Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017255.1 Corchorus olitorius cultivar O-4 contig17288, 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: 48031
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Found at i:1407 original size:25 final size:24
Alignment explanation
Indices: 1373--1419 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
1363 ACGTTTGCAC
1373 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
1398 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
1420 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:8621 original size:27 final size:27
Alignment explanation
Indices: 8588--8643 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
8578 TCATGAGGTC
8588 TTGGATTCAATTCTCACAGAATATGAG
1 TTGGATTCAATTCTCACAGAATATGAG
*
8615 TTGGATTCAATTCTCACAGAATGTGAG
1 TTGGATTCAATTCTCACAGAATATGAG
8642 TT
1 TT
8644 TAGTTTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (27 bp):
TTGGATTCAATTCTCACAGAATATGAG
Found at i:14947 original size:19 final size:19
Alignment explanation
Indices: 14897--14947 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
14887 TGTGGAATTT
14897 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
14915 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
14934 TTAATAATTAATTA
1 TTAATAATTAATTA
14948 ATTTCAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:21740 original size:46 final size:47
Alignment explanation
Indices: 21680--21780 Score: 122
Period size: 47 Copynumber: 2.2 Consensus size: 47
21670 TATTATTACT
21680 TTTTAC-T-TTTTAGCTTAATTAAC-CT-TACTACTGATTACT-CTTGC
1 TTTTACTTCTTTTAGCTTAATT-ACTCTATACTACTGATTACTCCTT-C
* **
21724 TTTTACTTCTTTTAGCTTAATTACTCTATTCTTTTGATTACTCCTTC
1 TTTTACTTCTTTTAGCTTAATTACTCTATACTACTGATTACTCCTTC
21771 TTTTACTTCT
1 TTTTACTTCT
21781 GATTACTCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
44 6 0.12
45 3 0.06
46 15 0.31
47 22 0.45
48 3 0.06
ACGTcount: A:0.19, C:0.21, G:0.05, T:0.55
Consensus pattern (47 bp):
TTTTACTTCTTTTAGCTTAATTACTCTATACTACTGATTACTCCTTC
Found at i:21865 original size:65 final size:65
Alignment explanation
Indices: 21754--21925 Score: 265
Period size: 65 Copynumber: 2.6 Consensus size: 65
21744 TTACTCTATT
*
21754 CTTTTGATTACTCCTTCTTTTACTTCTGATTACTCTTTCTTCTGCTTTTGATTACTCTTTCTTTT
1 CTTTTGATTACT-CTTCTTTTACTTCTGATTACTCTTTCTTCTGCTTTTGATTACTCTTCCTTTT
*
21819 G
65 A
*
21820 CTTTTGATTAGTCTTCCTTTTAC-TCTGATTACTCTTTCTTCTGCTTTTGATTACTCTTCCTTTT
1 CTTTTGATTACTCTT-CTTTTACTTCTGATTACTCTTTCTTCTGCTTTTGATTACTCTTCCTTTT
21884 A
65 A
**
21885 CTCCTGATTACTCTTTCTTTTACTTCTGATTACTCTTTCTT
1 CTTTTGATTACTC-TTCTTTTACTTCTGATTACTCTTTCTT
21926 TTACTGCTTA
Statistics
Matches: 97, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
65 60 0.62
66 37 0.38
ACGTcount: A:0.12, C:0.24, G:0.07, T:0.58
Consensus pattern (65 bp):
CTTTTGATTACTCTTCTTTTACTTCTGATTACTCTTTCTTCTGCTTTTGATTACTCTTCCTTTTA
Found at i:21871 original size:87 final size:87
Alignment explanation
Indices: 21758--21930 Score: 229
Period size: 87 Copynumber: 2.0 Consensus size: 87
21748 TCTATTCTTT
* * * ** *
21758 TGATTACTCCTTCTTTTACTTCTGATTACTCTTTCTTCTGCTTTTGATTACTCTTTCTTTTGCTT
1 TGATTACTCCTTCTTCTACTTCTGATTACTCTTCCTTCTACTCCTGATTACTCTTTCTTTTACTT
* *
21823 TTGATTAGTCTTCCTTTTACTC
66 CTGATTACTCTTCCTTTTACTC
* * * *
21845 TGATTACTCTTTCTTCTGCTTTTGATTACTCTTCCTTTTACTCCTGATTACTCTTTCTTTTACTT
1 TGATTACTCCTTCTTCTACTTCTGATTACTCTTCCTTCTACTCCTGATTACTCTTTCTTTTACTT
*
21910 CTGATTACTCTTTCTTTTACT
66 CTGATTACTCTTCCTTTTACT
21931 GCTTAGCTTG
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.12, C:0.24, G:0.07, T:0.57
Consensus pattern (87 bp):
TGATTACTCCTTCTTCTACTTCTGATTACTCTTCCTTCTACTCCTGATTACTCTTTCTTTTACTT
CTGATTACTCTTCCTTTTACTC
Found at i:21945 original size:28 final size:22
Alignment explanation
Indices: 21758--21930 Score: 222
Period size: 22 Copynumber: 7.9 Consensus size: 22
21748 TCTATTCTTT
*
21758 TGATTACTCCTTCTTTTACTTC
1 TGATTACTCTTTCTTTTACTTC
* * *
21780 TGATTACTCTTTCTTCTGCTTT
1 TGATTACTCTTTCTTTTACTTC
* *
21802 TGATTACTCTTTCTTTTGCTTT
1 TGATTACTCTTTCTTTTACTTC
* *
21824 TGATTAGTCTTCCTTTTAC-TC
1 TGATTACTCTTTCTTTTACTTC
* * *
21845 TGATTACTCTTTCTTCTGCTTT
1 TGATTACTCTTTCTTTTACTTC
* *
21867 TGATTACTCTTCCTTTTACTCC
1 TGATTACTCTTTCTTTTACTTC
21889 TGATTACTCTTTCTTTTACTTC
1 TGATTACTCTTTCTTTTACTTC
21911 TGATTACTCTTTCTTTTACT
1 TGATTACTCTTTCTTTTACT
21931 GCTTAGCTTG
Statistics
Matches: 129, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
21 16 0.12
22 113 0.88
ACGTcount: A:0.12, C:0.24, G:0.07, T:0.57
Consensus pattern (22 bp):
TGATTACTCTTTCTTTTACTTC
Found at i:22069 original size:141 final size:140
Alignment explanation
Indices: 21921--22321 Score: 552
Period size: 141 Copynumber: 2.8 Consensus size: 140
21911 TGATTACTCT
** * * ** * *
21921 TTCTTTTACTGCTTAGCTTGATTACCCAGAATCAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATCAAACTG-CATCTTCTTCTTTTGCTATTTAGTT
* *
21986 TAATTACCCAGAATTAAACTCTTTTCTTCTTCTTTTACTATTTAGTTTAATTACCCAG-AATTAA
65 TAATTACCAAGAATTAAACTATTTTCTTCTTCTTTTACTATTTAGTTTAATTACCC-GCAATTAA
22050 ACTAACATCTTC
129 ACTAACATCTTC
* *
22062 TTCTTTTACTATTTAGTTTAAGTACCCAGAATCAAACTAGCCTCTTCTTCTTTTGCTATTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATCAAACT-GCATCTTCTTCTTTTGCTATTTAGTT
* * ***
22127 TAATTACCTAGGATTAAACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCGCAATTAAA
65 TAATTACCAAGAATTAAACTATTTTCTTCTTCTTTTACTATTTAGTTTAATTACCCGCAATTAAA
22192 CTAACATCTTC
130 CTAACATCTTC
* *
22203 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGACATCTTCTTCTTTTACTATTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATCAAACTG-CATCTTCTTCTTTTGCTATTTAGTT
* * * *
22268 TAATTACCAAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTAC
65 TAATTACCAAGAATTAAACTATTTTCTTCTTCTTTTACTATTTAGTTTAATTAC
22322 TCTGATTTAA
Statistics
Matches: 229, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
140 2 0.01
141 226 0.99
142 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.46
Consensus pattern (140 bp):
TTCTTTTACTATTTAGTTTAATTACCCAGAATCAAACTGCATCTTCTTCTTTTGCTATTTAGTTT
AATTACCAAGAATTAAACTATTTTCTTCTTCTTTTACTATTTAGTTTAATTACCCGCAATTAAAC
TAACATCTTC
Found at i:22334 original size:47 final size:47
Alignment explanation
Indices: 21921--22321 Score: 482
Period size: 47 Copynumber: 8.5 Consensus size: 47
21911 TGATTACTCT
** * * * ***
21921 TTCTTTTACTGCTTAGCTTGATTACCCAGAATCAAACTGTTTTCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGACATCTTC
* * * ****
21968 TTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGACATCTTC
*
22015 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACATCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGACATCTTC
* * *
22062 TTCTTTTACTATTTAGTTTAAGTACCCAGAATCAAACT-AGCCTCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGA-CATCTTC
* * * * *
22109 TTCTTTTGCTATTTAGTTTAATTACCTAGGATTAAACTAACCTCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGACATCTTC
*
22156 TTCTTTTACTATTTAGTTTAATTACCC-GCAATTAAACTAACATCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAG-AATTAAACTGACATCTTC
22203 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGACATCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGACATCTTC
* ***
22250 TTCTTTTACTATTTAGTTTAATTACCAAGAATTAAACTGTTTTCTTC
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGACATCTTC
* * *
22297 TTCTCTTGCTCTTTAGTTTAATTAC
1 TTCTTTTACTATTTAGTTTAATTAC
22322 TCTGATTTAA
Statistics
Matches: 315, Mismatches: 35, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
46 2 0.01
47 311 0.99
48 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.46
Consensus pattern (47 bp):
TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTGACATCTTC
Found at i:35402 original size:15 final size:15
Alignment explanation
Indices: 35382--35412 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35372 TTTGATAAAA
*
35382 TAATAATTATTTAAT
1 TAATAATTAATTAAT
35397 TAATAATTAATTAAT
1 TAATAATTAATTAAT
35412 T
1 T
35413 TCAGCCCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATAATTAATTAAT
Found at i:35407 original size:19 final size:18
Alignment explanation
Indices: 35359--35409 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
35349 TGTGGGATTT
*
35359 TTAATAATAATTATTTGA
1 TTAATAATAATTATTTAA
*
35377 TAAAATAATAATTATTTAA
1 T-TAATAATAATTATTTAA
35396 TTAATAATTAATTA
1 TTAATAA-TAATTA
35410 ATTTCAGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATAATAATTATTTAA
Found at i:40881 original size:48 final size:48
Alignment explanation
Indices: 40826--40922 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
40816 TCATATAATT
40826 CATTAACAACTTCAACTCATTATTAACAAAATCTGTCCAAATTAGCAC
1 CATTAACAACTTCAACTCATTATTAACAAAATCTGTCCAAATTAGCAC
40874 CATTAACAACTTCAACTCATTATTAACAAAATCTGTCCAAATTAGCAC
1 CATTAACAACTTCAACTCATTATTAACAAAATCTGTCCAAATTAGCAC
40922 C
1 C
40923 GAAACCCCGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.41, C:0.26, G:0.04, T:0.29
Consensus pattern (48 bp):
CATTAACAACTTCAACTCATTATTAACAAAATCTGTCCAAATTAGCAC
Found at i:41827 original size:129 final size:130
Alignment explanation
Indices: 41598--41850 Score: 343
Period size: 129 Copynumber: 1.9 Consensus size: 130
41588 TTACTTTAAG
*
41598 CCCTCAATTAGTTTCTCACCATTCCTTTCTCCTCCAGCCCTTTTTTGTAATTGCAAGGGTTTTTA
1 CCCTCAATTAGTTTCTCACCATTCCTTTCTCCTCCAGCCCTTTTTTGTAATTACAAGGGTTTTTA
* * * *
41663 ATCAGTTGAATGTGAAAGCATTTATTGACCATAAAATCA-T-CTATTATTTATTTACTAAGAAGA
66 ACCACTTCAATGTGAAAACATTTATTGACCATAAAATCAGTACTATTATTTATTTACTAAGAAGA
* * ** * *
41726 CCCTCAATTAGTTTCTCAGCATTCCTTTTTCCTCC-GCTTTTTTTTTTTTTATTACAAGGGTTTT
1 CCCTCAATTAGTTTCTCACCATTCCTTTCTCCTCCAGC--CCTTTTTTGTAATTACAAGGGTTTT
41790 TAACCACTTCAATGT-AAACACATTTATTGACCATAAAATCATGTACTATTATTTATTTACT
64 TAACCACTTCAATGTGAAA-ACATTTATTGACCATAAAATCA-GTACTATTATTTATTTACT
41851 TCATCAAACC
Statistics
Matches: 108, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
127 2 0.02
128 36 0.33
129 53 0.49
131 1 0.01
132 16 0.15
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (130 bp):
CCCTCAATTAGTTTCTCACCATTCCTTTCTCCTCCAGCCCTTTTTTGTAATTACAAGGGTTTTTA
ACCACTTCAATGTGAAAACATTTATTGACCATAAAATCAGTACTATTATTTATTTACTAAGAAGA
Found at i:41910 original size:13 final size:13
Alignment explanation
Indices: 41892--41924 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
41882 CTAAATCTGG
41892 AAAAAAAAAACAA
1 AAAAAAAAAACAA
*
41905 AAAAAAGAAACAA
1 AAAAAAAAAACAA
41918 AAAAAAA
1 AAAAAAA
41925 CCAGAGGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.91, C:0.06, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:42777 original size:14 final size:15
Alignment explanation
Indices: 42758--42786 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42748 TATCCTTATA
42758 ACTATTTTA-TATTT
1 ACTATTTTACTATTT
42772 ACTATTTTACTATTT
1 ACTATTTTACTATTT
42787 TACTTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (15 bp):
ACTATTTTACTATTT
Found at i:42782 original size:8 final size:8
Alignment explanation
Indices: 42758--42790 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
42748 TATCCTTATA
42758 ACTATTTT
1 ACTATTTT
42766 A-TA-TTT
1 ACTATTTT
42772 ACTATTTT
1 ACTATTTT
42780 ACTATTTT
1 ACTATTTT
42788 ACT
1 ACT
42791 TTTATAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 4 0.17
7 4 0.17
8 15 0.65
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (8 bp):
ACTATTTT
Found at i:42783 original size:22 final size:22
Alignment explanation
Indices: 42758--42804 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
42748 TATCCTTATA
42758 ACTATTTTA-TATTTACTA-TTTT
1 ACTATTTTACT-TTTA-TAGTTTT
42780 ACTATTTTACTTTTATAGTTTT
1 ACTATTTTACTTTTATAGTTTT
42802 ACT
1 ACT
42805 TAACTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 2 0.09
22 20 0.87
23 1 0.04
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.62
Consensus pattern (22 bp):
ACTATTTTACTTTTATAGTTTT
Found at i:42817 original size:93 final size:93
Alignment explanation
Indices: 42695--42881 Score: 293
Period size: 93 Copynumber: 2.0 Consensus size: 93
42685 CATTGTTTAA
*
42695 ACTTTCATAGTTTTAGTCAACTAAAAACTCAATTTTTATTTAATTAAATCTAATATCCTTATAAC
1 ACTTTCATAGTTTTACTCAACTAAAAACTCAATTTTTATTTAATTAAATCTAATATCCTTATAAC
* * *
42760 TATTTTATATTTACTATTTTACTATTTT
66 TATTTTATATTTACCATATTACTAATTT
* * * *
42788 ACTTTTATAGTTTTACTTAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTCATAGTTTTACTCAACTAAAAACTCAATTTTTATTTAATTAAATCTAATATCCTTATAAC
*
42853 TATTTTATTTTTACCATATTACTAATTT
66 TATTTTATATTTACCATATTACTAATTT
42881 A
1 A
42882 ATTAAAAAGT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 85 1.00
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (93 bp):
ACTTTCATAGTTTTACTCAACTAAAAACTCAATTTTTATTTAATTAAATCTAATATCCTTATAAC
TATTTTATATTTACCATATTACTAATTT
Found at i:42865 original size:71 final size:70
Alignment explanation
Indices: 42781--43006 Score: 196
Period size: 71 Copynumber: 3.2 Consensus size: 70
42771 TACTATTTTA
* * *
42781 CTATTTTACTTTTATAGTTTTACTTAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCC
1 CTATTTTACTTTTATAGTTTTATTTAACTAAAAAATTTATTTTTATTTAATTAAAT-TAATATCC
42846 TTATAC
65 TTATAC
* * * * ** * *
42852 CTATTTTATTTTTACCATA-TTACTAATTTAATTAAAAAGTTTAGATATA-TTAGA-TATATT--
1 CTATTTTACTTTT---ATAGTT--TTATTTAACTAAAAAATTTATTTTTATTTA-ATTAAATTAA
*
42912 TA-CCATATTA-
60 TATCCTTA-TAC
*
42922 CTATTTTACTTTTATAGTCTTATTTAACTAAAAAATTTATTTTTATTTAATTAAATTTAATATCC
1 CTATTTTACTTTTATAGTTTTATTTAACTAAAAAATTTATTTTTATTTAATTAAA-TTAATATCC
42987 TTATAC
65 TTATAC
*
42993 CTATTTTATTTTTA
1 CTATTTTACTTTTA
43007 CCATTTTAAT
Statistics
Matches: 118, Mismatches: 22, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
66 21 0.18
67 9 0.08
68 3 0.03
70 20 0.17
71 33 0.28
73 3 0.03
74 10 0.08
75 19 0.16
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (70 bp):
CTATTTTACTTTTATAGTTTTATTTAACTAAAAAATTTATTTTTATTTAATTAAATTAATATCCT
TATAC
Found at i:43047 original size:12 final size:12
Alignment explanation
Indices: 43030--43055 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43020 CAATAAAAGA
43030 AATATTATTATC
1 AATATTATTATC
43042 AATATTATTATC
1 AATATTATTATC
43054 AA
1 AA
43056 GTTTAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (12 bp):
AATATTATTATC
Found at i:43561 original size:25 final size:25
Alignment explanation
Indices: 43529--43611 Score: 166
Period size: 25 Copynumber: 3.3 Consensus size: 25
43519 TAATTCTTAA
43529 ATTTATTTAATATCTTTATTATTCG
1 ATTTATTTAATATCTTTATTATTCG
43554 ATTTATTTAATATCTTTATTATTCG
1 ATTTATTTAATATCTTTATTATTCG
43579 ATTTATTTAATATCTTTATTATTCG
1 ATTTATTTAATATCTTTATTATTCG
43604 ATTTATTT
1 ATTTATTT
43612 TACAATCGAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (25 bp):
ATTTATTTAATATCTTTATTATTCG
Found at i:46526 original size:27 final size:27
Alignment explanation
Indices: 46465--46541 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
46455 CATTAGGGTT
* *
46465 ATCCATGGGCATTTTAGTCATTTGCAC
1 ATCCAGGGGCATTTTGGTCATTTGCAC
* *
46492 GTCCAGGGGCATTTTGGTCATTTGTAC
1 ATCCAGGGGCATTTTGGTCATTTGCAC
**
46519 ATTTAGGGGCATTTTGGTCATTT
1 ATCCAGGGGCATTTTGGTCATTT
46542 TAAGTTCACT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (27 bp):
ATCCAGGGGCATTTTGGTCATTTGCAC
Found at i:46973 original size:2 final size:2
Alignment explanation
Indices: 46966--46995 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46956 TTAGCATTAC
46966 AT 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 AT
46996 GTTTGATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.