Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009841.1 Corchorus capsularis cultivar CVL-1 contig09862, 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: 42810
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5229 original size:7 final size:7
Alignment explanation
Indices: 5213--5244 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5203 GAATTTTATT
*
5213 AATAACG
1 AATAATG
5220 AATAATG
1 AATAATG
5227 AATAATG
1 AATAATG
5234 AATAATG
1 AATAATG
5241 AATA
1 AATA
5245 TAGATGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.59, C:0.03, G:0.12, T:0.25
Consensus pattern (7 bp):
AATAATG
Found at i:6622 original size:23 final size:23
Alignment explanation
Indices: 6582--6653 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
6572 TCTTTGTTTA
* **
6582 TTTTGGAACTCCAATGTGAGAGC
1 TTTTGGGACTCCTTTGTGAGAGC
* * * *
6605 TTTTGGTATTTCTTTGTGAGAGT
1 TTTTGGGACTCCTTTGTGAGAGC
6628 TTTTGGGACTCCTTTGTGAGAGC
1 TTTTGGGACTCCTTTGTGAGAGC
6651 TTT
1 TTT
6654 GTCTATTGTC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.17, C:0.12, G:0.26, T:0.44
Consensus pattern (23 bp):
TTTTGGGACTCCTTTGTGAGAGC
Found at i:14834 original size:3 final size:3
Alignment explanation
Indices: 14826--14863 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
14816 GGAAAAAGAT
14826 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
14864 GGGCGGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:16087 original size:2 final size:2
Alignment explanation
Indices: 16076--16107 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16066 ATTCTTTGTT
16076 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16108 TCTTTCTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19211 original size:18 final size:18
Alignment explanation
Indices: 19190--19227 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
19180 ATAATCCTCT
*
19190 CCTTTTCCATTATCCCAC
1 CCTTTCCCATTATCCCAC
*
19208 CCTTTCCCATTATTCCAC
1 CCTTTCCCATTATCCCAC
19226 CC
1 CC
19228 CGCCCATCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.47, G:0.00, T:0.37
Consensus pattern (18 bp):
CCTTTCCCATTATCCCAC
Found at i:26016 original size:84 final size:84
Alignment explanation
Indices: 25914--26131 Score: 375
Period size: 84 Copynumber: 2.6 Consensus size: 84
25904 CACAGCAGTA
* * *
25914 GCATTCCTATTATACATCAAGGTATAATGGTGCGTCTGAATAAAATTTGGTGACAGGAATTTCTG
1 GCATTCCTATTATACATCAAGGTATAATGGTGCATCTGAATAAAAGTTGGTGACAGGAATTTCTA
25979 TTCTGCAGTAAAAGGGATG
66 TTCTGCAGTAAAAGGGATG
25998 GCATTCCTATTATACATCAAGGTATAATGGTGCATCTGAATAAAAGTTGGTGACAGGAATTTCTA
1 GCATTCCTATTATACATCAAGGTATAATGGTGCATCTGAATAAAAGTTGGTGACAGGAATTTCTA
* *
26063 TTTTGCAGTGAAAGGGATG
66 TTCTGCAGTAAAAGGGATG
*
26082 GCATTCCTATTATACATCAAGGTATAATGGTGCATC-GAATAAAGGTTGGT
1 GCATTCCTATTATACATCAAGGTATAATGGTGCATCTGAATAAAAGTTGGT
26132 AAGAATTCTT
Statistics
Matches: 128, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
83 13 0.10
84 115 0.90
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (84 bp):
GCATTCCTATTATACATCAAGGTATAATGGTGCATCTGAATAAAAGTTGGTGACAGGAATTTCTA
TTCTGCAGTAAAAGGGATG
Found at i:30332 original size:21 final size:21
Alignment explanation
Indices: 30306--30374 Score: 111
Period size: 21 Copynumber: 3.1 Consensus size: 21
30296 AGGCAGAAAC
30306 AGAAACAGAAACAGAGGGGGA
1 AGAAACAGAAACAGAGGGGGA
30327 AGAAACAGAAACAGAGGGGGAAA
1 AGAAACAGAAACAGAGGGGG--A
30350 CAGAAACAGAAACAGAGGGGGA
1 -AGAAACAGAAACAGAGGGGGA
30372 AGA
1 AGA
30375 GATCATAGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
21 23 0.51
22 1 0.02
23 1 0.02
24 20 0.44
ACGTcount: A:0.54, C:0.10, G:0.36, T:0.00
Consensus pattern (21 bp):
AGAAACAGAAACAGAGGGGGA
Found at i:40829 original size:325 final size:323
Alignment explanation
Indices: 40057--42238 Score: 2758
Period size: 325 Copynumber: 6.7 Consensus size: 323
40047 AAAAAATTGC
* *
40057 TTTTCCCTTTTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAA
1 TTTTCCC-ATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAA
* * * *
40122 ACAAATCTTTAAATCCAATGTGTCTGAGATTTGATTCGATGAATAGAGCTATTTCAAGGAGGCTA
65 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCT-
* * * ** * ***
40187 TT-TGCCAAAAATCACGCAGAACTGAACTTGGGCCCCGAAACGCATTTTTAGTCAATAACAACAA
129 TTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTGA
**
40251 TGGTTAGTACACGATTTCGGCTAAGAATTGACCCGAAAGTTTTTTTTTTCCTTTCTGAAATTTTT
194 TGGTTAGTACACGATTTCGGCTAAGAATTGACCCGAAA-----AATTTT--TTTCTGAAATTTTT
* *
40316 GCCACAATACTCAGT-AAAAATATATAATTCAACGCAAAAAAAAATTGAAAGATTTTTCACGCTT
252 GCCACAATACTC-GTAAAAAATATATAATTCAACGC-AAAAAAAATTGAAGGGTTTTTCACGCTT
40380 CCAATATCG
315 CCAATATCG
* * *
40389 TTTTCCTA-TTTTTTCCAAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCATAAAAA
1 TTTTCCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAA
* * *
40453 CAAATCCTTAAAACCAATGTGGCTGAGATTTGGTTCCATGAATAGAGATATTTCAAGGAGTCTTT
66 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTTT
**
40518 CTGCCAAAAATCATAAAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTGATG
131 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTGATG
* * * * *
40583 ATTAGTACACGATTTCGGCTAAGAATTGACCCGAAAAATTTTATTCTAAAATTTTTCCCACAAAA
196 GTTAGTACACGATTTCGGCTAAGAATTGACCCGAAAAATTTTTTTCTGAAATTTTTGCCACAATA
* *
40648 CTCGTAAAAAATATATAATTCAACGCAAAAACAAAATTTAAGGGTTTTTCACACTTCCAATATCG
261 CTCGTAAAAAATATATAATTCAACGC-AAAA-AAAATTGAAGGGTTTTTCACGCTTCCAATATCG
40713 TTTTCCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAA
1 TTTTCCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAA
* *
40778 CAAATTCC-TAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAGATATTTGAAGGAGTCTT
66 CAAA-TCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTT
** * * * *
40842 TCTGCCAAAAATCATAAAAAACTGAGCCGGAGCCCCGAAACACGTTTTTAGTCAATAACAGTAAC
130 TCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTGAT
* * * * * *
40907 GATTACTACACTATTTCGGCTTAGAATTGACCCG-TAAATTTTTTTTTGAAATTTTTGCCACAAT
195 GGTTAGTACACGATTTCGGCTAAGAATTGACCCGAAAAATTTTTTTCTGAAATTTTTGCCACAAT
* * * *
40971 ACTCG-GAAAAATGATATAATTCAACACAAAAAAAATTTAAGGGTTTTTCACACTTCCAATATCG
260 ACTCGTAAAAAAT-ATATAATTCAACGCAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATCG
* *
41035 TTTTACCATTCTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTTAGATGCTCGTAAAA
1 TTTTCCCATT-TTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAA
* * * * * *
41100 ACAAATCCTTAAATCCAATGTGACTGAAATTTGGTTCGATGAATAAAGATATTGCACGGAGGCTA
65 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTT
* * * * * * *
41165 TCTTCCAAATATCACGCAGAACTGAGTCGGGGCCCCGAAACACGTTTTTAGTCAATAAAAGTGAT
130 TCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTGAT
* * *
41230 GGTTAGTAC-CAATTTCGGCTAAGAATTGACCCGAAAAATTATTTTATTCTAAAATTTTTTCCAC
195 GGTTAGTACACGATTTCGGCTAAGAATTGACCCGAAAAA-T-TTTT-TTCTGAAATTTTTGCCAC
* * * *
41294 AACACTC-TGAAAAATTATATAATTCAATGCAAAAAAAAAATTGAA-GGATTTTCACGCTTCCAA
257 AATACTCGT-AAAAAATATATAATTCAACGC--AAAAAAAATTGAAGGGTTTTTCACGCTTCCAA
41357 TATCG
319 TATCG
* * *
41362 TTTTCCCAATTTTTTT-CGAATTTATTTTTAATTAAATTGAAAGAAAATTCAGATGCTCGTAAAA
1 TTTTCCC-ATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAA
* * * * *
41426 ACAAATCCTTAAATTCAATATGGCTGAGATTTGGCTCGATGAATAGAGCTATTTCAAGGAGGCTA
65 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTT
* * * *
41491 TCTGCCAAAAATCACGCAAAACTGAGCTGGGGCCCCGAAACGCGTTTTTAGCCCAATAATAGTGA
130 TCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAG-TCAATAACAGTGA
* * * * * *** *
41556 TGGTTACTACACGATTTCAGCTTATAATTGACGCGGAATTTTTTTTTTCTGAAATTTTTGCCCCA
194 TGGTTAGTACACGATTTCGGCTAAGAATTGAC-CCGAAAAATTTTTTTCTGAAATTTTTGCCACA
* * * *
41621 ATACTC--AGAAAAATATATAATTAAATGCAAAAAAAA-TGAAGAGTTTTACACGCTTCCAATAT
258 ATACTCGTA-AAAAATATATAATTCAACGCAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATAT
41683 CG
322 CG
*
41685 TTTTCCCATTTTCTTTCCGAATTTATCTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAA
1 TTTTCCCATTTT-TTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGT-AAA
* * * * *
41750 AACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTCAATGAATAGAAATCTTTTCAAGGAGTC
64 AACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAGAT-ATTTCAAGGAGGC
* * * * * *
41815 TTTCTGCAAAAAAT-ATGAAAAATTGAGCCGGGTCCCCGAAACACGTTTTTAGTCAATAACTGTG
128 TTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTG
* * * **
41879 ACGGTTACTACACGATTTCGGCTTAGAATTGACCCGTAAATTTTTTTTTCTGAAATTTTTGCCAC
193 ATGGTTAGTACACGATTTCGGCTAAGAATTGACCCG-AAAAATTTTTTTCTGAAATTTTTGCCAC
* * * * *
41944 AATACTTGGAAAAAATATATAATTAAATGCAAAAAAAATTGAAGGGCTTTTCACGCTTCCAATAT
257 AATACTCGTAAAAAATATATAATTCAACGCAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATAT
42009 CG
322 CG
* * *
42011 TTTTCCCA-TTTATTCCGAATTGATTTCTCATTAAATCGAAACAAAATTCAGATGCTCGTAAAAA
1 TTTTCCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAA
* * *
42075 CAAATCCTTAAATCCAATATCGCTGAGATTTGGTTCGATGAATAGAGATATTTAAAGGAGGCTTT
66 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTTT
* * * * * *
42140 CTGCCGAAAGTCATGCAAAACTGAGACGGGGCCCCG-AACGTGTTTTTAGGCTATAACAGTGATG
131 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTGATG
* **
42204 GTTAGAATGCGATTTCGGCTAAGAATTGACCCGAA
196 GTTAGTACACGATTTCGGCTAAGAATTGACCCGAA
42239 TTTTTTCCGA
Statistics
Matches: 1623, Mismatches: 196, Indels: 73
0.86 0.10 0.04
Matches are distributed among these distances:
321 2 0.00
322 149 0.09
323 336 0.21
324 235 0.14
325 339 0.21
326 259 0.16
327 61 0.04
328 33 0.02
329 6 0.00
330 197 0.12
332 6 0.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (323 bp):
TTTTCCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAA
CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTTT
CTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTGATG
GTTAGTACACGATTTCGGCTAAGAATTGACCCGAAAAATTTTTTTCTGAAATTTTTGCCACAATA
CTCGTAAAAAATATATAATTCAACGCAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATCG
Found at i:41600 original size:648 final size:646
Alignment explanation
Indices: 40067--42244 Score: 2880
Period size: 648 Copynumber: 3.4 Consensus size: 646
40057 TTTTCCCTTT
*
40067 TTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCTTT
1 TTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTT
* * * * *
40132 AAATCCAATGTGTCTGAGATTTGATTCGATGAATAGAGCTATTTCAAGGAGGCTATTTGCCAAAA
66 AAATCCAATATGGCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAA
* * * * ** *
40197 ATCACGCAGAACTGAACTTGGGCCCCGAAACGCATTTTTAGTCAATAACAACAATGGTTAGTACA
131 ATCACGCAAAACTGAGCTGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTAATGGTTACTACA
*
40262 CGATTTCGGCTAAGAATTGACCCGAAAGTTTTTTTTTTCCTTTCTGAAATTTTTGCCACAATACT
196 CGATTTCGGCTTAGAATTGACCCGAAA------TTTTT--TTTCTGAAATTTTTGCCACAATACT
* * *
40327 CAGTAAAAATATATAATTCAACGCAAAAAAAAATTGAAAGATTTTTCACGCTTCCAATATCGTTT
253 C-GGAAAAATATATAATTCAACGC-AAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATCGTTT
* *
40392 TCC-TATTTTTTCCAAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCATAAAAACAA
316 TCCAT-TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAA
* * *
40456 ATCCTTAAAACCAATGTGGCTGAGATTTGGTTCCATGAATAGAGATATTTCAAGGAGTCTTTCTG
380 ATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAATGAATAAAGATATTTCAAGGAGTCTTTCTG
* * *
40521 CCAAAAATCATAAAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTGATGATT
445 CCAAAAATCATGAAAAACTGAGCCGGGGCCCCGAAACACGTTTTTAGTCAATAACAGTGATGGTT
40586 AGTACACGATTTCGGCTAAGAATTGACCCGAAAA--ATTTTATTCTAAAATTTTTCCCACAAAAC
510 AGTACACGATTTCGGCTAAGAATTGACCCGAAAATTATTTTATTCTAAAATTTTTCCCACAAAAC
* * * * *
40649 TC-GTAAAAAATATATAATTCAACGCAAAAACAAAATTTAAGGGTTTTTCACACTTCCAATATCG
575 TCTG-AAAAAATATATAATTCAATGCAAAAAAAAAATTGAAGGGATTTTCACGCTTCCAATATCG
40713 TTTTCCCA
639 TTTTCCCA
40721 TTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATTCC
1 TTTTTTT-CGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAA-TCC
* * * *
40786 -TAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAGATATTTGAAGGAGTCTTTCTGCCAA
64 TTAAATCCAATATGGCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTGCCAA
*** * * * * *
40850 AAATCATAAAAAACTGAGCCGGAGCCCCGAAACACGTTTTTAGTCAATAACAGTAACGATTACTA
129 AAATCACGCAAAACTGAGCTGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTAATGGTTACTA
*
40915 CACTATTTCGGCTTAGAATTGACCCGTAAATTTTTTTT-TGAAATTTTTGCCACAATACTCGGAA
194 CACGATTTCGGCTTAGAATTGACCCG-AAATTTTTTTTCTGAAATTTTTGCCACAATACTCGGAA
* * *
40979 AAATGATATAATTCAACACAAAAAAAATTTAAGGGTTTTTCACACTTCCAATATCGTTTTACCAT
258 AAAT-ATATAATTCAACGCAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATCGTTTT-CCAT
*
41044 TCTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTTAGATGCTCGTAAAAACAAATCCT
321 T-TTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCT
* * * * * * * *
41109 TAAATCCAATGTGACTGAAATTTGGTTCGATGAATAAAGATATTGCACGGAGGCTATCTTCCAAA
385 TAAATCCAATGTGGCTGAGATTTGGTTCAATGAATAAAGATATTTCAAGGAGTCTTTCTGCCAAA
* * * * * *
41174 TATCACGCAGAACTGAGTCGGGGCCCCGAAACACGTTTTTAGTCAATAAAAGTGATGGTTAGTAC
450 AATCATGAAAAACTGAGCCGGGGCCCCGAAACACGTTTTTAGTCAATAACAGTGATGGTTAGTAC
* * *
41239 -CAATTTCGGCTAAGAATTGACCCGAAAAATTATTTTATTCTAAAATTTTTTCCACAACACTCTG
515 ACGATTTCGGCTAAGAATTGACCCG-AAAATTATTTTATTCTAAAATTTTTCCCACAAAACTCTG
*
41303 AAAAATTATATAATTCAATGCAAAAAAAAAATTGAA-GGATTTTCACGCTTCCAATATCGTTTTC
579 AAAAAATATATAATTCAATGCAAAAAAAAAATTGAAGGGATTTTCACGCTTCCAATATCGTTTTC
41367 CCAA
644 CC-A
* * *
41371 TTTTTTTCGAATTTATTTTTAATTAAATTGAAAGAAAATTCAGATGCTCGTAAAAACAAATCCTT
1 TTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTT
* * *
41436 AAATTCAATATGGCTGAGATTTGGCTCGATGAATAGAGCTATTTCAAGGAGGCTATCTGCCAAAA
66 AAATCCAATATGGCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAA
* * *
41501 ATCACGCAAAACTGAGCTGGGGCCCCGAAACGCGTTTTTAGCCCAATAATAGTGATGGTTACTAC
131 ATCACGCAAAACTGAGCTGGGGCCCCGAAACGCGTTTTTAG-TCAATAACAGTAATGGTTACTAC
* * * * * *
41566 ACGATTTCAGCTTATAATTGACGCGGAATTTTTTTTTTCTGAAATTTTTGCCCCAATACTCAGAA
195 ACGATTTCGGCTTAGAATTGAC-CCGAA-ATTTTTTTTCTGAAATTTTTGCCACAATACTCGGAA
* * * *
41631 AAATATATAATTAAATGCAAAAAAAA-TGAAGAGTTTTACACGCTTCCAATATCGTTTTCCCATT
258 AAATATATAATTCAACGCAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATCGTTTT-CCATT
*
41695 TTCTTTCCGAATTTATCTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAACAAATCCT
322 TT-TTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGT-AAAAACAAATCCT
* * *
41760 TAAATCCAATGTGGCTGAGATTTGATTCAATGAATAGAA-ATCTTTTCAAGGAGTCTTTCTGCAA
385 TAAATCCAATGTGGCTGAGATTTGGTTCAATGAATA-AAGAT-ATTTCAAGGAGTCTTTCTGCCA
* * * * *
41824 AAAAT-ATGAAAAATTGAGCCGGGTCCCCGAAACACGTTTTTAGTCAATAACTGTGACGGTTACT
448 AAAATCATGAAAAACTGAGCCGGGGCCCCGAAACACGTTTTTAGTCAATAACAGTGATGGTTAGT
* * * * * *
41888 ACACGATTTCGGCTTAGAATTGACCCGTAAATT-TTTTTTTCTGAAATTTTTGCCACAATACT-T
513 ACACGATTTCGGCTAAGAATTGACCCGAAAATTATTTTATTCTAAAATTTTTCCCACAAAACTCT
* *
41951 GGAAAAAATATATAATTAAATGC--AAAAAAAATTGAAGGGCTTTTCACGCTTCCAATATCGTTT
578 -GAAAAAATATATAATTCAATGCAAAAAAAAAATTGAAGGGATTTTCACGCTTCCAATATCGTTT
42014 TCCCA
642 TCCCA
* * * *
42019 TTTATTCCGAATTGATTTCTCATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTT
1 TTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTT
* * * *
42084 AAATCCAATATCGCTGAGATTTGGTTCGATGAATAGAGATATTTAAAGGAGGCTTTCTGCCGAAA
66 AAATCCAATATGGCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAA
* * * * * * ** *
42149 GTCATGCAAAACTGAGAC-GGGGCCCCG-AACGTGTTTTTAGGCTATAACAGTGATGGTTAGAAT
131 ATCACGCAAAACTGAG-CTGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTAATGGTTACTAC
* *
42212 GCGATTTCGGCTAAGAATTGACCCG-AATTTTTT
195 ACGATTTCGGCTTAGAATTGACCCGAAATTTTTT
42245 CCGAATTTAT
Statistics
Matches: 1338, Mismatches: 161, Indels: 61
0.86 0.10 0.04
Matches are distributed among these distances:
643 6 0.00
644 1 0.00
645 2 0.00
646 79 0.06
647 73 0.05
648 335 0.25
649 205 0.15
650 237 0.18
651 133 0.10
652 71 0.05
654 7 0.01
655 184 0.14
656 5 0.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (646 bp):
TTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTT
AAATCCAATATGGCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAA
ATCACGCAAAACTGAGCTGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTAATGGTTACTACA
CGATTTCGGCTTAGAATTGACCCGAAATTTTTTTTCTGAAATTTTTGCCACAATACTCGGAAAAA
TATATAATTCAACGCAAAAAAAATTGAAGGGTTTTTCACGCTTCCAATATCGTTTTCCATTTTTT
TCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATC
CAATGTGGCTGAGATTTGGTTCAATGAATAAAGATATTTCAAGGAGTCTTTCTGCCAAAAATCAT
GAAAAACTGAGCCGGGGCCCCGAAACACGTTTTTAGTCAATAACAGTGATGGTTAGTACACGATT
TCGGCTAAGAATTGACCCGAAAATTATTTTATTCTAAAATTTTTCCCACAAAACTCTGAAAAAAT
ATATAATTCAATGCAAAAAAAAAATTGAAGGGATTTTCACGCTTCCAATATCGTTTTCCCA
Found at i:41912 original size:974 final size:972
Alignment explanation
Indices: 40067--42238 Score: 3032
Period size: 974 Copynumber: 2.2 Consensus size: 972
40057 TTTTCCCTTT
* *
40067 TTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCTTT
1 TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTT
* *
40132 AAATCCAATGTGTCTGAGATTTGATTCGATGAATAGAGCTATTTCAAGGAGGCTAT-TTGCCAAA
66 AAATCCAATGTG-CTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTT-CC-AA
* * **
40196 AATCACGCAGAACTGA-ACTTGGGCCCCGAAACGCATTTTTAGTCAATAACAA-CAATGGTTAGT
128 AATCACGCAGAACTGAGAC-GGGGCCCCGAAACGCGTTTTTAGTCAATAA-AAGTGATGGTTAGT
** * * * *
40259 ACACGATTTCGGCTAAGAATTGACCCGAAAGTTTTTTTTTTCCTTTCTGAAATTTTTGCCACAAT
191 AC-CGATTTCGGCTAAGAATTGACCCGAAAG-AATTATTTT-CATTCTAAAATTTTTGCCACAAC
40324 ACTCAGTAAAAATATATAATTCAACGCAAAAAAAAATTGAAAGATTTTTCACGCTTCCAATATCG
253 ACTCAGTAAAAATATATAATTCAACGCAAAAAAAAATTGAAAGATTTTTCACGCTTCCAATATCG
*
40389 TTTTCCTATTTTTTCCAAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCATAAAAAC
318 TTTTCCAATTTTTTCCAAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCATAAAAAC
* * * *
40454 AAATCCTTAAAACCAATGTGGCTGAGATTTGGTTCCATGAATAGAGATATTTCAAGGAGTCTTTC
383 AAATCCTTAAAACCAATATGGCTGAGATTTGGCTCCATGAATAGAGATATTTCAAGGAGGCTATC
* *
40519 TGCCAAAAATCATAAAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGTCAATAACAGTGATGA
448 TGCCAAAAATCACAAAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAATAACAGTGATGA
* *
40584 TTAGTACACGATTTCGGCTAAGAATTGACCCGAAAAATTTTATTCTAAAATTTTTCCCACAAAAC
513 TTACTACACGATTTCAGCTAAGAATTGACCCGAAAAATTTTATTCTAAAATTTTTCCCACAAAAC
* * * *
40649 TCGTAAAAAATATATAATTCAACGCAAAAACAAAATTTAAGGGTTTTTCACACTTCCAATATCGT
578 TCG-AAAAAATATATAATTAAACGCAAAAACAAAATTGAAGAGTTTTACACACTTCCAATATCGT
*
40714 TTTCCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAC
642 TTTCCCATTTTTTTCCGAATTTATCTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAC
* * * *
40779 AAATTCCTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATAGAGATATTTGAAGGAGTCTTTC
707 AAATTCCTAAATCCAATGTGGCTGAGATTTGATTCAATGAATAGAAATATTTCAAGGAGTCTTTC
*
40844 TGCCAAAAATCATAAAAAACTGAGCCGGAGCCCCGAAACACGTTTTTAGTCAATAACAGTAACGA
772 TGCAAAAAATCATAAAAAACTGAGCCGGAGCCCCGAAACACGTTTTTAGTCAATAACAGTAACGA
*
40909 TTACTACACTATTTCGGCTTAGAATTGACCCGTAAA-TTTTTTTT-TGAAATTTTTGCCACAATA
837 TTACTACACGATTTCGGCTTAGAATTGACCCGTAAATTTTTTTTTCTGAAATTTTTGCCACAATA
* * *
40972 CTCGG-AAAAATGATATAATTCAACACAAAAAAAATTTAAGGGTTTTTCACACTTCCAATATCGT
902 CTCGGAAAAAAT-ATATAATTAAACACAAAAAAAATTGAAGGGCTTTTCACACTTCCAATATCGT
41036 TTTACCA
966 TTTACCA
*
41043 TTCTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTTAGATGCTCGTAAAAACAAATCC
1 -T-TTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCC
* * * *
41108 TTAAATCCAATGTGACTGAAATTTGGTTCGATGAATAAAGATATTGCACGGAGGCTATCTTCCAA
64 TTAAATCCAATGTG-CTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTTCCAA
* *
41173 ATATCACGCAGAACTGAGTCGGGGCCCCGAAACACGTTTTTAGTCAATAAAAGTGATGGTTAGTA
128 A-ATCACGCAGAACTGAGACGGGGCCCCGAAACGCGTTTTTAGTCAATAAAAGTGATGGTTAGTA
* *
41238 CCAATTTCGGCTAAGAATTGACCCGAAA-AATTATTTT-ATTCTAAAATTTTTTCCACAACACTC
192 CCGATTTCGGCTAAGAATTGACCCGAAAGAATTATTTTCATTCTAAAATTTTTGCCACAACACTC
* * *
41301 TG-AAAAATTATATAATTCAATGCAAAAAAAAAATTGAAGGA-TTTTCACGCTTCCAATATCGTT
257 AGTAAAAA-TATATAATTCAACGC-AAAAAAAAATTGAAAGATTTTTCACGCTTCCAATATCGTT
* * * * * *
41364 TTCCCAATTTTTTTCGAATTTATTTTTAATTAAATTGAAAGAAAATTCAGATGCTCGTAAAAACA
320 TT-CCAATTTTTTCCAAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCATAAAAACA
** * *
41429 AATCCTTAAATTCAATATGGCTGAGATTTGGCTCGATGAATAGAGCTATTTCAAGGAGGCTATCT
384 AATCCTTAAAACCAATATGGCTGAGATTTGGCTCCATGAATAGAGATATTTCAAGGAGGCTATCT
** * * *
41494 GCCAAAAATCACGCAAAACTGAGCTGGGGCCCCGAAACGCGTTTTTAGCCCAATAATAGTGATGG
449 GCCAAAAATCACAAAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAG-CCAATAACAGTGATGA
* * * *** * * *
41559 TTACTACACGATTTCAGCTTATAATTGACGCGGAATTTTTTTTTTCTGAAATTTTTGCCC-CAAT
513 TTACTACACGATTTCAGCTAAGAATTGAC-CCGAAAAATTTTATTCTAAAATTTTT-CCCACAAA
* *
41623 ACTC-AGAAAAATATATAATTAAATGC-AAAA-AAAA-TGAAGAGTTTTACACGCTTCCAATATC
576 ACTCGA-AAAAATATATAATTAAACGCAAAAACAAAATTGAAGAGTTTTACACACTTCCAATATC
41684 GTTTTCCCATTTTCTTTCCGAATTTATCTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAA
640 GTTTTCCCATTTT-TTTCCGAATTTATCTCTAATTAAATCGAAACAAAATTCAGATGCTCGT-AA
*
41749 AAACAAA-TCCTTAAATCCAATGTGGCTGAGATTTGATTCAATGAATAGAAATCTTTTCAAGGAG
703 AAACAAATTCC-TAAATCCAATGTGGCTGAGATTTGATTCAATGAATAGAAAT-ATTTCAAGGAG
* * *
41813 TCTTTCTGCAAAAAAT-ATGAAAAATTGAGCCGG-GTCCCCGAAACACGTTTTTAGTCAATAACT
766 TCTTTCTGCAAAAAATCATAAAAAACTGAGCCGGAG-CCCCGAAACACGTTTTTAGTCAATAACA
* *
41876 GTGACGGTTACTACACGATTTCGGCTTAGAATTGACCCGTAAATTTTTTTTTCTGAAATTTTTGC
830 GTAACGATTACTACACGATTTCGGCTTAGAATTGACCCGTAAATTTTTTTTTCTGAAATTTTTGC
* ** *
41941 CACAATACTTGGAAAAAATATATAATTAAATGCAAAAAAAATTGAAGGGCTTTTCACGCTTCCAA
895 CACAATACTCGGAAAAAATATATAATTAAACACAAAAAAAATTGAAGGGCTTTTCACACTTCCAA
*
42006 TATCGTTTTCCCA
960 TATCGTTTTACCA
* * *
42019 TTTATTCCGAATTGATTTCTCATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTT
1 TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTT
* * * *
42084 AAATCCAATATCGCTGAGATTTGGTTCGATGAATAGAGATATTTAAAGGAGGCTTTCTGCCGAAA
66 AAATCCAATGT-GCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTTCC-AAA
* * * * * * * * *
42149 GTCATGCAAAACTGAGACGGGGCCCCG-AACGTGTTTTTAGGCTATAACAGTGATGGTTAGAATG
129 ATCACGCAGAACTGAGACGGGGCCCCGAAACGCGTTTTTAGTCAATAAAAGTGATGGTTAGTA-C
42213 CGATTTCGGCTAAGAATTGACCCGAA
193 CGATTTCGGCTAAGAATTGACCCGAA
42239 TTTTTTCCGA
Statistics
Matches: 1061, Mismatches: 111, Indels: 49
0.87 0.09 0.04
Matches are distributed among these distances:
972 41 0.04
973 145 0.14
974 465 0.44
975 99 0.09
976 102 0.10
977 41 0.04
978 165 0.16
979 3 0.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (972 bp):
TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTT
AAATCCAATGTGCTGAGATTTGGTTCGATGAATAGAGATATTTCAAGGAGGCTATCTTCCAAAAT
CACGCAGAACTGAGACGGGGCCCCGAAACGCGTTTTTAGTCAATAAAAGTGATGGTTAGTACCGA
TTTCGGCTAAGAATTGACCCGAAAGAATTATTTTCATTCTAAAATTTTTGCCACAACACTCAGTA
AAAATATATAATTCAACGCAAAAAAAAATTGAAAGATTTTTCACGCTTCCAATATCGTTTTCCAA
TTTTTTCCAAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCATAAAAACAAATCCTT
AAAACCAATATGGCTGAGATTTGGCTCCATGAATAGAGATATTTCAAGGAGGCTATCTGCCAAAA
ATCACAAAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCAATAACAGTGATGATTACTACA
CGATTTCAGCTAAGAATTGACCCGAAAAATTTTATTCTAAAATTTTTCCCACAAAACTCGAAAAA
ATATATAATTAAACGCAAAAACAAAATTGAAGAGTTTTACACACTTCCAATATCGTTTTCCCATT
TTTTTCCGAATTTATCTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATTCCTA
AATCCAATGTGGCTGAGATTTGATTCAATGAATAGAAATATTTCAAGGAGTCTTTCTGCAAAAAA
TCATAAAAAACTGAGCCGGAGCCCCGAAACACGTTTTTAGTCAATAACAGTAACGATTACTACAC
GATTTCGGCTTAGAATTGACCCGTAAATTTTTTTTTCTGAAATTTTTGCCACAATACTCGGAAAA
AATATATAATTAAACACAAAAAAAATTGAAGGGCTTTTCACACTTCCAATATCGTTTTACCA
Done.