Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018196.1 Corchorus olitorius cultivar O-4 contig18229, 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: 95723
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:291 original size:154 final size:154
Alignment explanation
Indices: 1--903 Score: 1164
Period size: 154 Copynumber: 5.9 Consensus size: 154
* * **
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGCTC-GTTGGAACACTTGCAATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* *
64 TGTGCCTATCGAGGCCCATTAGT-TC-TGTTTGAATTGTCTTCGATTTGGCAAACCTCAATGCTT
66 TGGGCCTATCGAGGCCCATTAGTGACGT-TTTGAATTGTCTTCGATTTGGCAAACCTCAATGCTT
127 TTCTTTCCATTGTTTATGGCCTAAC
130 TTCTTTCCATTGTTTATGGCCTAAC
* * * **
152 TATAATCATTTAGGTGAGATTCGTCCTCTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* * * * * * * *
217 TGGGCTTATTGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGAC-AACCTTCGATGCCT
66 TGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATTGTCTTCGATTTGGCAAACC-TCAATGCTT
*
281 TTCTTTCCATTGTTTATTGCCTAAC
130 TTCTTTCCATTGTTTATGGCCTAAC
* * **
306 TATAATCACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCGTTTGGAACACTTGCAATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
** ** * *
371 TGTACCTATCGAGGCCCATTAGTTTCATTTTGAATTGTCTTCGATTTGGCAAACCACAATGCTTT
66 TGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATTGTCTTCGATTTGGCAAACCTCAATGCTTT
* *
436 TCTTTCCATTGTGTACGGCCTAAC
131 TCTTTCCATTGTTTATGGCCTAAC
* * *
460 TATAATTATTTTGGTGAGATTAGT-C-CTCGGCAGTTTTTAGCTCATTTGGAACACTTGTTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* * * ** *
523 TGGGCCTATCGAGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGAC-AACCTTTGATGCGT
66 TGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATTGTCTTCGATTTGGCAAACC-TCAATGCTT
587 TTCTTTCCATTGTTTATGGCCTAAC
130 TTCTTTCCATTGTTTATGGCCTAAC
* *
612 TATAATCACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCAATTGGAACACTTGTTATTT
1 TATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* * * *
677 TGGGCCTTTCG-GAGCCCATCA--GATCTGTATTGAATTGTCTTCGATTTGGCAAACCTCAATTC
66 TGGGCCTATCGAG-GCCCATTAGTGA-C-GTTTTGAATTGTCTTCGATTTGGCAAACCTCAATGC
*
739 TTTTCTTTCCATTGTTGATGGCCTAAC
128 TTTTCTTTCCATTGTTTATGGCCTAAC
* * *
766 TATAATCATTTTGGTGAGATTAGTCCATTGTTGAAGTTTTTAGCTCAATTGGAACACTTGTTATT
1 TATAATCATTTTGGTGAGATTAGTCCACTG-GGAAGTTTTTAGCTCATTTGGAACACTTGTTATT
* * *
831 TTGTGCCTATCGAGGCCCATTAGT-TCTGTTTTGTATTGTCTTCGATTTGGCAAACCTCAATGCT
65 TTGGGCCTATCGAGGCCCATTAGTGAC-GTTTTGAATTGTCTTCGATTTGGCAAACCTCAATGCT
895 TTTCTTTCC
129 TTTCTTTCC
904 TGATATGAAT
Statistics
Matches: 644, Mismatches: 91, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
151 35 0.05
152 136 0.21
153 42 0.07
154 326 0.51
155 104 0.16
156 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
TATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
TGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATTGTCTTCGATTTGGCAAACCTCAATGCTTT
TCTTTCCATTGTTTATGGCCTAAC
Found at i:556 original size:306 final size:303
Alignment explanation
Indices: 1--903 Score: 1321
Period size: 306 Copynumber: 2.9 Consensus size: 303
* *
1 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTAGCTCGTTGGAACACTTGCAATTTT
1 TATAATCACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCGTTGGAACACTTGCAATTTT
65 GTGCCTATCGAGGCCCATTAGTTCTGTTTGAATTGTCTTCGATTTGGCAAACCTCAATGCTTTTC
66 GTGCCTATCGAGGCCCATTAGTTCTGTTTGAATTGTCTTCGATTTGGCAAACCTCAATGCTTTTC
* * *
130 TTTCCATTGTTTATGGCCTAACTATAATCATTTAGGTGAGATTCGTCCTCTATGAAGTTTTTAGC
131 TTTCCATTG-TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCTC--GGAAGTTTTTAGC
* * *
195 TCATTTGGAACACTTGTTATTTTGGGCTTATTGGGGACCATTAGTGACGTTTTGAATCGTCTTCG
193 TCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAATCGTCTTCG
*
260 ATTTGACAACCTTCGATGCCTTTCTTTCCATTGTTTATTGCCTAAC
258 ATTTGACAACCTTCGATGCCTTTCTTTCCATTGTTTATGGCCTAAC
306 TATAATCACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCGTTTGGAACACTTGCAATTT
1 TATAATCACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCG-TTGGAACACTTGCAATTT
* *
371 TGTACCTATCGAGGCCCATTAGTTTCAT-TTTGAATTGTCTTCGATTTGGCAAACCACAATGCTT
65 TGTGCCTATCGAGGCCCATTAG-TTC-TGTTTGAATTGTCTTCGATTTGGCAAACCTCAATGCTT
* * *
435 TTCTTTCCATTGTGTACGGCCTAACTATAATTATTTTGGTGAGATTAGTCCTCGGCAGTTTTTAG
128 TTCTTTCCATTGT-TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCTCGGAAGTTTTTAG
500 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAATCGTCTTC
192 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAATCGTCTTC
* *
565 GATTTGACAACCTTTGATGCGTTTCTTTCCATTGTTTATGGCCTAAC
257 GATTTGACAACCTTCGATGCCTTTCTTTCCATTGTTTATGGCCTAAC
* **
612 TATAATCACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCAATTGGAACACTTGTTATTT
1 TATAATCACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTC-GTTGGAACACTTGCAATTT
* * * * *
677 TGGGCCTTTCG-GAGCCCATCAGATCTGTATTGAATTGTCTTCGATTTGGCAAACCTCAATTCTT
65 TGTGCCTATCGAG-GCCCATTAGTTCTGT-TTGAATTGTCTTCGATTTGGCAAACCTCAATGCTT
*
741 TTCTTTCCATTGTTGATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCATTGTTGAAGTTTT
128 TTCTTTCCATTGTT-ATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC-TCG--GAAGTTTT
* * * * * *
806 TAGCTCAATTGGAACACTTGTTATTTTGTGCCTATCGAGGCCCATTAGT-TCTGTTTTGTATTGT
189 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGACCATTAGTGAC-GTTTTGAATCGT
* * *
870 CTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCC
253 CTTCGATTTGAC-AACCTTCGATGCCTTTCTTTCC
904 TGATATGAAT
Statistics
Matches: 543, Mismatches: 40, Indels: 26
0.89 0.07 0.04
Matches are distributed among these distances:
304 1 0.00
305 38 0.07
306 283 0.52
307 42 0.08
308 86 0.16
309 89 0.16
310 4 0.01
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (303 bp):
TATAATCACTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCGTTGGAACACTTGCAATTTT
GTGCCTATCGAGGCCCATTAGTTCTGTTTGAATTGTCTTCGATTTGGCAAACCTCAATGCTTTTC
TTTCCATTGTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCTCGGAAGTTTTTAGCTCA
TTTGGAACACTTGTTATTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAATCGTCTTCGATT
TGACAACCTTCGATGCCTTTCTTTCCATTGTTTATGGCCTAAC
Found at i:6600 original size:15 final size:16
Alignment explanation
Indices: 6563--6593 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6553 TGGTCCGGCG
6563 GTTTGAACGTTGAAAA
1 GTTTGAACGTTGAAAA
6579 GTTTGAA-GTTGAAAA
1 GTTTGAACGTTGAAAA
6594 TGTTGAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (16 bp):
GTTTGAACGTTGAAAA
Found at i:11161 original size:25 final size:26
Alignment explanation
Indices: 11133--11182 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
11123 TGTTTATGGT
*
11133 TTTTCCTAGTAGGATTAGG-TTTTAC
1 TTTTCCTAGTAGAATTAGGATTTTAC
**
11158 TTTTCCTCTTAGAATTAGGATTTTA
1 TTTTCCTAGTAGAATTAGGATTTTA
11183 AGTTAAGCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (26 bp):
TTTTCCTAGTAGAATTAGGATTTTAC
Found at i:11940 original size:45 final size:45
Alignment explanation
Indices: 11891--12020 Score: 190
Period size: 45 Copynumber: 2.9 Consensus size: 45
11881 AGATCTTTTC
* *
11891 TTTGTTTGTAAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGGA
1 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGAA
11936 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGAA
1 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGAA
* * * *
11981 TTTGTTTGTGAGGGAGAGGAGTCTGAGTTTG-TCATTGATG
1 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTC-TTGATG
12021 GAAAAAGATT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
44 2 0.03
45 76 0.97
ACGTcount: A:0.24, C:0.05, G:0.30, T:0.42
Consensus pattern (45 bp):
TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGAA
Found at i:12518 original size:25 final size:26
Alignment explanation
Indices: 12490--12539 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
12480 TGTTTATGGT
*
12490 TTTTCCTAGTAGGATTAGG-TTTTAC
1 TTTTCCTAGTAGAATTAGGATTTTAC
**
12515 TTTTCCTCTTAGAATTAGGATTTTA
1 TTTTCCTAGTAGAATTAGGATTTTA
12540 AGTTAAGCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (26 bp):
TTTTCCTAGTAGAATTAGGATTTTAC
Found at i:13542 original size:10 final size:10
Alignment explanation
Indices: 13527--13557 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
13517 TAACACAAGT
13527 AAGAAAAAAA
1 AAGAAAAAAA
13537 AAG-AAAAAA
1 AAGAAAAAAA
13546 AAGAAAAAAA
1 AAGAAAAAAA
13556 AA
1 AA
13558 AGATGCTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:13545 original size:9 final size:9
Alignment explanation
Indices: 13531--13556 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
13521 ACAAGTAAGA
13531 AAAAAAAAG
1 AAAAAAAAG
13540 AAAAAAAAG
1 AAAAAAAAG
13549 AAAAAAAA
1 AAAAAAAA
13557 AAGATGCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:18036 original size:17 final size:17
Alignment explanation
Indices: 17991--18041 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
17981 AGGTTGATTC
*
17991 CGGCAGCAGGAATCGCG
1 CGGCAGCAGGAATCACG
*
18008 CGGCTGCAGGAATCACG
1 CGGCAGCAGGAATCACG
* *
18025 TGGCAGCGGGAATCACG
1 CGGCAGCAGGAATCACG
18042 AAACGACCGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.24, C:0.27, G:0.39, T:0.10
Consensus pattern (17 bp):
CGGCAGCAGGAATCACG
Found at i:21855 original size:72 final size:72
Alignment explanation
Indices: 21735--21940 Score: 342
Period size: 72 Copynumber: 2.9 Consensus size: 72
21725 CCCATGGTCC
* * *
21735 TCTTCTCCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGTAGTCCTTCGCACAATCCTTGC
1 TCTTCTACATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
21800 ATGATCA
66 ATGATCA
* * *
21807 TCTTCTTCGTTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCACACAATCCTTAC
1 TCTTCTACATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
21872 ATGATCA
66 ATGATCA
21879 TCTT-TCACATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCT
1 TCTTCT-ACATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCT
21941 CACTACTCCC
Statistics
Matches: 125, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
71 1 0.01
72 124 0.99
ACGTcount: A:0.20, C:0.30, G:0.19, T:0.32
Consensus pattern (72 bp):
TCTTCTACATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
ATGATCA
Found at i:22548 original size:16 final size:16
Alignment explanation
Indices: 22527--22558 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
22517 AATCCTTCCA
22527 GCAGCAGAATGCTACC
1 GCAGCAGAATGCTACC
*
22543 GCAGCAGAATTCTACC
1 GCAGCAGAATGCTACC
22559 ACAAGATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (16 bp):
GCAGCAGAATGCTACC
Found at i:22640 original size:29 final size:29
Alignment explanation
Indices: 22560--22640 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
22550 AATTCTACCA
* * *
22560 CAAGAT-ATTGCCACAACATAATGTTATTG
1 CAAGATCA-TGCCACAGCAAAATGTTAGTG
* * * *
22589 CAAAATCTTGCTACAGGAAAATGTTAGTG
1 CAAGATCATGCCACAGCAAAATGTTAGTG
*
22618 CAAGATCATGCCACAGCAGAATG
1 CAAGATCATGCCACAGCAAAATG
22641 CTACCGCAGC
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (29 bp):
CAAGATCATGCCACAGCAAAATGTTAGTG
Found at i:22658 original size:45 final size:45
Alignment explanation
Indices: 22608--22700 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 45
22598 GCTACAGGAA
* * *
22608 AATGTTAGTGCAAGATCATGCCAC-AGCAGAATGCTACCGCAGCAG
1 AATGTTACTGCAAAATCATGCCACTAG-AGAATGCTACCACAGCAG
* *
22653 AATGTTACTGCAAAATCTTGCCACTAGAGAATGTTACCACAGCAG
1 AATGTTACTGCAAAATCATGCCACTAGAGAATGCTACCACAGCAG
22698 AAT
1 AAT
22701 ATCACTGTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 40 0.95
46 2 0.05
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (45 bp):
AATGTTACTGCAAAATCATGCCACTAGAGAATGCTACCACAGCAG
Found at i:22699 original size:16 final size:16
Alignment explanation
Indices: 22628--22700 Score: 55
Period size: 16 Copynumber: 4.8 Consensus size: 16
22618 CAAGATCATG
*
22628 CCACAGCAGAATGCTA
1 CCACAGCAGAATGTTA
*
22644 CCGCAGCAGAATGTT-
1 CCACAGCAGAATGTTA
* * * *
22659 --ACTGCAAAATCTTG
1 CCACAGCAGAATGTTA
22673 CCACTAG-AGAATGTTA
1 CCAC-AGCAGAATGTTA
22689 CCACAGCAGAAT
1 CCACAGCAGAAT
22701 ATCACTGTAG
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
13 9 0.21
15 2 0.05
16 30 0.71
17 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (16 bp):
CCACAGCAGAATGTTA
Found at i:28879 original size:30 final size:25
Alignment explanation
Indices: 28800--28866 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
28790 CTTAGATAAA
28800 AAACTATAAGAAATCACAAA-A--C
1 AAACTATAAGAAATCACAAACATGC
*
28822 CAACTATAAGAAATCACAAACATGC
1 AAACTATAAGAAATCACAAACATGC
28847 AAACTATAAGAAATCACAAA
1 AAACTATAAGAAATCACAAA
28867 AACCACATGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
22 19 0.47
23 1 0.03
25 20 0.50
ACGTcount: A:0.60, C:0.19, G:0.06, T:0.15
Consensus pattern (25 bp):
AAACTATAAGAAATCACAAACATGC
Found at i:32911 original size:14 final size:15
Alignment explanation
Indices: 32888--32919 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
32878 AGGAAAATGA
32888 AAAAGTAAAAAAAAG
1 AAAAGTAAAAAAAAG
32903 AAAAG-AAAAAAAAG
1 AAAAGTAAAAAAAAG
32917 AAA
1 AAA
32920 CTCAACTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAGTAAAAAAAAG
Found at i:32913 original size:22 final size:22
Alignment explanation
Indices: 32870--32912 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
32860 TTACTGTTTG
* *
32870 GTAAAAATAGGAAAATGAAAAA
1 GTAAAAAAAAGAAAATGAAAAA
32892 GTAAAAAAAAGAAAA-GAAAAA
1 GTAAAAAAAAGAAAATGAAAAA
32913 AAAGAAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.09
Consensus pattern (22 bp):
GTAAAAAAAAGAAAATGAAAAA
Found at i:45626 original size:30 final size:30
Alignment explanation
Indices: 45592--45653 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
45582 AATTCCATGG
45592 CCCAAGTCTTAAATCAGATTGGCCCGCTGC
1 CCCAAGTCTTAAATCAGATTGGCCCGCTGC
45622 CCCAAGTCTTAAATCAGATTGGCCCGCTGC
1 CCCAAGTCTTAAATCAGATTGGCCCGCTGC
45652 CC
1 CC
45654 TAAGCCTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (30 bp):
CCCAAGTCTTAAATCAGATTGGCCCGCTGC
Found at i:49283 original size:40 final size:40
Alignment explanation
Indices: 49223--49302 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
49213 GAGAGATTAC
* * *
49223 AATTCTAGATAATTAAGGGGGATATGATTTATTATAACAT
1 AATTATAGATAATTAAGGGGGATAGGATTTATCATAACAT
49263 AATTATAGATAATTAAGGGGGATAGGATTTATCATAACAT
1 AATTATAGATAATTAAGGGGGATAGGATTTATCATAACAT
49303 TTATGTGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (40 bp):
AATTATAGATAATTAAGGGGGATAGGATTTATCATAACAT
Found at i:55848 original size:15 final size:15
Alignment explanation
Indices: 55818--55874 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
55808 TTACTTTGCT
55818 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
55834 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
55849 TTATTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
55864 TTGCTTTCTGT
1 TTGTTTTCTGT
55875 CAATCTCTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 29 0.76
16 9 0.24
ACGTcount: A:0.14, C:0.09, G:0.12, T:0.65
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:64367 original size:18 final size:19
Alignment explanation
Indices: 64330--64368 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
64320 CTCAACCTCT
64330 CTTAGCCCAAATCACAAACA
1 CTTAGCCCAAAT-ACAAACA
64350 CTTAGCCCAAAT-CAAACA
1 CTTAGCCCAAATACAAACA
64368 C
1 C
64369 AAAATACCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
20 12 0.63
ACGTcount: A:0.44, C:0.36, G:0.05, T:0.15
Consensus pattern (19 bp):
CTTAGCCCAAATACAAACA
Found at i:64982 original size:25 final size:24
Alignment explanation
Indices: 64947--65145 Score: 335
Period size: 25 Copynumber: 8.0 Consensus size: 24
64937 ATGGTTCAAC
64947 TCAAAGCCCACATCTATGTGGCAA
1 TCAAAGCCCACATCTATGTGGCAA
64971 TGCAAAGCCCACATCTATGTGGCAA
1 T-CAAAGCCCACATCTATGTGGCAA
64996 CTCAAAGCCCACATCTATGTGGCAA
1 -TCAAAGCCCACATCTATGTGGCAA
65021 CTCAAAGCCCACATCTATGTGGCAA
1 -TCAAAGCCCACATCTATGTGGCAA
65046 TACAAAGCCCACATCTATGTGGCAA
1 T-CAAAGCCCACATCTATGTGGCAA
65071 TGCAAAGCCCACATCTATGTGGCAA
1 T-CAAAGCCCACATCTATGTGGCAA
65096 CTCAAAGCCCACATCTATGTGGCAA
1 -TCAAAGCCCACATCTATGTGGCAA
65121 TACAAAGCCCACATCTATGTGGCAA
1 T-CAAAGCCCACATCTATGTGGCAA
65146 AGCATCATGC
Statistics
Matches: 169, Mismatches: 1, Indels: 9
0.94 0.01 0.05
Matches are distributed among these distances:
24 3 0.02
25 164 0.97
26 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (24 bp):
TCAAAGCCCACATCTATGTGGCAA
Found at i:65066 original size:75 final size:75
Alignment explanation
Indices: 64943--65145 Score: 381
Period size: 75 Copynumber: 2.7 Consensus size: 75
64933 CCCCATGGTT
*
64943 CAACTCAAAGCCCACATCTATGTGGCAATGCAAAGCCCACATCTATGTGGCAACT-CAAAGCCCA
1 CAACTCAAAGCCCACATCTATGTGGCAATACAAAGCCCACATCTATGTGGCAA-TGCAAAGCCCA
65007 CATCTATGTGG
65 CATCTATGTGG
65018 CAACTCAAAGCCCACATCTATGTGGCAATACAAAGCCCACATCTATGTGGCAATGCAAAGCCCAC
1 CAACTCAAAGCCCACATCTATGTGGCAATACAAAGCCCACATCTATGTGGCAATGCAAAGCCCAC
65083 ATCTATGTGG
66 ATCTATGTGG
65093 CAACTCAAAGCCCACATCTATGTGGCAATACAAAGCCCACATCTATGTGGCAA
1 CAACTCAAAGCCCACATCTATGTGGCAATACAAAGCCCACATCTATGTGGCAA
65146 AGCATCATGC
Statistics
Matches: 126, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
74 1 0.01
75 125 0.99
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (75 bp):
CAACTCAAAGCCCACATCTATGTGGCAATACAAAGCCCACATCTATGTGGCAATGCAAAGCCCAC
ATCTATGTGG
Found at i:67138 original size:16 final size:15
Alignment explanation
Indices: 67100--67141 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
67090 ACAGAGATTG
*
67100 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
67115 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
67130 ACTAGAAAACAA
1 AC-AGAAAACAA
67142 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:70437 original size:21 final size:21
Alignment explanation
Indices: 70411--70460 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
70401 TGAATGGTGA
70411 TGGCACGGGCATAG-CCGATGG
1 TGGCACGGG-ATAGACCGATGG
* *
70432 TGGCACGGGATTGACCGGTGG
1 TGGCACGGGATAGACCGATGG
70453 TGGCACGG
1 TGGCACGG
70461 TGAATGGGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.16, C:0.22, G:0.46, T:0.16
Consensus pattern (21 bp):
TGGCACGGGATAGACCGATGG
Found at i:70670 original size:11 final size:11
Alignment explanation
Indices: 70654--70711 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
70644 CTAGCCGGGC
70654 ATGAGGCTTGG
1 ATGAGGCTTGG
70665 ATGAGGCTT-G
1 ATGAGGCTTGG
*
70675 A-GATGGC-GGG
1 ATGA-GGCTTGG
70685 CATGAGGCTTGG
1 -ATGAGGCTTGG
70697 ATGAGGCTTGAG
1 ATGAGGCTTG-G
70709 ATG
1 ATG
70712 GCGGGCATGG
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 2 0.05
10 6 0.15
11 23 0.59
12 8 0.21
ACGTcount: A:0.21, C:0.10, G:0.45, T:0.24
Consensus pattern (11 bp):
ATGAGGCTTGG
Found at i:70688 original size:32 final size:32
Alignment explanation
Indices: 70649--70720 Score: 144
Period size: 32 Copynumber: 2.2 Consensus size: 32
70639 CGATCCTAGC
70649 CGGGCATGAGGCTTGGATGAGGCTTGAGATGG
1 CGGGCATGAGGCTTGGATGAGGCTTGAGATGG
70681 CGGGCATGAGGCTTGGATGAGGCTTGAGATGG
1 CGGGCATGAGGCTTGGATGAGGCTTGAGATGG
70713 CGGGCATG
1 CGGGCATG
70721 GCCGGGCATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.18, C:0.14, G:0.47, T:0.21
Consensus pattern (32 bp):
CGGGCATGAGGCTTGGATGAGGCTTGAGATGG
Found at i:71141 original size:21 final size:21
Alignment explanation
Indices: 71115--71157 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
71105 GGAGATGCCA
*
71115 AAGATGCCATTTGATCCATTG
1 AAGATGCCATTAGATCCATTG
*
71136 AAGATGCCATTAGGTCCATTG
1 AAGATGCCATTAGATCCATTG
71157 A
1 A
71158 CAAGAGCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (21 bp):
AAGATGCCATTAGATCCATTG
Found at i:74720 original size:2 final size:2
Alignment explanation
Indices: 74715--74773 Score: 86
Period size: 2 Copynumber: 30.0 Consensus size: 2
74705 ATAAGTCCAA
*
74715 AT AT AT -T AT AT AT AT AT AT A- AT AT AT AT GAT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
74756 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
74774 TATTCGTATA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
1 2 0.04
2 48 0.92
3 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:74731 original size:38 final size:38
Alignment explanation
Indices: 74689--74777 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 38
74679 ATATATAACT
74689 TATATATAATATTTAT-ATAAGTCCAAATATAT-TATATA
1 TATATATAATATTTATGATAAGT--AAATATATATATATA
* * *
74727 TATATATAATATATATGATATGTATATATATATATATA
1 TATATATAATATTTATGATAAGTAAATATATATATATA
*
74765 TATATATATTATT
1 TATATATAATATT
74778 CGTATAATAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
37 7 0.16
38 32 0.73
39 5 0.11
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (38 bp):
TATATATAATATTTATGATAAGTAAATATATATATATA
Found at i:80908 original size:21 final size:21
Alignment explanation
Indices: 80882--81016 Score: 211
Period size: 21 Copynumber: 6.4 Consensus size: 21
80872 TGCTAGGAGT
80882 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
80903 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
80924 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
80945 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
80966 TCATTGGAGAAGGTTCCAAAC
1 TCATTGGAGAAGGTTCCAAGC
* *
80987 TCGTTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
81008 TCATTGGAG
1 TCATTGGAG
81017 TTGCCTAAGA
Statistics
Matches: 106, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
20 4 0.04
21 100 0.94
22 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:82899 original size:15 final size:15
Alignment explanation
Indices: 82879--82907 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
82869 TGGAGGTTCG
82879 AAATCAACAAGCTCA
1 AAATCAACAAGCTCA
82894 AAATCAACAAGCTC
1 AAATCAACAAGCTC
82908 CACTTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.28, G:0.07, T:0.14
Consensus pattern (15 bp):
AAATCAACAAGCTCA
Found at i:83541 original size:33 final size:33
Alignment explanation
Indices: 83504--83574 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
83494 TGTTTTTAGC
83504 GATGATACTAAAACTAATTTGA-GTGTTGTTTGT
1 GATGATACTAAAACT-ATTTGAGGTGTTGTTTGT
* *
83537 GATGATACTAAATCTATTTTAGGTGTTGTTTGT
1 GATGATACTAAAACTATTTGAGGTGTTGTTTGT
83570 GATGA
1 GATGA
83575 ACCAAATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 5 0.14
33 30 0.86
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.44
Consensus pattern (33 bp):
GATGATACTAAAACTATTTGAGGTGTTGTTTGT
Found at i:84095 original size:16 final size:15
Alignment explanation
Indices: 84057--84098 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
84047 ACAGAGATTG
*
84057 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
84072 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
84087 ACTAGAAAACAA
1 AC-AGAAAACAA
84099 AGCAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:84874 original size:11 final size:11
Alignment explanation
Indices: 84858--84883 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
84848 CCTTTGCCTA
84858 AAAACTAGAAG
1 AAAACTAGAAG
84869 AAAACTAGAAG
1 AAAACTAGAAG
84880 AAAA
1 AAAA
84884 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:87434 original size:21 final size:21
Alignment explanation
Indices: 87410--87463 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
87400 GGCACTGAAT
* *
87410 GGTGATGGCACGGGCATAGCC
1 GGTGGTGGCACGGGCATAACC
*
87431 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATAACC
87452 GGTGGTGGCACG
1 GGTGGTGGCACG
87464 ACAATGGGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.15, C:0.22, G:0.46, T:0.17
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Found at i:90620 original size:21 final size:21
Alignment explanation
Indices: 90595--90634 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
90585 TTTTTTTTTC
* *
90595 AAAAACGCAACACAAAAAATA
1 AAAAACGCAAAAAAAAAAATA
*
90616 AAAAATGCAAAAAAAAAAA
1 AAAAACGCAAAAAAAAAAA
90635 ATCAAATATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.78, C:0.12, G:0.05, T:0.05
Consensus pattern (21 bp):
AAAAACGCAAAAAAAAAAATA
Found at i:90627 original size:15 final size:14
Alignment explanation
Indices: 90607--90640 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
90597 AAACGCAACA
90607 CAAAAAATAAAAAAT
1 CAAAAAA-AAAAAAT
90622 GCAAAAAAAAAAAAT
1 -CAAAAAAAAAAAAT
90637 CAAA
1 CAAA
90641 TATTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 7 0.39
16 7 0.39
ACGTcount: A:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (14 bp):
CAAAAAAAAAAAAT
Found at i:91022 original size:16 final size:15
Alignment explanation
Indices: 90984--91022 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
90974 ACAGAGATTG
*
90984 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
90999 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
91014 ACTAGAAAA
1 AC-AGAAAA
91023 TAAAGCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.64, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:91801 original size:11 final size:11
Alignment explanation
Indices: 91785--91810 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
91775 CCTTTGCCTA
91785 AAAACTAGAAG
1 AAAACTAGAAG
91796 AAAACTAGAAG
1 AAAACTAGAAG
91807 AAAA
1 AAAA
91811 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:94230 original size:21 final size:21
Alignment explanation
Indices: 94204--94338 Score: 227
Period size: 21 Copynumber: 6.4 Consensus size: 21
94194 TGCTAGGAGT
94204 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
94225 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
94246 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
94267 TCATTGGAGTAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
94288 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
94309 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
94330 TCATCGGAG
1 TCATTGGAG
94339 TTACCTAAGA
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
20 2 0.02
21 107 0.98
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.