Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010501.1 Corchorus capsularis cultivar CVL-1 contig10522, 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: 129553
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:631 original size:323 final size:321
Alignment explanation
Indices: 1--1032 Score: 1391
Period size: 323 Copynumber: 3.2 Consensus size: 321
* * * * *
1 ATTTCTGCTAAAAAGTGATCTGAAATTTTTTTTATGAAATTTTCA-CCATAATACTCT-GACAAA
1 ATTTCTGCTAAAAAGTGACCCGAAATTTTTTTTCTGAAATTTT-AGCCACAATACT-TAGAAAAA
* ** ** *
64 ATATTTAATTTAAAGCAAAAAAA-AAAGAAGGATTTTTCACACTTCCAATATTGTTTTTCCATTT
64 ATATGTAATTTAAAGCAAAAAAATATTGAAGGATTTTTCACGTTTCCAATATCGTTTTTCCATTT
**
128 TTTTTTCCAAATTTATTTCTAATTAAACCGAAACAAATTCAGATGCTCATAAAAACAAATCCTTA
129 TTCCTT---AATTTATTTCTAATTAAACCGAAACAAATTCAGATGCTCATAAAAACAAATCCTTA
* *
193 AATGCATTGTGGCTGAGATTTGGTTCCATGAATATAGATATTTCAAGGAGACTTTCTGCCAAAAA
191 AATGCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGGCTTTCTGCCAAAAA
* *
258 TCTTGAAAAACTGAGACGGGCCCTCAAAACGCATTTTTA-CCACAAAAACCGTGATGGTTAGTAC
256 TCATGAAAAACTGAGACGGGCCC-CAAAACGCGTTTTTACCCAC-AAAACCGTGATGGTTAGTAC
322 ACG
319 ACG
*
325 ATTTCTGCTAAAAAGTGACCCGAAATTTTATTTTTTGAAATTTTAGCCACAATACTTAGAAAAAA
1 ATTTCTGCTAAAAAGTGACCCGAAATTTT-TTTTCTGAAATTTTAGCCACAATACTTAGAAAAAA
* *
390 TATGTAATTGAAAGCAAAAAAATATTGAAGGATTTTTTACGTTTCCAATATCGTTTTTCCATTTT
65 TATGTAATTTAAAGCAAAAAAATATTGAAGGATTTTTCACGTTTCCAATATCGTTTTTCCATTTT
*
455 TCCTTAATTTATTTCTAATTAAACCGAAACAAATTCAGATGCTCGTAAAAACAAATCCTTAAATG
130 TCCTTAATTTATTTCTAATTAAACCGAAACAAATTCAGATGCTCATAAAAACAAATCCTTAAATG
* * *
520 CATTGTGGCTGAGGTATAGTTCGATGAATATAGATATTTCAAGGAGGCTTTCTGCCAAAAATCAT
195 CATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGGCTTTCTGCCAAAAATCAT
*
585 GGAAAACTGAGACGGGCCCACAAAACGCGTTTTTACCCACAAAACCGTGATGGTTAGTACACG
260 GAAAAACTGAGACGGGCCC-CAAAACGCGTTTTTACCCACAAAACCGTGATGGTTAGTACACG
* * *
648 ATTTCTACTAAAAAGTGACACGAAATTTTTTTTCTGAAATTTTAACCTA-AATACTTA-AAAAAA
1 ATTTCTGCTAAAAAGTGACCCGAAATTTTTTTTCTGAAATTTTAGCC-ACAATACTTAGAAAAAA
* *
711 TATGTAATTTAAAGCAAAAAAATATTGAAGAATTTTTCATGTTTCCAATATCAG-TTTTCCATTT
65 TATGTAATTTAAAGCAAAAAAATATTGAAGGATTTTTCACGTTTCCAATATC-GTTTTTCCATTT
* * * ** *
775 TTCCCTAATTTATTTTTAATTAAA-CGAAAACAAATTTAGATGCTCATAAAATTAAA-CCCTAAA
129 TTCCTTAATTTATTTCTAATTAAACCG-AAACAAATTCAGATGCTCATAAAAACAAATCCTTAAA
* * * * * *
838 TCCATTGTGGCTGAAATTTGGTTCGATGAATTTAGATATTTCAAGGAGGCATTCAGCAAAAAATC
193 TGCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGGCTTTCTGCCAAAAATC
* * *
903 ATGAAAAACTGAGAAGGGCCCCAAAACGCGTTTTTTATCCC-CAAAACCGTGATAGTTAATACAC
258 ATGAAAAACTGAGACGGGCCCCAAAACGCG-TTTTTA-CCCACAAAACCGTGATGGTTAGTACAC
*
967 A
321 G
* * * * * * *
968 ATTTCGGCTAAAAAGTGACCCGAAAGTTTTTTTCCGACATTTTCGTCACAATACTCAGAAAAAAT
1 ATTTCTGCTAAAAAGTGACCCGAAATTTTTTTTCTGAAATTTTAGCCACAATACTTAGAAAAAAT
1033 CAGATGCTCC
Statistics
Matches: 632, Mismatches: 64, Indels: 27
0.87 0.09 0.04
Matches are distributed among these distances:
319 10 0.02
320 155 0.25
321 121 0.19
322 25 0.04
323 201 0.32
324 33 0.05
325 48 0.08
326 39 0.06
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.33
Consensus pattern (321 bp):
ATTTCTGCTAAAAAGTGACCCGAAATTTTTTTTCTGAAATTTTAGCCACAATACTTAGAAAAAAT
ATGTAATTTAAAGCAAAAAAATATTGAAGGATTTTTCACGTTTCCAATATCGTTTTTCCATTTTT
CCTTAATTTATTTCTAATTAAACCGAAACAAATTCAGATGCTCATAAAAACAAATCCTTAAATGC
ATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGGCTTTCTGCCAAAAATCATG
AAAAACTGAGACGGGCCCCAAAACGCGTTTTTACCCACAAAACCGTGATGGTTAGTACACG
Found at i:1896 original size:321 final size:321
Alignment explanation
Indices: 1187--1977 Score: 1021
Period size: 321 Copynumber: 2.5 Consensus size: 321
1177 TTTAAAGCAA
** *
1187 AAAAAAAAGAGAAGGATTTTTCACGCTTCCAATATTGTTTTTCCACTTTTTTTCCAAATTTATTT
1 AAAAAAAATTGAAGGATTTTTCACGCTTCCAATATCGTTTTTCCA--TTTTTTCCAAATTTATTT
* *
1252 CTAATTAAACCGAAACAAATTCAGATGCTCATACAAAAAAAATCCTTAAATGCATTGTGGCTGAG
64 CTAATTAAACCGAAACAAATTCAGATGCTCTTA-AAAACAAATCCTTAAATGCATTGTGGCTGAG
* * * *
1317 ATTTGGTTCG---AT-GA-ATATTTCAATGAGGTTTTCTGCCATAAATCATGCAAAACTAAGACG
128 ATTTGGTTCGATAATATAGATATTTCAATGAGGGTTTCTGCAAAAAATCATGCAAAACTAAGACG
* * * *
1377 GGTCACCGAGACACGTTTTTACCCTAAAAACCGTGATGGTTAATACACGATTTTCGACTAAAAAG
193 GGTCACCGAAACACGTTTTTAACCAAAAAACCGTGATGGTTAATACACGAATTTCGACTAAAAAG
* * * * * *
1442 TGACCCAAAAATATTTTTCTGAAATTTTTGCCATAATACTCAGAAAGAATATGTAATTTAACAT
258 TGACCCAAAAATATTTTTCTGAAATTTTCGCCACAATACTAAGAAAAAATATGTAATTCAACAC
* * * * * *
1506 AAAAAAATTTGAAGGATTTATCACGCTTCCAATAACGTTTTTCC-TTTTTTCCTAATTTGTTTTT
1 AAAAAAAATTGAAGGATTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTCCAAATTTATTTCT
* * *
1570 AATTAAACCGAAACAAATTCATATGCTCTTAAAAACAAATCCTTAAATGCATTGTGACTAAGATT
66 AATTAAACCGAAACAAATTCAGATGCTCTTAAAAACAAATCCTTAAATGCATTGTGGCTGAGATT
* *
1635 TGGTTCGATTAATATAGATATTTCAA-GAAGGGTTTCTGCAAAAAATCTTGCAAAACTGAGACGG
131 TGGTTCGA-TAATATAGATATTTCAATG-AGGGTTTCTGCAAAAAATCATGCAAAACTAAGACGG
* * * * *
1699 GTCTCCGAAACGCTTTTTTAACCAAAAAACCGTGATGGTTAGTACAC-AATTTCGGCTAAAAAGT
194 GTCACCGAAACACGTTTTTAACCAAAAAACCGTGATGGTTAATACACGAATTTCGACTAAAAAGT
* *
1763 GACCCGAAAAT-TTTTTCCTGAAATTTTCGCCACAATACTAAGAAAAAATATGTAA-TCAACGC
259 GACCCAAAAATATTTTT-CTGAAATTTTCGCCACAATACTAAGAAAAAATATGTAATTCAACAC
*
1825 AAAAAAAATTGAAGGATTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTCCCCAATTTATTTC
1 AAAAAAAATTGAAGGATTTTTCACGCTTCCAATATCGTTTTTCCATTTTTT-CCAAATTTATTTC
* * * *
1890 TAATTAAACTGAAACAAAATT-AGATGCT-TGTAAAAACAAATCTTTAAATCCATTATGGCTGAG
65 TAATTAAACCGAAAC-AAATTCAGATGCTCT-TAAAAACAAATCCTTAAATGCATTGTGGCTGAG
*
1953 ATTTGGTTCGATGAACATAGATATT
128 ATTTGGTTCGAT-AATATAGATATT
1978 CACGTTTCAA
Statistics
Matches: 408, Mismatches: 51, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
315 38 0.09
316 46 0.11
319 90 0.22
320 69 0.17
321 160 0.39
322 5 0.01
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (321 bp):
AAAAAAAATTGAAGGATTTTTCACGCTTCCAATATCGTTTTTCCATTTTTTCCAAATTTATTTCT
AATTAAACCGAAACAAATTCAGATGCTCTTAAAAACAAATCCTTAAATGCATTGTGGCTGAGATT
TGGTTCGATAATATAGATATTTCAATGAGGGTTTCTGCAAAAAATCATGCAAAACTAAGACGGGT
CACCGAAACACGTTTTTAACCAAAAAACCGTGATGGTTAATACACGAATTTCGACTAAAAAGTGA
CCCAAAAATATTTTTCTGAAATTTTCGCCACAATACTAAGAAAAAATATGTAATTCAACAC
Found at i:2079 original size:130 final size:132
Alignment explanation
Indices: 1844--2107 Score: 356
Period size: 130 Copynumber: 2.0 Consensus size: 132
1834 TGAAGGATTT
* * *
1844 TTCACGCTTCCAATATCGTTTTTCCATTTTTTCCCCAATTTATTTCTAATTAAACTGAAACAAAA
1 TTCACGCTTCAAATATAGTTTTTCCATTTTTTCCCCAATTTATTTCTAATTAAACCGAAACAAAA
* * *
1909 TTAGATGCTTGTAAAAACAAATCTTTAAATCCATTATGGCTGAGATTTGGTTCGATGAACATAGA
66 TTAGATGCTCGTAAAAACAAATCCTTAAATCCATTATGGCTGAGATTTGATTCGATGAACATAGA
1974 TA
131 TA
* * * *
1976 TTCACGTTTCAAATATAGTTTTTCCA-TTTTT-CCTAATTTATTTTTAATTATACCGAAA-AAAA
1 TTCACGCTTCAAATATAGTTTTTCCATTTTTTCCCCAATTTATTTCTAATTAAACCGAAACAAAA
* * **
2038 TTCAGA-GACTCGTAAAAACAAGTCCTTAAATCCATTGTGGCTGAGATTTGATTCGATGAATTTA
66 TT-AGATG-CTCGTAAAAACAAATCCTTAAATCCATTATGGCTGAGATTTGATTCGATGAACATA
2102 GATA
129 GATA
2106 TT
1 TT
2108 TCAAGGAGGC
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
129 7 0.06
130 81 0.70
131 5 0.04
132 23 0.20
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (132 bp):
TTCACGCTTCAAATATAGTTTTTCCATTTTTTCCCCAATTTATTTCTAATTAAACCGAAACAAAA
TTAGATGCTCGTAAAAACAAATCCTTAAATCCATTATGGCTGAGATTTGATTCGATGAACATAGA
TA
Found at i:2871 original size:26 final size:26
Alignment explanation
Indices: 2831--4420 Score: 1716
Period size: 26 Copynumber: 59.1 Consensus size: 26
2821 TTGAAAAAAT
*
2831 TGAGCCCTACTGAATATGGAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
*
2857 TGAGCCCTACAGAATATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
* *
2883 TGAGCCCTACTAAATATGCAACTAAA
1 TGAGCCCTACTGAATATGCAACTATA
2909 TGAGCCCTACTGAATATGCAACAATATGGTA
1 TGAGCCCTACTGAATATGCAAC--TA---TA
* *
2940 TGACCCCTACTGAATATGCTACTATA
1 TGAGCCCTACTGAATATGCAACTATA
*
2966 TGAGCCCCTACTAAATATGCAACTATA
1 TGAG-CCCTACTGAATATGCAACTATA
* *
2993 TGAGCCCCAACT--ATATG----T-CA
1 TGAG-CCCTACTGAATATGCAACTATA
*
3013 TGATCCCTACTGAATATGCAACTATATGTCA
1 TGAGCCCTACTGAATATGCAAC--TA--T-A
3044 TGAGCCCTACTGAATATGCAACTATATGGCA
1 TGAGCCCTACTGAATATGCAAC--TAT---A
* *
3075 TGAGCCCTACTAAATATGCATCTATA
1 TGAGCCCTACTGAATATGCAACTATA
*
3101 TGGTATGGCCCTTATTGAATATGC--CTATA
1 T-G-A--GCCC-TACTGAATATGCAACTATA
3130 TG-GCCCCTACTGAATATGCAACTATA
1 TGAG-CCCTACTGAATATGCAACTATA
* * *
3156 TAAGCCGTACAGAATATGCAACTATATGTCA
1 TGAGCCCTACTGAATATGCAAC--TA--T-A
3187 TGAGCCCTACTGAATATGCAACTATATGGTA
1 TGAGCCCTACTGAATATGCAAC--TA---TA
* *
3218 TGAGCCTTACTAAATATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
3244 TGATATAGCCGCTACTGAATATGCAACTATATGGCA
1 TG----AGCC-CTACTGAATATGCAAC--TAT---A
*
3280 TGAGCCCTATTGAATATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
*
3306 TGGTATGGCCCCTACTGAATATGCTACTATA
1 T-G-A--G-CCCTACTGAATATGCAACTATA
3337 TGA-CCCTTACTGAATATGCAACTATA
1 TGAGCCC-TACTGAATATGCAACTATA
* *
3363 TGAGCCCCTACTGAAAATGAAACTATA
1 TGAG-CCCTACTGAATATGCAACTATA
*
3390 TAAGCCCTACTGAATATGCAACTATATGTCA
1 TGAGCCCTACTGAATATGCAAC--TA--T-A
3421 TGAGCCCTACTGAATATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
3447 TGGTATAAGCCCTACTGAATATGCAACTATA
1 T-G----AGCCCTACTGAATATGCAACTATA
3478 TG-GCCCCTACTGAATATGCAACTATA
1 TGAG-CCCTACTGAATATGCAACTATA
* *
3504 TGAGCCTTACTGAAAATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
3530 TG-GCCTCTACTGAATATGCAACTATA
1 TGAGCC-CTACTGAATATGCAACTATA
*
3556 TGAGCCCTACTGAATATGCAACTACA
1 TGAGCCCTACTGAATATGCAACTATA
**
3582 TGAGCCCTACTGAATATAAAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
*
3608 TG-GCCCCTACTGAATATGCAACTATT
1 TGAG-CCCTACTGAATATGCAACTATA
*
3634 TGAGCCCCTAATGAATATGCAACTATA
1 TGAG-CCCTACTGAATATGCAACTATA
3661 TG-GCCCCTACTGAATATGCAACTATA
1 TGAG-CCCTACTGAATATGCAACTATA
* *
3687 TGAGCCCTACTGAATATGCAACCACA
1 TGAGCCCTACTGAATATGCAACTATA
*
3713 TGAGCCCTACTGAAAATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
*
3739 TGAGCCCCTAATGAATATGCAACTATA
1 TGAG-CCCTACTGAATATGCAACTATA
3766 TG-GCCCCTACTGAATATGCAACTATA
1 TGAG-CCCTACTGAATATGCAACTATA
**
3792 TGTCCCCTACTGAATATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
* * * *
3818 TGAGTCCTACTGAATATGCACCCATG
1 TGAGCCCTACTGAATATGCAACTATA
3844 TGAGCCCTACTGAATATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
** * *
3870 TGTCCCCTATTGAATATGAAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
* *
3896 TG-GCTCTTACTGAATATGCAACTACA
1 TGAGC-CCTACTGAATATGCAACTATA
*
3922 TGA-CCCTTACTGAATATGCAACTACA
1 TGAGCCC-TACTGAATATGCAACTATA
3948 TG-GCCCTTACTGAATATGCAACTATA
1 TGAGCCC-TACTGAATATGCAACTATA
3974 TGAGCCCTACTGAATATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
*
4000 TGAGCCCTACTGAATATGCAATTATA
1 TGAGCCCTACTGAATATGCAACTATA
* *
4026 TGAGTCCTACTGAATATGCAACTACA
1 TGAGCCCTACTGAATATGCAACTATA
**
4052 TGCCCCCTACTGAATATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
*
4078 TG-GCCCCTACTGAATATGCAACTACA
1 TGAG-CCCTACTGAATATGCAACTATA
*
4104 TG-GCCCCTACTGAATATGCAACTACA
1 TGAG-CCCTACTGAATATGCAACTATA
4130 TG-GCCCCTACTGAATATGCAACTATA
1 TGAG-CCCTACTGAATATGCAACTATA
*
4156 TGCGCCCTACTGAATATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
* *
4182 TGCGCCCTACTGAATATGCAATTATA
1 TGAGCCCTACTGAATATGCAACTATA
**
4208 TGTCCCCTACTGAATATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
4234 TG-GCCCCTACTGAATATGCAACTATA
1 TGAG-CCCTACTGAATATGCAACTATA
*
4260 TGAGAGTCCTACTGAATATGCAACTATA
1 T--GAGCCCTACTGAATATGCAACTATA
*
4288 TG-TCCGCTACTGAATATGCAACTATA
1 TGAGCC-CTACTGAATATGCAACTATA
4314 TGAGCCCTACTGAATATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
* * *
4340 TGAACCATACTGAATATGCAACTAAA
1 TGAGCCCTACTGAATATGCAACTATA
*
4366 TGAGCCATACTGAATATGCAACTATA
1 TGAGCCCTACTGAATATGCAACTATA
* *
4392 TGAGCCCTACTAAATATGCAACTACA
1 TGAGCCCTACTGAATATGCAACTATA
4418 TGA
1 TGA
4421 TGCAGATGGC
Statistics
Matches: 1363, Mismatches: 116, Indels: 170
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.00
20 4 0.00
21 6 0.00
24 12 0.01
25 19 0.01
26 899 0.66
27 115 0.08
28 35 0.03
29 21 0.02
30 13 0.01
31 221 0.16
32 6 0.00
33 3 0.00
36 3 0.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (26 bp):
TGAGCCCTACTGAATATGCAACTATA
Found at i:3009 original size:73 final size:76
Alignment explanation
Indices: 2927--3071 Score: 199
Period size: 73 Copynumber: 1.9 Consensus size: 76
2917 ACTGAATATG
*
2927 CAACAATATGGT-ATGACCCCTACTGAATATGCTACTATATG-A-G-CCCCTACTAAATATGCAA
1 CAACAATAT-GTCATGACCCCTACTGAATATGCAACTATATGCATGACCCCTACTAAATATGCAA
2988 CTATATGAGCCC
65 CTATATGAGCCC
* * * *
3000 CAACTATATGTCATGATCCCTACTGAATATGCAACTATATGTCATGAGCCCTACTGAATATGCAA
1 CAACAATATGTCATGACCCCTACTGAATATGCAACTATATG-CATGACCCCTACTAAATATGCAA
3065 CTATATG
65 CTATATG
3072 GCATGAGCCC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
72 2 0.03
73 35 0.56
75 1 0.02
76 1 0.02
77 23 0.37
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (76 bp):
CAACAATATGTCATGACCCCTACTGAATATGCAACTATATGCATGACCCCTACTAAATATGCAAC
TATATGAGCCC
Found at i:35474 original size:620 final size:620
Alignment explanation
Indices: 34687--35925 Score: 2345
Period size: 620 Copynumber: 2.0 Consensus size: 620
34677 GTGGCACGTG
34687 ACCTAATATGTTTGAATTAAATTAAAATTAAAATTTTAAGTATATTACTAATTTTATCCTAAAGA
1 ACCTAATATGTTTGAATTAAATTAAAATTAAAATTTTAAGTATATTACTAATTTTATCCTAAAGA
*
34752 AGCCTATTAGCTGGCAAAATTTCACTCGAGTACGGGTATCCGACTCGATCGCCTGAAGCCAAACC
66 AGCCTATTAGCTAGCAAAATTTCACTCGAGTACGGGTATCCGACTCGATCGCCTGAAGCCAAACC
34817 TTATCCAACCCGATTCGACCAAAAAATCTGCTCAATCCGAAAATGATATCACCCGGCCTCAAATC
131 TTATCCAACCCGATTCGACCAAAAAATCTGCTCAATCCGAAAATGATATCACCCGGCCTCAAATC
34882 CTTAATAACCAAAACCTAAACCATTAAATCAAATAAAATAATTGCACGTTAGGGAAATAATATAT
196 CTTAATAACCAAAACCTAAACCATTAAATCAAATAAAATAATTGCACGTTAGGGAAATAATATAT
34947 TTTAATCATAATACATTAAACTATCAAATAGAACATGTCAATCACAATAACATTTCAAATTAAAA
261 TTTAATCATAATACATTAAACTATCAAATAGAACATGTCAATCACAATAACATTTCAAATTAAAA
*
35012 TGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGGGTCTTTGGTAAAA
326 TGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTCTTTGGTAAAA
35077 TAAAACTGTATATTAAAATTTTTAATATATCCAA-TTTTATTGTAAAAATAGTAAAATGGTAAAA
391 TAAAACTGTATATTAAAATTTTTAATATATCCAATTTTTATTG-AAAAATAGTAAAATGGTAAAA
35141 ATAAAGAAATTATAAAGAGATCAGATTTAATAATTGAATAAAAATTGAGTTTCTAGTAAAATAAA
455 ATAAAGAAATTATAAAGAGATCAGATTTAATAATTGAATAAAAATTGAGTTTCTAGTAAAATAAA
35206 ACTACAATTGTTTAACCAAGGCATTTAAGAGATATATTCAAAAAAATAAGGATATAATGGTCGAT
520 ACTACAATTGTTTAACCAAGGCATTTAAGAGATATATTCAAAAAAATAAGGATATAATGGTCGAT
35271 TCAAAAGTTTCTCAAAACTCGTACTTTTATATATAT
585 TCAAAAGTTTCTCAAAACTCGTACTTTTATATATAT
*
35307 ACCTAATATGTTTGAATTAAATTAAAATTAAAATTTTAAGTATATTACTAATTTTTTCCTAAAGA
1 ACCTAATATGTTTGAATTAAATTAAAATTAAAATTTTAAGTATATTACTAATTTTATCCTAAAGA
35372 AGCCTATTAGCTAGCAAAATTTCACTCGAGTACGGGTATCCGACTCGATCGCCTGAAGCCAAACC
66 AGCCTATTAGCTAGCAAAATTTCACTCGAGTACGGGTATCCGACTCGATCGCCTGAAGCCAAACC
* *
35437 TTATCCAACCCGATTCGACCAAAAAATCTGCTCAATCCGAAAATGATATGACCCGGTCTCAAATC
131 TTATCCAACCCGATTCGACCAAAAAATCTGCTCAATCCGAAAATGATATCACCCGGCCTCAAATC
* * * *
35502 CTTAATAACCCAAACCTAAATCATTAAATCAAATAAAATAATTGCGCGTTAGGGAAATAGTATAT
196 CTTAATAACCAAAACCTAAACCATTAAATCAAATAAAATAATTGCACGTTAGGGAAATAATATAT
*
35567 TTTAATCATAATACATTAAACTATCAAATAGAACATGTCAATCACAATAACATTTTAAATTAAAA
261 TTTAATCATAATACATTAAACTATCAAATAGAACATGTCAATCACAATAACATTTCAAATTAAAA
*
35632 TGGTAAGAATAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTCTTTGGTAAAA
326 TGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTCTTTGGTAAAA
35697 TAAAACTGTATATTAAAATTTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATGGTAAAAA
391 TAAAACTGTATATTAAAATTTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATGGTAAAAA
* *
35762 TAAAGAAATTATAAAGAGATCAGATTTAATAATTGAATAAAAATTGAGTTTTTAGTAGAATAAAA
456 TAAAGAAATTATAAAGAGATCAGATTTAATAATTGAATAAAAATTGAGTTTCTAGTAAAATAAAA
35827 CTACAATTGTTTAACCAAGGCATTTAAGAGATATATTCAAAAAAATAAGGATATAATGGTCGATT
521 CTACAATTGTTTAACCAAGGCATTTAAGAGATATATTCAAAAAAATAAGGATATAATGGTCGATT
35892 CAAAAGTTTCTCAAAACTCGTACTTTTATATATA
586 CAAAAGTTTCTCAAAACTCGTACTTTTATATATA
35926 GTATAGATTA
Statistics
Matches: 605, Mismatches: 13, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
620 597 0.99
621 8 0.01
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.31
Consensus pattern (620 bp):
ACCTAATATGTTTGAATTAAATTAAAATTAAAATTTTAAGTATATTACTAATTTTATCCTAAAGA
AGCCTATTAGCTAGCAAAATTTCACTCGAGTACGGGTATCCGACTCGATCGCCTGAAGCCAAACC
TTATCCAACCCGATTCGACCAAAAAATCTGCTCAATCCGAAAATGATATCACCCGGCCTCAAATC
CTTAATAACCAAAACCTAAACCATTAAATCAAATAAAATAATTGCACGTTAGGGAAATAATATAT
TTTAATCATAATACATTAAACTATCAAATAGAACATGTCAATCACAATAACATTTCAAATTAAAA
TGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTCTTTGGTAAAA
TAAAACTGTATATTAAAATTTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATGGTAAAAA
TAAAGAAATTATAAAGAGATCAGATTTAATAATTGAATAAAAATTGAGTTTCTAGTAAAATAAAA
CTACAATTGTTTAACCAAGGCATTTAAGAGATATATTCAAAAAAATAAGGATATAATGGTCGATT
CAAAAGTTTCTCAAAACTCGTACTTTTATATATAT
Found at i:68228 original size:15 final size:15
Alignment explanation
Indices: 68208--68238 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
68198 ACCCCACTAC
*
68208 ACCCACAGGGCGTTT
1 ACCCACAGGGCATTT
68223 ACCCACAGGGCATTT
1 ACCCACAGGGCATTT
68238 A
1 A
68239 AGTTGTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (15 bp):
ACCCACAGGGCATTT
Found at i:68335 original size:28 final size:28
Alignment explanation
Indices: 68278--68358 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
68268 TCTTAGCATA
* *
68278 CCCCATTACACCCACAGGGCGTTTAAATG
1 CCCCACTACACCCAGA-GGCGTTTAAATG
68307 CCCCACTACACCCAGAGGCGTTTAAATG
1 CCCCACTACACCCAGAGGCGTTTAAATG
68335 CCCCACTACACCCAG-GGCGTTTAA
1 CCCCACTACACCCAGAGGCGTTTAA
68359 GATGGAGGGG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
27 9 0.18
28 27 0.54
29 14 0.28
ACGTcount: A:0.27, C:0.37, G:0.17, T:0.19
Consensus pattern (28 bp):
CCCCACTACACCCAGAGGCGTTTAAATG
Found at i:72563 original size:6 final size:6
Alignment explanation
Indices: 72540--72573 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
72530 TGCTGCTGAC
* *
72540 TTTGGT TCTGGC TTTGGT TTTGGT TTTGGT TTTG
1 TTTGGT TTTGGT TTTGGT TTTGGT TTTGGT TTTG
72574 TTCCTGCGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.06, G:0.32, T:0.62
Consensus pattern (6 bp):
TTTGGT
Found at i:75683 original size:14 final size:14
Alignment explanation
Indices: 75664--75692 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
75654 CTTTGCTACA
75664 CTATCTATATTCAG
1 CTATCTATATTCAG
75678 CTATCTATATTCAG
1 CTATCTATATTCAG
75692 C
1 C
75693 GGTTGTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (14 bp):
CTATCTATATTCAG
Found at i:75946 original size:5 final size:5
Alignment explanation
Indices: 75936--75972 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
75926 AGGAAAAAGC
75936 ATATA ATATA ATATA ATATAA ATATA A-AT- ATATA ATA
1 ATATA ATATA ATATA ATAT-A ATATA ATATA ATATA ATA
75973 ATATTTATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 1 0.03
4 4 0.14
5 19 0.66
6 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:77994 original size:32 final size:32
Alignment explanation
Indices: 77934--77994 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
77924 ATAAGGCCCT
* *
77934 GAAATATTATTGCAAAATTTTCACCAAAAAAA
1 GAAATATTATTGCAAAATATTCAACAAAAAAA
77966 GAAATATTATTGCAAAATAATT-AACAAAA
1 GAAATATTATTGCAAAAT-ATTCAACAAAA
77995 GTGGTTAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.28
Consensus pattern (32 bp):
GAAATATTATTGCAAAATATTCAACAAAAAAA
Found at i:80774 original size:13 final size:14
Alignment explanation
Indices: 80744--80777 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
80734 ATAGAAACAG
*
80744 AAACAGAGTACAAA
1 AAACAGAGCACAAA
80758 AAACAGAGCAC-AA
1 AAACAGAGCACAAA
80771 AAACAGA
1 AAACAGA
80778 ACTAGGCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.65, C:0.18, G:0.15, T:0.03
Consensus pattern (14 bp):
AAACAGAGCACAAA
Found at i:103984 original size:42 final size:42
Alignment explanation
Indices: 103925--104008 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
103915 GACCGCAGTC
103925 TCCCATTTGGTAGGCAATCTGTAAATTTCGAAAAGCCCGACA
1 TCCCATTTGGTAGGCAATCTGTAAATTTCGAAAAGCCCGACA
103967 TCCCATTTGGTAGGCAATCTGTAAATTTCGAAAAGCCCGACA
1 TCCCATTTGGTAGGCAATCTGTAAATTTCGAAAAGCCCGACA
104009 AGTCCAATGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (42 bp):
TCCCATTTGGTAGGCAATCTGTAAATTTCGAAAAGCCCGACA
Found at i:104927 original size:18 final size:18
Alignment explanation
Indices: 104889--104928 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
104879 ACATAAAACC
*
104889 TAAATTCAAGACTTAATT
1 TAAATTCAAGACTTAACT
*
104907 TAAATTCAAGACTTGACT
1 TAAATTCAAGACTTAACT
104925 TAAA
1 TAAA
104929 AGAGAAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.35
Consensus pattern (18 bp):
TAAATTCAAGACTTAACT
Found at i:110147 original size:2 final size:2
Alignment explanation
Indices: 110140--110165 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
110130 GTATAAAGTC
110140 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
110166 CACATAACGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120267 original size:15 final size:14
Alignment explanation
Indices: 120249--120282 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
120239 ATAAAAACTT
120249 AAAAAACCGA-ACC
1 AAAAAACCGACACC
120262 GAAAAAACCGACACC
1 -AAAAAACCGACACC
120277 AAAAAA
1 AAAAAA
120283 TGAACAGCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.65, C:0.26, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAACCGACACC
Done.