Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023272.1 Corchorus olitorius cultivar O-4 contig23305, 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: 78868
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:1370 original size:137 final size:138
Alignment explanation
Indices: 1114--1367 Score: 419
Period size: 137 Copynumber: 1.9 Consensus size: 138
1104 AATAGAAAAA
* *
1114 TTTAAGTTCTTGTTTTATATATATACTTTTTATCCTACTCCAATAAAATTAACTTGTAAATAATT
1 TTTAAGTTCTTG-TTTATATATATACTTTTTATCCGACTCCAACAAAATTAACTTGTAAATAATT
*
1179 AAATATATATATATATAAATTTATTAAGGAATTTTATATCTATCAAAGCAAATAAACACAAATTA
65 AAATATATATATATATAAACTTATTAAGGAATTTTATATCTATCAAAGCAAATAAACACAAATTA
1244 TATATATAC
130 TATATATAC
*
1253 TTTAAGTTCTTG-TTATATATATACTTTTTATCCGACTCCAACAAAATTAACTTGTAAATACTTA
1 TTTAAGTTCTTGTTTATATATATACTTTTTATCCGACTCCAACAAAATTAACTTGTAAATAATTA
*
1317 AGTATATA-A-A-A-AAACTTATTAAGGAATTTTATATCTATCAAAGCAAATAAA
66 AATATATATATATATAAACTTATTAAGGAATTTTATATCTATCAAAGCAAATAAA
1368 TAACTTTCAC
Statistics
Matches: 110, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
133 39 0.35
134 1 0.01
135 1 0.01
136 1 0.01
137 56 0.51
139 12 0.11
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.41
Consensus pattern (138 bp):
TTTAAGTTCTTGTTTATATATATACTTTTTATCCGACTCCAACAAAATTAACTTGTAAATAATTA
AATATATATATATATAAACTTATTAAGGAATTTTATATCTATCAAAGCAAATAAACACAAATTAT
ATATATAC
Found at i:2412 original size:276 final size:276
Alignment explanation
Indices: 1919--2470 Score: 924
Period size: 276 Copynumber: 2.0 Consensus size: 276
1909 CTCCTAGAGC
*
1919 GCACTCTCCTACTCGATCCTCAAATTCAGAGCTCCCCTTTTTGGCATTCATGGAATATCTCTCAT
1 GCACTCTCCTACTCGATCATCAAATTCAGAGCTCCCCTTTTTGGCATTCATGGAATATCTCTCAT
*
1984 TCGTCTCACAGAGCACCATAGTTCGACAGAGGGGCGCACTACCAAATTGAGCATTCTACGATTCA
66 TCGTCTCACAGAGCACCATAGTTCGACAGAGGGGCACACTACCAAATTGAGCATTCTACGATTCA
* * *
2049 ACACTCTCCACATGGAGTATACATTGAGATCGTATACCCTTATGTCCGGCATTATCTAGTCTTGC
131 ACACTCTCCACATGGAGTATACATCGAAATCGTATACCCTTATGTCCAGCATTATCTAGTCTTGC
* * * * * *
2114 AATCAATAAACCTATTTAGCCCAGATCCTCCCAACCCGTCCACCTGACACTCAGTTTCATAGCCT
196 AATCAATAAACCTATTTAGCCCAAATCCTCCCAACCCGCCCACCTAACACGCAGTTTCATAACCG
*
2179 TTTGTGCAATCACTTT
261 TTTGTCCAATCACTTT
*
2195 GCACTCTCCTACTCGATCATCAAATTCAGTGCTCCCCTTTTTGGCATTCATGGAATATCTCTCAT
1 GCACTCTCCTACTCGATCATCAAATTCAGAGCTCCCCTTTTTGGCATTCATGGAATATCTCTCAT
*
2260 TCGTCTCACAGAGCACCATAGTTCGACAGAGGGGCACACTACCAAATTGAGCATTCTACGATTCG
66 TCGTCTCACAGAGCACCATAGTTCGACAGAGGGGCACACTACCAAATTGAGCATTCTACGATTCA
*
2325 ACACTCTCCACATGGAGTATACATCGAAATCGTATACCCTTATGTCTAGCATTATCTAGTCTTGC
131 ACACTCTCCACATGGAGTATACATCGAAATCGTATACCCTTATGTCCAGCATTATCTAGTCTTGC
** * * *
2390 AATCGGTAAACTTATTTAGCCCAAATCCTCCCAACCCGCCCACCTAACGCGCAGTTTTATAACCG
196 AATCAATAAACCTATTTAGCCCAAATCCTCCCAACCCGCCCACCTAACACGCAGTTTCATAACCG
2455 TTTGTCCAATCACTTT
261 TTTGTCCAATCACTTT
2471 AGAATAACTT
Statistics
Matches: 256, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
276 256 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (276 bp):
GCACTCTCCTACTCGATCATCAAATTCAGAGCTCCCCTTTTTGGCATTCATGGAATATCTCTCAT
TCGTCTCACAGAGCACCATAGTTCGACAGAGGGGCACACTACCAAATTGAGCATTCTACGATTCA
ACACTCTCCACATGGAGTATACATCGAAATCGTATACCCTTATGTCCAGCATTATCTAGTCTTGC
AATCAATAAACCTATTTAGCCCAAATCCTCCCAACCCGCCCACCTAACACGCAGTTTCATAACCG
TTTGTCCAATCACTTT
Found at i:8020 original size:21 final size:21
Alignment explanation
Indices: 7994--8073 Score: 103
Period size: 21 Copynumber: 3.9 Consensus size: 21
7984 GGGAGAGGAA
7994 TTTTTTTAAAAAAAAAAGTTC
1 TTTTTTTAAAAAAAAAAGTTC
**
8015 TTTTTTTTTAAAAAAAAGTTC
1 TTTTTTTAAAAAAAAAAGTTC
8036 -TTTTTT--AAAAAAAAGTTC
1 TTTTTTTAAAAAAAAAAGTTC
8054 TTTTTTTATTAAAAAAAAAG
1 TTTTTTTA--AAAAAAAAAG
8074 AAAAGAAAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
18 12 0.23
19 6 0.12
20 6 0.12
21 19 0.37
23 9 0.17
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (21 bp):
TTTTTTTAAAAAAAAAAGTTC
Found at i:8027 original size:18 final size:18
Alignment explanation
Indices: 8006--8068 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
7996 TTTTTAAAAA
8006 AAAAAGTTCTTTTTTTTT
1 AAAAAGTTCTTTTTTTTT
***
8024 AAAAAAAAGTTCTTTTTTAAA
1 ---AAAAAGTTCTTTTTTTTT
8045 AAAAAGTTCTTTTTTTATT
1 AAAAAGTTCTTTTTTT-TT
8064 AAAAA
1 AAAAA
8069 AAAAGAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 15 0.43
19 5 0.14
21 15 0.43
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (18 bp):
AAAAAGTTCTTTTTTTTT
Found at i:8039 original size:17 final size:18
Alignment explanation
Indices: 8003--8059 Score: 87
Period size: 18 Copynumber: 3.0 Consensus size: 18
7993 ATTTTTTTAA
8003 AAAAAAAAGTTCTTTTTTTTT
1 AAAAAAAAGTTC---TTTTTT
8024 AAAAAAAAGTTCTTTTTT
1 AAAAAAAAGTTCTTTTTT
8042 AAAAAAAAGTTCTTTTTT
1 AAAAAAAAGTTCTTTTTT
8060 TATTAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 24 0.67
21 12 0.33
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (18 bp):
AAAAAAAAGTTCTTTTTT
Found at i:14633 original size:31 final size:31
Alignment explanation
Indices: 14598--14767 Score: 160
Period size: 31 Copynumber: 5.5 Consensus size: 31
14588 GGTGTCCGAC
* *
14598 GTGGCATGCCACGTGTATTAAAAAGCGACAT
1 GTGGCACGCCACGTGTATCAAAAAGCGACAT
* *
14629 GTGGCATGCCACGTGTATCAAAAAGTGACAT
1 GTGGCACGCCACGTGTATCAAAAAGCGACAT
* * * *
14660 GTGGCACACCACTTGTACCGAAAAGCGACAT
1 GTGGCACGCCACGTGTATCAAAAAGCGACAT
* **
14691 GTGGCACGCCATGTGTATCAAAAAATGACAT
1 GTGGCACGCCACGTGTATCAAAAAGCGACAT
** ** * * *
14722 GTATCACGCCGTGTGTACCAAAAAGTGACAC
1 GTGGCACGCCACGTGTATCAAAAAGCGACAT
* *
14753 GTGGCATGTCACGTG
1 GTGGCACGCCACGTG
14768 CACAAAAGGA
Statistics
Matches: 112, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 112 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.21
Consensus pattern (31 bp):
GTGGCACGCCACGTGTATCAAAAAGCGACAT
Found at i:14695 original size:62 final size:62
Alignment explanation
Indices: 14617--14767 Score: 187
Period size: 62 Copynumber: 2.4 Consensus size: 62
14607 CACGTGTATT
* *
14617 AAAAAGCGACATGTGGCATGCCACGTGTATCAAAAAGTGACATGTGGCACACCACT-TGTACC
1 AAAAAGCGACATGTGGCATGCCACGTGTATCAAAAAATGACATGTAGCACACC-CTGTGTACC
* * * * * *
14679 GAAAAGCGACATGTGGCACGCCATGTGTATCAAAAAATGACATGTATCACGCCGTGTGTACC
1 AAAAAGCGACATGTGGCATGCCACGTGTATCAAAAAATGACATGTAGCACACCCTGTGTACC
* * *
14741 AAAAAGTGACACGTGGCATGTCACGTG
1 AAAAAGCGACATGTGGCATGCCACGTG
14768 CACAAAAGGA
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 1 0.01
62 73 0.99
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (62 bp):
AAAAAGCGACATGTGGCATGCCACGTGTATCAAAAAATGACATGTAGCACACCCTGTGTACC
Found at i:28076 original size:56 final size:56
Alignment explanation
Indices: 27990--28107 Score: 227
Period size: 56 Copynumber: 2.1 Consensus size: 56
27980 ACCGGCAATC
27990 TCTCCAAATTCAAGGCAAAGTTCTTCTCCATCAAAGCAGATCTGAAGCAAAGTTCT
1 TCTCCAAATTCAAGGCAAAGTTCTTCTCCATCAAAGCAGATCTGAAGCAAAGTTCT
*
28046 TCTCCAATTTCAAGGCAAAGTTCTTCTCCATCAAAGCAGATCTGAAGCAAAGTTCT
1 TCTCCAAATTCAAGGCAAAGTTCTTCTCCATCAAAGCAGATCTGAAGCAAAGTTCT
28102 TCTCCA
1 TCTCCA
28108 TCAACAAGGC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (56 bp):
TCTCCAAATTCAAGGCAAAGTTCTTCTCCATCAAAGCAGATCTGAAGCAAAGTTCT
Found at i:28178 original size:24 final size:23
Alignment explanation
Indices: 28129--28180 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
28119 ACAACAAAGC
28129 AGCAAAGTTCTTCGCAACAACAA
1 AGCAAAGTTCTTCGCAACAACAA
*
28152 AGCAAAGTTCTTTTC-CATCAACAA
1 AGCAAAGTTC--TTCGCAACAACAA
28176 AGCAA
1 AGCAA
28181 CAACAAAGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.38
24 13 0.50
25 3 0.12
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.21
Consensus pattern (23 bp):
AGCAAAGTTCTTCGCAACAACAA
Found at i:28409 original size:42 final size:42
Alignment explanation
Indices: 28342--28434 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
28332 TCAAATCTAG
* *
28342 CAAATCCGGCAACGAGAAATAACAAGCCTTCGGCCATTTCTCT
1 CAAATCC-ACAACGAGAAATAACAAGCCTTCGGCCATTCCTCT
* *
28385 CAAATCCACAACGAGGAATGACAAGCCTTCGGCCATTCCTCT
1 CAAATCCACAACGAGAAATAACAAGCCTTCGGCCATTCCTCT
28427 CAAATCCA
1 CAAATCCA
28435 TCTCATCGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 39 0.85
43 7 0.15
ACGTcount: A:0.33, C:0.32, G:0.15, T:0.19
Consensus pattern (42 bp):
CAAATCCACAACGAGAAATAACAAGCCTTCGGCCATTCCTCT
Found at i:32148 original size:28 final size:29
Alignment explanation
Indices: 32116--32192 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 29
32106 ATATGCGAGA
32116 AAATGAGTATTACTTAGTTTATATAAG-G
1 AAATGAGTATTACTTAGTTTATATAAGAG
* *
32144 AAATG-TTATT-C-T-GATT-TATAAGAG
1 AAATGAGTATTACTTAGTTTATATAAGAG
*
32168 AAGATGAGTTTTACTTAGTTTATAT
1 AA-ATGAGTATTACTTAGTTTATAT
32193 TATTGTACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
23 6 0.16
24 6 0.16
25 4 0.11
26 4 0.11
27 5 0.14
28 6 0.16
29 3 0.08
30 3 0.08
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (29 bp):
AAATGAGTATTACTTAGTTTATATAAGAG
Found at i:42826 original size:15 final size:16
Alignment explanation
Indices: 42793--42832 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
42783 TTACTTTGCT
42793 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
42809 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
42824 TTGCTTTCT
1 TTGTTTTCT
42833 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:43034 original size:28 final size:28
Alignment explanation
Indices: 42994--43078 Score: 118
Period size: 28 Copynumber: 3.0 Consensus size: 28
42984 ACCGATCAGT
*
42994 CATTTAGGGGGCATTTTGGTCATTTTTA
1 CATTCAGGGGGCATTTTGGTCATTTTTA
43022 CATTCAGGGGGCATTTTGGTCATTTTTGCA
1 CATTCAGGGGGCATTTTGGTCATTTTT--A
* *
43052 CATTCA-GGGGTATGTTGGTCATTTTTA
1 CATTCAGGGGGCATTTTGGTCATTTTTA
43079 AGTTCACGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
27 1 0.02
28 26 0.50
29 18 0.35
30 7 0.13
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.44
Consensus pattern (28 bp):
CATTCAGGGGGCATTTTGGTCATTTTTA
Found at i:43222 original size:26 final size:26
Alignment explanation
Indices: 43191--43250 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
43181 CATATTCAGC
43191 TTCATTTAGTAGTTGCATTTTAATCT
1 TTCATTTAGTAGTTGCATTTTAATCT
43217 TTCATTTAGTAGTTGCATTTTAATCT
1 TTCATTTAGTAGTTGCATTTTAATCT
*
43243 TTTATTTA
1 TTCATTTA
43251 AATCAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.57
Consensus pattern (26 bp):
TTCATTTAGTAGTTGCATTTTAATCT
Found at i:51500 original size:21 final size:21
Alignment explanation
Indices: 51471--51523 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
51461 GTCTTCAACT
*
51471 AATCTAATTATTCTACAATAC
1 AATCCAATTATTCTACAATAC
51492 AATCCAATTATTCTACAATAC
1 AATCCAATTATTCTACAATAC
51513 AATCCAATTAT
1 AATCCAATTAT
51524 CAAAACCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (21 bp):
AATCCAATTATTCTACAATAC
Found at i:51927 original size:19 final size:20
Alignment explanation
Indices: 51900--51937 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
51890 TACTATTATT
51900 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
51920 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
51938 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:52160 original size:22 final size:21
Alignment explanation
Indices: 52104--52335 Score: 149
Period size: 22 Copynumber: 10.5 Consensus size: 21
52094 GTCTCTGTGT
*
52104 GGTTATCAAAATTTCATACGA
1 GGTTATCAAAATTTCATAGGA
* * * *
52125 TAGTTATTATAATTTCAGGAGGA
1 -GGTTATCAAAATTTCA-TAGGA
* *
52148 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
52170 GGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
** *
52192 AATTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGG-A
* *
52214 GGTTATCCAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
52236 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* *
52260 GGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGG-A
** * *
52282 GGTTATTGAAATTTTATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* * *
52304 GGTTATCACAATTTTATAGAAA
1 GGTTATCAAAATTTCATAG-GA
52326 GGTTATCAAA
1 GGTTATCAAA
52336 GAGATTATCA
Statistics
Matches: 160, Mismatches: 41, Indels: 18
0.73 0.19 0.08
Matches are distributed among these distances:
21 5 0.03
22 132 0.82
23 6 0.04
24 17 0.11
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:52206 original size:66 final size:66
Alignment explanation
Indices: 52100--52317 Score: 215
Period size: 66 Copynumber: 3.3 Consensus size: 66
52090 TCTTGTCTCT
* * * * *
52100 GTGTGGTTATCAAAATTTCATACGATAGTTATTATAATTTCA-GGAGGAGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATACGATAATTATCAAAATTTCATGG-GAAGGTTATCAAAATTCCA
52164 TA
65 TA
* * *
52166 GTGTGGTTACCAAAATTTCATATGGA-AATTATCAAAATTTCATGGGAAGGTTATCCAAATTTCA
1 GTGTGGTTACCAAAATTTCATA-CGATAATTATCAAAATTTCATGGGAAGGTTATCAAAATTCCA
52230 TA
65 TA
* * * * * ** **
52232 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGGAAGGTTATTGAAATTTT
1 GTGTGGTTACCAAAATTTCATACGAT-A-ATTATCAAAATTTCATGGGAAGGTTATCAAAATTCC
52297 ATA
64 ATA
* *
52300 GTGTGGTTATCACAATTT
1 GTGTGGTTACCAAAATTT
52318 TATAGAAAGG
Statistics
Matches: 130, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
65 3 0.02
66 74 0.57
67 5 0.04
68 48 0.37
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATACGATAATTATCAAAATTTCATGGGAAGGTTATCAAAATTCCAT
A
Found at i:52361 original size:22 final size:22
Alignment explanation
Indices: 52336--52378 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
52326 GGTTATCAAA
52336 GAGATTATCAA-AATGTCATAGC
1 GAGATTAT-AAGAATGTCATAGC
*
52358 GAGATTATAAGAATTTCATAG
1 GAGATTATAAGAATGTCATAG
52379 TATGGTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (22 bp):
GAGATTATAAGAATGTCATAGC
Found at i:52394 original size:22 final size:22
Alignment explanation
Indices: 52369--52761 Score: 99
Period size: 22 Copynumber: 17.5 Consensus size: 22
52359 AGATTATAAG
*
52369 AATTTCATAGTATGGTTAACAA
1 AATTTCATAGTATGGTTATCAA
* * *
52391 AATTTTATTAGGA-GGTTA-CTAG
1 AATTTCA-TAGTATGGTTATC-AA
* *
52413 TATTTCATAGGGA-GGTTATCAA
1 AATTTCATA-GTATGGTTATCAA
* *
52435 ATTTTCATAGTGTGGTTATCAAA
1 AATTTCATAGTATGGTTATC-AA
** *
52458 AATTTTTTAGTGTGGTTATCAA
1 AATTTCATAGTATGGTTATCAA
*
52480 AATTTCATA-TGAAGGTTAT-AA
1 AATTTCATAGT-ATGGTTATCAA
* * * *
52501 AAGTCTCAATTTCA-TAAGGAGTACCAA
1 AA-TTTC-A--T-AGTATGG-TTATCAA
* *
52528 AATTTGATAGTAGAAGGTTATC-A
1 AATTTCATAGT--ATGGTTATCAA
* ** ** *
52551 AATCTCATAGCGTAATTATCGA
1 AATTTCATAGTATGGTTATCAA
*
52573 AATTTCATAGAGATCGGATTATCAA
1 AATTTCATAG-TAT-GG-TTATCAA
* * *
52598 AATTT-ATAGGAAGATTATCAA
1 AATTTCATAGTATGGTTATCAA
* *
52619 AATTTCAAAGCGA-GGTTATCAA
1 AATTTCATAG-TATGGTTATCAA
* * * *
52641 AATTACATAATGTGATTATCAA
1 AATTTCATAGTATGGTTATCAA
* * *
52663 AATTTCATAG-AGGGGTCAACAAA
1 AATTTCATAGTA-TGGTTATC-AA
*
52686 AATTT-ATAG-AGAGGTTATCAA
1 AATTTCATAGTA-TGGTTATCAA
** *
52707 AATTTCATAAAAAGGTTATCAA
1 AATTTCATAGTATGGTTATCAA
* * * * * *
52729 ATTTTCAAAATGTGATTACCAA
1 AATTTCATAGTATGGTTATCAA
52751 AATTTCATAGT
1 AATTTCATAGT
52762 GGTATTTCTG
Statistics
Matches: 275, Mismatches: 68, Indels: 56
0.69 0.17 0.14
Matches are distributed among these distances:
21 33 0.12
22 155 0.56
23 49 0.18
24 7 0.03
25 21 0.08
26 6 0.02
27 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
AATTTCATAGTATGGTTATCAA
Found at i:52664 original size:44 final size:43
Alignment explanation
Indices: 52542--52757 Score: 134
Period size: 44 Copynumber: 4.9 Consensus size: 43
52532 TGATAGTAGA
** * * *
52542 AGGTTATC-AAATCTCATAGCGTAATTATCGAAATTTCATAGAG
1 AGGTTATCAAAAT-TCATAATGTGATTATCAAAATTTCAAAGAG
* * * *
52585 ATCGGATTATCAAAATTTAT-AGGAAGATTATCAAAATTTCAAAGCG
1 A--GG-TTATCAAAATTCATAATG-TGATTATCAAAATTTCAAAGAG
*
52631 AGGTTATCAAAATTACATAATGTGATTATCAAAATTTCATAGAG
1 AGGTTATCAAAATT-CATAATGTGATTATCAAAATTTCAAAGAG
* * * * * * *
52675 GGGTCAACAAAAATTTATAGA-GAGGTTATCAAAATTTCATAA-AA
1 AGGTTATC-AAAATTCATA-ATGTGATTATCAAAATTTCA-AAGAG
* * *
52719 AGGTTATCAAATTTTCAAAATGTGATTACCAAAATTTCA
1 AGGTTATCAAA-ATTCATAATGTGATTATCAAAATTTCA
52758 TAGTGGTATT
Statistics
Matches: 131, Mismatches: 30, Indels: 23
0.71 0.16 0.12
Matches are distributed among these distances:
43 16 0.12
44 72 0.55
45 13 0.10
46 26 0.20
47 4 0.03
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (43 bp):
AGGTTATCAAAATTCATAATGTGATTATCAAAATTTCAAAGAG
Found at i:52707 original size:88 final size:88
Alignment explanation
Indices: 52596--52760 Score: 235
Period size: 88 Copynumber: 1.9 Consensus size: 88
52586 TCGGATTATC
** * *
52596 AAAATTTATAGGAAGATTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATTAT
1 AAAATTTATAGGAAGATTATCAAAATTTCATAA-AAAGGTTATCAAAATTACAAAATGTGATTAC
52660 CAAAATTTCATAGAGGGGTCAACA
65 CAAAATTTCATAGAGGGGTCAACA
* * *
52684 AAAATTTATA-GAGAGGTTATCAAAATTTCATAAAAAGGTTATCAAATTTTCAAAATGTGATTAC
1 AAAATTTATAGGA-AGATTATCAAAATTTCATAAAAAGGTTATCAAAATTACAAAATGTGATTAC
52748 CAAAATTTCATAG
65 CAAAATTTCATAG
52761 TGGTATTTCT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
87 2 0.03
88 64 0.94
89 2 0.03
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.32
Consensus pattern (88 bp):
AAAATTTATAGGAAGATTATCAAAATTTCATAAAAAGGTTATCAAAATTACAAAATGTGATTACC
AAAATTTCATAGAGGGGTCAACA
Found at i:52888 original size:22 final size:22
Alignment explanation
Indices: 52860--53330 Score: 199
Period size: 22 Copynumber: 21.7 Consensus size: 22
52850 TCAGGGAGGA
52860 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
52882 TATCAAAATTTCATGGTTTA-GT
1 TATCAAAATTTCAT-ATGAAGGT
* *
52904 TTTCAAAATTTC--AT-AAGAT
1 TATCAAAATTTCATATGAAGGT
* *
52923 TAACAAAATTTCACAATG-AGGT
1 TATCAAAATTTCA-TATGAAGGT
** * *
52945 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
* *
52967 TATCAAAATTTCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
52989 TATCAAAATTTTATATGAAGGTT
1 TATCAAAATTTCATATGAAGG-T
*
53012 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
53034 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
53056 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
53078 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * ** *
53100 TTTTAAATTTTCATAACATGGT
1 TATCAAAATTTCATATGAAGGT
** * *
53122 TATCAATGTATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
53144 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
53167 TATC--AATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
*
53187 TATCAAAATTTCATAGTG-ATGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
53209 CT-TCAAGATTCCTTA-G-AGGT
1 -TATCAAAATTTCATATGAAGGT
* *
53229 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** **
53251 TAAAAAAATTT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
53272 TATCAAAATATCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* * *
53294 TATTAAAATTACATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
*
53316 TATCAAAATTGCATA
1 TATCAAAATTTCATA
53331 AGGAGATCAT
Statistics
Matches: 339, Mismatches: 79, Indels: 62
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.00
19 14 0.04
20 19 0.06
21 32 0.09
22 238 0.70
23 33 0.10
24 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:52917 original size:44 final size:43
Alignment explanation
Indices: 52775--53325 Score: 191
Period size: 44 Copynumber: 12.8 Consensus size: 43
52765 ATTTCTGGAG
* * *
52775 AGGTTATCAAAATTTCATA-GTATGGTTAAC-AAA-TT-A-GGA
1 AGGTTATCAAAATTTCATATG-AAGGTTATCAAAATTTCATGGT
* * * * * *
52814 AGGTTATTAAACTTTTATTATGGA-GTAATCAAAATTTCA-GGG
1 AGGTTATCAAAATTTCA-TATGAAGGTTATCAAAATTTCATGGT
*
52856 AGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATGGTTT
1 AGGTTATCAAAATTTCATATGAAGGTTATCAAAATTTCATGG--T
* * * ***
52901 A-GTTTTCAAAATTTC--AT-AAGATTAACAAAATTTCACAAT
1 AGGTTATCAAAATTTCATATGAAGGTTATCAAAATTTCATGGT
** * *
52940 GAGGTTATCAAAAAATCATAGGGAGGTTATCAAAATTTCATAAGG-
1 -AGGTTATCAAAATTTCATATGAAGGTTATCAAAATTTCAT--GGT
*
52985 AGGTTATCAAAATTTTATATGAAGGTTTATCAAAATTTCATAGCG-
1 AGGTTATCAAAATTTCATATGAAGG-TTATCAAAATTTCAT-G-GT
* * *
53030 AGGTTATCACAATTTCATAGTG-TGATTATCAAAATTTCA-GAGT
1 AGGTTATCAAAATTTCATA-TGAAGGTTATCAAAATTTCATG-GT
* * * * ***
53073 -GTGATTA-CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAAC
1 AG-G-TTATC-AA-AATTTCATATGAAGGTTATCAAAATTTCATGGT
** * * * *
53117 ATGGTTATCAATGTATCATATGGAGGTTATCAACATCTCATAGTGT
1 A-GGTTATCAAAATTTCATATGAAGGTTATCAAAATTTCAT-G-GT
* *
53163 TGGTTATC--AATTTCAT-TGGGAA-GTTATCAAAATTTCATAGT
1 AGGTTATCAAAATTTCATAT--GAAGGTTATCAAAATTTCATGGT
* * * * * * *
53204 GATGTCT-TCAAGATTCCTTA-G-AGGTTAACAAAATTTCATAAGA
1 -AGGT-TATCAAAATTTCATATGAAGGTTATCAAAATTTCAT-GGT
** ** * *
53247 AGGTTAAAAAAATTT-ATAAAAAGGTTATCAAAATATCATAGT
1 AGGTTATCAAAATTTCATATGAAGGTTATCAAAATTTCATGGT
* * * *
53289 ATCGTTATTAAAATTACATAGGAAGGTTATCAAAATT
1 A-GGTTATCAAAATTTCATATGAAGGTTATCAAAATT
53326 GCATAAGGAG
Statistics
Matches: 372, Mismatches: 94, Indels: 87
0.67 0.17 0.16
Matches are distributed among these distances:
39 19 0.05
40 6 0.02
41 41 0.11
42 67 0.18
43 55 0.15
44 135 0.36
45 46 0.12
46 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (43 bp):
AGGTTATCAAAATTTCATATGAAGGTTATCAAAATTTCATGGT
Found at i:53201 original size:43 final size:45
Alignment explanation
Indices: 53118--53204 Score: 117
Period size: 43 Copynumber: 2.0 Consensus size: 45
53108 TTTCATAACA
* *
53118 TGGTTATCAATGTATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAATGTATCATATGGAAGTTATCAAAATCTCATAGTGT
*
53163 TGGTTATCAAT-T-TCAT-TGGGAAGTTATCAAAATTTCATAGTG
1 TGGTTATCAATGTATCATAT-GGAAGTTATCAAAATCTCATAGTG
53205 ATGTCTTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 1 0.03
43 25 0.66
44 1 0.03
45 11 0.29
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (45 bp):
TGGTTATCAATGTATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:53279 original size:21 final size:22
Alignment explanation
Indices: 53225--53286 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 22
53215 GATTCCTTAG
*
53225 AGGTTAACAAAATTTCATAAGA
1 AGGTTAACAAAATTTCATAAAA
*
53247 AGGTTAAAAAAATTT-ATAAAA
1 AGGTTAACAAAATTTCATAAAA
* *
53268 AGGTTATCAAAATATCATA
1 AGGTTAACAAAATTTCATA
53287 GTATCGTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.29
Consensus pattern (22 bp):
AGGTTAACAAAATTTCATAAAA
Found at i:53457 original size:3 final size:3
Alignment explanation
Indices: 53449--53517 Score: 120
Period size: 3 Copynumber: 22.3 Consensus size: 3
53439 ATAAAACTAG
53449 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53497 TAT TAT TAT ATAT ATAT TAT T
1 TAT TAT TAT -TAT -TAT TAT T
53518 TTTAGTTACC
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 58 0.89
4 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:54412 original size:18 final size:18
Alignment explanation
Indices: 54389--54423 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54379 ACAAAAATTG
54389 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
54407 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
54424 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:54576 original size:22 final size:20
Alignment explanation
Indices: 54549--54588 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
54539 TTTATAATTT
54549 TTATTAATAATATATATTATTA
1 TTATTAATAA-ATA-ATTATTA
54571 TTATTAATAAATAATTAT
1 TTATTAATAAATAATTAT
54589 ATAATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATTAATAAATAATTATTA
Found at i:54595 original size:15 final size:14
Alignment explanation
Indices: 54570--54599 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
54560 ATATATTATT
54570 ATTATTAATAAATA
1 ATTATTAATAAATA
54584 ATTATATAATAAATA
1 ATTAT-TAATAAATA
54599 A
1 A
54600 ACGTTCGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTATTAATAAATA
Found at i:54660 original size:35 final size:35
Alignment explanation
Indices: 54621--54695 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 35
54611 TTATATAAAC
54621 GAACACTTAAATGAACAATAAACGAGTC-TGTGCGT
1 GAACACTTAAATGAACAATAAACGAG-CATGTGCGT
* *
54656 GAACACTTAAATGAACAATAAGCGAGCATGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCATGTGCGT
54691 GAACA
1 GAACA
54696 TAAACGAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 1 0.03
35 36 0.97
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.21
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCATGTGCGT
Found at i:56778 original size:1 final size:1
Alignment explanation
Indices: 56772--56797 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
56762 TCTACTGCTC
56772 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
56798 AATGCTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:59167 original size:30 final size:31
Alignment explanation
Indices: 59125--59192 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
59115 AATTTCTCAA
59125 ACCCGA-CCAAATAACCTGAGAT-AAAAGTG
1 ACCCGACCCAAATAACCTGAGATAAAAAGTG
* *
59154 ACCCGACCCAAATAGCCTTAGATAAAAAGTG
1 ACCCGACCCAAATAACCTGAGATAAAAAGTG
59185 ACCCGACC
1 ACCCGACC
59193 GGTACTCACC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 6 0.17
30 14 0.40
31 15 0.43
ACGTcount: A:0.41, C:0.29, G:0.16, T:0.13
Consensus pattern (31 bp):
ACCCGACCCAAATAACCTGAGATAAAAAGTG
Found at i:59295 original size:23 final size:23
Alignment explanation
Indices: 59265--59312 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
59255 TCTGCAGTCG
59265 TTAGCAATTTAGGCATATATATC
1 TTAGCAATTTAGGCATATATATC
59288 TTAGCAATTTAGGCATATATATC
1 TTAGCAATTTAGGCATATATATC
59311 TT
1 TT
59313 CGTTGAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (23 bp):
TTAGCAATTTAGGCATATATATC
Found at i:72440 original size:12 final size:12
Alignment explanation
Indices: 72425--72450 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
72415 ACTTTTAAAC
72425 TTGATAATAATA
1 TTGATAATAATA
72437 TTGATAATAATA
1 TTGATAATAATA
72449 TT
1 TT
72451 TTTATAAGTT
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:0.00, G:0.08, T:0.46
Consensus pattern (12 bp):
TTGATAATAATA
Found at i:74640 original size:3 final size:3
Alignment explanation
Indices: 74632--74669 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
74622 CTGTTGCCAC
74632 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
74670 GGTTTTCAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:77856 original size:31 final size:31
Alignment explanation
Indices: 77818--77880 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
77808 TGACAATAGG
*
77818 ATCTAACTCATCTAAGAAGAGCAAAAGGCCT
1 ATCTAACTCATCTAAGAAAAGCAAAAGGCCT
77849 ATCTAACTCATCTAAGAAAAGCAAAAGGCCT
1 ATCTAACTCATCTAAGAAAAGCAAAAGGCCT
77880 A
1 A
77881 GATGAACATA
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:0.44, C:0.22, G:0.14, T:0.19
Consensus pattern (31 bp):
ATCTAACTCATCTAAGAAAAGCAAAAGGCCT
Done.