Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018143.1 Corchorus olitorius cultivar O-4 contig18176, 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: 99225
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:9093 original size:107 final size:104
Alignment explanation
Indices: 8832--9071 Score: 365
Period size: 107 Copynumber: 2.3 Consensus size: 104
8822 AATTTTTCTA
* **
8832 ACCCTTAAAATAAAATTTTAATTTTAATTTGGGCTAAATTTAGTG-AATTAGTTATATATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAATTTAGTGAAATTAGTTATATATTTTAT
* *
8896 TTCTAAAATCCAATAACAATATTATTAATTATGGAATTT
66 TTCTAAAACCCAATAACAATATTATTAATTATGAAATTT
* *
8935 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAATTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTT-GGGCTAAATTTAGTGAAATTAGTTATATATTTTA
* *
9000 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 TTTCTAAAACCCAATAACAAT--ATTATTAATTATGAAATTT
9042 ACCCTTAAAATAAAAATAAAATTTTAATTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTT
9072 ATGACTAAAC
Statistics
Matches: 124, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
103 27 0.22
104 15 0.12
105 35 0.28
107 47 0.38
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (104 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAATTTAGTGAAATTAGTTATATATTTTAT
TTCTAAAACCCAATAACAATATTATTAATTATGAAATTT
Found at i:20880 original size:15 final size:15
Alignment explanation
Indices: 20860--20889 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20850 TTTTTTTTGG
20860 TGGGGGGGGGGGGGC
1 TGGGGGGGGGGGGGC
20875 TGGGGGGGGGGGGGC
1 TGGGGGGGGGGGGGC
20890 ACAATTGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.87, T:0.07
Consensus pattern (15 bp):
TGGGGGGGGGGGGGC
Found at i:41224 original size:14 final size:15
Alignment explanation
Indices: 41199--41231 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
41189 TAAATTGAAG
*
41199 CTTTTTCGAGAAACA
1 CTTTTTCGAGAAAAA
41214 CTTTTTC-AGAAAAA
1 CTTTTTCGAGAAAAA
41228 CTTT
1 CTTT
41232 AAGTTAGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (15 bp):
CTTTTTCGAGAAAAA
Found at i:44328 original size:3 final size:3
Alignment explanation
Indices: 44320--44345 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44310 CTCAATAGGC
44320 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
44346 CTCCTCCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:44428 original size:24 final size:24
Alignment explanation
Indices: 44386--44437 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
44376 CTCAACAGAG
* *
44386 TCCTCTGCTTTTTCTTCAACTGGT
1 TCCTCTGCTTTTTCCTCAAATGGT
*
44410 TCCTCTG-TTTTCTCCTCAAATTGT
1 TCCTCTGCTTTT-TCCTCAAATGGT
44434 TCCT
1 TCCT
44438 GTTTGATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.10, C:0.31, G:0.10, T:0.50
Consensus pattern (24 bp):
TCCTCTGCTTTTTCCTCAAATGGT
Found at i:71734 original size:19 final size:19
Alignment explanation
Indices: 71710--71748 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
71700 ACATTGTTTA
*
71710 ACATTGTACATATGAGATT
1 ACATTGTACAGATGAGATT
*
71729 ACATTGTACAGATTAGATT
1 ACATTGTACAGATGAGATT
71748 A
1 A
71749 GGTACTGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (19 bp):
ACATTGTACAGATGAGATT
Found at i:72309 original size:60 final size:59
Alignment explanation
Indices: 72239--72402 Score: 206
Period size: 60 Copynumber: 2.7 Consensus size: 59
72229 ATTTACCATT
* * *
72239 TCAAATAAGGGTCTAATGTTTGCCAAAATGCTCAAATAAAGGTCCGATTTTTTAATTTGG
1 TCAAATAAGGGCCTAATGTTTG-CAAAATGCTCAAATAAAGGCCCGATATTTTAATTTGG
* *
72299 TCATATAAGGGCCTAATGTTATTG-AAAATGCTCAAATAAGGGCCCGATATTTTAATTTGG
1 TCAAATAAGGGCCTAATG-T-TTGCAAAATGCTCAAATAAAGGCCCGATATTTTAATTTGG
* *
72359 TCAAATAAGGGCCTAATATTAT-CGAAAATGCTCAAATAAGGGCC
1 TCAAATAAGGGCCTAATGTT-TGC-AAAATGCTCAAATAAAGGCC
72403 TAGCATCAGT
Statistics
Matches: 92, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
58 1 0.01
59 2 0.02
60 85 0.92
61 1 0.01
62 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (59 bp):
TCAAATAAGGGCCTAATGTTTGCAAAATGCTCAAATAAAGGCCCGATATTTTAATTTGG
Found at i:72341 original size:31 final size:31
Alignment explanation
Indices: 72303--72404 Score: 127
Period size: 31 Copynumber: 3.4 Consensus size: 31
72293 ATTTGGTCAT
*
72303 ATAAGGGCCTAATGTTATTGAAAATGCTCAA
1 ATAAGGGCCTAATATTATTGAAAATGCTCAA
** ** *
72334 ATAAGGGCCCGATATT-TT-AATTTGGTCAA
1 ATAAGGGCCTAATATTATTGAAAATGCTCAA
*
72363 ATAAGGGCCTAATATTATCGAAAATGCTCAA
1 ATAAGGGCCTAATATTATTGAAAATGCTCAA
72394 ATAAGGGCCTA
1 ATAAGGGCCTA
72405 GCATCAGTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
29 22 0.39
30 3 0.05
31 32 0.56
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (31 bp):
ATAAGGGCCTAATATTATTGAAAATGCTCAA
Found at i:72367 original size:29 final size:29
Alignment explanation
Indices: 72270--72371 Score: 96
Period size: 29 Copynumber: 3.4 Consensus size: 29
72260 GCCAAAATGC
* * *
72270 TCAAATAAAGGTCCGATTTTTTAATTTGG
1 TCAAATAAGGGCCCGATATTTTAATTTGG
* ** * ** *
72299 TCATATAAGGGCCTAATGTTATTGAAAATGC
1 TCAAATAAGGGCCCGATATT-TT-AATTTGG
72330 TCAAATAAGGGCCCGATATTTTAATTTGG
1 TCAAATAAGGGCCCGATATTTTAATTTGG
72359 TCAAATAAGGGCC
1 TCAAATAAGGGCC
72372 TAATATTATC
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
29 31 0.56
30 4 0.07
31 20 0.36
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (29 bp):
TCAAATAAGGGCCCGATATTTTAATTTGG
Found at i:72377 original size:29 final size:29
Alignment explanation
Indices: 72288--72378 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
72278 AGGTCCGATT
* *
72288 TTTTAATTTGGTCATATAAGGGCCTAATG
1 TTTTAATTTGGTCAAATAAGGGCCTAATA
** * **
72317 TTATTGAAAATGCTCAAATAAGGGCCCGATA
1 TT-TT-AATTTGGTCAAATAAGGGCCTAATA
72348 TTTTAATTTGGTCAAATAAGGGCCTAATA
1 TTTTAATTTGGTCAAATAAGGGCCTAATA
72377 TT
1 TT
72379 ATCGAAAATG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
29 24 0.50
30 4 0.08
31 20 0.42
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (29 bp):
TTTTAATTTGGTCAAATAAGGGCCTAATA
Found at i:72543 original size:60 final size:60
Alignment explanation
Indices: 72446--72604 Score: 214
Period size: 59 Copynumber: 2.7 Consensus size: 60
72436 GATGTCAGAC
* * * **
72446 CCTTATTTGAGCATTTTGGCAAATGTTAGG-CTCTTATTTGGCCAAATTAAAAGATCGGGT
1 CCTTATTTGAACATTTTGGCAAACGTTAGGCCT-TTATTTGGCCAAATTAAAAAATCAAGT
72506 CCTTATTTGAACATTTTGGCAAACGTTAGGCCTTTA-TTGGCCAAATTAAAAAATCAAGT
1 CCTTATTTGAACATTTTGGCAAACGTTAGGCCTTTATTTGGCCAAATTAAAAAATCAAGT
* * * *
72565 CCTTATTTGAACATTTTGACAAACATTAGACCCTTATTTG
1 CCTTATTTGAACATTTTGGCAAACGTTAGGCCTTTATTTG
72605 AGCGATTAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
59 52 0.59
60 34 0.39
61 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (60 bp):
CCTTATTTGAACATTTTGGCAAACGTTAGGCCTTTATTTGGCCAAATTAAAAAATCAAGT
Found at i:86638 original size:31 final size:29
Alignment explanation
Indices: 86596--86660 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 29
86586 GCTTAATACC
86596 CAAATTAGCCCCTTAACTATCCATTTTGGGA
1 CAAATTAGCCCCTTAACTATCC--TTTGGGA
* * *
86627 CAAATTGGCCCCTTAACTTTTCTTTGGGA
1 CAAATTAGCCCCTTAACTATCCTTTGGGA
86656 CAAAT
1 CAAAT
86661 AACTCCCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 12 0.39
31 19 0.61
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (29 bp):
CAAATTAGCCCCTTAACTATCCTTTGGGA
Found at i:93471 original size:40 final size:40
Alignment explanation
Indices: 93382--93753 Score: 543
Period size: 40 Copynumber: 9.2 Consensus size: 40
93372 ATTAAGGGCC
* * *
93382 AATGTAAATGAAGGAAAGTTCAATGTCAATTGGAAAAGTTG
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
93423 AATGTGAATCAAGGCAAGTTCAATGTCAATAGGG-AAGTTG
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* *
93463 AATGTGAATAAGGCAAGTTCAATGTTATTTGGGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* *
93503 AATGTGAATAAGGCAAGTTCAATGTTATTTGGGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
93543 AATGTGAATGAGGCAAGTTCAATGTCAATT-GGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
93582 AATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
1 AATGTGAA-TAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* *
93623 AATGTGAATCAAGGCAAGTTCAATGTCAGTTGGGAAAATTG
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
93664 GATGTGAATAAGGCAAGTTCAATGT-AAGTTGGGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAA-TTGGGAAAGTTG
* *
93704 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGAAAAGTTC
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
93745 AATGTGAAT
1 AATGTGAAT
93754 GTGCCATGTG
Statistics
Matches: 304, Mismatches: 20, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
39 39 0.13
40 145 0.48
41 118 0.39
42 2 0.01
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.28
Consensus pattern (40 bp):
AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
Found at i:94627 original size:11 final size:11
Alignment explanation
Indices: 94608--94637 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
94598 TATTCGGCTG
*
94608 TTTTCTTTTCT
1 TTTTTTTTTCT
94619 TTTTTTTTTCT
1 TTTTTTTTTCT
94630 TTTTTTTT
1 TTTTTTTT
94638 GGCACCAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:94627 original size:16 final size:15
Alignment explanation
Indices: 94608--94637 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
94598 TATTCGGCTG
94608 TTTTCTTTTCTTTTTT
1 TTTTCTTTT-TTTTTT
94624 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
94638 GGCACCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:97313 original size:340 final size:333
Alignment explanation
Indices: 96072--97719 Score: 1575
Period size: 328 Copynumber: 5.0 Consensus size: 333
96062 CGGGACCTCA
* * *
96072 TACACGGTTTCGGCTAAAATTTTGCAAAAATTGACCC-AAGGGATTTTTGCTCAA---TTGGGAA
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAA-GGATTTTTCCTCAATTTTTGGGCA
* * *
96133 AAATACTAATAAAAAAAAAT-TATAATT-AACCG-CAAAAAATATTGAAGGGCTTTTCACGCTTC
65 AAAT-CAAATAAGAAAAAATATATAATTCAA-CGTC-AAAAAGATTGAAGGGCTTTTCACGCTTC
* * *
96195 TAATATCTTTTTTCCTATTTTTTATCTAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATG
127 TAATATCGTTTTTCCTA-TTTTTA-C-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
* * * * *
96260 CTCGTAAAAACAAATCCTTAAATCTAAT-GTGGTTGAGA-TTAGTAAGATGGATATAGATATTTG
189 CTCGTAAAAACAAATCCTTAAATCCAATAG-GCTTGAGATTTAGTTAGATGAATATAGATATTTC
* * * * * **
96323 AAGGAGTCTTCG-CGCCAAAAATCATGCAAAACAGAT-CTGGGGCCCTGAAACGTGTTTGTAGTA
253 AAGGAGTCTT-GTCGCCAAAAATCATGCAAAACTGATACT-AGGTCCTGAAACGCGTTTTTAGCC
** * *
96386 AAAAAAAAGAGATGGTTAAG
316 AAAAACCA-TGATAGTT-AG
* * * * *
96406 TACATGATTTCGGCTAAAATTTTCCAAAATTTGACCCGAAAGATATTTCCAT-AATTTTT-GGCA
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAGGATTTTTCC-TCAATTTTTGGGCA
* * * * * *
96469 AAA--ATATTAA-TAAAAA-ATATAATTAAAC-TACAAAAAGATTGATGGGCTTTTTACACTTCT
65 AAATCA-AATAAGAAAAAATATATAATTCAACGT-CAAAAAGATTGAAGGGCTTTTCACGCTTCT
* * *
96529 AATATCG-TTTTCCTATTTTTCCGAATTAAGTTT-TAATTAAATTGAAACAAGATTCAAATGCTC
128 AATATCGTTTTTCCTATTTTTACGAATTAA-TTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * *
96592 GTAAAAACAAATCCTTAAGTCCAATATAGC-TGAGATTT-GATAAGATGAATATAGATATTTCAA
192 GTAAAAACAAATCCTTAAATCCAATA-GGCTTGAGATTTAG-TTAGATGAATATAGATATTTCAA
* * * * *
96655 GGAGTCTTGGCG-CAGAAAATCATGCAAAAATGAGAC--GGAGCCTCGGAACGCGTTTTTAGCCA
255 GGAGTCTTGTCGCCA-AAAATCATGCAAAACTGATACTAGG-TCCT-GAAACGCGTTTTTAGCCA
*
96717 AAAACCGTGATTA-TTAG
317 AAAACCATGA-TAGTTAG
** * * * * *
96734 TACACGAAATGGGC-AAAATTTTTGCAAAAATTGACCCAAAAGCTTTTTCCTCAATTTCT-GGC-
1 TACACGATTTCGGCTAAAA-TTTTGCAAAAATTGACCCGAAGGATTTTTCCTCAATTTTTGGGCA
* * * *
96796 -CAT--AATACAGATAACAATATATAATTCATCG-CTAAAAAGATTGAAGGGCTTTTCATGCTTC
65 AAATCAAATA-AGA-AAAAATATATAATTCAACGTC-AAAAAGATTGAAGGGCTTTTCACGCTTC
* * *
96857 TAATATGGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAAACGAAACAAGATTCAGATGCT
127 TAATATCGTTTTTCCTA-TTTTTACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
* * ***
96922 CGTAAAAACAAATCCTTAAGTCCAATAGGCTTGAGATTTAATTAGATGAATATAGATATTTTTTG
191 CGTAAAAACAAATCCTTAAATCCAATAGGCTTGAGATTTAGTTAGATGAATATAGATATTTCAAG
* * * *
96987 GAGTCTTGTCACCAAAAATCATGCAAAACTGATTCTAGGTCCTGGAACTCGTTTTTAGCCAAAAA
256 GAGTCTTGTCGCCAAAAATCATGCAAAACTGATACTAGGTCCTGAAACGCGTTTTTAGCCAAAAA
*
97052 TCATGATAGTTAG
321 CCATGATAGTTAG
* *
97065 TACACGATTTCGGCTAAAATTTT-AAAAAATTGACCTGAAGGATTTTTCCTCAATTTTTGGGCAA
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAGGATTTTTCCTCAATTTTTGGGCAA
*
97129 AATTCTAAAATATATATATAAATATATATAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGC
66 AA-TC--AAATA-AGA-A-AAA-ATATATAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGC
* * * *
97194 TTCTAATAACGTTTTCCCTACTCTTTTACGAATTAATTTCGAATTAAATCAAAACAAGATTCAGA
124 TTCTAATATCGTTTTTCCTA-T-TTTTACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
* * * *
97259 TGCTTGTAAAAA-AAATCATTAAATCCAATAGGCTTGTGATTTATTTAGATGAATATAGATATTT
187 TGCTCGTAAAAACAAATCCTTAAATCCAATAGGCTTGAGATTTAGTTAGATGAATATAGATATTT
** * * * * *
97323 TGAGGAGCCTTGTCGCCAAAAATCATGCAAAATTGATACTGGGTGCTGAAACGCGTTTTTAGTCA
252 CAAGGAGTCTTGTCGCCAAAAATCATGCAAAACTGATACTAGGTCCTGAAACGCGTTTTTAGCCA
* *
97388 AAAACCGTGATGGTTAG
317 AAAACCATGATAGTTAG
* * **
97405 T--ACGATTTCGGCTAAAATTTTACAAAGATTGACATGAAGGATTTTT-CTCAATTTTTGGGCAA
1 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAGGATTTTTCCTCAATTTTTGGGCAA
* ** *
97467 AATTC---TAAGAAAAAA-ATATAATTCAAAGTCAAAAAGATTGAAGGGCTTTTCACATTTTTAA
66 AA-TCAAATAAGAAAAAATATATAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAA
* * * * * *
97528 TATCGTTTTTTCTATTTTTTCTAAATTAATTTCAAATTAAATCGAAACAAGATTCAGTTGTTCGT
130 TATCGTTTTTCCTATTTTTAC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * * * * *
97593 AAAAACAAATCCTTAGATCCAATTTGGC-AGACATTTGGTTAGATGAATATAGATATTACAGGGA
194 AAAAACAAATCCTTAAATCCAA-TAGGCTTGAGATTTAGTTAGATGAATATAGATATTTCAAGGA
* * * *
97657 GTCTTGACGCCAAAAATCATGCAAAACTGATCCGA-GACCTCGAAACGCGTTTTTAGCCAAAAA
258 GTCTTGTCGCCAAAAATCATGCAAAACTGATACTAGGTCCT-GAAACGCGTTTTTAGCCAAAAA
97720 TCGATCAGAA
Statistics
Matches: 1096, Mismatches: 161, Indels: 120
0.80 0.12 0.09
Matches are distributed among these distances:
325 3 0.00
326 7 0.01
327 51 0.05
328 198 0.18
329 118 0.11
330 119 0.11
331 176 0.16
332 19 0.02
333 49 0.04
334 50 0.05
335 3 0.00
336 6 0.01
337 2 0.00
338 49 0.04
339 23 0.02
340 173 0.16
341 50 0.05
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (333 bp):
TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAGGATTTTTCCTCAATTTTTGGGCAA
AATCAAATAAGAAAAAATATATAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACGCTTCTAAT
ATCGTTTTTCCTATTTTTACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
AAACAAATCCTTAAATCCAATAGGCTTGAGATTTAGTTAGATGAATATAGATATTTCAAGGAGTC
TTGTCGCCAAAAATCATGCAAAACTGATACTAGGTCCTGAAACGCGTTTTTAGCCAAAAACCATG
ATAGTTAG
Found at i:97576 original size:668 final size:658
Alignment explanation
Indices: 96167--97721 Score: 1702
Period size: 668 Copynumber: 2.3 Consensus size: 658
96157 ATTAACCGCA
*
96167 AAAAATATTGAAGGGCTTTTCACGCTTCTAATATC-TTTTTTCCTATTTTTTATCTAAATTAATT
1 AAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTT-CTA-TTTTT-TCTAAATTAATT
* * * *
96231 TCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGTTGA
63 TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAGTCCAATG-GCTTGA
* * * *
96296 GA-TTAGTAAGATGGATATAGATATTTGAAGGAGTCTTCGCGCCAAAAATCATGCAAAACAGA-T
127 GATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTT-GCGCCAAAAATCATGCAAAACTGATT
* * * ** ** * *
96359 CTGGGGCCCTGAAACGT-GTTTGTAGTAAAAAAAAAGAGATGGTTAAGTACATGATTTCGGCTAA
191 CT-AGGACCTGAAAC-TCGTTTTTAGCCAAAAATCAGAGATAGTTAAGTACACGATTTCGGCTAA
* *
96423 AATTTTCCAAAATTTGACCCGAAAGATATTTCCATAATTTTTGGCAAAAATATTAATAAAAAATA
254 AATTTTCAAAAAATTGACCCGAAAGATATTTCCATAATTTTTGGCAAAAATATTAATAAAAAATA
* * * *
96488 TAATTAAACTACAAAAAGATTGATGGGCTTTTTACACTTCTAATATCGTTTTCCTATTTTTCCGA
319 TAATTAAACTACAAAAAGATTGAAGGGCTTTTCACACTTCTAATAACGTTTTCCTATTTTTACGA
* ** * *
96553 ATTAAGTTTTAATTAAATTGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAGTCCAATA
384 ATTAAGTTTGAATTAAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCATTAAATCCAATA
*
96618 TAGCTGAGATTTGATAAGATGAATATAGATATTTCAAGGAGTCTTGGCGCAGAAAATCATGCAAA
449 TAGCTGAGATTTGATAAGATGAATATAGATATTTCAAGGAGCCTTGGCGCAGAAAATCATGCAAA
* * *
96683 AATGAGACGGAGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATTATTAGTACACGAAATGGGC
514 AATGAGACGGAGCCTCGAAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTA-ACGAAATCGGC
* * * *
96748 AAAATTTTTGCAAAAATTGACCCAAAAGCTTTTTCCTCAATTTCTGGCCATAATACAGATAACAA
578 AAAATTTTTACAAAAATTGACACAAAAGATTTTTCCTCAATTTCTGGCCAAAATACAGATAACAA
* **
96813 TATATAATTCATCGCT
643 AATATAATTCAAAGCT
* * * **
96829 AAAAAGATTGAAGGGCTTTTCATGCTTCTAATATGGTTTTTCCTATTTTTTCCGAATTAATTTCT
1 AAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTTCTATTTTTTCTAAATTAATTTCT
*
96894 AATTAAAACGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAGTCCAATAGGCTTGAGAT
66 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAGTCCAAT-GGCTTGAGAT
* *** *
96959 TTAATTAGATGAATATAGATATTTTTTGGAGTCTTGTCACCAAAAATCATGCAAAACTGATTCTA
130 TTAGTTAGATGAATATAGATATTTCAAGGAGTCTTG-CGCCAAAAATCATGCAAAACTGATTCTA
* * *
97024 GGTCCTGGAACTCGTTTTTAGCCAAAAATCA-TGATAGTT-AGTACACGATTTCGGCTAAAATTT
194 GGACCTGAAACTCGTTTTTAGCCAAAAATCAGAGATAGTTAAGTACACGATTTCGGCTAAAATTT
* * *
97087 T-AAAAAATTGACCTGAAGGATTTTTCC-TCAATTTTTGGGCAAAATTCTAAAATATATATATAA
259 TCAAAAAATTGACCCGAAAGATATTTCCAT-AATTTTT-GGC---A----AAAATAT-TA-ATAA
* * *
97150 ATATATATAATTCAACGT-CAAAAAGATTGAAGGGCTTTTCACGCTTCTAATAACGTTTTCCCTA
313 A-AAATATAATTAAAC-TACAAAAAGATTGAAGGGCTTTTCACACTTCTAATAACGTTTT-CCTA
* *
97214 CTCTTTTACGAATTAA-TTTCGAATTAAATCAAAACAAGATTCAGATGCTTGTAAAAA-AAATCA
375 -T-TTTTACGAATTAAGTTT-GAATTAAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCA
* * * ** *
97277 TTAAATCCAATA-GGCTTGTGATTT-ATTTAGATGAATATAGATATTTTGAGGAGCCTTGTCGCC
437 TTAAATCCAATATAGC-TGAGATTTGA-TAAGATGAATATAGATATTTCAAGGAGCCTTGGCG-C
* * * * *
97340 A-AAAATCATGCAAAATTGATACTGG-GTGCT-GAAACGCGTTTTTAGTCAAAAACCGTGATGGT
499 AGAAAATCATGCAAAAATGAGAC-GGAG-CCTCGAAACGCGTTTTTAGCCAAAAACCGTGATGAT
** * ** * * *
97402 TAGT-ACGATTTCGGCTAAAA-TTTTACAAAGATTGACATGAAGGATTTTT-CTCAATTTTTGGG
562 TAGTAACGAAATCGGC-AAAATTTTTACAAAAATTGACACAAAAGATTTTTCCTCAATTTCTGGC
*
97464 CAAAATTCTAAGA-AA-AAAATATAATTCAAAG-T
626 CAAAATAC--AGATAACAAAATATAATTCAAAGCT
** *
97496 CAAAAAGATTGAAGGGCTTTTCACATTTTTAATATCGTTTTTTCTATTTTTTCTAAATTAATTTC
1 -AAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTTCTATTTTTTCTAAATTAATTTC
* * * *
97561 AAATTAAATCGAAACAAGATTCAGTTGTTCGTAAAAACAAATCCTT-AGATCCAATTTGGC-AGA
65 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAG-TCCAA--TGGCTTGA
* * * * *
97624 CATTTGGTTAGATGAATATAGATATTACAGGGAGTCTTGACGCCAAAAATCATGCAAAACTGATC
127 GATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTG-CGCCAAAAATCATGCAAAACTGATT
* *
97689 CGA-GACCTCGAAACGCGTTTTTAGCCAAAAATC
191 CTAGGACCT-GAAACTCGTTTTTAGCCAAAAATC
97722 GATCAGAAAG
Statistics
Matches: 750, Mismatches: 107, Indels: 66
0.81 0.12 0.07
Matches are distributed among these distances:
657 1 0.00
658 28 0.04
659 27 0.04
660 78 0.10
661 78 0.10
662 39 0.05
663 5 0.01
666 7 0.01
667 9 0.01
668 219 0.29
669 84 0.11
670 16 0.02
671 109 0.15
672 50 0.07
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (658 bp):
AAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTTCTATTTTTTCTAAATTAATTTCT
AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAGTCCAATGGCTTGAGATT
TAGTTAGATGAATATAGATATTTCAAGGAGTCTTGCGCCAAAAATCATGCAAAACTGATTCTAGG
ACCTGAAACTCGTTTTTAGCCAAAAATCAGAGATAGTTAAGTACACGATTTCGGCTAAAATTTTC
AAAAAATTGACCCGAAAGATATTTCCATAATTTTTGGCAAAAATATTAATAAAAAATATAATTAA
ACTACAAAAAGATTGAAGGGCTTTTCACACTTCTAATAACGTTTTCCTATTTTTACGAATTAAGT
TTGAATTAAATCAAAACAAGATTCAAATGCTCGTAAAAACAAATCATTAAATCCAATATAGCTGA
GATTTGATAAGATGAATATAGATATTTCAAGGAGCCTTGGCGCAGAAAATCATGCAAAAATGAGA
CGGAGCCTCGAAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTAACGAAATCGGCAAAATTTT
TACAAAAATTGACACAAAAGATTTTTCCTCAATTTCTGGCCAAAATACAGATAACAAAATATAAT
TCAAAGCT
Found at i:98005 original size:291 final size:302
Alignment explanation
Indices: 97476--99225 Score: 1354
Period size: 329 Copynumber: 5.5 Consensus size: 302
97466 AAATTCTAAG
* * ** * *
97476 AAAAAA-ATATAATTCAAAGTCAAAAAGATTGAAGGGCTTTTCACATTTTTAATATCGTTTTTTC
1 AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTC
* * ** * * *
97540 TATT-TTTTCTAAATTAATTTCAAATTAAATCGAAACAAGATTCAGTTGTTCGTAAAAACAAATC
66 AATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATC
* * * * * * ** *
97604 CTTAGATCCAATT-TGGCAGACATTT-GGTTAGATGAATATAGATATTACAGGGAGTCTTGACGC
131 CTTAAATCC-ATTGTGGCTGAGATTTGGGAT-GATTAATATAGATATTTCAATGAGTCTTGGCGC
* * * * * *
97667 CAAAAATCATGCAAAACTGA-TCCGAGACCTCGAAACGCGTTTTTAGCCAAAAATC-GA-TCAG-
194 CAAAAATCATGCAAAACAGAGT-CGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGGAGT-AGT
* * ** * * *
97728 A-AAG-TTT-T-TTTTTTC-AAGTTTTAACCG-CA-A-TACTCGT-
257 ACAAGATTTGTAATTTTGCAAAAATTGAACCGAAAGATTACTCCTC
**
97765 AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTAG
1 AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTC
97830 AATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATC
66 AATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATC
*
97895 CTTAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCACCA
131 CTTAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCGCCA
97960 AAAATCATGCAAAACAGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAGTAGTACA
196 AAAATCATGCAAAACAGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCG-GAGTAGTACA
* * *
98025 CGATTTCGGTAAAATTTTGCAAAAATTGATCCGAAAGATTTTTCCTCAATTTTTAACCGCAATAC
260 AGATTT--GT--AATTTTGCAAAAATTGAACCGAAAG-----------A---TT-A---C--TCC
98090 TC
301 TC
*
98092 GTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAATATCATTTTT
1 --AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTT
*
98157 TCAATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTGAAAACAAA
64 TCAATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAA
*
98222 TCCATAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCGC
129 TCCTTAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCGC
98287 CAAAAATCATGCAAAACTA-AGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTT
194 CAAAAATCATGCAAAAC-AGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCG-GA--G-T
* * * * *
98351 AATACACGATTTCGGCAAAATTTGGCAAAAATTGATCCGAAAGATTTTTCCTCAAGTTTTAACCG
254 AGTACAAGATTT--G--TAATTTTGCAAAAATTGAACCGAAAG-----------A---TT-A---
*
98416 CAATACTC
297 C--TCCTC
* * *
98424 GTAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGC-TTTCACACTTCTAATGTCATTTTT
1 --AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTT
** * * * *
98488 AGAATTCTTTCCCGAATTAAATTCTAATTAATTCGAAACAAGATTCGGATGATCGTAGAAACAAA
64 TCAATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAA
* * * * * *
98553 TCCTTAAATCCGTTGTGGCTGATATTT-GGTTACATTAATATAAATATTTCAGTGAGTCTTGGCG
129 TCCTTAAATCCATTGTGGCTGAGATTTGGGAT-GATTAATATAGATATTTCAATGAGTCTTGGCG
* * * * * *
98617 CACAAAAAACATGCAAAACTGAG-CTGGGGCCCCGGAACGCTTTTTTTTGTCAAAAATCGTGATG
193 C-CAAAAATCATGCAAAACAGAGTC-GGGGCCCCGGAACGC-GTTTTTAGCCAAAAACCG-GA--
* * * *
98681 GTTAGTACACGATTTCGGTAAAAATTTTACAAAAATTG-ACTCGAAAGATAATTCCTC
252 G-TAGTACAAGATTT--GT---AATTTTGCAAAAATTGAAC-CGAAAGATTACTCCTC
98738 AATTTTTAACCGCAATACTCGTGAAAAATATATAAATCAACGCCAAAAAGATTGAAGGG-TTTAT
1 AA-----AA----AATA----T-----ATA-AT---TCAACGCCAAAAAGATTGAAGGGCTTT-T
** * *
98802 CACGCTTCTAATATCATTTTTAGAATTCTTTCACGAATTAATTTCTAATTAAATCGAAATAAGAT
43 CACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGAT
*
98867 TCAGATGATCGTAAAAATAAATCCTTAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGA
108 TCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGA
* * * *
98932 TATTTCAATGTGTCTTGGCACCAAAAATCATGCAAAACAAAGTCGGGGACCCGGAACGCGTTTTT
173 TATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACAGAGTCGGGGCCCCGGAACGCGTTTTT
* *
98997 AGCCAAAAACCGTGA-TAACGTACACGATTTCGTTAAAATTTTGCAAAAATTGATCCGAAAGTTT
238 AGCCAAAAACCG-GAGT-A-GTACAAGATTT-G-T--AATTTTGCAAAAATTGAACCGAAAG---
*
99061 TTTCCTCAAATTTTAACCGCAATACTC
293 ---------A--TT-A---C--TCCTC
*
99088 ATAAAAAATATATAATTCAACGCCAAAAAGATAGAAGGGCTTTTCACGCTTCTAATATCATTTTT
1 --AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTT
** *
99153 AGAATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAA-TAA
64 TCAATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAA
99217 TCCTTAAAT
129 TCCTTAAAT
Statistics
Matches: 1230, Mismatches: 119, Indels: 184
0.80 0.08 0.12
Matches are distributed among these distances:
289 6 0.00
290 56 0.05
291 146 0.12
292 4 0.00
293 4 0.00
294 2 0.00
295 2 0.00
296 3 0.00
299 1 0.00
302 5 0.00
303 8 0.01
304 1 0.00
312 2 0.00
314 4 0.00
316 1 0.00
317 2 0.00
319 1 0.00
320 2 0.00
321 5 0.00
323 1 0.00
324 1 0.00
325 1 0.00
326 2 0.00
329 256 0.21
330 135 0.11
331 154 0.13
332 139 0.11
333 56 0.05
334 79 0.06
335 132 0.11
336 3 0.00
339 1 0.00
342 1 0.00
343 4 0.00
344 1 0.00
345 1 0.00
347 2 0.00
350 4 0.00
352 2 0.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (302 bp):
AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTC
AATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATC
CTTAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCGCCA
AAAATCATGCAAAACAGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGGAGTAGTACAA
GATTTGTAATTTTGCAAAAATTGAACCGAAAGATTACTCCTC
Found at i:98344 original size:329 final size:330
Alignment explanation
Indices: 97714--99225 Score: 2335
Period size: 329 Copynumber: 4.6 Consensus size: 330
97704 CGTTTTTAGC
* * * **
97714 CAAAAATCGATCAGAAAGTTTTTTTTTTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAAT
1 CAAAAATTGATCCGAAAG-ATTTTTCCTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAAT
97779 TCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGAA
65 TCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGAA
97844 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGT
130 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGT-AAAACAAATCCTTAAATCCATTGT
97909 GGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCACCAAAAATCATGCAAAA
194 GGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCACCAAAAATCATGCAAAA
97974 C-AGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGA-G-TAGTACACGATTTCGGTA
259 CTA-AGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAGGTTAGTACACGATTTCGGTA
98036 AAATTTTG
323 AAATTTTG
*
98044 CAAAAATTGATCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATT
1 CAAAAATTGATCCGAAAGATTTTTCCTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAATT
* **
98109 CAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAAT
66 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGAAT
*
98174 TAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTGAAAACAAATCCATAAATCCATTGTG
131 TAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGT-AAAACAAATCCTTAAATCCATTGTG
*
98239 GCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAAC
195 GCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCACCAAAAATCATGCAAAAC
* *
98304 TAAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCAA
260 TAAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGA-GGTTAGTACACGATTTCGGTAA
*
98369 AATTTGG
324 AATTTTG
98376 CAAAAATTGATCCGAAAGATTTTTCCTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAATT
1 CAAAAATTGATCCGAAAGATTTTTCCTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAATT
* * *
98441 CAATGCCAAAAAGATTGAAGGGC-TTTCACACTTCTAATGTCATTTTTAGAATTCTTTCCCGAAT
66 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGAAT
* * * *
98505 TAAATTCTAATTAATTCGAAACAAGATTCGGATGATCGTAGAAACAAATCCTTAAATCCGTTGTG
131 TAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTA-AAACAAATCCTTAAATCCATTGTG
* * * * * * *
98570 GCTGATATTT-GGTTACATTAATATAAATATTTCAGTGAGTCTTGGCGCACAAAAAACATGCAAA
195 GCTGAGATTTGGGAT-GATTAATATAGATATTTCAATGAGTCTTGGCAC-CAAAAATCATGCAAA
* * * * *
98634 ACTGAG-CTGGGGCCCCGGAACGCTTTTTTTTGTCAAAAATCGTGATGGTTAGTACACGATTTCG
258 ACTAAGTC-GGGGCCCCGGAACGC-GTTTTTAGCCAAAAACCGTGA-GGTTAGTACACGATTTCG
*
98698 GTAAAAATTTTA
320 GT-AAAATTTTG
** * * *
98710 CAAAAATTGA-CTCGAAAGATAATTCCTCAATTTTTAACCGCAATACTCGTGAAAAATATATAAA
1 CAAAAATTGATC-CGAAAGATTTTTCCTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAAT
*
98774 TCAACGCCAAAAAGATTGAAGGG-TTTATCACGCTTCTAATATCATTTTTAGAATTCTTTCACGA
65 TCAACGCCAAAAAGATTGAAGGGCTTT-TCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGA
* *
98838 ATTAATTTCTAATTAAATCGAAATAAGATTCAGATGATCGTAAAAATAAATCCTTAAATCCATTG
129 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGT-AAAACAAATCCTTAAATCCATTG
*
98903 TGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGTGTCTTGGCACCAAAAATCATGCAAA
193 TGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCACCAAAAATCATGCAAA
* * * *
98968 ACAAAGTCGGGGACCCGGAACGCGTTTTTAGCCAAAAACCGTGA--TAACGTACACGATTTCGTT
258 ACTAAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAGGTTA-GTACACGATTTCGGT
99031 AAAATTTTG
322 AAAATTTTG
* * *
99040 CAAAAATTGATCCGAAAGTTTTTTCCTCAAATTTTAACCGCAATACTCATAAAAAATATATAATT
1 CAAAAATTGATCCGAAAGATTTTTCCTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAATT
*
99105 CAACGCCAAAAAGATAGAAGGGCTTTTCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGAAT
66 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGAAT
99170 TAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAA-ATAATCCTTAAAT
131 TAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAACA-AATCCTTAAAT
Statistics
Matches: 1077, Mismatches: 85, Indels: 41
0.90 0.07 0.03
Matches are distributed among these distances:
328 1 0.00
329 287 0.27
330 184 0.17
331 154 0.14
332 142 0.13
333 54 0.05
334 120 0.11
335 131 0.12
336 4 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (330 bp):
CAAAAATTGATCCGAAAGATTTTTCCTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAATT
CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGAAT
TAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAACAAATCCTTAAATCCATTGTGG
CTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCACCAAAAATCATGCAAAACT
AAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAGGTTAGTACACGATTTCGGTAAAA
TTTTG
Found at i:99007 original size:666 final size:657
Alignment explanation
Indices: 97714--99225 Score: 2381
Period size: 666 Copynumber: 2.3 Consensus size: 657
97704 CGTTTTTAGC
* * **
97714 CAAAAATCGATCAGAAAGTTTTTTTTTTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAAT
1 CAAAAATTGATCCGAAAG-TTTTTTCCTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAAT
97779 TCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGAA
65 TCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGAA
97844 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGT
130 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGT-AAAACAAATCCTTAAATCCATTGT
* * *
97909 GGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCACCAAAAATCATGCAAAA
194 GGCTGAGATTTGGGATCATTAATATAAATATTTCAATGAGTCTTGGCACCAAAAAACATGCAAAA
97974 CAGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAGTAGTACACGATTTCGGTAAAA
259 CAGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAGTAGTACACGATTTCGGTAAAA
* **
98039 TTTTGCAAAAATTGATCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATA
324 TTTTACAAAAATTGATCCGAAAGATAATTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATA
* * *
98104 TAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCC
389 TAAATCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAATATCATTTTTACAATTCTTTCA
*
98169 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTGAAAACAAATCCATAAATCCA
454 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCATAAATCCA
*
98234 TTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGC
519 TTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCACCAAAAATCATGC
* *
98299 AAAACTAAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAA-TACACGATTT
584 AAAACAAAGTCGGGGACCCGGAACGCGTTTTTAGCCAAAAACCGTGA----TAACTACACGATTT
98363 CGGCAAAATTTGG
645 CGGCAAAATTTGG
*
98376 CAAAAATTGATCCGAAAGATTTTTCCTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAATT
1 CAAAAATTGATCCGAAAGTTTTTTCCTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAATT
* * *
98441 CAATGCCAAAAAGATTGAAGGGC-TTTCACACTTCTAATGTCATTTTTAGAATTCTTTCCCGAAT
66 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGAAT
* * * *
98505 TAAATTCTAATTAATTCGAAACAAGATTCGGATGATCGTAGAAACAAATCCTTAAATCCGTTGTG
131 TAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTA-AAACAAATCCTTAAATCCATTGTG
* * * *
98570 GCTGATATTT-GGTTACATTAATATAAATATTTCAGTGAGTCTTGGCGCACAAAAAACATGCAAA
195 GCTGAGATTTGGGAT-CATTAATATAAATATTTCAATGAGTCTTGGCAC-CAAAAAACATGCAAA
* * * * *
98634 ACTGAG-CTGGGGCCCCGGAACGCTTTTTTTTGTCAAAAATCGTGATGGTTAGTACACGATTTCG
258 ACAGAGTC-GGGGCCCCGGAACGC-GTTTTTAGCCAAAAACCGTGA--G-TAGTACACGATTTCG
*
98698 GTAAAAATTTTACAAAAATTGA-CTCGAAAGATAATTCCTCAATTTTTAACCGCAATACTCGTGA
318 GT-AAAATTTTACAAAAATTGATC-CGAAAGATAATTCCTCAATTTTTAACCGCAATACTCGTAA
* *
98762 AAAATATATAAATCAACGCCAAAAAGATTGAAG-GGTTTATCACGCTTCTAATATCATTTTTAGA
381 AAAATATATAAATCAACGCCAAAAAGATTGAAGAGCTTT-TCACGCTTCTAATATCATTTTTACA
* *
98826 ATTCTTTCACGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGATCGTAAAAATAAATCC
445 ATTCTTTCACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCC
* *
98891 TTAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGTGTCTTGGCACCAA
510 ATAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCACCAA
98956 AAATCATGCAAAACAAAGTCGGGGACCCGGAACGCGTTTTTAGCCAAAAACCGTGATAACGTACA
575 AAATCATGCAAAACAAAGTCGGGGACCCGGAACGCGTTTTTAGCCAAAAACCGTGATAAC-TACA
** *
99021 CGATTTCGTTAAAATTTTG
639 CGATTTCGGCAAAATTTGG
* *
99040 CAAAAATTGATCCGAAAGTTTTTTCCTCAAATTTTAACCGCAATACTCATAAAAAATATATAATT
1 CAAAAATTGATCCGAAAGTTTTTTCCTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAATT
*
99105 CAACGCCAAAAAGATAGAAGGGCTTTTCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGAAT
66 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGAAT
99170 TAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAA-ATAATCCTTAAAT
131 TAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAACA-AATCCTTAAAT
Statistics
Matches: 781, Mismatches: 54, Indels: 28
0.90 0.06 0.03
Matches are distributed among these distances:
659 4 0.01
660 137 0.18
661 100 0.13
662 36 0.05
663 1 0.00
664 118 0.15
665 98 0.13
666 287 0.37
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (657 bp):
CAAAAATTGATCCGAAAGTTTTTTCCTCAAGTTTTAACCGCAATACTCGTAAAAAATATATAATT
CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTAGAATTCTTTCCCGAAT
TAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAACAAATCCTTAAATCCATTGTGG
CTGAGATTTGGGATCATTAATATAAATATTTCAATGAGTCTTGGCACCAAAAAACATGCAAAACA
GAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAGTAGTACACGATTTCGGTAAAATT
TTACAAAAATTGATCCGAAAGATAATTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATATA
AATCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAATATCATTTTTACAATTCTTTCACG
AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCATAAATCCATT
GTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCACCAAAAATCATGCAA
AACAAAGTCGGGGACCCGGAACGCGTTTTTAGCCAAAAACCGTGATAACTACACGATTTCGGCAA
AATTTGG
Done.