Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006560.1 Corchorus capsularis cultivar CVL-1 contig06581, 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: 106878
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:372 original size:110 final size:111
Alignment explanation
Indices: 196--397 Score: 316
Period size: 110 Copynumber: 1.8 Consensus size: 111
186 CCGGCGCGTT
* * *
196 GAGCATTCTTGATTTGTGGCTAGCTAGTAAATTATTTTAGTTTTAGAGGTTTTTTTTCCTCTCGG
1 GAGCATTCTTGATATGTGGCTAGC---TAAATCATTTTAGTTATAGAGGTTTTTTTTCCTCTCGG
*
261 TTCTTATCATATATGTGAGTAGGTGGTTATCGGCTCGAGCTGACGGGTC
63 TTCTTATCATATATGTCAGTAGGTGGTTATCGGCTCGAGCTGACGGGTC
* *
310 GAGCATTCTTGATATGTGGCTAGC-AAATCATTTTAGTTATAGAGTTTTTTTTTTCTCTCGGTTC
1 GAGCATTCTTGATATGTGGCTAGCTAAATCATTTTAGTTATAGAGGTTTTTTTTCCTCTCGGTTC
374 TTATCATATATGTCAGTAGGTGGT
66 TTATCATATATGTCAGTAGGTGGT
398 CAACAAATTC
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
110 59 0.72
114 23 0.28
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.44
Consensus pattern (111 bp):
GAGCATTCTTGATATGTGGCTAGCTAAATCATTTTAGTTATAGAGGTTTTTTTTCCTCTCGGTTC
TTATCATATATGTCAGTAGGTGGTTATCGGCTCGAGCTGACGGGTC
Found at i:2610 original size:950 final size:950
Alignment explanation
Indices: 763--3614 Score: 5616
Period size: 950 Copynumber: 3.0 Consensus size: 950
753 TTCACCTTTA
*
763 GCAAAAGACCAAAAGGTAGAGTTATCCGTCTCAACATTAACCAACGTTTAGCTTTAATGTCTTTG
1 GCAAAAGACCAAAAGGTAGAGTTATCCATCTCAACATTAACCAACGTTTAGCTTTAATGTCTTTG
828 GCTAGACCTTTCCATTGTCTATTCTTCAAGGAGGATCTTTCCACCTCAAAGCAAAAAGAAAATAT
66 GCTAGACCTTTCCATTGTCTATTCTTCAAGGAGGATCTTTCCACCTCAAAGCAAAAAGAAAATAT
*
893 GAAACAAATTCAAAAATTTGCAAATATAAGAATAAAATAAAATTAAAGAGATATGAAAAGAAGTC
131 GAAACAAATTCAAAAATTTGCAAATATAAGAATAAAATAAAATTAAAGAGATATGGAAAGAAGTC
958 GCCAATTTTGCTTAAAGGAACTCCATGAATGGCTAGTAAAGCCAATGCCCTTGTTGTTGCTGTGG
196 GCCAATTTTGCTTAAAGGAACTCCATGAATGGCTAGTAAAGCCAATGCCCTTGTTGTTGCTGTGG
1023 TGGGTTTATGCAAGAGCTTCTTCGAGTGAAAGAAATTGACTTTAGACTCCTCCTGCATTCTCAGC
261 TGGGTTTATGCAAGAGCTTCTTCGAGTGAAAGAAATTGACTTTAGACTCCTCCTGCATTCTCAGC
1088 ATCTTGGCAACTTTACGAAACTTGCAGGCATCATCATTCTTAAAGAATGGCTCCGTTGTCACCCA
326 ATCTTGGCAACTTTACGAAACTTGCAGGCATCATCATTCTTAAAGAATGGCTCCGTTGTCACCCA
1153 TTCATCATAGGAATCACCATTGAAGCATCCAAACTCCAAAAACTTCTCAATCCCTAGGAAATCTT
391 TTCATCATAGGAATCACCATTGAAGCATCCAAACTCCAAAAACTTCTCAATCCCTAGGAAATCTT
1218 GATTCTCACATCTCAAAATCTCAATTGGAGGAGATTTATCAACCAAATTGGCTTTAGATGAGGAG
456 GATTCTCACATCTCAAAATCTCAATTGGAGGAGATTTATCAACCAAATTGGCTTTAGATGAGGAG
1283 TTTTCACTTAAAGTTGGCTTGGGAAGGAGTTGAGGTTGATCCACTAAAGAAGTTATGTCTTCAAG
521 TTTTCACTTAAAGTTGGCTTGGGAAGGAGTTGAGGTTGATCCACTAAAGAAGTTATGTCTTCAAG
1348 TTCATCTAGGCAAAGTGTTGTTTCGACCTCTATGAAGGTCCTTTCCAGAGGTTGAATTAGGAGAT
586 TTCATCTAGGCAAAGTGTTGTTTCGACCTCTATGAAGGTCCTTTCCAGAGGTTGAATTAGGAGAT
1413 TTTCTGAATTCTGCCCAGTTCAACCCTTAATAAGGTCCAATTCGACCTTCTCGAAGGTTGAAATA
651 TTTCTGAATTCTGCCCAGTTCAACCCTTAATAAGGTCCAATTCGACCTTCTCGAAGGTTGAAATA
1478 GAGTTCGTTTTCTCTTCTTTTTCAGCTTTATCCTCAACTTGATTCACTTCCCATGCTTCATTTTC
716 GAGTTCGTTTTCTCTTCTTTTTCAGCTTTATCCTCAACTTGATTCACTTCCCATGCTTCATTTTC
1543 TTCTTCCTCAAGGGCATTGAGGTAAGCTTCGATCCTTCCTAAGGAAACAATAATTTCCCCCATTT
781 TTCTTCCTCAAGGGCATTGAGGTAAGCTTCGATCCTTCCTAAGGAAACAATAATTTCCCCCATTT
1608 GATTCTTAATGTTTGTGAGCTCTTCATCATGTCTCAACAAGGTCTCATTTCTTTTCAACTGACTC
846 GATTCTTAATGTTTGTGAGCTCTTCATCATGTCTCAACAAGGTCTCATTTCTTTTCAACTGACTC
1673 TCAGTCAACTTCTGCAAAATTGCTTCCAAATTCGAGTTCT
911 TCAGTCAACTTCTGCAAAATTGCTTCCAAATTCGAGTTCT
1713 GCAAAAGACCAAAAGGTAGAGTTATCCATCTCAACATTAACCAACGTTTAGCTTTAATGTCTTTG
1 GCAAAAGACCAAAAGGTAGAGTTATCCATCTCAACATTAACCAACGTTTAGCTTTAATGTCTTTG
1778 GCTAGACCTTTCCATTGTCTATTCTTCAAGGAGGATCTTTCCACCTCAAAGCAAAAAGAAAATAT
66 GCTAGACCTTTCCATTGTCTATTCTTCAAGGAGGATCTTTCCACCTCAAAGCAAAAAGAAAATAT
1843 GAAACAAATTCAAAAATTTGCAAATATAAGAATAAAATAAAATTAAAGAGATATGGAAAGAAGTC
131 GAAACAAATTCAAAAATTTGCAAATATAAGAATAAAATAAAATTAAAGAGATATGGAAAGAAGTC
1908 GCCAATTTTGCTTAAAGGAACTCCATGAATGGCTAGTAAAGCCAATGCCCTTGTTGTTGCTGTGG
196 GCCAATTTTGCTTAAAGGAACTCCATGAATGGCTAGTAAAGCCAATGCCCTTGTTGTTGCTGTGG
1973 TGGGTTTATGCAAGAGCTTCTTCGAGTGAAAGAAATTGACTTTAGACTCCTCCTGCATTCTCAGC
261 TGGGTTTATGCAAGAGCTTCTTCGAGTGAAAGAAATTGACTTTAGACTCCTCCTGCATTCTCAGC
2038 ATCTTGGCAACTTTACGAAACTTGCAGGCATCATCATTCTTAAAGAATGGCTCCGTTGTCACCCA
326 ATCTTGGCAACTTTACGAAACTTGCAGGCATCATCATTCTTAAAGAATGGCTCCGTTGTCACCCA
2103 TTCATCATAGGAATCACCATTGAAGCATCCAAACTCCAAAAACTTCTCAATCCCTAGGAAATCTT
391 TTCATCATAGGAATCACCATTGAAGCATCCAAACTCCAAAAACTTCTCAATCCCTAGGAAATCTT
2168 GATTCTCACATCTCAAAATCTCAATTGGAGGAGATTTATCAACCAAATTGGCTTTAGATGAGGAG
456 GATTCTCACATCTCAAAATCTCAATTGGAGGAGATTTATCAACCAAATTGGCTTTAGATGAGGAG
2233 TTTTCACTTAAAGTTGGCTTGGGAAGGAGTTGAGGTTGATCCACTAAAGAAGTTATGTCTTCAAG
521 TTTTCACTTAAAGTTGGCTTGGGAAGGAGTTGAGGTTGATCCACTAAAGAAGTTATGTCTTCAAG
*
2298 TTCATCTAGGCAAAGTGTTGTTTCGACCTCTATGAAGGTCCATTCCAGAGGTTGAATTAGGAGAT
586 TTCATCTAGGCAAAGTGTTGTTTCGACCTCTATGAAGGTCCTTTCCAGAGGTTGAATTAGGAGAT
2363 TTTCTGAATTCTGCCCAGTTCAACCCTTAATAAGGTCCAATTCGACCTTCTCGAAGGTTGAAATA
651 TTTCTGAATTCTGCCCAGTTCAACCCTTAATAAGGTCCAATTCGACCTTCTCGAAGGTTGAAATA
2428 GAGTTCGTTTTCTCTTCTTTTTTCAGCTTTATCCTCAACTTGATTCACTTCCCATGCTTCATTTT
716 GAGTTCGTTTTCTCTTC-TTTTTCAGCTTTATCCTCAACTTGATTCACTTCCCATGCTTCATTTT
2493 CTTCTTCCTCAAGGGCATTGAGGTAAGCTTCGATCCTTCCTAAGGAAACAATAATTTCCCCCATT
780 CTTCTTCCTCAAGGGCATTGAGGTAAGCTTCGATCCTTCCTAAGGAAACAATAATTTCCCCCATT
2558 TGATTCTTAATGTTTGTGAGCTCTTCATCATGTCTCAACAAGGTCT-ATTTCTTTTCAACTGACT
845 TGATTCTTAATGTTTGTGAGCTCTTCATCATGTCTCAACAAGGTCTCATTTCTTTTCAACTGACT
2622 CTCAGTCAACTTCTGCAAAATTGCTTCCAAATTCGAGTTCT
910 CTCAGTCAACTTCTGCAAAATTGCTTCCAAATTCGAGTTCT
2663 GCAAAAGACCAAAAGGTAGAGTTATCCATCTCAACATTAACCAACGTTTAGCTTTAATGTCTTTG
1 GCAAAAGACCAAAAGGTAGAGTTATCCATCTCAACATTAACCAACGTTTAGCTTTAATGTCTTTG
2728 GCTAGACCTTTCCATTGTCTATTCTTCAAGGAGGATCTTTCCACCTCAAAGCAAAAAGAAAATAT
66 GCTAGACCTTTCCATTGTCTATTCTTCAAGGAGGATCTTTCCACCTCAAAGCAAAAAGAAAATAT
2793 GAAACAAATTCAAAAATTTGCAAATATAAGAATAAAATAAAATTAAAGAGATATGGAAAGAAGTC
131 GAAACAAATTCAAAAATTTGCAAATATAAGAATAAAATAAAATTAAAGAGATATGGAAAGAAGTC
*
2858 GCCAATTTTGCTTAAAGGAACTCCATGAATGGCTAGTAAAGCCAATGCCCTTGTTGTTGCTATGG
196 GCCAATTTTGCTTAAAGGAACTCCATGAATGGCTAGTAAAGCCAATGCCCTTGTTGTTGCTGTGG
* *
2923 TGGGTTTGTGCAAGAGCTTCTTCAAGTGAAAGAAATTGACTTTAGACTCCTCCTGCATTCTCAGC
261 TGGGTTTATGCAAGAGCTTCTTCGAGTGAAAGAAATTGACTTTAGACTCCTCCTGCATTCTCAGC
2988 ATCTTGGCAACTTTACGAAACTTGCAGGCATCATCATTCTTAAAGAATGGCTCCGTTGTCACCCA
326 ATCTTGGCAACTTTACGAAACTTGCAGGCATCATCATTCTTAAAGAATGGCTCCGTTGTCACCCA
3053 TTCATCATAGGAATCACCATTGAAGCATCCAAACTCCAAAAACTTCTCAATCCCTAGGAAATCTT
391 TTCATCATAGGAATCACCATTGAAGCATCCAAACTCCAAAAACTTCTCAATCCCTAGGAAATCTT
3118 GATTCTCACATCTCAAAATCTCAATTGGAGGAGATTTATCAACCAAATTGGCTTTAGATGAGGAG
456 GATTCTCACATCTCAAAATCTCAATTGGAGGAGATTTATCAACCAAATTGGCTTTAGATGAGGAG
3183 TTTTCACTTAAAGTTGGCTTGGGAAGGAGTTGAGGTTGATCCACTAAAGAAGTTATGTCTTCAAG
521 TTTTCACTTAAAGTTGGCTTGGGAAGGAGTTGAGGTTGATCCACTAAAGAAGTTATGTCTTCAAG
3248 TTCATCTAGGCAAAGTGTTGTTTCGACCTCTATGAAGGTCCTTTCCAGAGGTTGAATTAGGAGAT
586 TTCATCTAGGCAAAGTGTTGTTTCGACCTCTATGAAGGTCCTTTCCAGAGGTTGAATTAGGAGAT
*
3313 TTTCTGAATTCTGCCCAGTTCGACCCTTAATAAGGTCCAATTCGACCTTCTCGAAGGTTGAAATA
651 TTTCTGAATTCTGCCCAGTTCAACCCTTAATAAGGTCCAATTCGACCTTCTCGAAGGTTGAAATA
3378 GAGTTCGTTTTCTCTTCTTTTTCAGCTTTATCCTCAACTTGATTCACTTCCCATGCTTCATTTTC
716 GAGTTCGTTTTCTCTTCTTTTTCAGCTTTATCCTCAACTTGATTCACTTCCCATGCTTCATTTTC
*
3443 TTCTTCCTCAAGGGCATTGAGGTAAGCTTCGATCCTTCCTAAGGAAACAACAATTTCCCCCATTT
781 TTCTTCCTCAAGGGCATTGAGGTAAGCTTCGATCCTTCCTAAGGAAACAATAATTTCCCCCATTT
3508 GATTCTTAATGTTTGTGAGCTCTTCATCATGTCTCAACAAGGTCTCATTTCTTTTCAACTGACTC
846 GATTCTTAATGTTTGTGAGCTCTTCATCATGTCTCAACAAGGTCTCATTTCTTTTCAACTGACTC
3573 TCAGTCAACTTCTGCAAAATTGCTTCCAAATTCGAGTTCT
911 TCAGTCAACTTCTGCAAAATTGCTTCCAAATTCGAGTTCT
3613 GC
1 GC
3615 TCATGATTTG
Statistics
Matches: 1891, Mismatches: 9, Indels: 4
0.99 0.00 0.00
Matches are distributed among these distances:
949 157 0.08
950 1576 0.83
951 158 0.08
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (950 bp):
GCAAAAGACCAAAAGGTAGAGTTATCCATCTCAACATTAACCAACGTTTAGCTTTAATGTCTTTG
GCTAGACCTTTCCATTGTCTATTCTTCAAGGAGGATCTTTCCACCTCAAAGCAAAAAGAAAATAT
GAAACAAATTCAAAAATTTGCAAATATAAGAATAAAATAAAATTAAAGAGATATGGAAAGAAGTC
GCCAATTTTGCTTAAAGGAACTCCATGAATGGCTAGTAAAGCCAATGCCCTTGTTGTTGCTGTGG
TGGGTTTATGCAAGAGCTTCTTCGAGTGAAAGAAATTGACTTTAGACTCCTCCTGCATTCTCAGC
ATCTTGGCAACTTTACGAAACTTGCAGGCATCATCATTCTTAAAGAATGGCTCCGTTGTCACCCA
TTCATCATAGGAATCACCATTGAAGCATCCAAACTCCAAAAACTTCTCAATCCCTAGGAAATCTT
GATTCTCACATCTCAAAATCTCAATTGGAGGAGATTTATCAACCAAATTGGCTTTAGATGAGGAG
TTTTCACTTAAAGTTGGCTTGGGAAGGAGTTGAGGTTGATCCACTAAAGAAGTTATGTCTTCAAG
TTCATCTAGGCAAAGTGTTGTTTCGACCTCTATGAAGGTCCTTTCCAGAGGTTGAATTAGGAGAT
TTTCTGAATTCTGCCCAGTTCAACCCTTAATAAGGTCCAATTCGACCTTCTCGAAGGTTGAAATA
GAGTTCGTTTTCTCTTCTTTTTCAGCTTTATCCTCAACTTGATTCACTTCCCATGCTTCATTTTC
TTCTTCCTCAAGGGCATTGAGGTAAGCTTCGATCCTTCCTAAGGAAACAATAATTTCCCCCATTT
GATTCTTAATGTTTGTGAGCTCTTCATCATGTCTCAACAAGGTCTCATTTCTTTTCAACTGACTC
TCAGTCAACTTCTGCAAAATTGCTTCCAAATTCGAGTTCT
Found at i:4214 original size:24 final size:25
Alignment explanation
Indices: 4187--4237 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
4177 ATTAAGGAAC
*
4187 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
* *
4211 AATAAAATTAAGCAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
4236 AA
1 AA
4238 ATACTCCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:4239 original size:21 final size:21
Alignment explanation
Indices: 4174--4239 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
4164 TGGGGTTTTG
* *
4174 TAAATTAAGGAACAATA-AAA
1 TAAATTAAGCAACAAAATAAA
* *
4194 TAAA-TAAACAAGAAAAT-AA
1 TAAATTAAGCAACAAAATAAA
*
4213 TAAAATTAAGCAACAAGATAAA
1 T-AAATTAAGCAACAAAATAAA
4235 TAAAT
1 TAAAT
4240 ACTCCAATCC
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
19 11 0.31
20 7 0.20
21 14 0.40
22 3 0.09
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.20
Consensus pattern (21 bp):
TAAATTAAGCAACAAAATAAA
Found at i:7098 original size:166 final size:165
Alignment explanation
Indices: 6732--7173 Score: 570
Period size: 166 Copynumber: 2.7 Consensus size: 165
6722 GAGTCATTTG
*
6732 TCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCTCTCAAGAATCAAAAGTTAGGACATT
1 TCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCC-CTCAAGAATTAAAAGTTAGGACATT
* * * ** * *
6797 TAAGTAATCTGCAAAGTAGGTAAAGACGAAAAAAATTAGTTATCTAGCTCATCATCAATCCTTAA
65 TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTATCTAACTCAAAAGCAAGCCTTAA
* * *
6862 TGGAGATCTTTTATTAATTCCACTACTCTATTCAAG
130 TGGAGATCTTTTAGTAATTCCACTACTCTATTAAAA
* * *
6898 TCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCACCTCAAGAATTAAAAGTTAGGACATT
1 TCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATC-CCTCAAGAATTAAAAGTTAGGACATT
* * *
6963 TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTTTCTAACTCCAAAAGCAAGCCTTG
65 TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTATCTAACT-CAAAAGCAAGCCTTA
* *
7028 GTAGG-GATCTTTTAGTAATTGCACTACTCTATTAAAA
129 AT-GGAGATCTTTTAGTAATTCCACTACTCTATTAAAA
* **
7065 TCAATTGAGAAATGACC-AAAA-TTCTAGTTATTTAATCCCCTCAAGAATTAAAATTTAGGGTAT
1 TCAATTGAGAAATGACCAAAAAGTT-TAGTTATTTAAT-CCCTCAAGAATTAAAAGTTAGGACAT
*
7128 TTAAGTAATC-GATCAAGT-GTGAAAAGACGAAAAAAATTAGTTATCT
64 TTAAGTAATCTG-CCAAGTAG-GAAAAGACGAAAAAAATTAGTTATCT
7174 CGCTCCTCAT
Statistics
Matches: 241, Mismatches: 28, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
165 3 0.01
166 179 0.74
167 57 0.24
168 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (165 bp):
TCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCTCAAGAATTAAAAGTTAGGACATTT
AAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTATCTAACTCAAAAGCAAGCCTTAAT
GGAGATCTTTTAGTAATTCCACTACTCTATTAAAA
Found at i:7960 original size:30 final size:31
Alignment explanation
Indices: 7915--7973 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
7905 TCACTTCAAA
7915 GAAAATTTTAAGATATTGATCCCA-TAAATT
1 GAAAATTTTAAGATATTGATCCCACTAAATT
* * *
7945 GAAAGTTTTAGGATATTGATTCCACTAAA
1 GAAAATTTTAAGATATTGATCCCACTAAA
7974 AGATTTGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (31 bp):
GAAAATTTTAAGATATTGATCCCACTAAATT
Found at i:11372 original size:15 final size:15
Alignment explanation
Indices: 11352--11384 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11342 AAATTTGTTA
11352 ATGCACTTATTTTAT
1 ATGCACTTATTTTAT
11367 ATGCACTTATTTTAT
1 ATGCACTTATTTTAT
11382 ATG
1 ATG
11385 AACTCTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (15 bp):
ATGCACTTATTTTAT
Found at i:24221 original size:15 final size:15
Alignment explanation
Indices: 24200--24234 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
24190 AGTCGCCCCT
*
24200 CCTCCTCCTCCGCCA
1 CCTCCTCCACCGCCA
*
24215 GCTCCTCCACCGCCA
1 CCTCCTCCACCGCCA
24230 CCTCC
1 CCTCC
24235 ACCGCCGCCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.66, G:0.09, T:0.17
Consensus pattern (15 bp):
CCTCCTCCACCGCCA
Found at i:49367 original size:244 final size:244
Alignment explanation
Indices: 48928--49660 Score: 1295
Period size: 244 Copynumber: 3.0 Consensus size: 244
48918 AATCCGATGC
48928 GCTCAGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAGGAACT
1 GCTCAGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAGGAACT
* *
48993 AAATAGCAGTTCTGTCGAGGAAATTTTCACATTTGAGAAATGATCCCTTGCCTTACTCTCACACT
66 AAATAGCAGTTCTGTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTCACACT
* * *
49058 TCACTAGGGGTAGTAGACTTCCTGCATTCTTGACAGATTGTAAGCTCTGCTGGAACAATCCCTTT
131 TCACTAGGGGTAGTAGACTTCCTGCATCCTTGACAGATTGTAAGCTCTGCTGGAATAAGCCCTTT
** *
49123 CCATCTAAAGTGGGGTACTTGATCGCAGCAGGCTCAATTGTTGGAGCAG
196 CCATCTAAAGTGGGGTACTCAATCGCACCAGGCTCAATTGTTGGAGCAG
49172 GCTCAGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAGGAACT
1 GCTCAGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAGGAACT
* * *
49237 AAATAGCAGTTCTTTCGACGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACCCTCACACT
66 AAATAGCAGTTCTGTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTCACACT
*
49302 TCACTAGGGGTAGTAGACTTCCTGCATCCTTGACCGATTGTAAGCTCTGCTGGAATAAGCCCTTT
131 TCACTAGGGGTAGTAGACTTCCTGCATCCTTGACAGATTGTAAGCTCTGCTGGAATAAGCCCTTT
* *
49367 CCATCTAAAGTGGGGTACTCAATCACACCAGACTCAATTGTTGGAGCAG
196 CCATCTAAAGTGGGGTACTCAATCGCACCAGGCTCAATTGTTGGAGCAG
*
49416 GCTCAGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAGAAAGCAGTCAACTTTAGGAACT
1 GCTCAGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAGGAACT
*
49481 AAATAGCAGTTCTGTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTCACACC
66 AAATAGCAGTTCTGTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTCACACT
* *
49546 TCAGTAGGGGTAGTAGACTTCGTGCATCCTTGACAGATTGTAAGCTCTGCTGGAATAAGCCCTTT
131 TCACTAGGGGTAGTAGACTTCCTGCATCCTTGACAGATTGTAAGCTCTGCTGGAATAAGCCCTTT
*
49611 CCATCTAAAGTGGGGTACTCAATCGCACCAGGCTCAATTCTTGGAGCAG
196 CCATCTAAAGTGGGGTACTCAATCGCACCAGGCTCAATTGTTGGAGCAG
49660 G
1 G
49661 TGCAAGAAAA
Statistics
Matches: 464, Mismatches: 25, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
244 464 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (244 bp):
GCTCAGCATATTTGCACACTTCAACCTCTAGTTCCTATTGTAAAAAGCAGTCAACTTTAGGAACT
AAATAGCAGTTCTGTCGAGGAAATTTTCACATTTGAGAAATGTTCCCTTACCTTACTCTCACACT
TCACTAGGGGTAGTAGACTTCCTGCATCCTTGACAGATTGTAAGCTCTGCTGGAATAAGCCCTTT
CCATCTAAAGTGGGGTACTCAATCGCACCAGGCTCAATTGTTGGAGCAG
Found at i:61398 original size:6 final size:6
Alignment explanation
Indices: 61387--61443 Score: 98
Period size: 6 Copynumber: 9.7 Consensus size: 6
61377 GTTTGCTGAT
*
61387 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAA-GG AAAGGG
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG
61434 GAAGGG GAAG
1 GAAGGG GAAG
61444 ACGAAGAGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
5 4 0.08
6 44 0.92
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:85203 original size:42 final size:42
Alignment explanation
Indices: 85149--85235 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
85139 TGAACCTGGG
*
85149 TTTAAGTCTCACGAAATGTGAGTTTAGTTTGTAATTTGTTTA
1 TTTAAGTCTCACGAAATGTGAATTTAGTTTGTAATTTGTTTA
85191 TTTAAGTCTCACGAAATGTGAATTTAGTTTGTAATTTGTTTA
1 TTTAAGTCTCACGAAATGTGAATTTAGTTTGTAATTTGTTTA
85233 TTT
1 TTT
85236 TTGTATTTGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.49
Consensus pattern (42 bp):
TTTAAGTCTCACGAAATGTGAATTTAGTTTGTAATTTGTTTA
Found at i:93000 original size:32 final size:32
Alignment explanation
Indices: 92917--92992 Score: 152
Period size: 32 Copynumber: 2.4 Consensus size: 32
92907 CTTACGTGAA
92917 ATGCCACGTCAGGTGAAAAATTGCCATGTAGC
1 ATGCCACGTCAGGTGAAAAATTGCCATGTAGC
92949 ATGCCACGTCAGGTGAAAAATTGCCATGTAGC
1 ATGCCACGTCAGGTGAAAAATTGCCATGTAGC
92981 ATGCCACGTCAG
1 ATGCCACGTCAG
92993 CATAAAAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (32 bp):
ATGCCACGTCAGGTGAAAAATTGCCATGTAGC
Found at i:94378 original size:1 final size:1
Alignment explanation
Indices: 94372--94402 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
94362 CTAGAAGTAG
94372 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
94403 CCCTTGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:96222 original size:3 final size:3
Alignment explanation
Indices: 96214--96240 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
96204 AGGAGCCCCG
96214 ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA
96241 GGAAAGTTCT
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:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Done.