Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013619.1 Corchorus capsularis cultivar CVL-1 contig13640, 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: 45746
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1208 original size:20 final size:20
Alignment explanation
Indices: 1183--1225 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1173 GTATCATATT
*
1183 ACTCACCAGCTCCAACTTTA
1 ACTCACCAACTCCAACTTTA
1203 ACTCACCAACTCCAACTTTA
1 ACTCACCAACTCCAACTTTA
1223 ACT
1 ACT
1226 GGATCGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.40, G:0.02, T:0.26
Consensus pattern (20 bp):
ACTCACCAACTCCAACTTTA
Found at i:1839 original size:6 final size:6
Alignment explanation
Indices: 1828--1864 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
1818 ACAACCTGAA
1828 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAGAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG
1865 TATCAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 26 0.87
7 4 0.13
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2294 original size:30 final size:29
Alignment explanation
Indices: 2232--2301 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
2222 ACCGAACCAT
****
2232 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
2261 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTATT-AAAAAGGC
2291 CAAATAAGCCC
1 CAAATAAGCCC
2302 TGATGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Found at i:5636 original size:54 final size:53
Alignment explanation
Indices: 5539--5641 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 53
5529 TCTCCATTAA
*
5539 CCAATACCAATGGCTCTCAGTCCCGCTGAACCATTAGTCTCATCATTATCATG
1 CCAATACCAATGGCTCTCAGTCCCGCTGAACCATCAGTCTCATCATTATCATG
* * * *
5592 CCAATCACCGATGGCTCTTAGTCCCGCTGAGCCATC-GGCTTCATCATTAT
1 CCAAT-ACCAATGGCTCTCAGTCCCGCTGAACCATCAGTC-TCATCATTAT
5642 TACGCTAAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
53 7 0.16
54 36 0.84
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.28
Consensus pattern (53 bp):
CCAATACCAATGGCTCTCAGTCCCGCTGAACCATCAGTCTCATCATTATCATG
Found at i:7707 original size:19 final size:20
Alignment explanation
Indices: 7668--7709 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
7658 ACAATGGTGA
*
7668 TGAAAAGTAAGAGACAAGGT
1 TGAAAAATAAGAGACAAGGT
*
7688 TGAAAAATAA-AGATAAGGT
1 TGAAAAATAAGAGACAAGGT
7707 TGA
1 TGA
7710 TTAAACAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.52, C:0.02, G:0.26, T:0.19
Consensus pattern (20 bp):
TGAAAAATAAGAGACAAGGT
Found at i:8604 original size:20 final size:20
Alignment explanation
Indices: 8576--8615 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
8566 TTTGTTTGGT
*
8576 TGGAAGGTTTTGGAGGGGTG
1 TGGAAGGTTTTAGAGGGGTG
*
8596 TGGAGGGTTTTAGAGGGGTG
1 TGGAAGGTTTTAGAGGGGTG
8616 GACCTTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.55, T:0.30
Consensus pattern (20 bp):
TGGAAGGTTTTAGAGGGGTG
Found at i:9145 original size:18 final size:18
Alignment explanation
Indices: 9122--9159 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
9112 CTAATTCTTC
9122 TTGTTTAATTCTTCTTTT
1 TTGTTTAATTCTTCTTTT
* *
9140 TTGTTTATTTTTTCTTTT
1 TTGTTTAATTCTTCTTTT
9158 TT
1 TT
9160 AATTCCTGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.79
Consensus pattern (18 bp):
TTGTTTAATTCTTCTTTT
Found at i:13367 original size:29 final size:31
Alignment explanation
Indices: 13332--13398 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
13322 TATCAATTTG
* *
13332 GGATATAACGTTTC-AAAAACG-CCAATTCA
1 GGATATAACGTTACAAAAAACGACCAAATCA
13361 GGATATAACGTTACAAAAAACGACCAAATCA
1 GGATATAACGTTACAAAAAACGACCAAATCA
13392 GGATATA
1 GGATATA
13399 GTCTGACGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 13 0.38
30 7 0.21
31 14 0.41
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACAAAAAACGACCAAATCA
Found at i:15017 original size:29 final size:30
Alignment explanation
Indices: 14973--15029 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
14963 TGATTTGATT
*
14973 GTTTTATGTAACGTTATATC-CTAAATTGGC
1 GTTTTATGAAACGTTATATCAC-AAATTGGC
15003 GTTTT-TGAAACGTTATATCACAAATTG
1 GTTTTATGAAACGTTATATCACAAATTG
15030 ATCATTGCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (30 bp):
GTTTTATGAAACGTTATATCACAAATTGGC
Found at i:23458 original size:21 final size:20
Alignment explanation
Indices: 23432--23505 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 20
23422 TGTTGTTATT
23432 TTGTAGATCTAGGGTTTAAA
1 TTGTAGATCTAGGGTTTAAA
23452 CTTGTAGATCTAGGGTTTAAGA
1 -TTGTAGATCTAGGGTTTAA-A
**
23474 TTGTAGATCTAGGGTTTTAGG
1 TTGTAGATCTAGGG-TTTAAA
23495 TTGTAGATCTA
1 TTGTAGATCTA
23506 AGAAAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
21 44 0.90
22 5 0.10
ACGTcount: A:0.26, C:0.07, G:0.27, T:0.41
Consensus pattern (20 bp):
TTGTAGATCTAGGGTTTAAA
Found at i:23909 original size:30 final size:31
Alignment explanation
Indices: 23875--23987 Score: 112
Period size: 30 Copynumber: 3.8 Consensus size: 31
23865 TTAAAATTAG
*
23875 TTATTGATAATATTT-ATTAATTATATTTAT
1 TTATTGATAATATTTAATTAATTATATATAT
*
23905 TTATTGAT--TATTTAATT-GTTA-ATCATAT
1 TTATTGATAATATTTAATTAATTATAT-ATAT
* * *
23933 TTATTAATTATATTTAATTAATTATA-ATAA
1 TTATTGATAATATTTAATTAATTATATATAT
* *
23963 TTATTGATAATAATTATTTAATTAT
1 TTATTGATAATATTTAATTAATTAT
23988 TAATTTTATT
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
27 2 0.03
28 18 0.26
29 3 0.04
30 41 0.60
31 3 0.04
32 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.57
Consensus pattern (31 bp):
TTATTGATAATATTTAATTAATTATATATAT
Found at i:23933 original size:32 final size:30
Alignment explanation
Indices: 23891--23951 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 30
23881 ATAATATTTA
* *
23891 TTAATTATATTTATTTATTGATTATTTAATTG
1 TTAATCATATTTATTAATT-A-TATTTAATTG
23923 TTAATCATATTTATTAATTATATTTAATT
1 TTAATCATATTTATTAATTATATTTAATT
23952 AATTATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 9 0.33
31 1 0.04
32 17 0.63
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (30 bp):
TTAATCATATTTATTAATTATATTTAATTG
Found at i:23963 original size:13 final size:13
Alignment explanation
Indices: 23935--23992 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
23925 AATCATATTT
*
23935 ATTAATTATATTTA
1 ATTAATTATA-ATA
23949 ATTAATTATAATA
1 ATTAATTATAATA
23962 ATT-ATTGATAATA
1 ATTAATT-ATAATA
*
23975 ATT-ATT-TAATT
1 ATTAATTATAATA
23986 ATTAATT
1 ATTAATT
23993 TTATTTAATC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
11 7 0.17
12 6 0.15
13 17 0.43
14 10 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
ATTAATTATAATA
Found at i:24124 original size:10 final size:10
Alignment explanation
Indices: 24111--24165 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
24101 TAATTATTTA
24111 TAATAATTAT
1 TAATAATTAT
24121 TAATAACTTA-
1 TAATAA-TTAT
24131 TAATAATTAT
1 TAATAATTAT
*
24141 TGATAATTAT
1 TAATAATTAT
*
24151 TATTTAATTAT
1 TA-ATAATTAT
24162 TAAT
1 TAAT
24166 TTTATTTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 3 0.08
10 23 0.61
11 12 0.32
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (10 bp):
TAATAATTAT
Found at i:24138 original size:92 final size:92
Alignment explanation
Indices: 24042--24314 Score: 268
Period size: 92 Copynumber: 3.1 Consensus size: 92
24032 TTGTGAAATT
*
24042 TAATTATGATTAAGTATTGCTAATTAGTTTATTAGTATTAATTAGTTTAGGGTGAAATTTAATTA
1 TAATTATGATTAAGTATTGCTAATTAGTTTATTAGTATTAATTAGTTTACGGTGAAATTTAATTA
24107 TTTATAATAATTATTAATAACTTATAA
66 TTTATAATAATTATTAATAACTTATAA
* ** * * * * ** * *
24134 TAATTATTGA-TAATTATTATTTAATTA-TTAATT-TTATTTAATCA-TTTACTGTTTAA-TCAT
1 TAATTA-TGATTAAGTATT-GCTAATTAGTTTATTAGTA-TTAATTAGTTTACGGTGAAATTTAA
* * *
24194 TTAATTT-TGA-AATT-GTGA-AA--T-T--
63 TT-ATTTATAATAATTATTAATAACTTATAA
*
24216 TAATTACGATTAAGTATTGCTAATTAGTTTATTAGTATTAATTAGTTTACGGTGAAATTTAATTA
1 TAATTATGATTAAGTATTGCTAATTAGTTTATTAGTATTAATTAGTTTACGGTGAAATTTAATTA
24281 TTTATAATAATTATTAATAACTTATAA
66 TTTATAATAATTATTAATAACTTATAA
24308 TAATTAT
1 TAATTAT
24315 TGATAATAAT
Statistics
Matches: 132, Mismatches: 31, Indels: 36
0.66 0.16 0.18
Matches are distributed among these distances:
81 8 0.06
82 24 0.18
83 15 0.11
84 7 0.05
85 5 0.04
86 2 0.02
87 4 0.03
88 2 0.02
89 5 0.04
90 7 0.05
91 14 0.11
92 30 0.23
93 9 0.07
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (92 bp):
TAATTATGATTAAGTATTGCTAATTAGTTTATTAGTATTAATTAGTTTACGGTGAAATTTAATTA
TTTATAATAATTATTAATAACTTATAA
Found at i:24155 original size:174 final size:174
Alignment explanation
Indices: 23946--24430 Score: 891
Period size: 174 Copynumber: 2.8 Consensus size: 174
23936 TTAATTATAT
23946 TTAATTAA-TTATAATAATTATTGATAATAATTATTTAATTATTAATTTTATTTAATCATTTACT
1 TTAA-TAACTTATAATAATTATTGATAATAATTATTTAATTATTAATTTTATTTAATCATTTACT
24010 GTTTAATTATTTAATTTTGAAATTGTGAAATTTAATTATGATTAAGTATTGCTAATTAGTTTATT
65 GTTTAATTATTTAATTTTGAAATTGTGAAATTTAATTATGATTAAGTATTGCTAATTAGTTTATT
*
24075 AGTATTAATTAGTTTAGGGTGAAATTTAATTATTTATAATAATTA
130 AGTATTAATTAGTTTACGGTGAAATTTAATTATTTATAATAATTA
*
24120 TTAATAACTTATAATAATTATTGATAATTATTATTTAATTATTAATTTTATTTAATCATTTACTG
1 TTAATAACTTATAATAATTATTGATAATAATTATTTAATTATTAATTTTATTTAATCATTTACTG
* *
24185 TTTAATCATTTAATTTTGAAATTGTGAAATTTAATTACGATTAAGTATTGCTAATTAGTTTATTA
66 TTTAATTATTTAATTTTGAAATTGTGAAATTTAATTATGATTAAGTATTGCTAATTAGTTTATTA
24250 GTATTAATTAGTTTACGGTGAAATTTAATTATTTATAATAATTA
131 GTATTAATTAGTTTACGGTGAAATTTAATTATTTATAATAATTA
24294 TTAATAACTTATAATAATTATTGATAATAATTATTTAATTATTAATTTTATTTAATCATTTACTG
1 TTAATAACTTATAATAATTATTGATAATAATTATTTAATTATTAATTTTATTTAATCATTTACTG
* *
24359 TTTAATTTTTTTAATTTTGAAATTGGGAAATTTAATTATGATTAAGTATTGCTAATTAGTTTATT
66 TTTAA-TTATTTAATTTTGAAATTGTGAAATTTAATTATGATTAAGTATTGCTAATTAGTTTATT
24424 AGTATTA
130 AGTATTA
24431 GTTTAAGGTG
Statistics
Matches: 300, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
173 3 0.01
174 235 0.78
175 62 0.21
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.52
Consensus pattern (174 bp):
TTAATAACTTATAATAATTATTGATAATAATTATTTAATTATTAATTTTATTTAATCATTTACTG
TTTAATTATTTAATTTTGAAATTGTGAAATTTAATTATGATTAAGTATTGCTAATTAGTTTATTA
GTATTAATTAGTTTACGGTGAAATTTAATTATTTATAATAATTA
Found at i:24293 original size:13 final size:13
Alignment explanation
Indices: 24275--24330 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 13
24265 CGGTGAAATT
24275 TAATTATTTATAA
1 TAATTATTTATAA
24288 TAATTA--T-TAA
1 TAATTATTTATAA
*
24298 T-A--ACTTATAA
1 TAATTATTTATAA
*
24308 TAATTATTGATAA
1 TAATTATTTATAA
24321 TAATTATTTA
1 TAATTATTTA
24331 ATTATTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
7 1 0.03
9 2 0.06
10 8 0.24
11 2 0.06
13 21 0.62
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (13 bp):
TAATTATTTATAA
Found at i:24297 original size:20 final size:20
Alignment explanation
Indices: 24282--24320 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
24272 ATTTAATTAT
24282 TTATAATAATTATTAATAAC
1 TTATAATAATTATTAATAAC
*
24302 TTATAATAATTATTGATAA
1 TTATAATAATTATTAATAA
24321 TAATTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (20 bp):
TTATAATAATTATTAATAAC
Found at i:24355 original size:25 final size:24
Alignment explanation
Indices: 24321--24373 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
24311 TTATTGATAA
*
24321 TAATTATTTAAT-TATTAATTTTATT
1 TAATCATTTAATGT-TTAATTTT-TT
*
24346 TAATCATTTACTGTTTAATTTTTT
1 TAATCATTTAATGTTTAATTTTTT
24370 TAAT
1 TAAT
24374 TTTGAAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 18 0.72
26 1 0.04
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (24 bp):
TAATCATTTAATGTTTAATTTTTT
Found at i:24415 original size:82 final size:81
Alignment explanation
Indices: 23981--24416 Score: 245
Period size: 82 Copynumber: 5.1 Consensus size: 81
23971 AATAATTATT
*
23981 TAATTATTAATTTTATTTAATCATTTACTGTTTAA-TTATTTAATTTTGAAATTGTGAAATTTAA
1 TAATTATTAATTTTATTTAATCATTTACTGTTTAATTTTTTTAATTTTGAAATTG-GAAATTTAA
24045 TTATGATTAAGTATTGC
65 TTATGATTAAGTATTGC
* * * * *
24062 TAATTAGTTTATTAGTA-TTAATTAGTTTAGGGTGAAATTTAATTATTTATAATAATTATTAATA
1 TAATTA-TTAATT-TTATTTAATCA-TTTA--CTG---TTTAATT-TTT-T--TAATT-TTGA-A
* **
24126 ACTT--ATAA--TAATTATTGA-TAATTATTATT
52 A-TTGGA-AATTTAATTA-TGATTAAGTATT-GC
**
24155 TAATTATTAATTTTATTTAATCATTTACTGTTTAA-TCATTTAATTTTGAAATTGTGAAATTTAA
1 TAATTATTAATTTTATTTAATCATTTACTGTTTAATTTTTTTAATTTTGAAATTG-GAAATTTAA
*
24219 TTACGATTAAGTATTGC
65 TTATGATTAAGTATTGC
* * * *
24236 TAATTAGTTTATTAGTA-TTAATTAGTTTACGGTGAAATTTAATTATTTATAATAATTATTAATA
1 TAATTA-TTAATT-TTATTTAATCA-TTTAC--TG---TTTAATT-TTT-T--TAATT-TTGA-A
**
24300 ACTT--ATAA--TAATTATTGA-TAA-TAATTATT
52 A-TTGGA-AATTTAATTA-TGATTAAGT-ATT-GC
24329 TAATTATTAATTTTATTTAATCATTTACTGTTTAATTTTTTTAATTTTGAAATTGGGAAATTTAA
1 TAATTATTAATTTTATTTAATCATTTACTGTTTAATTTTTTTAATTTTGAAATT-GGAAATTTAA
24394 TTATGATTAAGTATTGC
65 TTATGATTAAGTATTGC
24411 TAATTA
1 TAATTA
24417 GTTTATTAGT
Statistics
Matches: 266, Mismatches: 35, Indels: 107
0.65 0.09 0.26
Matches are distributed among these distances:
78 2 0.01
79 4 0.02
80 7 0.03
81 25 0.09
82 50 0.19
83 26 0.10
84 3 0.01
85 8 0.03
86 12 0.05
88 10 0.04
89 6 0.02
90 3 0.01
91 16 0.06
92 47 0.18
93 29 0.11
94 10 0.04
95 4 0.02
96 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.51
Consensus pattern (81 bp):
TAATTATTAATTTTATTTAATCATTTACTGTTTAATTTTTTTAATTTTGAAATTGGAAATTTAAT
TATGATTAAGTATTGC
Found at i:24588 original size:24 final size:24
Alignment explanation
Indices: 24556--24684 Score: 141
Period size: 24 Copynumber: 5.4 Consensus size: 24
24546 CTCCGCTCGT
*
24556 AGGGAGAGAGAGGCTCAGATTGAG
1 AGGGAGAGAGAGGATCAGATTGAG
**
24580 AGGGAGAGAGCCGATCAGATTGAG
1 AGGGAGAGAGAGGATCAGATTGAG
* * * *
24604 AGGAAGAGAGAGGATTAGATTCAT
1 AGGGAGAGAGAGGATCAGATTGAG
** *
24628 AGGGAGAGAGTCGTTCAGATTGAG
1 AGGGAGAGAGAGGATCAGATTGAG
* * *
24652 AGGGGGAGAGAGGCTCGGATTGAG
1 AGGGAGAGAGAGGATCAGATTGAG
24676 AGGGAGAGA
1 AGGGAGAGA
24685 CCCGCTATGA
Statistics
Matches: 83, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 83 1.00
ACGTcount: A:0.33, C:0.08, G:0.44, T:0.15
Consensus pattern (24 bp):
AGGGAGAGAGAGGATCAGATTGAG
Found at i:27115 original size:17 final size:17
Alignment explanation
Indices: 27093--27126 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27083 GAACATTAAG
* *
27093 TTAAAAATAAGAAAAAA
1 TTAAAAAAAACAAAAAA
27110 TTAAAAAAAACAAAAAA
1 TTAAAAAAAACAAAAAA
27127 AATAAAGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (17 bp):
TTAAAAAAAACAAAAAA
Found at i:28768 original size:7 final size:7
Alignment explanation
Indices: 28666--28895 Score: 59
Period size: 7 Copynumber: 32.9 Consensus size: 7
28656 TGATTAATAT
28666 TTTACTC
1 TTTACTC
28673 TTTAC-C
1 TTTACTC
**
28679 ATTTTTTC
1 -TTTACTC
*
28687 TTTACTA
1 TTTACTC
*
28694 ATTACTC
1 TTTACTC
28701 TTTA-TCC
1 TTTACT-C
28708 TTTAC-C
1 TTTACTC
*
28714 ATTTTACTA
1 --TTTACTC
*
28723 ATTACTC
1 TTTACTC
*
28730 TTCACTC
1 TTTACTC
* *
28737 CTTACTA
1 TTTACTC
*
28744 TTTTC-C
1 TTTACTC
*
28750 TTTACTA
1 TTTACTC
*
28757 ATTACTC
1 TTTACTC
28764 TTTACTC
1 TTTACTC
28771 TTTAC-C
1 TTTACTC
*
28777 ATTTTC-C
1 -TTTACTC
*
28784 TTTACTGA
1 TTTACT-C
* *
28792 TTT-TTA
1 TTTACTC
28798 TATTACTC
1 T-TTACTC
28806 TTTAC-C
1 TTTACTC
28812 ATTT-CTC
1 -TTTACTC
*
28819 TTTACTG
1 TTTACTC
* *
28826 ATTACTT
1 TTTACTC
28833 TTTACTC
1 TTTACTC
*
28840 TTTACTA
1 TTTACTC
*
28847 TTTCACTG
1 TTT-ACTC
*
28855 TTTACTA
1 TTTACTC
*
28862 ATTAC-C
1 TTTACTC
* *
28868 ATTACTT
1 TTTACTC
28875 TTTAC-C
1 TTTACTC
28881 ATTTTACTC
1 --TTTACTC
28890 TTTACT
1 TTTACT
28896 GATTGCCTTT
Statistics
Matches: 159, Mismatches: 43, Indels: 42
0.65 0.18 0.17
Matches are distributed among these distances:
6 24 0.15
7 112 0.70
8 22 0.14
9 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.01, T:0.54
Consensus pattern (7 bp):
TTTACTC
Found at i:28843 original size:34 final size:33
Alignment explanation
Indices: 28666--28885 Score: 191
Period size: 34 Copynumber: 6.5 Consensus size: 33
28656 TGATTAATAT
28666 TTTACTCTTTACCATTTTTTCTTTACTAATTACTC
1 TTTACTCTTTACCA--TTTTCTTTACTAATTACTC
28701 TTTA-TCCTTTACCA---T-TTTACTAATTACTC
1 TTTACT-CTTTACCATTTTCTTTACTAATTACTC
* * *
28730 TTCACTCCTTACTATTTTCCTTTACTAATTACTC
1 TTTACTCTTTACCATTTT-CTTTACTAATTACTC
* ** *
28764 TTTACTCTTTACCATTTTCCTTTACTGATTTTTA
1 TTTACTCTTTACCATTTT-CTTTACTAATTACTC
* *
28798 TATTACTCTTTACCATTTCTCTTTACTGATTACTT
1 T-TTACTCTTTACCATTT-TCTTTACTAATTACTC
* *
28833 TTTACTCTTTACTATTTCACTGTTTACTAATTAC-C
1 TTTACTCTTTACCATTT---TCTTTACTAATTACTC
* *
28868 ATTACTTTTTACCATTTT
1 TTTACTCTTTACCATTTT
28886 ACTCTTTACT
Statistics
Matches: 154, Mismatches: 20, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
29 23 0.15
30 2 0.01
32 2 0.01
34 58 0.38
35 55 0.36
36 14 0.09
ACGTcount: A:0.21, C:0.23, G:0.01, T:0.55
Consensus pattern (33 bp):
TTTACTCTTTACCATTTTCTTTACTAATTACTC
Found at i:28879 original size:13 final size:14
Alignment explanation
Indices: 28799--28883 Score: 50
Period size: 13 Copynumber: 6.2 Consensus size: 14
28789 TGATTTTTAT
*
28799 ATTACTCTTTAC-C
1 ATTACTTTTTACTC
* * *
28812 ATTTCTCTTTACTG
1 ATTACTTTTTACTC
28826 ATTACTTTTTACTC
1 ATTACTTTTTACTC
* * *
28840 TTTACTATTTCACTG
1 ATTACT-TTTTACTC
* **
28855 TTTACTAATTAC-C
1 ATTACTTTTTACTC
28868 ATTACTTTTTAC-C
1 ATTACTTTTTACTC
28881 ATT
1 ATT
28884 TTACTCTTTA
Statistics
Matches: 55, Mismatches: 15, Indels: 4
0.74 0.20 0.05
Matches are distributed among these distances:
13 24 0.44
14 19 0.35
15 12 0.22
ACGTcount: A:0.22, C:0.22, G:0.02, T:0.53
Consensus pattern (14 bp):
ATTACTTTTTACTC
Found at i:28906 original size:21 final size:21
Alignment explanation
Indices: 28876--29294 Score: 153
Period size: 22 Copynumber: 19.1 Consensus size: 21
28866 CCATTACTTT
28876 TTACCATTTTACTCTTTACTGA
1 TTACC-TTTTACTCTTTACTGA
*
28898 TTGCCTTTTCACAT-TTTACTGA
1 TTACCTTTT-AC-TCTTTACTGA
* **
28920 TT-TCAATTACTCTTTACTGA
1 TTACCTTTTACTCTTTACTGA
* * * *
28940 TCATCTTCTTTAAT-TTTATTGA
1 TTA-CCT-TTTACTCTTTACTGA
*
28962 TTGCCATTTTACTCTTTTACTGA
1 TTACC-TTTTACTC-TTTACTGA
* *
28985 TTACTATTTTTTGCTCCTTTTTTACTGA
1 TTAC---CTTTTACT-C---TTTACTGA
* *
29013 CTACCCCTTTTACT-TTCTACTGG
1 TTA--CCTTTTACTCTT-TACTGA
* * * *
29036 TTGCCTCTTGCTTTTTACTGA
1 TTACCTTTTACTCTTTACTGA
*
29057 TTACCTTTTTACT-TCTTGCTGA
1 TTACC-TTTTACTCT-TTACTGA
*
29079 TTAGCTTTTTACTCTTTACTGA
1 TTA-CCTTTTACTCTTTACTGA
*
29101 TCACCTTTTTACTC-TTACTGA
1 TTACC-TTTTACTCTTTACTGA
* *
29122 TTTCCTTTTACT-TATTACTTA
1 TTACCTTTTACTCT-TTACTGA
* *
29143 TTACTTTTTTACTC-TCACTGA
1 TTAC-CTTTTACTCTTTACTGA
* *
29164 TTACTATTTTACTTTTTACTGA
1 TTAC-CTTTTACTCTTTACTGA
* **
29186 CTATTATTTTACTCTTGT--TGA
1 TTA-CCTTTTACTCTT-TACTGA
29207 TTACCTTCTTACGT-TTTACTGA
1 TTACCTT-TTAC-TCTTTACTGA
* * *
29229 TTACTATTTTACTCCTTACTAA
1 TTAC-CTTTTACTCTTTACTGA
* *
29251 TTACCATTTTACCCTTT-CAGA
1 TTACC-TTTTACTCTTTACTGA
*
29272 -TACCTTTTTACTTTTTACTGA
1 TTACC-TTTTACTCTTTACTGA
29293 TT
1 TT
29295 GGACGCTATC
Statistics
Matches: 293, Mismatches: 64, Indels: 80
0.67 0.15 0.18
Matches are distributed among these distances:
19 1 0.00
20 34 0.12
21 84 0.29
22 123 0.42
23 26 0.09
25 6 0.02
26 1 0.00
27 6 0.02
28 11 0.04
30 1 0.00
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.53
Consensus pattern (21 bp):
TTACCTTTTACTCTTTACTGA
Found at i:29081 original size:22 final size:22
Alignment explanation
Indices: 29050--29294 Score: 179
Period size: 22 Copynumber: 11.4 Consensus size: 22
29040 CTCTTGCTTT
29050 TTACTGATTACCTTTTTACTTC
1 TTACTGATTACCTTTTTACTTC
* *
29072 TTGCTGATTAGCTTTTTAC-TC
1 TTACTGATTACCTTTTTACTTC
*
29093 TTTACTGATCACCTTTTTAC-TC
1 -TTACTGATTACCTTTTTACTTC
* *
29115 TTACTGATTTCC-TTTTACTTA
1 TTACTGATTACCTTTTTACTTC
* *
29136 TTACTTATTACTTTTTTAC-TC
1 TTACTGATTACCTTTTTACTTC
* *
29157 TCACTGATTA-CTATTTTACTTT
1 TTACTGATTACCT-TTTTACTTC
* *
29179 TTACTGACTA-TTATTTTAC-TC
1 TTACTGATTACCT-TTTTACTTC
** *
29200 TTGTTGATTACCTTCTTACGTT-
1 TTACTGATTACCTTTTTAC-TTC
*
29222 TTACTGATTA-CTATTTTACTCC
1 TTACTGATTACCT-TTTTACTTC
* * *
29244 TTACTAATTACCATTTTAC-CC
1 TTACTGATTACCTTTTTACTTC
* * *
29265 TTTCAGA-TACCTTTTTACTTT
1 TTACTGATTACCTTTTTACTTC
29286 TTACTGATT
1 TTACTGATT
29295 GGACGCTATC
Statistics
Matches: 171, Mismatches: 39, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
20 17 0.10
21 64 0.37
22 88 0.51
23 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.53
Consensus pattern (22 bp):
TTACTGATTACCTTTTTACTTC
Found at i:29196 original size:43 final size:43
Alignment explanation
Indices: 29046--29262 Score: 167
Period size: 43 Copynumber: 5.0 Consensus size: 43
29036 TTGCCTCTTG
* *
29046 CTTTTTACTGATTACCT-TTTTACTTCTTGCTGATTAGCT-TTTTA
1 CTTTTTACTGATTA-TTATTTTAC-TCTTACTGATTA-CTATTTTA
* * * * *
29090 CTCTTTACTGATCACCT-TTTTACTCTTACTGATTTC-CTTTTA
1 CTTTTTACTGATTA-TTATTTTACTCTTACTGATTACTATTTTA
* * *
29132 CTTATTACTTATTACTT-TTTTACTCTCACTGATTACTATTTTA
1 CTTTTTACTGATTA-TTATTTTACTCTTACTGATTACTATTTTA
* ** *
29175 CTTTTTACTGACTATTATTTTACTCTTGTTGATTACCT-TCTTA
1 CTTTTTACTGATTATTATTTTACTCTTACTGATTA-CTATTTTA
* * * *
29218 CGTTTTACTGATTACTATTTTACTCCTTACTAATTACCATTTTA
1 CTTTTTACTGATTATTATTTTACT-CTTACTGATTACTATTTTA
29262 C
1 C
29263 CCTTTCAGAT
Statistics
Matches: 140, Mismatches: 27, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
42 37 0.26
43 67 0.48
44 36 0.26
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.54
Consensus pattern (43 bp):
CTTTTTACTGATTATTATTTTACTCTTACTGATTACTATTTTA
Found at i:29600 original size:26 final size:25
Alignment explanation
Indices: 29571--29712 Score: 72
Period size: 26 Copynumber: 5.2 Consensus size: 25
29561 TACCTTGACT
29571 CTGATTAACCTCTTTTTACTTAATTA
1 CTGATTAA-CTCTTTTTACTTAATTA
* * * *
29597 CTGATTTACTGATTATTA-TTACCTTGA
1 CTGATTAACT-CTTTTTACTTA-ATT-A
29624 CTCTGATTAATCTCTTTTTACTTAATTA
1 --CTGATTAA-CTCTTTTTACTTAATTA
* * * *
29652 CTGATTTACTGATTACTATTACTTTGACT-
1 CTGATTAACT-CTT--T-TTAC-TTAATTA
*
29681 CTGATTAATCTCTTTTTCCTTAATTA
1 CTGATTAA-CTCTTTTTACTTAATTA
29707 CTGATT
1 CTGATT
29713 TACTGATTAC
Statistics
Matches: 85, Mismatches: 17, Indels: 28
0.65 0.13 0.22
Matches are distributed among these distances:
25 11 0.13
26 32 0.38
27 2 0.02
28 2 0.02
29 27 0.32
30 11 0.13
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.51
Consensus pattern (25 bp):
CTGATTAACTCTTTTTACTTAATTA
Found at i:29742 original size:55 final size:55
Alignment explanation
Indices: 29479--29726 Score: 435
Period size: 55 Copynumber: 4.5 Consensus size: 55
29469 CATTTTAACT
*
29479 CTTAATTA-TCGATTTACTGATTACTATTACCTTGACTCTAATTAATCTCTTTTTA
1 CTTAATTACT-GATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
*
29534 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAACCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
*
29589 CTTAATTACTGATTTACTGATTATTATTACCTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* *
29644 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTC
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
29699 CTTAATTACTGATTTACTGATTACTATT
1 CTTAATTACTGATTTACTGATTACTATT
29727 TATTTTCACC
Statistics
Matches: 185, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
55 184 0.99
56 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.50
Consensus pattern (55 bp):
CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
Found at i:29822 original size:22 final size:22
Alignment explanation
Indices: 29762--29822 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
29752 CTGATTTCTA
**
29762 TTACTCTTTACTGATTATCACT
1 TTACTCTTTACTGATTGCCACT
29784 TTACTCTTTACTGATTGCCACT
1 TTACTCTTTACTGATTGCCACT
29806 TTAC-CTTTTACTGATTG
1 TTACTC-TTTACTGATTG
29823 TATCTTTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.20, C:0.23, G:0.08, T:0.49
Consensus pattern (22 bp):
TTACTCTTTACTGATTGCCACT
Found at i:29829 original size:22 final size:21
Alignment explanation
Indices: 29748--29829 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 21
29738 GATTACATGA
29748 TTTACTGATT-T-CTATTACTC
1 TTTACTGATTGTACT-TTACTC
*
29768 TTTACTGATTATCACTTTACTC
1 TTTACTGATTGT-ACTTTACTC
*
29790 TTTACTGATTGCCACTTTAC-C
1 TTTACTGATTG-TACTTTACTC
29811 TTTTACTGATTGTATCTTT
1 -TTTACTGATTGTA-CTTT
29830 CTTATTGAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
20 10 0.19
21 3 0.06
22 38 0.72
23 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTACTGATTGTACTTTACTC
Found at i:33247 original size:28 final size:28
Alignment explanation
Indices: 33174--33247 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
33164 GTAGATTAAG
* *
33174 AATGACCAAAATACCCCCTAAATGCAAA
1 AATGACCAAAATGCCCCTTAAATGCAAA
* **
33202 AATGACCAAAATGCCCCTTAGATGTGAA
1 AATGACCAAAATGCCCCTTAAATGCAAA
33230 AATGACCAAAATGCCCCT
1 AATGACCAAAATGCCCCT
33248 GGATGACCCT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (28 bp):
AATGACCAAAATGCCCCTTAAATGCAAA
Found at i:41625 original size:74 final size:75
Alignment explanation
Indices: 41503--41641 Score: 208
Period size: 74 Copynumber: 1.9 Consensus size: 75
41493 TTTAAAAAAA
* *
41503 TTAAACTCTTATTAAAAAGAAAACAATAAATTTTAATCACAAGAAATTAAACTATCAATACACAC
1 TTAAACTCTTATTAAAAAGAAAACAATAAATTATAATCACAAGAAATTAAACTACCAATACACAC
41568 TCCGAATACT
66 TCCGAATACT
* * * * *
41578 TTAAATTCTTATT-AAAAGGAAAGAATAAATTATAATCACAATAAATTAAACTACCAATAGACAC
1 TTAAACTCTTATTAAAAAGAAAACAATAAATTATAATCACAAGAAATTAAACTACCAATACACAC
41642 CTCAAATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
74 45 0.79
75 12 0.21
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.28
Consensus pattern (75 bp):
TTAAACTCTTATTAAAAAGAAAACAATAAATTATAATCACAAGAAATTAAACTACCAATACACAC
TCCGAATACT
Done.