Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008186.1 Corchorus capsularis cultivar CVL-1 contig08207, 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: 70780
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:9191 original size:154 final size:154
Alignment explanation
Indices: 8897--10660 Score: 2408
Period size: 154 Copynumber: 11.5 Consensus size: 154
8887 TTGGTGCATC
* * * * *
8897 AACAGCTCTAACGAGCCCCGAGAGGCCCAAAATAACAAGTGGTCGAAATGAG-TTAAAAACTTCA
1 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTT-AAAACTTCA
* * * *
8961 TAATGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAAAGGAAAGAAAAGCTTTGTT
65 CAGTGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTG
* * * *
9026 ATTTACCAAATCAAATACGATTCAA
130 GTTTGCCAAATCGAAGACGATTCAA
* *
9051 AACAACACTAATGTGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTTAAAACTTCAC
1 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTTAAAACTTCAC
* * * * *
9116 AGTGAACTAAACTCACAAAAATTATTATAGTTAGGCCATAAAGAATGGAAAGAAAAGCTTTGTGG
66 AGTGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGG
* *
9181 TTTGTCAAATCGAAGACGATTGAA
131 TTTGCCAAATCGAAGACGATTCAA
* * * *
9205 AACAGCACTAATGGGCCCTGAAAGGCCAAAAATAACAAGTGCTCGAAATGAGCTAAAAACATCAC
1 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTTAAAACTTCAC
* * * * * ** *
9270 AATGAACTAATCTCATCAAAATGATTATTGTTAGGACATAAGCAATGGAAAGACAATATTTGTGT
66 AGTGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGG
* * *
9335 TTTGTCAAATTGAAGATGATTCAA
131 TTTGCCAAATCGAAGACGATTCAA
* * *
9359 AACAGCTCTAATTGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAG-TTAAAAACTTGA
1 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTT-AAAACTTCA
* *
9423 CAATGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAATAATGGAAAGAAAAAGCTTTGT
65 CAGTGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAG-AAAAGCTTTGT
* * *
9488 GGTTTACCGAATCGAATACGATTCAA
129 GGTTTGCCAAATCGAAGACGATTCAA
* * * * *
9514 AACAGCACTAATGGACCCCAAAAGACCCAAAATAACAAGTGCTCAAAATGAGATTAAAACTTCAC
1 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTTAAAACTTCAC
* * *
9579 AGTGAACTAATCTCACAAAAATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGG
66 AGTGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGG
*
9644 TTTGCCAAATCGAGGACGATTCAA
131 TTTGCCAAATCGAAGACGATTCAA
** ** *
9668 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTATTTAAAATGAGCTAAAAACTTCAC
1 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTTAAAACTTCAC
* * * * *
9733 AGTGGACTAATCTCACCAAAATGGTTATAGTTAGGCCATAAACAATGCAAAGAAATGCTTTGTGG
66 AGTGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGG
* *
9798 TTTGCCAACTCGAAGATGATTCAA
131 TTTGCCAAATCGAAGACGATTCAA
* * *
9822 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGC-GAAATAC-TC-
1 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTTAAA-ACTTCA
* * * * * * *
9884 CAGTGGACTAATCTCACCAAAATGATTCTGGTTAGGACTTAAACAATGGAAAGAAAAGGTTTATG
65 CAGTGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTG
*
9949 GTTTGCCAATTCGAAGACGATTCAA
130 GTTTGCCAAATCGAAGACGATTCAA
* * *
9974 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGATCTAAAAACATCAC
1 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTTAAAACTTCAC
* * * ** *
10039 AATGAACTAATCTCACTAAAATAATTATTGTTAGGTTATAAACAATGGAACA-AAAATCTTTGTG
66 AGTGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAA-AGAAAAGCTTTGTG
* *
10103 TTTTGCCAAATCCAAGACGATTCAA
130 GTTTGCCAAATCGAAGACGATTCAA
* ** ** * * *
10128 AACAACTTTAATTAGCCCCGAAAGGCCCAAAATAACAACTGCTCGAAATTAGCTAAAAACTTCAC
1 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTTAAAACTTCAC
* *
10193 AATGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGTTTTGTGG
66 AGTGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGG
* *
10258 TTTACCAAATCGAATACGATTCAA
131 TTTGCCAAATCGAAGACGATTCAA
* **
10282 AACAGAACTAATGGGCCCTAAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTTAAAACTTCAC
1 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTTAAAACTTCAC
*
10347 AGTGAACTAATCTCACCAAAAT-ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGG
66 AGTGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGG
10411 TTTGCCAAATCGAAGACGATTCAA
131 TTTGCCAAATCGAAGACGATTCAA
* * *
10435 AACAACACTAATGGGCCCTGAAAGGCCCAAAATAACAAGTGCTCGAAATGACCTTAAAACTTCAC
1 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTTAAAACTTCAC
* * * *
10500 AGTGAACTAATATCACCAAAATGATTATTGTTAGGACATAAACAATGGAAAGAAAATCTTTGTGT
66 AGTGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGG
*
10565 TTTGCCAAGTCGAAGACGATTCAA
131 TTTGCCAAATCGAAGACGATTCAA
* *
10589 AACAGCTCTAATGGGCCCCGAAAGGTCCAAAATAACAAGTGCTCGAAATGAGCTTAAAACTTCAC
1 AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTTAAAACTTCAC
10654 AGTGAAC
66 AGTGAAC
10661 AATACATTAT
Statistics
Matches: 1418, Mismatches: 181, Indels: 22
0.87 0.11 0.01
Matches are distributed among these distances:
152 131 0.09
153 156 0.11
154 997 0.70
155 132 0.09
156 2 0.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (154 bp):
AACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGCTCGAAATGAGCTTAAAACTTCAC
AGTGAACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGG
TTTGCCAAATCGAAGACGATTCAA
Found at i:11664 original size:11 final size:10
Alignment explanation
Indices: 11624--11676 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
11614 TGCTCCTTGA
11624 AATAATTCTTC
1 AATAA-TCTTC
*
11635 AATGATCTTC
1 AATAATCTTC
11645 -AT-ATCTTC
1 AATAATCTTC
11653 AATAAGTCTTC
1 AATAA-TCTTC
11664 AATAAATCTTC
1 AAT-AATCTTC
11675 AA
1 AA
11677 ACACGAACTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
8 6 0.16
9 4 0.11
10 6 0.16
11 19 0.51
12 2 0.05
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.40
Consensus pattern (10 bp):
AATAATCTTC
Found at i:12523 original size:17 final size:18
Alignment explanation
Indices: 12486--12525 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
12476 TTTTCTCCTC
12486 TTTTATGAAAACACTTCT
1 TTTTATGAAAACACTTCT
*
12504 TTTTATGAAAA-ACTTTT
1 TTTTATGAAAACACTTCT
12521 TTTTA
1 TTTTA
12526 ACTACCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTTATGAAAACACTTCT
Found at i:13626 original size:8 final size:7
Alignment explanation
Indices: 13606--13644 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
13596 AGTTATAATT
13606 TTAAAAA
1 TTAAAAA
13613 TTAAAAA
1 TTAAAAA
13620 TTAAAAA
1 TTAAAAA
*
13627 TT-GAAA
1 TTAAAAA
13633 TT-AAAA
1 TTAAAAA
13639 TTAAAA
1 TTAAAA
13645 TTGGGTTGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 10 0.34
7 19 0.66
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (7 bp):
TTAAAAA
Found at i:13640 original size:12 final size:13
Alignment explanation
Indices: 13606--13646 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
13596 AGTTATAATT
13606 TTAAAAATTAAAAA
1 TTAAAAATT-AAAA
*
13620 TTAAAAATTGAAA
1 TTAAAAATTAAAA
13633 TT-AAAATTAAAA
1 TTAAAAATTAAAA
13645 TT
1 TT
13647 GGGTTGCCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.44
13 5 0.20
14 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (13 bp):
TTAAAAATTAAAA
Found at i:17014 original size:474 final size:474
Alignment explanation
Indices: 15708--17139 Score: 2452
Period size: 475 Copynumber: 3.0 Consensus size: 474
15698 CTTGCATGTC
*
15708 TTCTTTGGATACTACATGGCCTAGAACAATGCCTTGTTCTACCATGAAGTGGCACTTTTCAGAAT
1 TTCTTTGGATACTACATGGCCTAGAACAATGCCTTGTTCTACCATGAAGTGGCACTTTTCAGCAT
*
15773 TTAATACCAATTTGGTTTCAGCACACCTTTTTAATTAAGATGAGTTCTAGATTATGGAGGCATTG
66 TTAATACCAATTTGGTTTCAACACACC--TTT--TTAAGATGAGTTCTAGATTATGGAGGCATTG
* **
15838 ATTGAAGCTATCTCCATAGATTGTGAAATCGTCCATGAATACTTCCATTTTATCTCTGACATAAT
127 ATTGAAGCTATCTCCATAGACTGTGAAATCGTCCATGAATACTT-CATTTTATCTCCCACATAAT
15903 CTTGAAAGATGCTCATCAAACACCTTTGAAAAGTTGCAGGTGCATTGCATAAACCAAAAGGCATT
191 CTTGAAAGATGCTCATCAAACACCTTTGAAAAGTTGCAGGTGCATTGCATAAACCAAAAGGCATT
*
15968 CTTGTATAGGCATACGTACCAAAGGGGCATGTAAAGGTGGTTTTCTCTTGATCTTCAGGTGCAAT
256 CTTGTGTAGGCATACGTACCAAAGGGGCATGTAAAGGTGGTTTTCTCTTGATCTTCAGGTGCAAT
*
16033 TGGAATCTAGAAGTATCCTGAATACCCATCCAGAAAATAGTAGTAGGCTTTGCAAGCTAATCTTT
321 TGGAATCTAGAAGTATCCTGAATACCCATCCAGAAAACAGTAGTAGGCTTTGCAAGCTAATCTTT
* * *
16098 CCAGCATTTGGTCAATAAATGGCAATGGAAAGTAGTCTTTCCTTGTGGCAGCATTCAGCTTTCTG
386 CCAGCATTTAGTCAATAAATGGCAATGGAAAGTGGTCCTTCCTTGTGGCAGCATTCAGCTTTCTG
* *
16163 TAGTTGATGCATACTCTGCATCCA
451 TAGTCGATGCATACTCTCCATCCA
*
16187 TTCTTTAGATACTACATGGCCTAGAACAATGCCTTGTTCTACCATGAAGTGGCACTTTTCAGCAT
1 TTCTTTGGATACTACATGGCCTAGAACAATGCCTTGTTCTACCATGAAGTGGCACTTTTCAGCAT
16252 TTAATACCAATTTGGTTTCAACACACCTTTTTAAGATGAGTTCTAGATTATGGAGGCATTGATTG
66 TTAATACCAATTTGGTTTCAACACACCTTTTTAAGATGAGTTCTAGATTATGGAGGCATTGATTG
*
16317 AAGCTATCTCCATAGACTATGAAATCGTCCATGAATACTTGCATTTTATCTCCCACATAATCTTG
131 AAGCTATCTCCATAGACTGTGAAATCGTCCATGAATACTT-CATTTTATCTCCCACATAATCTTG
16382 AAAGATGCTCATCAAACACCTTTGAAAAGTTGCAGGTGCATTGCATAAACCAAAAGGCATTCTTG
195 AAAGATGCTCATCAAACACCTTTGAAAAGTTGCAGGTGCATTGCATAAACCAAAAGGCATTCTTG
*
16447 TGTAGGCATACGTACCAAAGGGGCATGTAAAAGTGGTTTTCTCTTGATCTTCAGGTGCAATTGGA
260 TGTAGGCATACGTACCAAAGGGGCATGTAAAGGTGGTTTTCTCTTGATCTTCAGGTGCAATTGGA
* * * *
16512 ATCTAGAAGTATCCTGAATACTCATCCAGGAAACAGTAGTAGCCGTTGCAAGCTAATCTTTCCAG
325 ATCTAGAAGTATCCTGAATACCCATCCAGAAAACAGTAGTAGGCTTTGCAAGCTAATCTTTCCAG
* *
16577 CATTTAGTCAATAAATGGCAATGGAAAGTGGTCCTTCCTCGTGGCAGCATTCAGTTTTCTGTAGT
390 CATTTAGTCAATAAATGGCAATGGAAAGTGGTCCTTCCTTGTGGCAGCATTCAGCTTTCTGTAGT
*
16642 GGATGCATACTCTCCATCCA
455 CGATGCATACTCTCCATCCA
* * *
16662 TTCTTTGGATATTACATGGCCTAAAACAATGCCTTGTTTTACCATGAAGTGGCACTTTTCAGCAT
1 TTCTTTGGATACTACATGGCCTAGAACAATGCCTTGTTCTACCATGAAGTGGCACTTTTCAGCAT
* *
16727 TTACTACCAATTTGATTTCAACACACC-TTTTAAGATGAGTTCTAGATTATGGAGGCATTGATTG
66 TTAATACCAATTTGGTTTCAACACACCTTTTTAAGATGAGTTCTAGATTATGGAGGCATTGATTG
* * *
16791 AAGTTATCTCAATAGACTGTGAACTCGTCCATGAATACTTCAATTTTATCTCCCACATAATCTTG
131 AAGCTATCTCCATAGACTGTGAAATCGTCCATGAATACTTC-ATTTTATCTCCCACATAATCTTG
* *
16856 AATGATGCTCATTAAACACCTTTGAAAAGTTGCAGGTGCATTGCATAAACCAAAAGGCATTCTTG
195 AAAGATGCTCATCAAACACCTTTGAAAAGTTGCAGGTGCATTGCATAAACCAAAAGGCATTCTTG
* * *
16921 TGTAGGCATACATACCAAAGGGGCATGTAAAGGTGGTTTTCTCTTGATTTTCTGGTGCAATTGGA
260 TGTAGGCATACGTACCAAAGGGGCATGTAAAGGTGGTTTTCTCTTGATCTTCAGGTGCAATTGGA
*
16986 ATCTGGAAGTATCCTGAATACCCATCCAGAAAACAGTAGTAGGCTTTGCAAGCTAATCTTTCCAG
325 ATCTAGAAGTATCCTGAATACCCATCCAGAAAACAGTAGTAGGCTTTGCAAGCTAATCTTTCCAG
*
17051 CATTTCGTCAATAAATGGCAATGGAAAGTGGTCCTTCCTTGTGGCAGCATTCAGCTTTCTGTAGT
390 CATTTAGTCAATAAATGGCAATGGAAAGTGGTCCTTCCTTGTGGCAGCATTCAGCTTTCTGTAGT
*
17116 CGATACATACTCTCCATCCA
455 CGATGCATACTCTCCATCCA
17136 TTCT
1 TTCT
17140 GCAGTCTTTG
Statistics
Matches: 904, Mismatches: 48, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
473 1 0.00
474 364 0.40
475 447 0.49
477 3 0.00
479 89 0.10
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (474 bp):
TTCTTTGGATACTACATGGCCTAGAACAATGCCTTGTTCTACCATGAAGTGGCACTTTTCAGCAT
TTAATACCAATTTGGTTTCAACACACCTTTTTAAGATGAGTTCTAGATTATGGAGGCATTGATTG
AAGCTATCTCCATAGACTGTGAAATCGTCCATGAATACTTCATTTTATCTCCCACATAATCTTGA
AAGATGCTCATCAAACACCTTTGAAAAGTTGCAGGTGCATTGCATAAACCAAAAGGCATTCTTGT
GTAGGCATACGTACCAAAGGGGCATGTAAAGGTGGTTTTCTCTTGATCTTCAGGTGCAATTGGAA
TCTAGAAGTATCCTGAATACCCATCCAGAAAACAGTAGTAGGCTTTGCAAGCTAATCTTTCCAGC
ATTTAGTCAATAAATGGCAATGGAAAGTGGTCCTTCCTTGTGGCAGCATTCAGCTTTCTGTAGTC
GATGCATACTCTCCATCCA
Found at i:23248 original size:26 final size:27
Alignment explanation
Indices: 23193--23257 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
23183 GTGGACTAAG
**
23193 AATGACCAAAATACCCCTGAATGTGCA
1 AATGACCAAAATACCCCTGAATGTAAA
* *
23220 AATGACTAAAATA-CCCTTAATGTAAA
1 AATGACCAAAATACCCCTGAATGTAAA
23246 AATGACCAAAAT
1 AATGACCAAAAT
23258 GTCCCTATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
26 21 0.64
27 12 0.36
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.22
Consensus pattern (27 bp):
AATGACCAAAATACCCCTGAATGTAAA
Found at i:30223 original size:41 final size:41
Alignment explanation
Indices: 30170--30254 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
30160 GTTCATATTT
* *
30170 TTTCTTTTTATCTCACCTAGGGTTTA-ATATGTTTTTTGAGGG
1 TTTCTTTTTATCTCACCTAAGGTTTATAT-TGTTTGTT-AGGG
30212 TTTC-TTTTATCTCACCTAAGGTTTATATTGTTTGTTAGGG
1 TTTCTTTTTATCTCACCTAAGGTTTATATTGTTTGTTAGGG
30252 TTT
1 TTT
30255 GGGTTTCATA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 7 0.17
41 27 0.68
42 6 0.15
ACGTcount: A:0.16, C:0.12, G:0.18, T:0.54
Consensus pattern (41 bp):
TTTCTTTTTATCTCACCTAAGGTTTATATTGTTTGTTAGGG
Found at i:31841 original size:29 final size:29
Alignment explanation
Indices: 31799--31888 Score: 145
Period size: 29 Copynumber: 3.3 Consensus size: 29
31789 GAGTTCTGAA
31799 TATTTTCCAAAATTTTATGTTTTTTTGTG
1 TATTTTCCAAAATTTTATGTTTTTTTGTG
31828 TATTTTCCAAAATTTTATG---TTTT-T-
1 TATTTTCCAAAATTTTATGTTTTTTTGTG
31852 TATTTTCCAAAATTTTATGTTTTTTTGTG
1 TATTTTCCAAAATTTTATGTTTTTTTGTG
31881 TATTTTCC
1 TATTTTCC
31889 TGTCAAACTT
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
24 19 0.34
25 1 0.02
26 4 0.07
27 4 0.07
28 1 0.02
29 27 0.48
ACGTcount: A:0.21, C:0.09, G:0.08, T:0.62
Consensus pattern (29 bp):
TATTTTCCAAAATTTTATGTTTTTTTGTG
Found at i:31856 original size:24 final size:24
Alignment explanation
Indices: 31799--31876 Score: 111
Period size: 24 Copynumber: 3.0 Consensus size: 24
31789 GAGTTCTGAA
31799 TATTTTCCAAAATTTTATGTTTTTTTGT
1 TATTTTCCAAAATTTTATG---TTTT-T
31827 GTATTTTCCAAAATTTTATGTTTTT
1 -TATTTTCCAAAATTTTATGTTTTT
31852 TATTTTCCAAAATTTTATGTTTTT
1 TATTTTCCAAAATTTTATGTTTTT
31876 T
1 T
31877 TGTGTATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
24 25 0.51
25 1 0.02
26 4 0.08
29 19 0.39
ACGTcount: A:0.23, C:0.08, G:0.06, T:0.63
Consensus pattern (24 bp):
TATTTTCCAAAATTTTATGTTTTT
Found at i:37283 original size:20 final size:20
Alignment explanation
Indices: 37258--37302 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
37248 GCAACTCATT
37258 CTTCATTCACTACTTGGGGG
1 CTTCATTCACTACTTGGGGG
37278 CTTCATTCACTACTTGGGGG
1 CTTCATTCACTACTTGGGGG
37298 CTTCA
1 CTTCA
37303 CTAATTGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.36
Consensus pattern (20 bp):
CTTCATTCACTACTTGGGGG
Found at i:37304 original size:16 final size:18
Alignment explanation
Indices: 37260--37310 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
37250 AACTCATTCT
37260 TCATTCACTACTTGGGGG
1 TCATTCACTACTTGGGGG
37278 CTTCATTCACTACTTGGGGG
1 --TCATTCACTACTTGGGGG
*
37298 -C-TTCACTAATTGG
1 TCATTCACTACTTGG
37311 TCATTTTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 11 0.37
17 1 0.03
20 18 0.60
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (18 bp):
TCATTCACTACTTGGGGG
Found at i:40920 original size:48 final size:48
Alignment explanation
Indices: 40832--41151 Score: 331
Period size: 48 Copynumber: 6.4 Consensus size: 48
40822 ATTATAGTTC
* * * *
40832 TGCCCTTCCCGGTTGGAAGGTGCCGTCTTCAGTGTCTATTTCCAGATT
1 TGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCCAGATT
*
40880 TGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGCTCTTTATTTCGGTCTTTATTTCCAG-TT
1 TGCCCTTCCCGGTCGGAAGGTGCA------G-TC-----TTCGGTGTTTATTTCCAGATT
* * *
40939 GTGCCCTTCCCCGTCGGAAGGTGCATTTTTCGGTGTTTATTTCCAG-TT
1 -TGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCCAGATT
* * ** *
40987 TCGCCCTTCCCGGTCGGAAGTTGCCGTCTTCAATGTCTATTTCCAGATT
1 T-GCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCCAGATT
* *
41036 TGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTCTTTATTTCCAGTTT
1 TGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCCAGATT
* *
41084 TGCCATTCCCGGTCGGAAGGTGCAGTTTTCGGTGTTTATTTCCAG-TT
1 TGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCCAGATT
41131 TCGCCCTTCCCGGTCGGAAGG
1 T-GCCCTTCCCGGTCGGAAGG
41152 CGCTAGATTT
Statistics
Matches: 228, Mismatches: 28, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
47 4 0.02
48 177 0.78
49 3 0.01
53 1 0.00
54 1 0.00
55 2 0.01
59 2 0.01
60 38 0.17
ACGTcount: A:0.12, C:0.27, G:0.25, T:0.37
Consensus pattern (48 bp):
TGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGGTGTTTATTTCCAGATT
Found at i:40961 original size:60 final size:60
Alignment explanation
Indices: 40868--40981 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
40858 CTTCAGTGTC
*
40868 TATTTCCAGATTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGCTCTTTATTTCGGTCTT
1 TATTTCCAGATTTGCCCTTCCCCGTCGGAAGGTGCAGTCTTCGCTCTTTATTTCGGTCTT
* * * *
40928 TATTTCCAG-TTGTGCCCTTCCCCGTCGGAAGGTGCATTTTTCGGTGTTTATTTC
1 TATTTCCAGATT-TGCCCTTCCCCGTCGGAAGGTGCAGTCTTCGCTCTTTATTTC
40982 CAGTTTCGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.04
60 46 0.96
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.41
Consensus pattern (60 bp):
TATTTCCAGATTTGCCCTTCCCCGTCGGAAGGTGCAGTCTTCGCTCTTTATTTCGGTCTT
Found at i:49305 original size:48 final size:48
Alignment explanation
Indices: 49233--49698 Score: 578
Period size: 48 Copynumber: 9.8 Consensus size: 48
49223 GGATTTTAGA
* *
49233 TGTCTA-TTACAGTTTTGCCCTTCCCGGTCGGAAGGTGCCGTCTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAG
* *
49280 TATCTATTTCCAGTTTTGCGCTTCCCGGTCGGAAGGTGCAGTCTT-AG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAG
* * **
49327 ATGTCTA-TTACAGTCTTGCCCTTCCCGGTCGGAAGGTGCCTTCTTCAG
1 -TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAG
* *
49375 TGTCTATTTCCAGATTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCGG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAG
* * * * *
49423 TCTTTATTTCCAGTTTTGCCCTTCCCAGTCGGAAGGTGCAGTTTTCGG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAG
* *
49471 TGTTTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTTTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAG
* * * *
49519 TGTTTATTTCCAGTTTCGCCCTTCCTGGTCGGAAGGTGCTGTCTTCAG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAG
* * **
49567 TGTCTATTTCCAGATTTGCCTTTCCCGGTCGGAAGGTGCAGTCTTTGG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAG
* * * * * *
49615 TCTTTATTTTCAGTTTTGCCATTCCCGGTCGGAAGGTGCAGTTTTCGG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAG
* * * * *
49663 AGTTTATTTCTAGTTTCGCCCTTTCCGGTCGGAAGG
1 TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGG
49699 CGCTAGATTT
Statistics
Matches: 365, Mismatches: 50, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
47 46 0.13
48 319 0.87
ACGTcount: A:0.13, C:0.25, G:0.25, T:0.37
Consensus pattern (48 bp):
TGTCTATTTCCAGTTTTGCCCTTCCCGGTCGGAAGGTGCAGTCTTCAG
Found at i:60705 original size:72 final size:73
Alignment explanation
Indices: 60588--60950 Score: 504
Period size: 72 Copynumber: 5.1 Consensus size: 73
60578 AACGACCGGT
** * * *
60588 CACAATCCTTACATGATAATCTTCCAT-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGTA
1 CACAATCCTTATGTGATAATATTCCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCA
60652 GTCCTTCG
66 GTCCTTCG
* ** * * *
60660 CACAATTCTTACATGATAATATTCCAT-ATTGTGGTTGTAGTCGAGGCAGTTCCCACATTTGGCA
1 CACAATCCTTATGTGATAATATTCCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCA
*
60724 GACCTTCG
66 GTCCTTCG
* * * *
60732 CACAACCCTTATGCGATTATATT-CATCATTGCGATTGTAGCCGAGACAGTTCCCACATTTGGCA
1 CACAATCCTTATGTGATAATATTCCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCA
60796 GTCCTTCG
66 GTCCTTCG
* * *
60804 CACAACCCTTATGCGATTATATT-CATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCA
1 CACAATCCTTATGTGATAATATTCCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCA
60868 GTCCTTCG
66 GTCCTTCG
*
60876 CACAATCCTTATGTGATAATCTTCC-TCATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCA
1 CACAATCCTTATGTGATAATATTCCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCA
60939 GTCCTTCG
66 GTCCTTCG
60947 CACA
1 CACA
60951 GTCCATGCTA
Statistics
Matches: 267, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
71 21 0.08
72 245 0.92
73 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (73 bp):
CACAATCCTTATGTGATAATATTCCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCA
GTCCTTCG
Found at i:62166 original size:16 final size:16
Alignment explanation
Indices: 62145--62179 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
62135 GTAACACTAA
*
62145 ATTTGAGAGATTTGGT
1 ATTTGAGAGAGTTGGT
62161 ATTTGAGAGAGTTGGT
1 ATTTGAGAGAGTTGGT
62177 ATT
1 ATT
62180 CAACCGGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (16 bp):
ATTTGAGAGAGTTGGT
Found at i:65542 original size:33 final size:33
Alignment explanation
Indices: 65500--65608 Score: 173
Period size: 33 Copynumber: 3.3 Consensus size: 33
65490 TTCTTTTCAC
** *
65500 CCAAAACAGAATTATTTTTAATGCTATAATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
* *
65533 CCAAAACAGAATTATTTGCAATGTTATGATTAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
65566 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
65599 CCAAAACAGA
1 CCAAAACAGA
65609 TTTGTTTCCA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:65671 original size:33 final size:33
Alignment explanation
Indices: 65634--65738 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
65624 ATTAGCATCC
*
65634 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* * * *
65667 AAAACAGATTTAGTGTCATTGCAAACAAGACTC
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
** *
65700 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
65733 AAAACA
1 AAAACA
65739 CTCTCTACAA
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
32 1 0.02
33 56 0.98
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:68183 original size:12 final size:12
Alignment explanation
Indices: 68166--68196 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
68156 GTTGTGGCCG
68166 GATGGCCCATGC
1 GATGGCCCATGC
*
68178 GATGGCCCGTGC
1 GATGGCCCATGC
68190 GATGGCC
1 GATGGCC
68197 GGTTGTGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.32, G:0.39, T:0.16
Consensus pattern (12 bp):
GATGGCCCATGC
Found at i:68221 original size:42 final size:42
Alignment explanation
Indices: 68149--68232 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
68139 AAAGGGTCGA
*
68149 ATGGCCAGTTGTGGCCGGATGGCCCATGCGATGGCCCGTGCG
1 ATGGCCAGTTGTGGCCGGATGACCCATGCGATGGCCCGTGCG
* * *
68191 ATGGCCGGTTGTGGCCGGATGACTCC-TGCGATGTCCTGTGCG
1 ATGGCCAGTTGTGGCCGGATGAC-CCATGCGATGGCCCGTGCG
68233 TTGTCCCATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 35 0.95
43 2 0.05
ACGTcount: A:0.11, C:0.27, G:0.39, T:0.23
Consensus pattern (42 bp):
ATGGCCAGTTGTGGCCGGATGACCCATGCGATGGCCCGTGCG
Found at i:68638 original size:86 final size:86
Alignment explanation
Indices: 68479--68802 Score: 261
Period size: 86 Copynumber: 3.9 Consensus size: 86
68469 AGATTAACAA
* * * *
68479 AATTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGATATATTTTAAGA
1 AATTAATAATGAGAATATTTTCTAAATCTTGCAAAATTGTGGAAGATTTAGGAGATATTCTAAGA
68544 AAATAAATAAATTAAAAATAG
66 AAATAAATAAATTAAAAATAG
68565 AATTAATAATGAGAATATTTTCTAAATCTTGCAAAATTGT-GAGAGATTTAGGAGATATTCTAAG
1 AATTAATAATGAGAATATTTTCTAAATCTTGCAAAATTGTGGA-AGATTTAGGAGATATTCTAAG
*
68629 -AAAT--A-AAA-TAATAAT--
65 AAAATAAATAAATTAAAAATAG
* * * * ** * *
68644 AA--AGT--TGAGAATATTTTCT-AAATCT-TGCCAAATT-GTGGAAGATTTAGGAGATATTTTA
1 AATTAATAATGAGAAT-ATTT-TCTAA-ATCTTGCAAAATTGTGGAAGATTTAGGAGATATTCTA
*
68702 AGAAAA-AAATAAATAATAAAAATTG
63 AGAAAATAAATAAAT--TAAAAATAG
* * * * * * *
68727 AA-TAGTAATGAGAATATTTATCTAAATCTTGCCAGATAGTGGGAGATTTAGGAGATATT-AAAT
1 AATTAATAATGAGAATATTT-TCTAAATCTTGCAAAATTGTGGAAGATTTAGGAGATATTCTAAG
68790 AATAATAAATAAA
65 AA-AATAAATAAA
68803 AAGTTAAGAT
Statistics
Matches: 190, Mismatches: 26, Indels: 42
0.74 0.10 0.16
Matches are distributed among these distances:
75 29 0.15
76 16 0.08
77 5 0.03
78 3 0.02
79 2 0.01
81 12 0.06
82 3 0.02
83 3 0.02
84 3 0.02
85 11 0.06
86 74 0.39
87 22 0.12
88 7 0.04
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (86 bp):
AATTAATAATGAGAATATTTTCTAAATCTTGCAAAATTGTGGAAGATTTAGGAGATATTCTAAGA
AAATAAATAAATTAAAAATAG
Found at i:68660 original size:161 final size:161
Alignment explanation
Indices: 68488--68785 Score: 483
Period size: 161 Copynumber: 1.8 Consensus size: 161
68478 AAATTAATAA
* *
68488 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGATATATTTTAAGAAAATAAATA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAAA-AAATA
*
68553 AAT-TAAAAATAGAATTAATAATGAGAATATTT-TCTAAATCTTGCAAAATTGTGAGAGATTTAG
65 AATATAAAAATAGAA-TAATAATGAGAATATTTATCTAAATCTTGCAAAATAGTGAGAGATTTAG
68616 GAGATATTCTAAGAAATAAAATAATAATAAAGT
129 GAGATATTCTAAGAAATAAAATAATAATAAAGT
68649 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAAAAAATAA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAAAAAATAA
* * * * *
68714 ATAATAAAAATTGAATAGTAATGAGAATATTTATCTAAATCTTGCCAGATAGTGGGAGATTTAGG
66 AT-ATAAAAATAGAATAATAATGAGAATATTTATCTAAATCTTGCAAAATAGTGAGAGATTTAGG
68779 AGATATT
130 AGATATT
68786 AAATAATAAT
Statistics
Matches: 126, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
160 8 0.06
161 73 0.58
162 45 0.36
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.34
Consensus pattern (161 bp):
TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAAAAAATAA
ATATAAAAATAGAATAATAATGAGAATATTTATCTAAATCTTGCAAAATAGTGAGAGATTTAGGA
GATATTCTAAGAAATAAAATAATAATAAAGT
Found at i:68971 original size:12 final size:14
Alignment explanation
Indices: 68945--68985 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
68935 TTAGAAATTC
*
68945 AATTATAAGAGTAAT
1 AATTAAAAGA-TAAT
68960 AA-TAAAA-ATAAT
1 AATTAAAAGATAAT
68972 AATTAAAAGATAAT
1 AATTAAAAGATAAT
68986 TTTAGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 6 0.26
13 6 0.26
14 9 0.39
15 2 0.09
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (14 bp):
AATTAAAAGATAAT
Done.