 Consensus size: 65
2994 TTTATAGAAA
* ** * *
3004 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAGAA--GAGGTTATCAAAATTACATAAT
3068 GT
64 GT
* * * *
3070 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATGAAGAGGTTATCAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCA-GAAGAGGTTATCAAAATTACATAATG
*
3135 A
65 T
* *
3136 GGTTATCAAATTTTCA
1 GATTATCAAAATTTCA
3152 AAATGTGATT
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
66 65 0.97
68 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (65 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAGAAGAGGTTATCAAAATTACATAATGT
Found at i:3440 original size:22 final size:22
Alignment explanation
Indices: 3297--3844 Score: 109
Period size: 22 Copynumber: 25.0 Consensus size: 22
3287 AAAATTCAGG
*
3297 GAGGATATCAAAATTTCAT-AT
1 GAGGTTATCAAAATTTCATAAT
* * * *
3318 GAAGCTTATTAAAATTCCATAGTT
1 G-AGGTTATCAAAATTTCATA-AT
* * *
3342 TA-GTTTTCAAAATTTCACAA-
1 GAGGTTATCAAAATTTCATAAT
*
3362 GAGGATTATCAAAATTTCATAGT
1 GAGG-TTATCAAAATTTCATAAT
* * **
3385 -ATGTAGATCAAAATTTCATAGG
1 GAGGT-TATCAAAATTTCATAAT
* *
3407 GAGATTAACAAAATTTCATAAT
1 GAGGTTATCAAAATTTCATAAT
** * **
3429 GAGGTTATCAAAAAATCAGAGG
1 GAGGTTATCAAAATTTCATAAT
*
3451 GAGGTTATCAAAA-TT--T-GT
1 GAGGTTATCAAAATTTCATAAT
*
3469 -A-GTTATCAAGATTTCATAA-
1 GAGGTTATCAAAATTTCATAAT
* * **
3488 GAAAGTTATCAAAATTTTATAGG
1 G-AGGTTATCAAAATTTCATAAT
* *
3511 GAGATTTATCAAAATTT-ATAGGAA
1 GAG-GTTATCAAAATTTCATA--AT
** **
3535 GATTTTTATC-AAATTTCATAGC
1 GA-GGTTATCAAAATTTCATAAT
* * *
3557 GAGATTATCACAATTTCATAGT
1 GAGGTTATCAAAATTTCATAAT
* * * * *
3579 GTGATTATCAAAATTTTAGAGT
1 GAGGTTATCAAAATTTCATAAT
* *
3601 GTGATTA-CTAACAA-TTCAT-AT
1 GAGGTTATC-AA-AATTTCATAAT
* * *
3622 GGAGGTGT-TTAAATTTTCATAAC
1 -GAGGT-TATCAAAATTTCATAAT
* * *
3645 GTGGTTATCAATATATCAT-AT
1 GAGGTTATCAAAATTTCATAAT
* * *
3666 GGAGGTTATCAACATCTCATAGT
1 -GAGGTTATCAAAATTTCATAAT
* *
3689 GCTGGTTATCAAAATTTCATATT
1 G-AGGTTATCAAAATTTCATAAT
* * **
3712 GAGGTCT-TCAAAATTACTTAGG
1 GAGGT-TATCAAAATTTCATAAT
* * *
3734 GAGGTTAACCAAACTTCATAA-
1 GAGGTTATCAAAATTTCATAAT
** *
3755 GAAGGTTAAAAAAAATTT-ATAAA
1 G-AGGTT-ATCAAAATTTCATAAT
* * * *
3778 AAGGTTCTCGAAA-TTCTATAGT
1 GAGGTTATCAAAATTTC-ATAAT
* * *
3800 -ATCGTTATTAAAATTTCAT-AG
1 GA-GGTTATCAAAATTTCATAAT
3821 GAAGGTTATCAAAATTTCATAAT
1 G-AGGTTATCAAAATTTCATAAT
3844 G
1 G
3845 GGATCATAAA
Statistics
Matches: 375, Mismatches: 107, Indels: 88
0.66 0.19 0.15
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 1 0.00
19 1 0.00
20 3 0.01
21 21 0.06
22 266 0.71
23 59 0.16
24 12 0.03
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAAT
Found at i:3699 original size:23 final size:22
Alignment explanation
Indices: 3646--3710 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
3636 TTTCATAACG
* *
3646 TGGTTATCAATATATCATATGG
1 TGGTTATCAAAATATCATATGC
* * *
3668 AGGTTATCAACATCTCATAGTGC
1 TGGTTATCAAAATATCATA-TGC
*
3691 TGGTTATCAAAATTTCATAT
1 TGGTTATCAAAATATCATAT
3711 TGAGGTCTTC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATATCATATGC
Found at i:4694 original size:44 final size:44
Alignment explanation
Indices: 4358--4891 Score: 396
Period size: 43 Copynumber: 12.3 Consensus size: 44
4348 TTGTTGATAT
* *
4358 GGTTACCAAAATTTCAT-ATGGAGATTACCAAAATTTCATTGTGA
1 GGTTACCAAAATTTCATAAT-GAGGTTACCAAAATTTCATAGTGA
* * * * *
4402 GGTTA-CTAAATTTCA-GA-G-GTGTTACCCAATATTTTATAGGGA
1 GGTTACCAAAATTTCATAATGAG-GTTA-CCAAAATTTCATAGTGA
** * * * * * * * *
4444 GACTACAAAAATTTCATACTAAGCTTGCAAAAATTTAATTGTGA
1 GGTTACCAAAATTTCATAATGAGGTTACCAAAATTTCATAGTGA
* *
4488 GGTTACCAAAATTTCATAA-GGGGTTACCCAAATTT-ATAGTGA
1 GGTTACCAAAATTTCATAATGAGGTTACCAAAATTTCATAGTGA
* ** * * * *
4530 GGTTACAAAAATTTCATAGCGCGGTTACTAAAATATCATAGAG-
1 GGTTACCAAAATTTCATAATGAGGTTACCAAAATTTCATAGTGA
* * * *
4573 GGTAACCAAAATTTCAT-ATGGAGATTTCCAAAATTTCATAG-GG
1 GGTTACCAAAATTTCATAAT-GAGGTTACCAAAATTTCATAGTGA
* * *
4616 GGTCACTAAAATTTCATAA-GAAGGTTACAAAAATTTTCATAGTGA
1 GGTTACCAAAATTTCATAATG-AGGTTACCAAAA-TTTCATAGTGA
* *
4661 TGTTACAAAAATTTCATAATGAGGTTACC-AAATTTCATAAG-G-
1 GGTTACCAAAATTTCATAATGAGGTTACCAAAATTTCAT-AGTGA
* * * * *
4703 GATTACCAAAATTTCATAATAAGGTTACCAAAATTTCAAAACTTA
1 GGTTACCAAAATTTCATAATGAGGTTACCAAAATTTC-ATAGTGA
* * * *
4748 GCTTACCAAAATTTCATACTTAGGTTACCAAAATTTCATAGTCA
1 GGTTACCAAAATTTCATAATGAGGTTACCAAAATTTCATAGTGA
* ** * *
4792 AGTTACCAAAATTTCATAGGGAAGTTACCAAAATATCATAGTGA
1 GGTTACCAAAATTTCATAATGAGGTTACCAAAATTTCATAGTGA
** * * *
4836 GGTTACCAAAATTTCATAGGGAGGTTACC-AAATTTTATTGTTA
1 GGTTACCAAAATTTCATAATGAGGTTACCAAAATTTCATAGTGA
*
4879 GGTTACCGAAATT
1 GGTTACCAAAATT
4892 ATTATCATAT
Statistics
Matches: 384, Mismatches: 85, Indels: 43
0.75 0.17 0.08
Matches are distributed among these distances:
40 1 0.00
41 4 0.01
42 66 0.17
43 132 0.34
44 119 0.31
45 60 0.16
46 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (44 bp):
GGTTACCAAAATTTCATAATGAGGTTACCAAAATTTCATAGTGA
Found at i:4710 original size:20 final size:22
Alignment explanation
Indices: 4358--4867 Score: 330
Period size: 22 Copynumber: 23.5 Consensus size: 22
4348 TTGTTGATAT
4358 GGTTACCAAAATTTCAT-ATGGA
1 GGTTACCAAAATTTCATAAT-GA
* **
4380 GATTACCAAAATTTCATTGTGA
1 GGTTACCAAAATTTCATAATGA
* *
4402 GGTTA-CTAAATTTCA-GA-G-
1 GGTTACCAAAATTTCATAATGA
* * **
4420 GTGTTACCCAATATTTTATAGGGA
1 G-GTTA-CCAAAATTTCATAATGA
** * * *
4444 GACTACAAAAATTTCATACTAA
1 GGTTACCAAAATTTCATAATGA
* * * * **
4466 GCTTGCAAAAATTTAATTGTGA
1 GGTTACCAAAATTTCATAATGA
*
4488 GGTTACCAAAATTTCATAA-GG
1 GGTTACCAAAATTTCATAATGA
* *
4509 GGTTACCCAAATTT-ATAGTGA
1 GGTTACCAAAATTTCATAATGA
* ** *
4530 GGTTACAAAAATTTCATAGCGC
1 GGTTACCAAAATTTCATAATGA
* *
4552 GGTTACTAAAATATCAT-A-GA
1 GGTTACCAAAATTTCATAATGA
*
4572 GGGTAACCAAAATTTCAT-ATGGA
1 -GGTTACCAAAATTTCATAAT-GA
* * * *
4595 GATTTCCAAAATTTCAT-AGGG
1 GGTTACCAAAATTTCATAATGA
* *
4616 GGTCACTAAAATTTCATAA-GAA
1 GGTTACCAAAATTTCATAATG-A
* *
4638 GGTTACAAAAATTTTCATAGTGA
1 GGTTACCAAAA-TTTCATAATGA
* *
4661 TGTTACAAAAATTTCATAATGA
1 GGTTACCAAAATTTCATAATGA
4683 GGTTACC-AAATTTCATAA-G-
1 GGTTACCAAAATTTCATAATGA
*
4702 GGATTACCAAAATTTCATAATAA
1 GG-TTACCAAAATTTCATAATGA
* *
4725 GGTTACCAAAATTTCAAAACTTA
1 GGTTACCAAAATTTCATAA-TGA
* * *
4748 GCTTACCAAAATTTCATACTTA
1 GGTTACCAAAATTTCATAATGA
* *
4770 GGTTACCAAAATTTCATAGTCA
1 GGTTACCAAAATTTCATAATGA
* **
4792 AGTTACCAAAATTTCATAGGGA
1 GGTTACCAAAATTTCATAATGA
* * *
4814 AGTTACCAAAATATCATAGTGA
1 GGTTACCAAAATTTCATAATGA
**
4836 GGTTACCAAAATTTCATAGGGA
1 GGTTACCAAAATTTCATAATGA
4858 GGTTACCAAA
1 GGTTACCAAA
4868 TTTTATTGTT
Statistics
Matches: 386, Mismatches: 81, Indels: 42
0.76 0.16 0.08
Matches are distributed among these distances:
18 1 0.00
19 7 0.02
20 10 0.03
21 95 0.25
22 227 0.59
23 44 0.11
24 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAATGA
Found at i:4864 original size:66 final size:65
Alignment explanation
Indices: 4358--4867 Score: 383
Period size: 64 Copynumber: 7.8 Consensus size: 65
4348 TTGTTGATAT
* * * * *
4358 GGTTACCAAAATTTCATATGGAGATTACCAAAATTTCATTGTGAGGTTA-CTAAATTTCAGAG-G
1 GGTTACCAAAATTTCATAAGG-GGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATAGCG
4421 -
65 A
* * * * * * * * * * * *
4421 TGTTACCCAATATTTTAT-AGGGAGACTACAAAAATTTCATACTAAGCTTGCAAAAATTTAATTG
1 GGTTA-CCAAAATTTCATAAGGG-G-TTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATAG
*
4485 TGA
63 CGA
* * *
4488 GGTTACCAAAATTTCATAAGGGGTTACCCAAATTT-ATAGTGAGGTTACAAAAATTTCATAGCGC
1 GGTTACCAAAATTTCATAAGGGGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATAGCGA
* * * * *
4552 GGTTACTAAAATATCAT-AGAGGGTAACCAAAATTTCATA-TGGAGATTTCCAAAATTTCATAG-
1 GGTTACCAAAATTTCATAAG-GGGTTACCAAAATTTCATAGT-GAGGTTACCAAAATTTCATAGC
*
4614 GG
64 GA
* * * * * * **
4616 GGTCACTAAAATTTCATAAGAAGGTTACAAAAATTTTCATAGTGATGTTACAAAAATTTCATAAT
1 GGTTACCAAAATTTCATAAG-GGGTTACCAAAA-TTTCATAGTGAGGTTACCAAAATTTCATAGC
4681 GA
64 GA
* * * * * *
4683 GGTTACC-AAATTTCATAAGGGATTACCAAAATTTCATAATAAGGTTACCAAAATTTCAAAACTT
1 GGTTACCAAAATTTCATAAGGGGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATAGC-G
4747 A
65 A
* *** * * *
4748 GCTTACCAAAATTTCATACTTAGGTTACCAAAATTTCATAGTCAAGTTACCAAAATTTCATAGGG
1 GGTTACCAAAATTTCATA-AGGGGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATAGCG
4813 A
65 A
* * *
4814 AGTTACCAAAATATCAT-AGTGAGGTTACCAAAATTTCATAGGGAGGTTACCAAA
1 GGTTACCAAAATTTCATAAG-G-GGTTACCAAAATTTCATAGTGAGGTTACCAAA
4868 TTTTATTGTT
Statistics
Matches: 345, Mismatches: 83, Indels: 35
0.75 0.18 0.08
Matches are distributed among these distances:
62 1 0.00
63 8 0.02
64 119 0.34
65 66 0.19
66 101 0.29
67 50 0.14
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (65 bp):
GGTTACCAAAATTTCATAAGGGGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATAGCGA
Found at i:5585 original size:333 final size:327
Alignment explanation
Indices: 4911--5904 Score: 1032
Period size: 333 Copynumber: 3.0 Consensus size: 327
4901 TTTAATATAT
* * * * * * * *
4911 TTTGGTTAGGTGAATATAGATATTTCAAGGAATCTTGGCGCTAAAAATCATTCAAAATTAACCGA
1 TTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCAAAAAATCATGCAAAATGAGCCGA
** * * *
4976 -GCCCCGAAACATGTTTTTAGCCAAAAATCATGATGATT-ATCACACGATTTCGACTAAAATTTT
66 GGCCCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTAAT-ACACGATTTCGGCTAAAATTTT
* * * * * *
5039 -CCAAAATTGACCCGGAAGATATTTCCTCAATTTTTAGCCATAATACTCATAAAATATATATATA
130 GCAAAAATTGACCC-GAAAATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAA-A-ATATATA
* **
5103 ATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTCTTGATATTTTTTCTGA
192 ATTCAACGCCAAAAAGATTGAAGGG-TTTTTACG-TTTTAATATCGTT-TTTCTATTTTTTCTGA
* * * * * *
5168 ATTAATTTCAAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATGCAATG
254 ATTAATTTCTAATTAAATCGAAACAATATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
*
5233 TGGCTAAAA
319 TGACTAAAA
* * *
5242 TTTTATTAGATGAATATAGTTATTTCAAGGAGTGTCGGCGCAAAAAATCATGCAAAACTGAGCCG
1 TTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCAAAAAATCATGCAAAA-TGAGCCG
* *
5307 AGGCCCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTAATACATGATTTTGGCTAAAATTTT
65 AGGCCCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTAATACACGATTTCGGCTAAAATTTT
*
5372 GCAAAAAAATT-ACCCGAACAATTTTTCCTCAAATTTTGGCTAAAATACTCATAAAAAATATATA
130 GC--AAAAATTGACCCGAA-AATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATA
* * *
5436 ATTCAACGCCAAAAAGATTGAAGGGTTTTTGACGTTTCTAAAATAGTTTTTCCTATTTTTTCCGA
192 ATTCAACGCCAAAAAGATTGAAGGGTTTTT-ACGTTT-TAATATCGTTTTT-CTATTTTTTCTGA
* *
5501 ATTAATTTCTAATTAAATCGAAATAATATTTAGATGCTCGTAAAAACAAATCCTTGAATCCAATG
254 ATTAATTTCTAATTAAATCGAAACAATATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* *
5566 TGACTGAGA
319 TGACTAAAA
* * * * * * **
5575 TTTGATTAGATGAATATAGATATTTCGAGTAGTCTCAGAGCCAAAAATTATGCAAAATTGAG-AA
1 TTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCAAAAAATCATGCAAAA-TGAGCCG
* * * * * * *
5639 AGATCACCGGAACGCGTTTTTAGCAAAAAAACTATGATCGATGGTTTGTTAATACACGATCTCAG
65 AG-GCCCCGAAACGCGTTTTTAGC-CAAAAA-T-CG-T-GAT-G---GTTAATACACGATTTCGG
* * * *
5704 TTAAAATTTTGCAAAAATTGACACGAAAGATTTCTCCTCAATTTTTGGCTAAAGTACTCAT-AAA
120 CTAAAATTTTGCAAAAATTGACCCGAAA-ATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAA
* * * * *
5768 AATATATATTTCAATGCCAAAAAGATTGGAGGGCTTTTTACGCTTGTAATATCGTATTTCTGATT
184 AATATATAATTCAACGCCAAAAAGATTGAAGGG-TTTTTACG-TTTTAATATCGTTTTTCT-ATT
* * * *
5833 TTTT-TAAATTAATTTCTAATTAAATCGAAACAATA-TTAGATGTTCATAAAAACAAATTCTTAA
246 TTTTCTGAATTAATTTCTAATTAAATCGAAACAATATTTAGATGCTCGTAAAAACAAATCCTTAA
*
5896 ATTCAATGT
311 ATCCAATGT
5905 TGCAGAGCCT
Statistics
Matches: 555, Mismatches: 83, Indels: 43
0.81 0.12 0.06
Matches are distributed among these distances:
331 48 0.09
332 17 0.03
333 240 0.43
334 12 0.02
335 36 0.06
336 7 0.01
337 1 0.00
338 35 0.06
339 31 0.06
340 61 0.11
341 42 0.08
342 25 0.05
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (327 bp):
TTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCAAAAAATCATGCAAAATGAGCCGA
GGCCCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTAATACACGATTTCGGCTAAAATTTTG
CAAAAATTGACCCGAAAATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
AACGCCAAAAAGATTGAAGGGTTTTTACGTTTTAATATCGTTTTTCTATTTTTTCTGAATTAATT
TCTAATTAAATCGAAACAATATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTAA
AA
Found at i:12810 original size:2 final size:2
Alignment explanation
Indices: 12803--12831 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12793 GAATTGTTAC
12803 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 T
12832 CTTTGGCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18919 original size:2 final size:2
Alignment explanation
Indices: 18912--18947 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18902 AGCTATAAAC
18912 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
18948 AATGTCATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:28644 original size:39 final size:39
Alignment explanation
Indices: 28590--28667 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
28580 AATAGATTTG
28590 ATATAATTAGTTTTTCTTTTCCATTGAGATTCACACAAA
1 ATATAATTAGTTTTTCTTTTCCATTGAGATTCACACAAA
28629 ATATAATTAGTTTTTCTTTTCCATTGAGATTCACACAAA
1 ATATAATTAGTTTTTCTTTTCCATTGAGATTCACACAAA
28668 TTTGGTTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (39 bp):
ATATAATTAGTTTTTCTTTTCCATTGAGATTCACACAAA
Found at i:47100 original size:2 final size:2
Alignment explanation
Indices: 47095--47119 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47085 TTTGCAAAAA
47095 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
47120 CACAAATGTA
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:49762 original size:53 final size:53
Alignment explanation
Indices: 49705--49811 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
49695 CGGCTGTTTT
* *
49705 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
1 ATTTTATAAATTCTCTTAAGAAAATTCAGATAAGAAATCAAATTTTGTTGTGA
49758 ATTTTATAAATTCTCTTAAGAAAATTCAGATAAGAAATCAAATTTTGTTGTGA
1 ATTTTATAAATTCTCTTAAGAAAATTCAGATAAGAAATCAAATTTTGTTGTGA
49811 A
1 A
49812 ATGATAACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (53 bp):
ATTTTATAAATTCTCTTAAGAAAATTCAGATAAGAAATCAAATTTTGTTGTGA
Found at i:53337 original size:21 final size:22
Alignment explanation
Indices: 53281--53339 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 22
53271 GATTGAAAGT
*
53281 TGTCACTGTTTA-GTGTAATGA
1 TGTCACTATTTAGGTGTAATGA
53302 T-TC-CTATTT-GGTGTAATGA
1 TGTCACTATTTAGGTGTAATGA
53321 TGTCACT-TTTAGGTGTAAT
1 TGTCACTATTTAGGTGTAAT
53340 AAGAATTTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 15 0.45
20 7 0.21
21 11 0.33
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.46
Consensus pattern (22 bp):
TGTCACTATTTAGGTGTAATGA
Found at i:58081 original size:31 final size:32
Alignment explanation
Indices: 58038--58102 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
58028 ATATATTTAC
* **
58038 TTATCATTTGAAT-TCTCAAATTCATGACAAT
1 TTATCATTTGAATATCCCAAATTCAAAACAAT
58069 TTATC-TTATGAATATCCCAAATTCAAAACAAT
1 TTATCATT-TGAATATCCCAAATTCAAAACAAT
58101 TT
1 TT
58103 GCTATATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 2 0.07
31 10 0.34
32 17 0.59
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (32 bp):
TTATCATTTGAATATCCCAAATTCAAAACAAT
Found at i:60994 original size:21 final size:22
Alignment explanation
Indices: 60968--61013 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
60958 TGAAGTGGAG
60968 AAAAGAACAG-AGAAAAAGAGA
1 AAAAGAACAGCAGAAAAAGAGA
* *
60989 AAAAGAAGAGCAGAAAAGGAGA
1 AAAAGAACAGCAGAAAAAGAGA
61011 AAA
1 AAA
61014 GAAGCTACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.70, C:0.04, G:0.26, T:0.00
Consensus pattern (22 bp):
AAAAGAACAGCAGAAAAAGAGA
Found at i:61014 original size:21 final size:20
Alignment explanation
Indices: 60964--61017 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
60954 AAGTTGAAGT
*
60964 GGAGAAAAGAACAGAGAAAA
1 GGAGAAAAGAAGAGAGAAAA
*
60984 AGAGAAAAAGAAGAGCAGAAAA
1 GGAG-AAAAGAAGAG-AGAAAA
61006 GGAGAAAAGAAG
1 GGAGAAAAGAAG
61018 CTACCCAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.10
21 17 0.59
22 9 0.31
ACGTcount: A:0.65, C:0.04, G:0.31, T:0.00
Consensus pattern (20 bp):
GGAGAAAAGAAGAGAGAAAA
Found at i:70904 original size:21 final size:21
Alignment explanation
Indices: 70880--70923 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
70870 ATAAGGGTCC
70880 TAAAACACA-ATTTCAATAAAT
1 TAAAACACATATTT-AATAAAT
* *
70901 TAAAATACATATTTAGTAAAT
1 TAAAACACATATTTAATAAAT
70922 TA
1 TA
70924 TGACATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAAACACATATTTAATAAAT
Found at i:72208 original size:31 final size:31
Alignment explanation
Indices: 72167--72242 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
72157 GTGTCCGACG
*
72167 TGGCATGCCACGTGGATAAAAAAGTAACACA
1 TGGCACGCCACGTGGATAAAAAAGTAACACA
* * * * **
72198 TGGCAGGCCACATGGATCAAAAAGTGACATG
1 TGGCACGCCACGTGGATAAAAAAGTAACACA
72229 TGGCACGCCACGTG
1 TGGCACGCCACGTG
72243 TGCCAAAAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.34, C:0.22, G:0.28, T:0.16
Consensus pattern (31 bp):
TGGCACGCCACGTGGATAAAAAAGTAACACA
Found at i:77387 original size:2 final size:2
Alignment explanation
Indices: 77380--77404 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
77370 AATAACAACA
77380 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
77405 ATAGCAACAA
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
Done.