Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022071.1 Corchorus olitorius cultivar O-4 contig22104, 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: 112135
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:661 original size:11 final size:11
Alignment explanation
Indices: 618--655 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
608 TTCGTATTTA
*
618 AAATAAATTAT
1 AAATTAATTAT
629 CAAA-TAATTAT
1 -AAATTAATTAT
640 AAATTAATTAT
1 AAATTAATTAT
651 AAATT
1 AAATT
656 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:27499 original size:12 final size:12
Alignment explanation
Indices: 27482--27510 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
27472 AACCAATCGC
27482 CCCATCTTATGA
1 CCCATCTTATGA
27494 CCCATCTTATGA
1 CCCATCTTATGA
27506 CCCAT
1 CCCAT
27511 TTTTTCAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.38, G:0.07, T:0.31
Consensus pattern (12 bp):
CCCATCTTATGA
Found at i:29789 original size:28 final size:28
Alignment explanation
Indices: 29749--29805 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
29739 TAGTATGTGC
29749 TTAACTTTTTTCTGCAACTATTTCAAAT
1 TTAACTTTTTTCTGCAACTATTTCAAAT
29777 TTAACTTTTTTCTGCAACTATTTCAAAT
1 TTAACTTTTTTCTGCAACTATTTCAAAT
29805 T
1 T
29806 GTTATGAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.51
Consensus pattern (28 bp):
TTAACTTTTTTCTGCAACTATTTCAAAT
Found at i:40443 original size:24 final size:24
Alignment explanation
Indices: 40408--40455 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
40398 TTTCCCCTTC
40408 TCTTTCTCCTCAGCTTTTTTCTTG
1 TCTTTCTCCTCAGCTTTTTTCTTG
40432 TCTTTCAT-CTCAGCTTTTTTCTTG
1 TCTTTC-TCCTCAGCTTTTTTCTTG
40456 ACAACCTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.06, C:0.27, G:0.08, T:0.58
Consensus pattern (24 bp):
TCTTTCTCCTCAGCTTTTTTCTTG
Found at i:41556 original size:1 final size:1
Alignment explanation
Indices: 41537--41579 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
41527 CATACCAAGC
* * * *
41537 AAAAAGAAAGAAAAGAAAAAAAAAAAAAAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
41580 TTTCCTTCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.91, C:0.02, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:45176 original size:30 final size:32
Alignment explanation
Indices: 45142--45215 Score: 116
Period size: 30 Copynumber: 2.3 Consensus size: 32
45132 AAAAAAAAAT
45142 CAGGGGATTTTCCGGCC-AAAAAAA-TTAAGA
1 CAGGGGATTTTCCGGCCAAAAAAAATTTAAGA
45172 CAGGGGATTTTCCGGCCAAAAAAAAAATTTAAGA
1 CAGGGGATTTTCCGGCC--AAAAAAAATTTAAGA
45206 CAGGGGATTT
1 CAGGGGATTT
45216 GTTTACAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
30 17 0.43
33 7 0.17
34 16 0.40
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (32 bp):
CAGGGGATTTTCCGGCCAAAAAAAATTTAAGA
Found at i:50815 original size:21 final size:21
Alignment explanation
Indices: 50791--50834 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
50781 TGGAGGAGGC
*
50791 GGTGGAGGTGGAGGCAGCAGT
1 GGTGGAAGTGGAGGCAGCAGT
* *
50812 GGTGGAAGTGGTGGTAGCAGT
1 GGTGGAAGTGGAGGCAGCAGT
50833 GG
1 GG
50835 GAGTGGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.07, G:0.57, T:0.18
Consensus pattern (21 bp):
GGTGGAAGTGGAGGCAGCAGT
Found at i:53256 original size:13 final size:13
Alignment explanation
Indices: 53238--53262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53228 TTGGGGCTGA
53238 TGTGATGAGTTTT
1 TGTGATGAGTTTT
53251 TGTGATGAGTTT
1 TGTGATGAGTTT
53263 CAGGGAGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (13 bp):
TGTGATGAGTTTT
Found at i:61639 original size:3 final size:3
Alignment explanation
Indices: 61631--61657 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
61621 ATATGTTCTT
61631 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
61658 ATTTTTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:64586 original size:29 final size:29
Alignment explanation
Indices: 64532--64589 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
64522 GCAACGTGGA
* * * *
64532 ATAAAAATAAAACATTAGGGTGCAAAGTG
1 ATAAAAATAAAAAATAAGGATACAAAGTG
64561 ATAAAAATAAAAAATAAGGATACAAAGTG
1 ATAAAAATAAAAAATAAGGATACAAAGTG
64590 GCAATTCGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.59, C:0.05, G:0.17, T:0.19
Consensus pattern (29 bp):
ATAAAAATAAAAAATAAGGATACAAAGTG
Found at i:64677 original size:21 final size:21
Alignment explanation
Indices: 64651--64692 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
64641 TTGTTTATTC
64651 TAATCAAAAACTTACCTATCT
1 TAATCAAAAACTTACCTATCT
64672 TAATCAAAAACTTACCTATCT
1 TAATCAAAAACTTACCTATCT
64693 CAAATGGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATCAAAAACTTACCTATCT
Found at i:80354 original size:22 final size:22
Alignment explanation
Indices: 80129--80501 Score: 235
Period size: 22 Copynumber: 16.9 Consensus size: 22
80119 AAATGTCTAC
*
80129 TTATCAAAATTTCATA-TGAAAG
1 TTATCAAAATTTCATAGTG-AGG
* * * *
80151 TTATGAAAATTTTAT-GAAGAGT
1 TTATCAAAATTTCATAG-TGAGG
* *
80173 TTATCAAAATTACATAGAGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
80195 ATATCAAAGTTTCATTCTCATAGGGAGG
1 TTATCAAA-----ATT-TCATAGTGAGG
* * * *
80223 TTATCGAAATTGCATGGTGTGG
1 TTATCAAAATTTCATAGTGAGG
*
80245 CTATCAAAATTT--TA-TGAGG
1 TTATCAAAATTTCATAGTGAGG
*
80264 TTATCAAAATTTTCATAGTGCGG
1 TTATCAAAA-TTTCATAGTGAGG
* *
80287 TTA-C-CAATTTTATATCGTGA--
1 TTATCAAAATTTCATA--GTGAGG
* **
80307 TTATCAAAATTTCATAGGGAAA
1 TTATCAAAATTTCATAGTGAGG
* *
80329 TTATCAAAATTTCATACTAAGG
1 TTATCAAAATTTCATAGTGAGG
** *
80351 TTATCAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
*
80373 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
80395 TTATCAAATTTTCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
80417 TTATCGAAATTTAATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
80439 TTATCAAATTTTCACAGAT-AGG
1 TTATCAAAATTTCATAG-TGAGG
* *
80461 TTATCGAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
80483 TTATCAAATTTTCACAGTG
1 TTATCAAAATTTCATAGTG
80502 TGATTGTCAA
Statistics
Matches: 266, Mismatches: 64, Indels: 42
0.72 0.17 0.11
Matches are distributed among these distances:
19 12 0.05
20 16 0.06
21 4 0.02
22 203 0.76
23 13 0.05
27 3 0.01
28 15 0.06
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:95007 original size:18 final size:18
Alignment explanation
Indices: 94984--95020 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
94974 AGTTTGTCCG
94984 TACATCAAACTATACAAT
1 TACATCAAACTATACAAT
95002 TACATCAAACTATACAAT
1 TACATCAAACTATACAAT
95020 T
1 T
95021 TGCTAGCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (18 bp):
TACATCAAACTATACAAT
Found at i:96909 original size:109 final size:109
Alignment explanation
Indices: 96748--96966 Score: 438
Period size: 109 Copynumber: 2.0 Consensus size: 109
96738 GGCTTCCAAA
96748 GAAAGCCTTTCTTTTATCAATCCTCTCGCTATTGCTCGAGAACACAATAACCTAAACGGACTCTT
1 GAAAGCCTTTCTTTTATCAATCCTCTCGCTATTGCTCGAGAACACAATAACCTAAACGGACTCTT
96813 ATGTATTCGCTCAATCCGAAGTTAGTCAAGAAAATGTCATATTG
66 ATGTATTCGCTCAATCCGAAGTTAGTCAAGAAAATGTCATATTG
96857 GAAAGCCTTTCTTTTATCAATCCTCTCGCTATTGCTCGAGAACACAATAACCTAAACGGACTCTT
1 GAAAGCCTTTCTTTTATCAATCCTCTCGCTATTGCTCGAGAACACAATAACCTAAACGGACTCTT
96922 ATGTATTCGCTCAATCCGAAGTTAGTCAAGAAAATGTCATATTG
66 ATGTATTCGCTCAATCCGAAGTTAGTCAAGAAAATGTCATATTG
96966 G
1 G
96967 GGCCTAATCT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (109 bp):
GAAAGCCTTTCTTTTATCAATCCTCTCGCTATTGCTCGAGAACACAATAACCTAAACGGACTCTT
ATGTATTCGCTCAATCCGAAGTTAGTCAAGAAAATGTCATATTG
Found at i:102828 original size:19 final size:18
Alignment explanation
Indices: 102804--102842 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
102794 TTTCAAAGTG
102804 AAACAGT-CAAATAAAAATA
1 AAACAGTAC-AAT-AAAATA
102823 AAACAGTACAATAAAATA
1 AAACAGTACAATAAAATA
102841 AA
1 AA
102843 TAAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 10 0.53
20 1 0.05
ACGTcount: A:0.69, C:0.10, G:0.05, T:0.15
Consensus pattern (18 bp):
AAACAGTACAATAAAATA
Found at i:103107 original size:24 final size:24
Alignment explanation
Indices: 103062--103107 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
103052 GTTAGTCAGT
* *
103062 GATGAAGACGAGTTCACGTTGGCA
1 GATGAAGACGAGCTCACATTGGCA
* *
103086 GATGCAGACGAGCTCGCATTGG
1 GATGAAGACGAGCTCACATTGG
103108 ACTACCTCGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.26, C:0.20, G:0.35, T:0.20
Consensus pattern (24 bp):
GATGAAGACGAGCTCACATTGGCA
Found at i:103673 original size:125 final size:127
Alignment explanation
Indices: 103530--103786 Score: 405
Period size: 125 Copynumber: 2.0 Consensus size: 127
103520 CATTGTTTAA
*
103530 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-C-AT-TA-
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTATCTAT
*
103591 TAATTTTTACCATTTTACTATTTTAATTAAAAAAATCTTTTATATATTAGAATTTTTTAAATAT
66 TAATTTTTACCATTTTACTATTTTAATT-AAAAAA-CTTATATATATTAGAATTTTTTAAATAT
103655 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCC-TAT--C
*
103720 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
63 TA-TTAATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
103785 T
127 T
103786 A
1 A
103787 TTTCTTAAAT
Statistics
Matches: 121, Mismatches: 3, Indels: 10
0.90 0.02 0.07
Matches are distributed among these distances:
125 55 0.45
126 1 0.01
128 2 0.02
131 30 0.25
132 6 0.05
133 27 0.22
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (127 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTATCTAT
TAATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:105567 original size:15 final size:15
Alignment explanation
Indices: 105547--105582 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
105537 TTATTTTTAG
105547 ATTATAATATAATTA
1 ATTATAATATAATTA
105562 ATTATAATATAATTA
1 ATTATAATATAATTA
*
105577 TTTATA
1 ATTATA
105583 GTCATGAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAATATAATTA
Found at i:108552 original size:328 final size:327
Alignment explanation
Indices: 107181--108684 Score: 1193
Period size: 326 Copynumber: 4.6 Consensus size: 327
107171 AAGACTCAAC
* * * * * ** * * *
107181 CACATTGAATTTAAGGATTTG-TTCTAAGAGAATCTAAATCTTG-AACTATTTAATAAAAAATTA
1 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * * *
107244 ATTTAGAAAAAACATGAAAAACGATATTAAAAGCCTGAAAAA-TCCTTCAATCTTTTTGGCGTTG
66 A-TTAG--AAAATAGGAAAAACGATATTAGAAGCGT-AAAAAGCCCTTCAATCTTTTTGGCATTG
* * * * *
107308 AATTATACATATTTTATGAGTATTGC-AGCTAAAAATTGAGGAAAAATATTTTGGATCATTTTTT
127 AATTATATATTTTTTATGAGTATT-CTAGCTAAAAATTGAGGAAAAATCTTTCGG-TCAATTTTT
* * *
107372 GCAAAATTTTAGCCGAAATCGTGTACTAA-TCA-CA-GATTTTTTGCTAAAAACGCGTTCAAGGG
190 GCAAAATTTTAGCCGAAATCGTGTACTAACACATCACGATTTTTGGCTAAAAACGCGTTC-CGGG
* * * *
107434 -CCCTAGGTCA--GTTTTGCATGATTTTTGGTGGC-AAACTCATTGAAATATCTTTATTCATCTA
254 TCCC--GG-CACTGTTTTGCATGATTTTTGGCGCCGAGACTC-TTGAAATATCTATATTCATCTA
* *
107495 ACCAAATCTTAGC
315 ACCAAATCTCAGT
** * * * *
107508 CACATTGGATTTAAGGATTAATTTTTACGAGCATTTGAATCATGTTTCGTTTTAATTAAAAATTA
1 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * * *
107573 ATTTGAAAAAAATTAGGGAAACCGATATTAGAAGCGTGAGAAGCCCTTCAATCTTTTTGGCGTTG
66 A-TT--AGAAAA-TAGGAAAAACGATATTAGAAGCGTAAAAAGCCCTTCAATCTTTTTGGCATTG
* *
107638 AATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAAT-TTTCGGGTCAATTTTTG
127 AATTATATATTTTTTATGAGTATTCTAGCTAAAAATTGAGGAAAAATCTTTC-GGTCAATTTTTG
* * * * ** **** * *
107702 CAAAATTTTAGCTGAAATCTTGTACCATCATGGT-TTTTTTTTTGGCTAAAAACGCATTCCGGGG
191 CAAAATTTTAGCCGAAATCGTGTACTAACA-CATCACGATTTTTGGCTAAAAACGCGTTCCGGGT
* * * * *
107766 CCCTGTATCAGTTTTGCATGATTTTT--C-ACG-G---C--AAATATATCTATATTCATCTAACC
255 CCCGGCA-CTGTTTTGCATGATTTTTGGCGCCGAGACTCTTGAA-ATATCTATATTCATCTAACC
*
107822 AAAGCTCAGT
318 AAATCTCAGT
* ** * * * * *
107832 CACATTGTATTTAAGGATTTGTTTTTACGAGTTTCTAAATTTTGTTTTGATTTAATCAGAAATGA
1 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
*
107897 ATTTAGATATAAAATAGGAAAAACGATATTAGAAGCGTGAAAAAG-CCTTCAATTTTTTTTGGC-
66 A-TTAG----AAAATAGGAAAAACGATATTAGAAGCGT-AAAAAGCCCTTCAA-TCTTTTTGGCA
* * * *
107960 TATGAATTATATATTTTTTATGA-TATTTTCAG-TAGAAATCGAGGAAAAATCTTTCGAGTCCAT
124 T-TGAATTATATATTTTTTATGAGTATTCT-AGCTAAAAATTGAGGAAAAATCTTTCG-GTCAAT
* * * *
108023 TTATGCAAAATTTTAGCCGAAATCGTGCACTAAC-CATCACGGTTTATGGCTAAAAACGCGTT-C
186 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACACATCACGATTTTTGGCTAAAAACGCGTTCC
* * **** * * * * *
108086 TGCTGCCCGATTTTGTTTTTCATGATTTTCGGTGCCAAGACTCCTTGAAATATCTATAATCATCT
251 GGGT-CCCGGCACTGTTTTGCATGATTTTTGGCGCCGAGACT-CTTGAAATATCTATATTCATCT
* * *
108151 TACCCAATCTCAGG
314 AACCAAATCTCAGT
* * * * *
108165 CACATTAGTTTTAAGGATTTGTTTTTACGTGTATCTGAATCTTGTCTCGATTTAATTAGAAATTA
1 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * ** * ***
108230 ATTCG-GAATAGGAAAAATAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTTATATTGAA-T
66 ATTAGAAAATAGGAAAAACGATATTAGAAGCGTAAAAAGCCCTTCAATCTTTTTGGCATTGAATT
* *
108293 ATATATTTTTTATGAGTATTCTAGCAAAAAATTGAGGAAATATCTTTCAGGTCAATTTTTGCAAA
131 ATATATTTTTTATGAGTATTCTAGCTAAAAATTGAGGAAAAATCTTTC-GGTCAATTTTTGCAAA
* *
108358 AGTTTAGCCGAAATCGTGTACTAACACTATCACGATTTTTGGCTAAAAACGCGTTCCAGGGTCAC
195 ATTTTAGCCGAAATCGTGTACTAACAC-ATCACGATTTTTGGCTAAAAACGCGTTCC-GGGTCCC
* * * * * *
108423 GGCACTGTTTTGCATTATTTTTGACGCCGTGACTTCTTGAATTATCTTTATTCATCTAATCAAAT
258 GGCACTGTTTTGCATGATTTTTGGCGCCGAGAC-TCTTGAAATATCTATATTCATCTAACCAAAT
108488 CTCAGT
322 CTCAGT
*
108494 CACATTGGATTTAAGGATTT-TTTTTA-TATGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
1 CACATTGGATTTAAGGATTTGTTTTTACGA-GCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * * * *
108557 AATTTAGAGAAAATATGAAAAACGATATTATTAAAAGCGT-GAAAGTCCTCCAATCTTTTTGGCG
65 AA-TT--AGAAAATAGGAAAAACG--A-TATTAGAAGCGTAAAAAGCCCTTCAATCTTTTTGGCA
* * * *
108621 TTGAATTATATATGTATATATATTATGAGTATTTTTGCCAAAGAAATGAGGAAAAATCTTTCGG
124 TTGAATTATATA--T-T-T-T-TTATGAGTATTCTAGCTAAA-AATTGAGGAAAAATCTTTCGG
108685 GTCATATTCA
Statistics
Matches: 924, Mismatches: 187, Indels: 118
0.75 0.15 0.10
Matches are distributed among these distances:
322 1 0.00
323 2 0.00
324 98 0.11
325 92 0.10
326 152 0.16
327 53 0.06
328 82 0.09
329 138 0.15
330 87 0.09
331 5 0.01
332 52 0.06
333 80 0.09
334 25 0.03
335 17 0.02
337 1 0.00
338 1 0.00
339 1 0.00
340 1 0.00
341 19 0.02
342 17 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (327 bp):
CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
ATTAGAAAATAGGAAAAACGATATTAGAAGCGTAAAAAGCCCTTCAATCTTTTTGGCATTGAATT
ATATATTTTTTATGAGTATTCTAGCTAAAAATTGAGGAAAAATCTTTCGGTCAATTTTTGCAAAA
TTTTAGCCGAAATCGTGTACTAACACATCACGATTTTTGGCTAAAAACGCGTTCCGGGTCCCGGC
ACTGTTTTGCATGATTTTTGGCGCCGAGACTCTTGAAATATCTATATTCATCTAACCAAATCTCA
GT
Found at i:110375 original size:66 final size:66
Alignment explanation
Indices: 110298--110433 Score: 240
Period size: 66 Copynumber: 2.1 Consensus size: 66
110288 TATGAGCCAA
110298 CAAA-CCCCTTCCCCAACAAACAAACCCAATGAAATCTCATTACAA-TCTAAATAAATCTCTATG
1 CAAACCCCCTTCCCCAACAAACAAACCCAATGAAATCTCATTACAATTC-AAATAAATCTCTATG
110361 CC
65 CC
*
110363 CAAACCCCCTTCCCCAACAAACAAACCCAGTGAAATCTCATTACAATTCAAATAAATCTCTATGC
1 CAAACCCCCTTCCCCAACAAACAAACCCAATGAAATCTCATTACAATTCAAATAAATCTCTATGC
110428 C
66 C
110429 CAAAC
1 CAAAC
110434 ATCTAAATGA
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
65 4 0.06
66 62 0.91
67 2 0.03
ACGTcount: A:0.41, C:0.35, G:0.04, T:0.21
Consensus pattern (66 bp):
CAAACCCCCTTCCCCAACAAACAAACCCAATGAAATCTCATTACAATTCAAATAAATCTCTATGC
C
Found at i:110889 original size:49 final size:47
Alignment explanation
Indices: 110786--110927 Score: 160
Period size: 49 Copynumber: 3.0 Consensus size: 47
110776 GAGCGTGCCA
* * * *
110786 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
110833 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * * * *
110882 TTTAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAATGAAAAATAAA
110928 GGATTGCTTG
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
47 12 0.15
48 28 0.35
49 41 0.51
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:111780 original size:9 final size:9
Alignment explanation
Indices: 111766--111790 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
111756 ATTTCTTTTC
111766 TTATTTTAA
1 TTATTTTAA
111775 TTATTTTAA
1 TTATTTTAA
111784 TTATTTT
1 TTATTTT
111791 TGGGTTCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTATTTTAA
Found at i:112022 original size:3 final size:3
Alignment explanation
Indices: 112005--112083 Score: 140
Period size: 3 Copynumber: 26.3 Consensus size: 3
111995 TTGCTTTCTC
* *
112005 TTA TTA TCA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
112053 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
112084 AAATATCGAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Done.