Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017909.1 Corchorus olitorius cultivar O-4 contig17942, 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: 122033
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2247 original size:11 final size:11
Alignment explanation
Indices: 2203--2272 Score: 51
Period size: 11 Copynumber: 6.7 Consensus size: 11
2193 CAATTTTTAG
2203 TATATAT-TAA
1 TATATATATAA
* *
2213 -ATATTTATAT
1 TATATATATAA
2223 TATATATATAA
1 TATATATATAA
* *
2234 TATATATCTGA
1 TATATATATAA
*
2245 TATCATA-ATAT
1 TAT-ATATATAA
2256 TA-ATAT-TAA
1 TATATATATAA
2265 TATATATA
1 TATATATA
2273 CTTTTCCATT
Statistics
Matches: 44, Mismatches: 10, Indels: 11
0.68 0.15 0.17
Matches are distributed among these distances:
9 12 0.27
10 6 0.14
11 23 0.52
12 3 0.07
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (11 bp):
TATATATATAA
Found at i:21717 original size:14 final size:16
Alignment explanation
Indices: 21685--21714 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21675 ATTAATAAGC
21685 AAATTATATACAAATT
1 AAATTATATACAAATT
21701 AAATTATATA-AAAT
1 AAATTATATACAAAT
21715 AAAAAGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATTATATACAAATT
Found at i:25448 original size:69 final size:70
Alignment explanation
Indices: 25362--25501 Score: 219
Period size: 69 Copynumber: 2.0 Consensus size: 70
25352 AAAACTAACA
** * *
25362 ACTAAGGAAAAAATGGTGAAAACAGTATTAATTACATCCAAATGCTAAAA-TTACATGTAAAGAC
1 ACTAAGGAAAAAATGGTGAAAACACCATTAATTACATCAAAATGCTAAAATTTACATATAAAGAC
25426 AATGC
66 AATGC
* *
25431 ACTAAGGAATAAATGGTGGAAACACCATTAATTACATCAAAATGCTAAAATTTACATATAAAGAC
1 ACTAAGGAAAAAATGGTGAAAACACCATTAATTACATCAAAATGCTAAAATTTACATATAAAGAC
25496 AATGC
66 AATGC
25501 A
1 A
25502 TTTCAATAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
69 45 0.70
70 19 0.30
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (70 bp):
ACTAAGGAAAAAATGGTGAAAACACCATTAATTACATCAAAATGCTAAAATTTACATATAAAGAC
AATGC
Found at i:29085 original size:60 final size:60
Alignment explanation
Indices: 29005--29194 Score: 147
Period size: 60 Copynumber: 3.4 Consensus size: 60
28995 TGTCTATAAA
*
29005 TTATAGTTTATGGT-TCAAATTGCCCAAAATTAAAGTTTAGGATGCAAATTGTCCATTTAC
1 TTATAGTTTAAGGTGT-AAATTGCCCAAAATTAAAGTTTAGGATGCAAATTGTCCATTTAC
* * ** * **
29065 TTATAGTTTAAGGTGTAAATTG---TACATT--AG---AGGAAAC-TATTACCCA--TAGC
1 TTATAGTTTAAGGTGTAAATTGCCCAAAATTAAAGTTTAGGATGCAAATTGTCCATTTA-C
** * **
29115 --CCAGTTTATGGTTCAAATTGCCCAAAATTAAAGTTTAGGATGCAAATTGTCCATTTAC
1 TTATAGTTTAAGGTGTAAATTGCCCAAAATTAAAGTTTAGGATGCAAATTGTCCATTTAC
29173 TTATAGTTTAAGGTGTAAATTG
1 TTATAGTTTAAGGTGTAAATTG
29195 TACATTAGAG
Statistics
Matches: 90, Mismatches: 25, Indels: 30
0.62 0.17 0.21
Matches are distributed among these distances:
48 15 0.17
49 2 0.02
50 1 0.01
51 10 0.11
52 5 0.06
53 2 0.02
55 2 0.02
56 5 0.06
57 10 0.11
58 1 0.01
59 2 0.02
60 34 0.38
61 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (60 bp):
TTATAGTTTAAGGTGTAAATTGCCCAAAATTAAAGTTTAGGATGCAAATTGTCCATTTAC
Found at i:29198 original size:108 final size:108
Alignment explanation
Indices: 29009--29225 Score: 434
Period size: 108 Copynumber: 2.0 Consensus size: 108
28999 TATAAATTAT
29009 AGTTTATGGTTCAAATTGCCCAAAATTAAAGTTTAGGATGCAAATTGTCCATTTACTTATAGTTT
1 AGTTTATGGTTCAAATTGCCCAAAATTAAAGTTTAGGATGCAAATTGTCCATTTACTTATAGTTT
29074 AAGGTGTAAATTGTACATTAGAGGAAACTATTACCCATAGCCC
66 AAGGTGTAAATTGTACATTAGAGGAAACTATTACCCATAGCCC
29117 AGTTTATGGTTCAAATTGCCCAAAATTAAAGTTTAGGATGCAAATTGTCCATTTACTTATAGTTT
1 AGTTTATGGTTCAAATTGCCCAAAATTAAAGTTTAGGATGCAAATTGTCCATTTACTTATAGTTT
29182 AAGGTGTAAATTGTACATTAGAGGAAACTATTACCCATAGCCC
66 AAGGTGTAAATTGTACATTAGAGGAAACTATTACCCATAGCCC
29225 A
1 A
29226 TAGGCACCCG
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (108 bp):
AGTTTATGGTTCAAATTGCCCAAAATTAAAGTTTAGGATGCAAATTGTCCATTTACTTATAGTTT
AAGGTGTAAATTGTACATTAGAGGAAACTATTACCCATAGCCC
Found at i:30804 original size:15 final size:15
Alignment explanation
Indices: 30784--30816 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
30774 CATATCTCAA
30784 TCATGAATTGAATCG
1 TCATGAATTGAATCG
*
30799 TCATGAATTGAATTG
1 TCATGAATTGAATCG
30814 TCA
1 TCA
30817 CCAATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (15 bp):
TCATGAATTGAATCG
Found at i:34347 original size:19 final size:19
Alignment explanation
Indices: 34323--34359 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
34313 CTGTTTAGCA
*
34323 ACTGTATAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
*
34342 ACTGTACAGATTAGATTA
1 ACTGTACAGATGAGATTA
34360 GATATTGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:34370 original size:21 final size:21
Alignment explanation
Indices: 34344--34422 Score: 140
Period size: 21 Copynumber: 3.8 Consensus size: 21
34334 GAGATTACAC
34344 TGTACAGATTAGATTAGATAT
1 TGTACAGATTAGATTAGATAT
*
34365 TGTACATATTAGATTAGATAT
1 TGTACAGATTAGATTAGATAT
34386 TGTACAGATTAGATTAGATAT
1 TGTACAGATTAGATTAGATAT
*
34407 TGTACAGATGAGATTA
1 TGTACAGATTAGATTA
34423 TTAGAGCAGC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (21 bp):
TGTACAGATTAGATTAGATAT
Found at i:35663 original size:23 final size:22
Alignment explanation
Indices: 35628--35674 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
35618 CCCGCTTCCA
*
35628 TCTCTCTTTTCTTCTCCTTCCTT
1 TCTCTCTTTTCTTCT-CTCCCTT
35651 TCTC-CTTTCTCTTCTCTCCCTT
1 TCTCTCTTT-TCTTCTCTCCCTT
35673 TC
1 TC
35675 AACTTCTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (22 bp):
TCTCTCTTTTCTTCTCTCCCTT
Found at i:36084 original size:7 final size:7
Alignment explanation
Indices: 36072--36123 Score: 68
Period size: 7 Copynumber: 7.1 Consensus size: 7
36062 ATATAGAGAT
36072 ATTTATA
1 ATTTATA
36079 ATTTATA
1 ATTTATA
36086 ATTTTATA
1 A-TTTATA
*
36094 ATTTTATG
1 A-TTTATA
36102 ATTTATA
1 ATTTATA
36109 ATTTATA
1 ATTTATA
*
36116 ATATATA
1 ATTTATA
36123 A
1 A
36124 GTGATTCTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
7 27 0.66
8 14 0.34
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (7 bp):
ATTTATA
Found at i:36093 original size:15 final size:15
Alignment explanation
Indices: 36073--36117 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
36063 TATAGAGATA
36073 TTTATAATTTATAAT
1 TTTATAATTTATAAT
*
36088 TTTATAATTTTATGA-
1 TTTATAA-TTTATAAT
36103 TTTATAATTTATAAT
1 TTTATAATTTATAAT
36118 ATATAAGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 6 0.23
15 14 0.54
16 6 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TTTATAATTTATAAT
Found at i:40532 original size:76 final size:76
Alignment explanation
Indices: 40406--40560 Score: 310
Period size: 76 Copynumber: 2.0 Consensus size: 76
40396 GTCTTCTTAA
40406 TGTTGAATTAAGTTCATTAATAATGATTAAACATTAATCTTCATTACCAAATTTAAGGTTCAGGA
1 TGTTGAATTAAGTTCATTAATAATGATTAAACATTAATCTTCATTACCAAATTTAAGGTTCAGGA
40471 GTTCGATTACG
66 GTTCGATTACG
40482 TGTTGAATTAAGTTCATTAATAATGATTAAACATTAATCTTCATTACCAAATTTAAGGTTCAGGA
1 TGTTGAATTAAGTTCATTAATAATGATTAAACATTAATCTTCATTACCAAATTTAAGGTTCAGGA
40547 GTTCGATTACG
66 GTTCGATTACG
40558 TGT
1 TGT
40561 AAGGAAGGTA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.39
Consensus pattern (76 bp):
TGTTGAATTAAGTTCATTAATAATGATTAAACATTAATCTTCATTACCAAATTTAAGGTTCAGGA
GTTCGATTACG
Found at i:42535 original size:45 final size:45
Alignment explanation
Indices: 42484--42610 Score: 200
Period size: 45 Copynumber: 2.8 Consensus size: 45
42474 AATTCTACTT
*
42484 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAACTAATATTATACTCCTC
* *
42529 CATCTCTAGGTAATTCATCAAAATAAAACTAATATTCTACTCCTT
1 CATCTCTAGGTAATTCATCAAAATAAAACTAATATTATACTCCTC
* * *
42574 CATCTTTAGGTCATTCATCAAAATAAACCTAATATTA
1 CATCTCTAGGTAATTCATCAAAATAAAACTAATATTA
42611 ATTGTTGCTT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.35
Consensus pattern (45 bp):
CATCTCTAGGTAATTCATCAAAATAAAACTAATATTATACTCCTC
Found at i:47976 original size:18 final size:18
Alignment explanation
Indices: 47955--47996 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
47945 AAATAGAAAC
*
47955 TAATTAATTA-ATAGATTT
1 TAATAAATTATATA-ATTT
47973 TAATAAATTATATAATTT
1 TAATAAATTATATAATTT
47991 T-ATAAA
1 TAATAAA
47997 AAAAAAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 14 0.64
19 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TAATAAATTATATAATTT
Found at i:64734 original size:15 final size:15
Alignment explanation
Indices: 64714--64743 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
64704 TCTTTCTATT
64714 TAGATCTATTTTGGC
1 TAGATCTATTTTGGC
64729 TAGATCTATTTTGGC
1 TAGATCTATTTTGGC
64744 ATTGCAGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (15 bp):
TAGATCTATTTTGGC
Found at i:75632 original size:49 final size:48
Alignment explanation
Indices: 75561--75696 Score: 145
Period size: 49 Copynumber: 2.8 Consensus size: 48
75551 ATTTTTTACA
*
75561 TTTCC-TGCACCTTTTTCTCAATTTTTACAACAAAATTGAATC-TTTAAT
1 TTTCCTTGCA-CTTTTTCACAATTTTTACAACAAAATTG-ATCATTTAAT
** *
75609 TTTCCTTGCACATTTTTCACAATTTTTATGACAAAATTGATCATTTACT
1 TTTCCTTGCAC-TTTTTCACAATTTTTACAACAAAATTGATCATTTAAT
* **
75658 TTTCATTGCACTTTTT-ATCAATTTTT-TGACAAAATTGAT
1 TTTCCTTGCACTTTTTCA-CAATTTTTACAACAAAATTGAT
75697 TGGCACGCTC
Statistics
Matches: 79, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
47 14 0.18
48 22 0.28
49 43 0.54
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.48
Consensus pattern (48 bp):
TTTCCTTGCACTTTTTCACAATTTTTACAACAAAATTGATCATTTAAT
Found at i:78215 original size:197 final size:196
Alignment explanation
Indices: 77871--78263 Score: 723
Period size: 197 Copynumber: 2.0 Consensus size: 196
77861 AGAAACAATA
77871 AAAATAAGAAGTGAAGTTACCAAAAAACCAATGTAAAGAATTGATTTTATGAATTCATTCACAAA
1 AAAATAAGAAGTGAAGTTACCAAAAAACCAATGTAAAGAATTGATTTTATGAATTCATTCACAAA
* *
77936 TAGAGAGGGGTATTTTTGTCATTTCATGCTTGGTTTTTTCGTTATTTGGGTTGATGATAGAGGGT
66 TAGAGAGGGGTATTTTGGTCATTTCATGCTTGGTTTTTTCGTTATTTGGGTTGATGATAGAGGGG
*
78001 ATTTTGGGAATTTTGTGAAAAAATTACTATTTGTGGGTCCCATTCTTCATAAACTAATATTTTTT
131 ATTTTGGGAACTTTGTGAAAAAATTACTATTTGTGGGTCCCATTCTTCATAAACTAAT-TTTTTT
78066 TT
195 TT
*
78068 AAAATAGGAAGTGAAGTTACCAAAAAACCAATGTAAAGAATTGATTTTATGAATTCATTCACAAA
1 AAAATAAGAAGTGAAGTTACCAAAAAACCAATGTAAAGAATTGATTTTATGAATTCATTCACAAA
78133 TAGAGAGGGGTATTTTGGTCATTTCATGCTTGGTTTTTTCGTTATTTGGGTTGATGATAGAGGGG
66 TAGAGAGGGGTATTTTGGTCATTTCATGCTTGGTTTTTTCGTTATTTGGGTTGATGATAGAGGGG
* *
78198 ATTTTGGGAACTTTGTGAGAAAGTTACTATTTGTGGGTCCCATTCTTCATAAACTAATTTTTTTT
131 ATTTTGGGAACTTTGTGAAAAAATTACTATTTGTGGGTCCCATTCTTCATAAACTAATTTTTTTT
78263 T
196 T
78264 GGATTATTTA
Statistics
Matches: 190, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
196 8 0.04
197 182 0.96
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (196 bp):
AAAATAAGAAGTGAAGTTACCAAAAAACCAATGTAAAGAATTGATTTTATGAATTCATTCACAAA
TAGAGAGGGGTATTTTGGTCATTTCATGCTTGGTTTTTTCGTTATTTGGGTTGATGATAGAGGGG
ATTTTGGGAACTTTGTGAAAAAATTACTATTTGTGGGTCCCATTCTTCATAAACTAATTTTTTTT
T
Found at i:79133 original size:434 final size:435
Alignment explanation
Indices: 78353--79404 Score: 1225
Period size: 434 Copynumber: 2.4 Consensus size: 435
78343 CGCGTTGGCT
* * *
78353 TTTATTTTTGTATT-TTTTTTCTATTTGTCCGATTAAGGTGACTCAAGTGTCTATTAAAAGGTAA
1 TTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAA
* * * * * * **
78417 TTTGATGATCTGCAATTTTCATTAAGAACTTAAAAGCCAATTTTAATGTTTTGATTCTAAAAAAT
66 TTTGATGATCTACAATCTTCATGAAGGACTCAAAAGCTAA-TTT-ATGTTTAAATTCTAAAAAAT
* ** * *
78482 GCTTCCGAAATTTTGTGGTTTTGATTGTCGGT-TAATTTAAT--ATAGTATAATTTTTTGTCCAC
129 GCTT-CTAAATTTTGT-GTTTTGATTGTTAGTCT-ATTTAATACATA-TATAATTGTTCGTCCAC
** * * * * * *
78544 ATGTCCGGTTGAAGTTATTGAAGAGTCGGTTAAAAGGTTATTGCATGATTTACGACTTCCATGAA
190 ATGTCCAATTAAAGTTATTCAAGAGTCGGTTAAAAGGTTACTACATAATCTACGACTTCCATGAA
* *
78609 GGACCCGAAAGCTCAATTTGATATACGAGTTTCGTGAAGGGTTCAAAAGGGAATTTTTATGTTTC
255 GAACCCGAAAGCTCAATTTGATATACGAGTTTCGTGAAGGGTTCAAAAGAGAATTTTTATGTTTC
* * * * * *
78674 AAGATCTCCATTAACAAACATTTTCTTTTTTGGATTATTTATCAAATGACCCTCATGCTTTTCTC
320 AAGATCTCCATTAACAAACATTTTCTTGTTTGAATTAGTTATCAAATCACCCTCATACTTTTCTA
* *
78739 TTTT-TACTACTTAGTCCTTTACAAATTCTATCTTA-ATTTAAAGT-TTCAGC
385 TTTTATACTACTTAGTCCTTTACAAATTCTATCTTACATTT-AACTCTTCA-A
* *
78789 TTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGTTGATTCATGTGTCTATTAAAAGGTAA
1 TTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAA
* * *
78854 TTTCATGAGCTACAATCTTCATGAAGGACTCAAAAG-TAA-TTATGTTTAAATTCAAAAAAATGC
66 TTTGATGATCTACAATCTTCATGAAGGACTCAAAAGCTAATTTATGTTTAAATTCTAAAAAATGC
* *
78917 TTGCTAAATTTGGTCGTTTCGATTGTTAGTCTATTTAATACCATATATAA-TGTTCGATCCACAT
131 TT-CTAAATTTTGT-GTTTTGATTGTTAGTCTATTTAATA-CATATATAATTGTTCG-TCCACAT
* * *
78981 GTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACTATATAATCTACGACTTTCATGAAGA
192 GTCCAATTAAAGTTATTCAAGAGTCGGTTAAAAGGTTACTACATAATCTACGACTTCCATGAAGA
* * * * *
79046 ACCCGAAAG-TTAATTTGATCTATGAGTTTCTTGAAGGGTTTAAAAGAGAATTTTTATGTTTCAA
257 ACCCGAAAGCTCAATTTGATATACGAGTTTCGTGAAGGGTTCAAAAGAGAATTTTTATGTTTCAA
*
79110 GATCTCCATTAACAAATATTTTCTTGTTTGAATTAGTTATCAAATCACCCTCATACTTTTCTATT
322 GATCTCCATTAACAAACATTTTCTTGTTTGAATTAGTTATCAAATCACCCTCATACTTTTCTATT
*
79175 TTATGCTACTTAGTCCTTTACAAATTCTATCTTACTCGATTTAACTCTTCAA
387 TTATACTACTTAGTCCTTTACAAATTCTATCTTA--C-ATTTAACTCTTCAA
* * * * *
79227 TTT-TTTTTAATT-TTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTGTCTATTGAAAGAT
1 TTTATTTTT--TTATTCTTTGTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGT
* * *
79290 AATTTGATGATCTACAA-CTTTTATGAAAGG-TTCAAAAGCTAATTTTTATGTTTCAATTCTAAA
64 AATTTGATGATCTACAATC-TTCATG-AAGGACTCAAAAGCTAA--TTTATGTTTAAATTCTAAA
* * *
79353 AAATGCTTTTGAAATTTTGTGATTTTGATTGATAATCTATTTAATATCATAT
125 AAATGCTTCT-AAATTTTGTG-TTTTGATTGTTAGTCTATTTAATA-CATAT
79405 TATTTTTATC
Statistics
Matches: 523, Mismatches: 71, Indels: 38
0.83 0.11 0.06
Matches are distributed among these distances:
433 49 0.09
434 116 0.22
435 104 0.20
436 18 0.03
437 81 0.15
438 78 0.15
439 17 0.03
441 2 0.00
442 58 0.11
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (435 bp):
TTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAA
TTTGATGATCTACAATCTTCATGAAGGACTCAAAAGCTAATTTATGTTTAAATTCTAAAAAATGC
TTCTAAATTTTGTGTTTTGATTGTTAGTCTATTTAATACATATATAATTGTTCGTCCACATGTCC
AATTAAAGTTATTCAAGAGTCGGTTAAAAGGTTACTACATAATCTACGACTTCCATGAAGAACCC
GAAAGCTCAATTTGATATACGAGTTTCGTGAAGGGTTCAAAAGAGAATTTTTATGTTTCAAGATC
TCCATTAACAAACATTTTCTTGTTTGAATTAGTTATCAAATCACCCTCATACTTTTCTATTTTAT
ACTACTTAGTCCTTTACAAATTCTATCTTACATTTAACTCTTCAA
Found at i:79923 original size:168 final size:168
Alignment explanation
Indices: 79614--79934 Score: 509
Period size: 168 Copynumber: 1.9 Consensus size: 168
79604 TTAATTCAAC
* * * *
79614 CATTGACTAAAAACTTTTTATTGTTTCTATAAAAATGAAATATTAATTCTTCATGAATTTTTGTA
1 CATTAACTAAAAACATTTTATTGTTTCTATAAAAATGAAATACTAATTCCTCATGAATTTTTGTA
*
79679 AATATTTGAGGAAAAGGAAATTGAGAGAAAATGCCAAATGGCATATCTCTTTAGTCTCCTTTAAG
66 AATATTTGAGGAAAAGGAAATTAAGAGAAAATGCCAAATGGCATATCTCTTTAGTCTCCTTTAAG
79744 GATAGGATTAATAGTATGGTATATATGGTATAGACAAG
131 GATAGGATTAATAGTATGGTATATATGGTATAGACAAG
* *
79782 CATTAACTAGAAACATTTTATTGTTTCTATTAAAATGAAATACTAATTCCTCATGAATTTTTGTA
1 CATTAACTAAAAACATTTTATTGTTTCTATAAAAATGAAATACTAATTCCTCATGAATTTTTGTA
* * * *
79847 AATATTTGAGGAAAATGAAATTAAGAGAAAATGGCAAGTGGCATATCTCTTTAGTCTTCTTT-AG
66 AATATTTGAGGAAAAGGAAATTAAGAGAAAATGCCAAATGGCATATCTCTTTAGTCTCCTTTAAG
* *
79911 GATTATGATTAATATTATGGTATA
131 GA-TAGGATTAATAGTATGGTATA
79935 GATGTTTAAG
Statistics
Matches: 139, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
167 4 0.03
168 135 0.97
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (168 bp):
CATTAACTAAAAACATTTTATTGTTTCTATAAAAATGAAATACTAATTCCTCATGAATTTTTGTA
AATATTTGAGGAAAAGGAAATTAAGAGAAAATGCCAAATGGCATATCTCTTTAGTCTCCTTTAAG
GATAGGATTAATAGTATGGTATATATGGTATAGACAAG
Found at i:80477 original size:15 final size:15
Alignment explanation
Indices: 80457--80513 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
80447 CGTTCAAATG
80457 TCGGGTCATTTGGGT
1 TCGGGTCATTTGGGT
*
80472 TCGGGTCAATTCTAGGT
1 TCGGGTC-ATT-TGGGT
*
80489 T-GGGTCATTTTCGGTT
1 TCGGGTCA-TTT-GGGT
80505 TCGGGTCAT
1 TCGGGTCAT
80514 ACGGTTCGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
15 9 0.26
16 14 0.41
17 11 0.32
ACGTcount: A:0.11, C:0.16, G:0.33, T:0.40
Consensus pattern (15 bp):
TCGGGTCATTTGGGT
Found at i:80512 original size:17 final size:15
Alignment explanation
Indices: 80457--80513 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
80447 CGTTCAAATG
*
80457 TCGGGTCATTTGGGT
1 TCGGGTCATTTTGGT
*
80472 TCGGGTCAATTCTAGGT
1 TCGGGTC-ATT-TTGGT
80489 T-GGGTCATTTTCGGTT
1 TCGGGTCATTTT-GG-T
80505 TCGGGTCAT
1 TCGGGTCAT
80514 ACGGTTCGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 1 0.03
15 12 0.34
16 10 0.29
17 12 0.34
ACGTcount: A:0.11, C:0.16, G:0.33, T:0.40
Consensus pattern (15 bp):
TCGGGTCATTTTGGT
Found at i:82141 original size:16 final size:17
Alignment explanation
Indices: 82116--82159 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
82106 CGGGTTGATT
82116 GGGTTCGGGTCA-TTTC
1 GGGTTCGGGTCATTTTC
*
82132 GGGTTTGGGTCATTTTC
1 GGGTTCGGGTCATTTTC
82149 GGGTTCGGGTC
1 GGGTTCGGGTC
82160 GTTTGGATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.05, C:0.16, G:0.41, T:0.39
Consensus pattern (17 bp):
GGGTTCGGGTCATTTTC
Found at i:82150 original size:17 final size:16
Alignment explanation
Indices: 82116--82173 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
82106 CGGGTTGATT
82116 GGGTTCGGGTCATTTC
1 GGGTTCGGGTCATTTC
*
82132 GGGTTTGGGTCATTTTC
1 GGGTTCGGGTCA-TTTC
*
82149 GGGTTCGGGTCGTTT-
1 GGGTTCGGGTCATTTC
*
82164 GGATTCGGGT
1 GGGTTCGGGT
82174 ATCCAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 9 0.24
16 14 0.38
17 14 0.38
ACGTcount: A:0.05, C:0.14, G:0.41, T:0.40
Consensus pattern (16 bp):
GGGTTCGGGTCATTTC
Found at i:103565 original size:23 final size:23
Alignment explanation
Indices: 103539--103588 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
103529 TTTCCTTATT
*
103539 TTCTGTTTTCTCTTCCCTT-TCCC
1 TTCTATTTTCTCTTCCCTTCT-CC
*
103562 TTCTATTTTCTCTTTCCTTCTCC
1 TTCTATTTTCTCTTCCCTTCTCC
103585 TTCT
1 TTCT
103589 TCCTTCTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.02, C:0.36, G:0.02, T:0.60
Consensus pattern (23 bp):
TTCTATTTTCTCTTCCCTTCTCC
Found at i:103594 original size:30 final size:30
Alignment explanation
Indices: 103535--103595 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
103525 TTTTTTTCCT
*
103535 TATTTTCTGTTTTCTCTTCCCTTTCCCTTC
1 TATTTTCTGCTTTCTCTTCCCTTTCCCTTC
*
103565 TATTTTCT-CTTTC-CTTCTCCTTCTTCCTTC
1 TATTTTCTGCTTTCTCTTC-CCTT-TCCCTTC
103595 T
1 T
103596 TCAAAACTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.15
29 8 0.30
30 15 0.56
ACGTcount: A:0.03, C:0.34, G:0.02, T:0.61
Consensus pattern (30 bp):
TATTTTCTGCTTTCTCTTCCCTTTCCCTTC
Found at i:105515 original size:31 final size:31
Alignment explanation
Indices: 105480--105542 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
105470 CAAAAAAAAT
105480 CTAAATTGATCCAATTCTAAAACGTTTAGTA
1 CTAAATTGATCCAATTCTAAAACGTTTAGTA
*
105511 CTAAATTGATCCAATTTTAAAACGTTTAGTA
1 CTAAATTGATCCAATTCTAAAACGTTTAGTA
105542 C
1 C
105543 CTATTTGAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (31 bp):
CTAAATTGATCCAATTCTAAAACGTTTAGTA
Found at i:105582 original size:19 final size:19
Alignment explanation
Indices: 105558--105612 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 19
105548 TGAGCTGGTT
105558 TAAAAATATTTAAAAAAAA
1 TAAAAATATTTAAAAAAAA
*
105577 T-AAAA-ATTCAAAAAAAA
1 TAAAAATATTTAAAAAAAA
105594 TAAAAAAATATTTAAAAAA
1 T--AAAAATATTTAAAAAA
105613 GCCATGTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 12 0.40
18 4 0.13
19 1 0.03
20 4 0.13
21 9 0.30
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAAATATTTAAAAAAAA
Found at i:105740 original size:29 final size:30
Alignment explanation
Indices: 105682--105740 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
105672 ACCTGAAAAA
*
105682 GTACTAAATTGGACCATTAATAAAACGTTTG
1 GTACCAAATTGGACCA-TAATAAAACGTTTG
* *
105713 GTACCAAATTGGACGA-AATAAAAGGTTT
1 GTACCAAATTGGACCATAATAAAACGTTT
105741 CATACTAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.44
31 14 0.56
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.29
Consensus pattern (30 bp):
GTACCAAATTGGACCATAATAAAACGTTTG
Found at i:108597 original size:42 final size:40
Alignment explanation
Indices: 108550--108632 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 40
108540 AGGTGGTAAA
* * *
108550 AGACAAGGGTGAAAAATACAAGTTCGATCCCTCCGGAAACGC
1 AGACAAGGGTG-AAAACACAAGTTCAATCCC-CCGAAAACGC
*
108592 AGACAAGGGTGAAAGCACAAGTTCAATCCCCCGAAAACGC
1 AGACAAGGGTGAAAACACAAGTTCAATCCCCCGAAAACGC
108632 A
1 A
108633 TTTCTTAGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 10 0.27
41 16 0.43
42 11 0.30
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.12
Consensus pattern (40 bp):
AGACAAGGGTGAAAACACAAGTTCAATCCCCCGAAAACGC
Found at i:108702 original size:27 final size:27
Alignment explanation
Indices: 108664--108718 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
108654 CAGACCCGAA
108664 ATGGATTAATCTCAAGCCTAAATAGTT
1 ATGGATTAATCTCAAGCCTAAATAGTT
* *
108691 ATGGATTAATCTCAAGTCTAAATGGTT
1 ATGGATTAATCTCAAGCCTAAATAGTT
108718 A
1 A
108719 GGAATACTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (27 bp):
ATGGATTAATCTCAAGCCTAAATAGTT
Found at i:117443 original size:21 final size:24
Alignment explanation
Indices: 117419--117461 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
117409 TTCACATCTT
117419 ATTTAATT-CTC-T-GTTTTTATA
1 ATTTAATTACTCATAGTTTTTATA
117440 ATTTAATTACTCATAGTTTTTA
1 ATTTAATTACTCATAGTTTTTA
117462 ATTGTCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 1 0.05
24 7 0.37
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.58
Consensus pattern (24 bp):
ATTTAATTACTCATAGTTTTTATA
Done.