Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018416.1 Corchorus olitorius cultivar O-4 contig18449, 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: 58017
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:282 original size:36 final size:36
Alignment explanation
Indices: 235--304 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
225 TTCAATAACC
* *
235 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
271 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
305 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:1188 original size:204 final size:205
Alignment explanation
Indices: 812--1225 Score: 697
Period size: 204 Copynumber: 2.0 Consensus size: 205
802 GCTTAATAAC
* *
812 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCCAAGATTACTATCAAAGTTGAAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTATAAGTCCAAGATTACTAACAAAGTTGAAGTGAATAA
* *
877 GATACAACACATTATTATTATTATTATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTG
66 GATACAACACATTACTATTATTATTATATAGAACTATACCAAAAAAAAGTAGTTGAACATTAGTG
942 GTTGATTTATTAAATTAAATTAGATCAATGTCAAAAAAAATTTCAAAATTATAAAAGATATTAAA
131 GTTGATTTATTAAATTAAATTAGATCAATGTCAAAAAAAATTTCAAAATTATAAAAGATATT-AA
*
1007 GATCTGATTTA
195 GATCCGATTTA
* *
1018 TTTATCAATGGTGAATGTTATTAATTTTATAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTATAAGTCCAAGATTACTAACAAAGTTGAAGTGAATAA
* **
1083 GATACAACACATTACTATTA-TA-TATATAGGACTATACCAAAAAAATTTAGTTGAACATTAGTG
66 GATACAACACATTACTATTATTATTATATAGAACTATACCAAAAAAAAGTAGTTGAACATTAGTG
* *
1146 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTTAAAATTATAAAAGATATTAAG
131 GTTGATTTATTAAATTAAATTAGATCAATGTCAAAAAAAATTTCAAAATTATAAAAGATATTAAG
1211 ATCCGATTTA
196 ATCCGATTTA
1221 TTTAT
1 TTTAT
1226 TATTAAGGAA
Statistics
Matches: 196, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
203 17 0.09
204 97 0.49
205 2 0.01
206 80 0.41
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.37
Consensus pattern (205 bp):
TTTATCAATGGTGAATGTTATTAATTTTATAAGTCCAAGATTACTAACAAAGTTGAAGTGAATAA
GATACAACACATTACTATTATTATTATATAGAACTATACCAAAAAAAAGTAGTTGAACATTAGTG
GTTGATTTATTAAATTAAATTAGATCAATGTCAAAAAAAATTTCAAAATTATAAAAGATATTAAG
ATCCGATTTA
Found at i:1332 original size:25 final size:24
Alignment explanation
Indices: 1298--1344 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
1288 ACGTTTGCAC
1298 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
1323 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
1345 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:1389 original size:39 final size:40
Alignment explanation
Indices: 1335--1415 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
1325 ATACCTAAGA
*
1335 ATTTAATTAATGTAAGTATTCCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTCCAGTTATTATATATATTAC
**
1374 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTCCAGTTATTATATATATTAC
1414 AT
1 AT
1416 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTCCAGTTATTATATATATTAC
Found at i:12593 original size:15 final size:15
Alignment explanation
Indices: 12570--12613 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
12560 AAAGAAGTCT
*
12570 TTTCCTTCCTTCCCC
1 TTTCTTTCCTTCCCC
12585 TTTCTTTCC-TCCCC
1 TTTCTTTCCTTCCCC
12599 TCTTCTTTCCTTCCC
1 T-TTCTTTCCTTCCC
12614 ACTTCCTCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 6 0.23
15 16 0.62
16 4 0.15
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTCTTTCCTTCCCC
Found at i:12618 original size:15 final size:14
Alignment explanation
Indices: 12575--12618 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
12565 AGTCTTTTCC
12575 TTCCTTCCCCTTTCT
1 TTCCTTCCCC-TTCT
*
12590 TTCCTCCCCTCTTCT
1 TTCCTTCCC-CTTCT
12605 TTCCTTCCCACTTC
1 TTCCTTCCC-CTTC
12619 CTCCCTACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 24 0.96
16 1 0.04
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (14 bp):
TTCCTTCCCCTTCT
Found at i:17169 original size:1 final size:1
Alignment explanation
Indices: 17163--17199 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
17153 GGCTCTCACC
17163 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17200 GACAATGCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:27726 original size:17 final size:17
Alignment explanation
Indices: 27696--27737 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
27686 CTACCTTCAT
27696 GTCAAC-TC-AACCCAA
1 GTCAACGTCAAACCCAA
27711 GTCAACGTCAAACCCAA
1 GTCAACGTCAAACCCAA
27728 GTCAACGTCA
1 GTCAACGTCA
27738 TTTTGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.24
16 2 0.08
17 17 0.68
ACGTcount: A:0.38, C:0.36, G:0.12, T:0.14
Consensus pattern (17 bp):
GTCAACGTCAAACCCAA
Found at i:40592 original size:763 final size:757
Alignment explanation
Indices: 38900--41186 Score: 3170
Period size: 763 Copynumber: 3.0 Consensus size: 757
38890 ATGACTTGTT
38900 ATGATTAATAGTAATTAATAATTTCTTTAGGGAATAGTAATTAATAATTTTGATTTGCCTATAGG
1 ATGATTAATAGTAATTAATAATTT-TTTAGGGAATAGTAATTAATAATTTTGATTTGCCTATAGG
*
38965 AATAAATCCCGTGTAATATCCAAAGTTCCAAGTCCAAATCTTTATAATTATCTAAAAACATAGTA
65 AATAAATCCCGTGTAATATCC--A-----AAGTCCAAATCTTTAAAATTATCTAAAAACATAGTA
* * ** *
39030 GCAACCCAATTATCCAAAAAAAAAAAAATGTTTTATGGCCAATATAAGGAGAGTTTGGCTTTATA
123 GCAAACCAATTATCC--CAAAAAAAATCTGTTTTATGGCCAATATGAGGAGAGTTTGGC-TT-TA
* *
39095 TATAGAAAAGACATCCATA-TTTATTTTTCATTAAAAAAGGGGTTTTTTGGTGGGCGTCATCGAC
184 TATAGAAAAGACATCCATATTTTTTTTTTCATTAAAAAAGGGGTCTTTTGGTGGGCGTCATCGAC
* *
39159 TCGAGGGGCTCTAAGTCCCCCACTCCCTCTTAAACCCCGGTGACTCCATGGCGAGGGGCACAACT
249 -CGAGGGGCTCTAAGTCCCCCACTCCCTCTTAAACCCCGGTGACTTCATGGCGAGGGGCACACCT
* * * *
39224 GCGGACAGTAGTGAGACGTGCCAAGAGTGGATTTTAACATAGGATGAAAACAAACAAGAGTCTAT
313 GCGGACAGTAGTGGGGCGTGCCAAGAGTGGATTTTAACACAGGATGGAAACAAACAAGAGTC---
* *
39289 ATATGTGAGAAAAACATAGTGTTTACTTAGACTCGAACCCATGACCACACCTGCAGGAATCTTAC
375 -TATGTGAGAAAAACATTGTGTTTACTCAGACTCGAACCCATGACCACACCTGCAGGAATCTTAC
* * *
39354 ACATCTTAGAGTGATGATCCTATAGACTCGAGTCCATGGGAGTTACCATGCAATCGAAGCTAGAT
439 ACATCTTAGAGTGATG-TCCTATAGACTCGAGTCCGTGGGAGTTACCACGCAATCGAAGCTAAAT
* *
39419 CACACATATAATCATGTAATCATTCTAAAACCATACCATAATCCATGTTTAGCAGTCCATATCTA
503 CACACATATAATCATGTATTCATTCTAAAACC-TACCATAATCCATGTTTAGAAGTCCATATCTA
* * *
39484 CCCATAAAATAAATAAAAAATTTATTTGGA---AAACTTCATACTAAAATTGTATCTTAATTAAT
567 CCCATAAAATAAATAAAAAATTTATTTGGAGCTAAAATTCATATTAAAATTGTATCTTAATTATT
*
39546 AATGTCCTTAATTGAACAACAAAAAAAATTGTATCTTAATTCCCTT-TTTTATTTAATTTAATTT
632 AATGTCCTTAATTGAACAACAGAAAAAATTGTATCTTAATT-CCTTCTTTTATTTAATTTAATTT
39610 T--CATAT-ATC-----TTACTTTTAAAAAAGGGGAAATATCATTCATCATCTATCAATATC
696 TCACATATCATCTTTTATTACTTTTAAAAAAGGGGAAATATCATTCATCATCTATCAATATC
* * * *
39664 ATGATTAATATTAATTAATATTTTTTTAGGGAATAGTAATTAATAATTTTGATTTGCCTACAGTA
1 ATGATTAATAGTAATTAATAATTTTTTAGGGAATAGTAATTAATAATTTTGATTTGCCTATAGGA
* *
39729 ATAAATCCCATGTAATATCCAAAGTTCCAAAGTCCAAATCTTTAAAATTATCTAAAAACATAATA
66 ATAAATCCCGTGT-A-AT----A--TCCAAAGTCCAAATCTTTAAAATTATCTAAAAACATAGTA
*
39794 GCAAACCAATTATCCCAAGAAAAAATCTATTTTATGGCCAATATGAGGAGAGTTTGGCTTTATAT
123 GCAAACCAATTATCCCAA-AAAAAATCTGTTTTATGGCCAATATGAGGAGAGTTTGGCTTTATAT
*
39859 AGAAAAGACATCCATATTTCTTTTTTTTCATTAAAAAAGGGGTCTCTTGGTGGGCGTCATCGACC
187 AGAAAAGACATCCATA-TT-TTTTTTTTCATTAAAAAAGGGGTCTTTTGGTGGGCGTCATCGACC
* * *
39924 GAAGGACTCTTAAGTCCCCC-CTCCCTCTTAAACCCCGGTGACTTCATGGCGAGGGGCACACCTA
250 GAGGGGCTC-TAAGTCCCCCACTCCCTCTTAAACCCCGGTGACTTCATGGCGAGGGGCACACCTG
* ** ** *
39988 CAGACAGTAGTGGGGCGTGGTAAGAGTGGATTTTAACACAAAATGGAAACAAACAATAGTCTATG
314 CGGACAGTAGTGGGGCGTGCCAAGAGTGGATTTTAACACAGGATGGAAACAAACAAGAGTCTATG
* * *
40053 TGAGAAAAACATTGTGTTTAGTCAGACTGGAATCCATGACCACACCTGCAGGAATCTTACACATC
379 TGAGAAAAACATTGTGTTTACTCAGACTCGAACCCATGACCACACCTGCAGGAATCTTACACATC
* *
40118 TTAGAGTGATGTTCCTATAGACTCGAGTCCGTGGGAGTTACCACGCAATCGAAGCAAAACCACAC
444 TTAGAGTGATG-TCCTATAGACTCGAGTCCGTGGGAGTTACCACGCAATCGAAGCTAAATCACAC
* * *
40183 ATATAATCATGTATTCATTCTAAAACCTGACCATAATCCATGTTTAAAAGACCCTATCTACCCAT
508 ATATAATCATGTATTCATTCTAAAACCT-ACCATAATCCATGTTTAGAAGTCCATATCTACCCAT
* * *
40248 AAAGTAAATAAATAATTTATTTGGAGCTAAAATTCATATTAAAATCGTATCTTAATTATTAATGT
572 AAAATAAATAAAAAATTTATTTGGAGCTAAAATTCATATTAAAATTGTATCTTAATTATTAATGT
* *
40313 CCTTAATTGAACAA-AGAAAAAATTATATCTTAACTCCTTCTTTTATTTAATTTAATTTTCACAT
637 CCTTAATTGAACAACAGAAAAAATTGTATCTTAATTCCTTCTTTTATTTAATTTAATTTTCACAT
*
40377 ATCATACGTTTTATTACTTTT-AAAAAGGGGAGATATCATTCATCATCTATCAATATC
702 ATCAT-C-TTTTATTACTTTTAAAAAAGGGGAAATATCATTCATCATCTATCAATATC
40434 ATGATTAATAGTAATTAATAATTATTTTAGGGAATAGTAATTAATAATTTTGATTTGCCTATAGG
1 ATGATTAATAGTAATTAATAATT-TTTTAGGGAATAGTAATTAATAATTTTGATTTGCCTATAGG
* *
40499 AATAAATCACGTGTAATATCCAAAGTCCAAATCTTTAAAATTACCTAAAAACATAGTAGCAAACC
65 AATAAATCCCGTGTAATATCCAAAGTCCAAATCTTTAAAATTATCTAAAAACATAGTAGCAAACC
* *
40564 AATTATCCCTAAAAAATATCCGTTTTATGGCCAATATGAGGAGAGTTTGGCTTTATATAGAAAAG
130 AATTATCCC-AAAAAAAATCTGTTTTATGGCCAATATGAGGAGAGTTTGGCTTTATATAGAAAAG
* * *
40629 GCATCTATATTTTTTTTTTCATTAAAAAAGGGGTCTTTTGGTGGTCGTCATCGACCCGAGGGGCT
194 ACATCCATATTTTTTTTTTCATTAAAAAAGGGGTCTTTTGGTGGGCGTCATCGA-CCGAGGGGCT
* *
40694 CTAAGTCCCCCGCTCCCTCTTAAACCCCGGTGA-TTCCATGGCAAGGGGGCACACCTGCGGACAG
258 CTAAGTCCCCCACTCCCTCTTAAACCCCGGTGACTT-CATGGCGA-GGGGCACACCTGCGGACAG
* * *
40758 TAATGGGGCATGCCAAGAGTGGATTTTAACACAGGAT-GAAACAAACAAGAGTCTATGTGAGTAA
321 TAGTGGGGCGTGCCAAGAGTGGATTTTAACACAGGATGGAAACAAACAAGAGTCTATGTGAGAAA
* * * * * *
40822 AACATTGTGTTTACTGAGACTCAAACCCATGACCACACTTGTAGGAATCTTATACAACTTAGA--
386 AACATTGTGTTTACTCAGACTCGAACCCATGACCACACCTGCAGGAATCTTACACATCTTAGAGT
* *
40885 G-TG----AT-GA-TCGAGTCGGTGGGAGTTACCACACAATCGAAGCTAAATCACACATATAATC
451 GATGTCCTATAGACTCGAGTCCGTGGGAGTTACCACGCAATCGAAGCTAAATCACACATATAATC
** * * *
40943 ATGTATTCATTCTAAAACCCTATTATAATACATGTTTGGAAGTCCATATCTACCAATAAAATAAA
516 ATGTATTCATTCTAAAA-CCTACCATAATCCATGTTTAGAAGTCCATATCTACCCATAAAATAAA
*** * *
41008 TAAAAAAAAAATTTGGAGCTAAAATTCATATTAAAATTGTATCTTTATTATTAATGCCCTTAATT
580 TAAAAAATTTATTTGGAGCTAAAATTCATATTAAAATTGTATCTTAATTATTAATGTCCTTAATT
* * * * *
41073 GAACAACAGAAAAAATCGTATCTTAGTTCATTCTTTTATTTAATTTAATTTTCATATATCACCCT
645 GAACAACAGAAAAAATTGTATCTTAATTCCTTCTTTTATTTAATTTAATTTTCACATATCA-TC-
41138 TTTTATTACTTTTAAAAAAGGGGAAATATCATTCATCATCTATCAATAT
708 TTTTATTACTTTTAAAAAAGGGGAAATATCATTCATCATCTATCAATAT
41187 TTATATGCTA
Statistics
Matches: 1362, Mismatches: 123, Indels: 86
0.87 0.08 0.05
Matches are distributed among these distances:
752 163 0.12
753 67 0.05
754 36 0.03
758 1 0.00
759 206 0.15
760 5 0.00
761 111 0.08
762 169 0.12
763 351 0.26
764 126 0.09
765 4 0.00
769 4 0.00
770 57 0.04
771 62 0.05
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (757 bp):
ATGATTAATAGTAATTAATAATTTTTTAGGGAATAGTAATTAATAATTTTGATTTGCCTATAGGA
ATAAATCCCGTGTAATATCCAAAGTCCAAATCTTTAAAATTATCTAAAAACATAGTAGCAAACCA
ATTATCCCAAAAAAAATCTGTTTTATGGCCAATATGAGGAGAGTTTGGCTTTATATAGAAAAGAC
ATCCATATTTTTTTTTTCATTAAAAAAGGGGTCTTTTGGTGGGCGTCATCGACCGAGGGGCTCTA
AGTCCCCCACTCCCTCTTAAACCCCGGTGACTTCATGGCGAGGGGCACACCTGCGGACAGTAGTG
GGGCGTGCCAAGAGTGGATTTTAACACAGGATGGAAACAAACAAGAGTCTATGTGAGAAAAACAT
TGTGTTTACTCAGACTCGAACCCATGACCACACCTGCAGGAATCTTACACATCTTAGAGTGATGT
CCTATAGACTCGAGTCCGTGGGAGTTACCACGCAATCGAAGCTAAATCACACATATAATCATGTA
TTCATTCTAAAACCTACCATAATCCATGTTTAGAAGTCCATATCTACCCATAAAATAAATAAAAA
ATTTATTTGGAGCTAAAATTCATATTAAAATTGTATCTTAATTATTAATGTCCTTAATTGAACAA
CAGAAAAAATTGTATCTTAATTCCTTCTTTTATTTAATTTAATTTTCACATATCATCTTTTATTA
CTTTTAAAAAAGGGGAAATATCATTCATCATCTATCAATATC
Found at i:42363 original size:18 final size:18
Alignment explanation
Indices: 42340--42374 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42330 ACAAAAACTG
42340 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
42358 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
42375 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:42542 original size:29 final size:30
Alignment explanation
Indices: 42486--42553 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
42476 TACCCAGAAA
* *
42486 AATCCCTTATGTTTTGCTTTTGGGACAAAAT
1 AATCCCTTATGTTTT-CTTTCGAGACAAAAT
* *
42517 CATCCCTTATGTTTT-TTTCGAGACAAATT
1 AATCCCTTATGTTTTCTTTCGAGACAAAAT
42546 AATCCCTT
1 AATCCCTT
42554 GCGTTTCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 18 0.56
31 14 0.44
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.43
Consensus pattern (30 bp):
AATCCCTTATGTTTTCTTTCGAGACAAAAT
Found at i:42884 original size:15 final size:16
Alignment explanation
Indices: 42860--42892 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
42850 AAATTGATTT
42860 TTTTTCCTTTTTTTCC
1 TTTTTCCTTTTTTTCC
42876 TTTTT-CTTTTTTTCC
1 TTTTTCCTTTTTTTCC
42891 TT
1 TT
42893 CTCCTCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTCCTTTTTTTCC
Found at i:43148 original size:125 final size:124
Alignment explanation
Indices: 42978--43214 Score: 327
Period size: 125 Copynumber: 1.9 Consensus size: 124
42968 ATTCCCTAAA
* *
42978 AAAATGGTAAAGATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGA-ATTTTTG
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAGA-TTTTA
* *
43042 GTAAAATAAAACTGTAAAAGTTTAAATAAT-GTCATTTAAGAATATATTTAATTAAAATAGT
65 ATAAAATAAAACTGTAAAAGTTTAAA-AATGGT-ATTTAAAAATATATTTAATTAAAATAGT
* *
43103 AAAATGGTAAAAATAAAATAGTTATAAATATATT-AGATTTGATTAAATAAAAATAGAGATTTTA
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTGA-ATTTAATTAAATAAAAATAGAGATTTTA
** * *
43167 ATTGAGTAAAATTGTAAAAGTTTAAAAATGGTATTTAAAAATATATTT
65 ATAAAATAAAACTGTAAAAGTTTAAAAATGGTATTTAAAAATATATTT
43215 GAAAAATAAG
Statistics
Matches: 99, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
124 19 0.19
125 79 0.80
126 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.36
Consensus pattern (124 bp):
AAAATGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAGATTTTAA
TAAAATAAAACTGTAAAAGTTTAAAAATGGTATTTAAAAATATATTTAATTAAAATAGT
Found at i:43869 original size:31 final size:31
Alignment explanation
Indices: 43833--43929 Score: 158
Period size: 31 Copynumber: 3.1 Consensus size: 31
43823 ACTAAATACT
* * *
43833 AAAAAAATTCTCTTATATTTTTCTTTTTGGAC
1 AAAAAAA-TCCCTTATGTTTTTCTTTTGGGAC
43865 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
43896 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
43927 AAA
1 AAA
43930 TCAGTCTCTT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
31 55 0.89
32 7 0.11
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.43
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:44095 original size:29 final size:31
Alignment explanation
Indices: 44053--44126 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 31
44043 CTCATTTTTG
* *
44053 AAACGTAAGGGATTAATTTGTCCC-GAAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAAACA
* *
44082 AAACATAAGTGATTATTTTGTCCCAAAAACA
1 AAACATAAGGGATTAATTTGTCCCAAAAACA
44113 AAACATAAGGGATT
1 AAACATAAGGGATT
44127 TTTTTGGGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 21 0.55
30 3 0.08
31 14 0.37
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.26
Consensus pattern (31 bp):
AAACATAAGGGATTAATTTGTCCCAAAAACA
Found at i:45365 original size:20 final size:20
Alignment explanation
Indices: 45340--45381 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
45330 TTGGTGTGGC
45340 AATATCTCTTTTAATAGTAA
1 AATATCTCTTTTAATAGTAA
*
45360 AATATCTCTTTTGATAGTAA
1 AATATCTCTTTTAATAGTAA
45380 AA
1 AA
45382 CAAGCAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (20 bp):
AATATCTCTTTTAATAGTAA
Found at i:57583 original size:32 final size:32
Alignment explanation
Indices: 57536--57596 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
57526 TGTAAAAATT
* *
57536 TTGAATCGACTATTATACCCTTATTTTTCTAA
1 TTGAATCAACCATTATACCCTTATTTTTCTAA
*
57568 TTGAATCAACCATTATATCCTTATTTTTC
1 TTGAATCAACCATTATACCCTTATTTTTC
57597 AAACATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.48
Consensus pattern (32 bp):
TTGAATCAACCATTATACCCTTATTTTTCTAA
Done.