Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012376.1 Corchorus olitorius cultivar O-4 contig12409, 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: 126669
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1524 original size:26 final size:26
Alignment explanation
Indices: 1495--1546 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1485 TTTTTACTCT
**
1495 TTTCATATTTCGATGCCAAAAAAAAC
1 TTTCATATTTCGATGAAAAAAAAAAC
*
1521 TTTCATATTTTGATGAAAAAAAAAAC
1 TTTCATATTTCGATGAAAAAAAAAAC
1547 CATCATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (26 bp):
TTTCATATTTCGATGAAAAAAAAAAC
Found at i:1552 original size:26 final size:26
Alignment explanation
Indices: 1497--1553 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1487 TTTACTCTTT
** **
1497 TCATATTTCGATGCCAAAAAAAACTT
1 TCATATTTCGATGAAAAAAAAAACCA
*
1523 TCATATTTTGATGAAAAAAAAAACCA
1 TCATATTTCGATGAAAAAAAAAACCA
1549 TCATA
1 TCATA
1554 ATTCATAGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (26 bp):
TCATATTTCGATGAAAAAAAAAACCA
Found at i:7356 original size:104 final size:105
Alignment explanation
Indices: 7115--7375 Score: 400
Period size: 106 Copynumber: 2.5 Consensus size: 105
7105 AGTTTAGTCT
*
7115 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
*
7180 AATAATTTATTGTTATATGGTTTTAGAAATAAAATACAAAAC
65 AATAA-TTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* * *
7222 TAATTTCACTAAGTTTAACCCAAATTAAATTTTTATTTTTATTTTAAGGGTAAATTCCATAATTA
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
* *
7287 ATAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 ATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
** *
7326 TAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
7376 TAAGAAAAAT
Statistics
Matches: 142, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
103 42 0.30
104 35 0.25
106 48 0.34
107 17 0.12
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:7651 original size:29 final size:28
Alignment explanation
Indices: 7606--7682 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 28
7596 TTCAACTTGC
* *
7606 AAGTTCAAGGGGTAAAATATCCAAAATTA
1 AAGTTCAAGGGGCAAAACAT-CAAAATTA
*
7635 AAGTTTAAGGGGCAAAACATCAAAATCATA
1 AAGTTCAAGGGGCAAAACATCAAAAT--TA
7665 CAAGTTC-AGGAGGCAAAA
1 -AAGTTCAAGG-GGCAAAA
7683 AGGGCATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 6 0.15
29 17 0.43
30 5 0.12
31 12 0.30
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.19
Consensus pattern (28 bp):
AAGTTCAAGGGGCAAAACATCAAAATTA
Found at i:7829 original size:29 final size:31
Alignment explanation
Indices: 7768--7830 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
7758 TACAGTACAT
*
7768 GTCCCTCTATTTACAAAAATGGATCAATTTG
1 GTCCCTCTATTTACAAAAATGGATCAATCTG
*
7799 GTCCCTCTA-TTACAAAAATTG-TCAATCTG
1 GTCCCTCTATTTACAAAAATGGATCAATCTG
7828 GTC
1 GTC
7831 TATCTACTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 10 0.33
30 11 0.37
31 9 0.30
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (31 bp):
GTCCCTCTATTTACAAAAATGGATCAATCTG
Found at i:7836 original size:29 final size:31
Alignment explanation
Indices: 7768--7843 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
7758 TACAGTACAT
* * *
7768 GTCCCTCTATTTACAAAAATGGATCAATTTG
1 GTCCATCTACTTACAAAAATGGATCAATCTG
* *
7799 GTCCCTCTA-TTACAAAAATTG-TCAATCTG
1 GTCCATCTACTTACAAAAATGGATCAATCTG
*
7828 GTCTATCTACTTACAA
1 GTCCATCTACTTACAA
7844 TTTGGTGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 14 0.35
30 17 0.43
31 9 0.22
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.36
Consensus pattern (31 bp):
GTCCATCTACTTACAAAAATGGATCAATCTG
Found at i:16552 original size:2 final size:2
Alignment explanation
Indices: 16545--16590 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
16535 GGTTTCAATC
16545 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
16587 AT AT
1 AT AT
16591 GCAATTGATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20094 original size:2 final size:2
Alignment explanation
Indices: 20087--20114 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20077 TTATGCAAGA
20087 AT 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 AT
20115 GCATGTAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50989 original size:6 final size:6
Alignment explanation
Indices: 50980--51004 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
50970 CAGCGTCAGG
50980 ACCCTA ACCCTA ACCCTA ACCCTA A
1 ACCCTA ACCCTA ACCCTA ACCCTA A
51005 TTCTTTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (6 bp):
ACCCTA
Found at i:52147 original size:2 final size:2
Alignment explanation
Indices: 52140--52164 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52130 CTAGCCAGCC
52140 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 T
52165 CATGCATGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61317 original size:37 final size:37
Alignment explanation
Indices: 61267--61339 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
61257 CAAATTCATA
* *
61267 ATTGTTACATGAAGTAGATGCACCAGACACGGGCATT
1 ATTGTTACATGAAGTAGATGCACCACACACAGGCATT
61304 ATTGTTACATGAAGTAGATGCACCACACACAGGCAT
1 ATTGTTACATGAAGTAGATGCACCACACACAGGCAT
61340 GTACAGGGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (37 bp):
ATTGTTACATGAAGTAGATGCACCACACACAGGCATT
Found at i:64468 original size:19 final size:19
Alignment explanation
Indices: 64446--64497 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
64436 TAATTAGGAG
*
64446 TAATTTTTAAATAAAAATA
1 TAATATTTAAATAAAAATA
* *
64465 TAATATATAAATAAAAATT
1 TAATATTTAAATAAAAATA
*
64484 TAATATTAAAATAA
1 TAATATTTAAATAA
64498 TTAATTAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAATATTTAAATAAAAATA
Found at i:73319 original size:60 final size:60
Alignment explanation
Indices: 73226--73430 Score: 392
Period size: 60 Copynumber: 3.4 Consensus size: 60
73216 CACTAAATTG
*
73226 GAAGGAAATGTACCAACTGATAGGGCAGGGTCTGCAAAGAACATTATTGACTTGACTGTT
1 GAAGGAAATGTACCGACTGATAGGGCAGGGTCTGCAAAGAACATTATTGACTTGACTGTT
73286 GAAGGAAATGTACCGACTGATAGGGCAGGGTCTGCAAAGAACATTATTGACTTGACTGTT
1 GAAGGAAATGTACCGACTGATAGGGCAGGGTCTGCAAAGAACATTATTGACTTGACTGTT
*
73346 GAAGGAAATGAACCGACTGATAGGGCAGGGTCTGCAAAGAACATTATTGACTTGACTGTT
1 GAAGGAAATGTACCGACTGATAGGGCAGGGTCTGCAAAGAACATTATTGACTTGACTGTT
73406 GAAGGAAATGTACCGACTGATAGGG
1 GAAGGAAATGTACCGACTGATAGGG
73431 ATTGGTGAAG
Statistics
Matches: 142, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 142 1.00
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (60 bp):
GAAGGAAATGTACCGACTGATAGGGCAGGGTCTGCAAAGAACATTATTGACTTGACTGTT
Found at i:81157 original size:8 final size:8
Alignment explanation
Indices: 81144--81173 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
81134 TTCTAGCAAA
81144 AAAAAAAC
1 AAAAAAAC
81152 AAAAAAAC
1 AAAAAAAC
81160 -AAAAAAC
1 AAAAAAAC
81167 AAAAAAA
1 AAAAAAA
81174 AACAGTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:81165 original size:15 final size:14
Alignment explanation
Indices: 81141--81175 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
81131 ACTTTCTAGC
81141 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
81155 AAAACAAAAAACAAA
1 AAAA-AAAAAACAAA
81170 AAAAAA
1 AAAAAA
81176 CAGTAATGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:81165 original size:17 final size:17
Alignment explanation
Indices: 81142--81177 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
81132 CTTTCTAGCA
*
81142 AAAAAAAAACAAAAAAAC
1 AAAAAACAA-AAAAAAAC
81160 AAAAAACAAAAAAAAAC
1 AAAAAACAAAAAAAAAC
81177 A
1 A
81178 GTAATGCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAACAAAAAAAAAC
Found at i:87779 original size:6 final size:6
Alignment explanation
Indices: 87768--87804 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
87758 TTCTTATATC
87768 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA T
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA T
87805 TTATTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:89728 original size:2 final size:2
Alignment explanation
Indices: 89721--89751 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
89711 TAAAAAGGGA
89721 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
89752 GAAAGCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:102585 original size:31 final size:31
Alignment explanation
Indices: 102550--102616 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
102540 TGGGCCGGAC
102550 GGGGAAGAGATAAGAACTCACAAGTGAATCG
1 GGGGAAGAGATAAGAACTCACAAGTGAATCG
102581 GGGGAAGAGATAAGAACTCACAAGTGAATCG
1 GGGGAAGAGATAAGAACTCACAAGTGAATCG
*
102612 AGGGA
1 GGGGA
102617 GATTGTTGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.42, C:0.12, G:0.34, T:0.12
Consensus pattern (31 bp):
GGGGAAGAGATAAGAACTCACAAGTGAATCG
Found at i:104495 original size:333 final size:326
Alignment explanation
Indices: 103860--108985 Score: 3907
Period size: 333 Copynumber: 15.4 Consensus size: 326
103850 ACAAACTCTA
* * ** *
103860 GATTTAATTAGAAATTAATTCAGAAAAAGTATGAAAAACGATATTAAAAGTATGAAAAACACTTT
1 GATTTAATTAGAAATTAATTGAGAAAAA-TATGAAAAACGATATTAGAAGCGTG-AAAAC-CCTT
* * * * * * ** *
103925 TAATCTTTTTGGTGTTAAATTATATATATTTTATGAATATTTTATCCAAAAATTGAGGAAAAATT
63 CAATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAA-T
* *
103990 TTTCGGGTCAATTTTTGTAAAATTTTAGCCAAAATC--GT-GTACCATCACGG-TTTTGGCTAAA
127 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGTACCATCACGGTTTTTGGCTAAA
* * * * *
104051 AACGCGTTTCGAGGCCTCGACTCAGTTTTGCATGATTTTTGGTGCCGAGACTCCTTGAATTATCT
192 AACGCGTTCCG-GGCCCCGA-TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCT
* * * * ** *
104116 ATATTTATCTAATAAAATCTTAGCCACATTGCATTTAAGGATTTGTTTTTATAACCATCTGAATC
255 ATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
*
104181 TTATTTC
320 TTGTTTC
* *
104188 GATTTAATTAGAAATTAATTGAGAAAAATATGAAAAACGCTATTAAAAGCGTGAAAACCCTTCAA
1 GATTTAATTAGAAATTAATTGAGAAAAATATGAAAAACGATATTAGAAGCGTGAAAACCCTTCAA
* * *
104253 TATTTTTGGTGTTGAATTATATATCTTTTATGAGTATTGTGGCTAAAAATTGAGGAAATATCTTT
66 TATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAAT-TTT
* * * ** *
104318 CGGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGCAGTATTCATCACTTTTTTTTTTTGGCTG
130 CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGTA-CCATCAC----GGTTTTTGGCTA
104383 AAAACGCGTTCCGGGCCCCGGATCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATC
190 AAAACGCGTTCCGGGCCCC-GATCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATC
* * * * *
104448 TATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGTATTTGTTTTTATGAGAATCTAAAT
254 TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
104513 CTTGTTTC
319 CTTGTTTC
* * * *
104521 GATTTAATTAGAAATCAATTCG-GAAAAAGTATGAAAAACGATATTAGAAGCGTAAAAAATCCAT
1 GATTTAATTAGAAATTAATT-GAGAAAAA-TATGAAAAACGATATTAGAAGCGT-GAAAACCCTT
** * * *
104585 CAATATTTTTTACGTTGAATTATATATTTTTTATGAGTATTTTAGGCTTTTAGCAAAAAATTAAG
63 CAATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGT-GGC---T----AAAAATTGAG
* * * *
104650 GAAATATTTTTCGGGTCAATTTTTGCAAAATGTTAGCCGAAATCGTGTAATAATCATCACGGTTT
120 GAAA-AATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGT-ACCATCACGGTTT
* * * * *** *
104715 TTGGTTCAAAACGGCGCCTTCCAGGACCCCGAGTCAGTTTTGCATAATTTTTGGCATTAAAACTC
183 TTGGCTAAAAAC-GCG--TTCC-GGGCCCCGA-TCAGTTTTGCATGATTTTTGGCGCCAAGACTC
* * * * * * *
104780 CTT-AAGATATCCATATTCATCTAATTAAATCTTAGCGATATTGCATTTAAGGATTTATTTTTTT
243 CTTGAA-ATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGA-TT-TGTTTTT
*
104844 ACGAACATCTGAATCTTGTTTC
305 ACGAGCATCTGAATCTTGTTTC
* * * * * * * * *
104866 AATTTAATTAAAAATTAATTCTAAAAAAAAGATGAAAAACGAAATGAAAAGCTTGAAAAGTCCTC
1 GATTTAATTAGAAATTAA-T-TGAGAAAAATATGAAAAACGATATTAGAAGCGTGAAAA---C-C
* * * * *
104931 CAATTTTTTTGCCAA-ATTATTTTGGCGTTAAATTATATATATTTCATGATTATTTTAGCTAAAA
60 C-------TT--CAATA-T-TTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAA
* * * * * * *
104995 ATTTAGAAAAAATTTCCGGCTC-TTTTTTCGCAAAATTTTAGCCGAAATTGTGTATTAACCATCA
114 ATTGAGGAAAAATTTTCGGGTCAATTTTT-GCAAAATTTTAGCCGAAATCGTGTAGT-ACCATCA
* * * * * *
105059 CAGTTTTTTTTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGTATGACTTTTGGT
177 C-G------GTTTTTGGCTAAAAACGCG-TTCCGGGCCCCGA-TCAGTTTTGCATGATTTTTGGC
* * * *
105124 GTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATT
233 GCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATT
*
105189 TGTTTTTACGAGCATCTGAATCTTGTTTT
298 TGTTTTTACGAGCATCTGAATCTTGTTTC
* * * * * *
105218 AATTTAATTGGAAATTAATTCAGAAAAATATGTAAAACGATATTAAAAGCGTGAAAAGTCCTTCA
1 GATTTAATTAGAAATTAATTGAGAAAAATATGAAAAACGATATTAGAAGCGTGAAAA-CCCTTCA
* ** * * * * *
105283 ATCTTTTCAGAGTTGAATTATATATATTTTATGATTATTTTAGAC-AAACATTGAGGAAAAATAT
65 ATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGT-GGCTAAAAATTGAGGAAAAAT-T
* * * * *
105347 TTCTGGTCAATTTTTGTAAAATATTAGCCGAAATCGTGTACGTTAGTCGAAATCACGG-TTTTGA
128 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-G-TA--C--CATCACGGTTTTTGG
* * * * * * * * *
105411 CTAAAAACGCGTTCCGAGCCCCGGTTCAATGTTGCATGATTTTTGCCTCCGAGACTCTTTGAAGT
187 CTAAAAACGCGTTCCGGGCCCC-GATCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
* *** *
105476 ATCTATATTCATCTAATCAAATCTCAGGCACATTGGATTTAAGGATTTG-TAAAACAAGCATCTG
251 ATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTG
*
105540 AATCATGTTTC
316 AATCTTGTTTC
* *
105551 GATTTAATTAGAAATTAATTCG-GAAAATAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCT
1 GATTTAATTAGAAATTAATT-GAG-AAA-AATATGAAAAACGATATTAGAAGCGTGAAAA-CCCT
* * * * * *
105615 TCAATTTTTTTGGCGTTGAATTATACAAATTTTATGAGTTTTGTGACTAAAAATTCAGGAAATAA
62 TCAATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAA-AA
* ** * ** * * *
105680 CTTTCGACTCAATTTTTGCAAAAATTTTAGCCAAAATTATGTAATAATCATCACGGTTTTTGGTT
126 TTTTCGGGTCAATTTTTGC-AAAATTTTAGCCGAAATCGTGTAGT-ACCATCACGGTTTTTGGCT
* * * * * * * * * *
105745 AAAAACGCGTTCCAAGGCCCCGGCTAAATTTTACATAATTTTTGGCACCAAGAATCTTTGAGATA
189 AAAAACGCGTTCC-GGGCCCC-GATCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATA
* * * * *
105810 TCCATATTCTTCTAATCAAATCCCAGCTACATTGGATTTAAGAATTT-TCTTTTACGAGCATCTG
252 TCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGT-TTTTACGAGCATCTG
105874 AATCTTGTTTC
316 AATCTTGTTTC
* * * *
105885 GATTTAAATAGAAATTAATTGAG-AAAATATGAAAAACGATATTAAAAGCGT-AAAAGTCCTCCA
1 GATTTAATTAGAAATTAATTGAGAAAAATATGAAAAACGATATTAGAAGCGTGAAAA-CCCTTCA
* * * * * *
105948 ATCTTTTTGGCGTTAAATAATATATATATATATATATTGTATGAGTATTTTAGCCAAATATTGAG
65 ATATTTTTGGCG-T---T--GA-AT-TATATATAT-TT-TATGAGTATTGTGGCTAAAAATTGAG
* * * * *
106013 GAAAAATTTTCGGGCCATTTTTTGCAAAATTTTAGCTGATAT-G-GT-TTACCATCACGGTTTTT
120 GAAAAATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGTACCATCACGGTTTTT
* ** * * * * * *
106075 GCCTAAAAACTAGTTTCGGGGCTCCGGCTTAGTTTTGTATGATTTTTGGCACCAAGACAGACTCC
185 GGCTAAAAACGCG-TTCCGGGC-CCCGATCAGTTTTGCATGATTTTTGGCGCC---A-AGACTCC
* * * * ** *
106140 TTGAAATATCTATATTCATCTAATTAAATCTCACCCGCATTGAATTTATTGATTTGTTTTTATGA
244 TTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGA
*
106205 GCATTTGAATCTTGTTTC
309 GCATCTGAATCTTGTTTC
* * * * * * *
106223 TATTTAATTAGAAATTAATTCAGAATAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCA
1 GATTTAATTAGAAATTAATTGAGAAAAATATGAAAAACGATATTAGAAGCGTGAAAA-CCCTTCA
* * *
106288 A-ACTTTTTCGCGTTGAATTATATATATATTATGAGTATTGTGGCTAGAAATTGAGGAAAAATAT
65 ATA-TTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAAT-T
* * * ***
106352 TTCGGGTCAATTTTTGCATAATTTTAGCCGAAATCGTGAACTACCA-CAATTTTTTTTTTGGCTA
128 TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGTACCATC-A--CGGTTTTTGGCTA
** * * * **
106416 AAAACG-GATTCCGGAGCCCCGAGTCAGTTTTGCATGATTTTTTGTTG-AAATACTCCGTGAAGC
190 AAAACGCG-TTCCGG-GCCCCGA-TCAGTTTTGCATGA-TTTTTGGCGCCAAGACTCCTTGAAAT
* * * * * *
106479 ATCTATATTCATCTAACCTAATTTTAGCCACATTGAATTTAAGGATTTGTTTTTA-GTAGCATTT
251 ATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG-AGCATCT
* *
106543 TAATCATGTTTC
315 GAATCTTGTTTC
* * * * * *
106555 GATTTAATT-GAAAATTAATTTGGGAAAAAAGTAGGAAAAATGAAATTAGAAGCGTGAGAAGCCG
1 GATTTAATTAG-AAATTAA-TTGAG-AAAAA-TATGAAAAACGATATTAGAAGCGTGA-AAACCC
* * * * * * *
106619 TTCAATCTTTTTGACATAGAATTATATATTTTTTATGATTATTGTGGCTGAAAATTGA-GAAAAT
61 TTCAATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAAA-
* * *
106683 ATTTT-GGGTCAATTTTTGCAAAATTTCAGCCAAAATC--GT-GTACCATCACAGTTTTTTTGG-
125 ATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGTACCATCAC-G-GTTTTTGGC
** * * * * * * * * ***
106743 TTGAAACGTGTTTCGGGGCCTCGACGCAATTTTGTATGGTTTTTCGCATAAAGACTCCTTGAAAT
188 TAAAAACGCG-TTCCGGGCCCCGA-TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
* * * * * * *
106808 AACTATATTCATCTAACCAAAATCTCAACCACACTGGATTTAAAGCTTTGTTTTTACAAGCATCT
251 ATCTATATTCATCTAATC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
*
106873 GAATTTTGTTTC
315 GAATCTTGTTTC
* *
106885 GATTTAATTAGAAATAAATTCG-GAAAAA-ATGGAAAAACGATATTAGATGCGTGAAAAACCCTT
1 GATTTAATTAGAAATTAATT-GAGAAAAATAT-GAAAAACGATATTAGAAGCGTG-AAAACCCTT
* ** * * * *
106948 CAATTTTTTTTGGAATTGAATTATATTTTTTTTTCTGAGTATTGTGGC-AAAAATAGAGGAAAAA
63 CAA-TATTTTTGGCGTTGAATTATA-TATATTTTATGAGTATTGTGGCTAAAAATTGAGG--AAA
** * * * *
107012 AATTTTCGAATCAGTTTTTGCAAAATTTTA-CCGAAATCGTGTACTAACCATTACAGTTTTTGGC
124 AATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGT-ACCATCACGGTTTTTGGC
* * * * * *
107076 TAAAAATGCGTTCCGGAGTCCCGACTCAATATTTGCATGATTTTTGGCACAAAAACTCCTTGAAA
188 TAAAAACGCGTTCCGG-GCCCCGA-TCAGT-TTTGCATGATTTTTGGCGCCAAGACTCCTTGAAA
* * * * * * *
107141 TATCTTTATTCATCGAACCAAATCTCTGCCACATTGGATATAAGGATTTGTTTTTATGAGCATGT
250 TATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
107206 GAATCTTGTTTC
315 GAATCTTGTTTC
* * *
107218 GATTTAATTAGAAATTAATTCG-GAAAAAAAACTGGAAAAACGATAGTAGAAGCGTGAAAACCCG
1 GATTTAATTAGAAATTAATT-GAG-AAAAATA-T-GAAAAACGATATTAGAAGCGTGAAAACCCT
* * * * *
107282 TCAATCGTTTTT-CCATTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAAAATTGA-GAAA
62 TCAAT-ATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGC--TAAAAATTGAGGAAA
** * *
107345 AACTTTTTAGGT-AA-----G----TTTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTTTG
124 AA-TTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGT-ACCATCACGG-TTTTTG
* * *
107400 G-TAAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCAATGATTTTTGGCAG-AAAGACTCCTTG
186 GCTAAAAACGCGTTCCG-GGCCCC-GATCAGTTTTGC-ATGATTTTTGGC-GCCAAGACTCCTTG
* * * *
107463 AAATATCTATATTCAGCTAACCAAATCTCAGCCACAATT-GATTTAAGCATTTGTTTTTATGAGC
247 AAATATCTATATTCATCTAATCAAATCTCAGCCAC-ATTGGATTTAAGGATTTGTTTTTACGAGC
107527 ATCTGAATCTTGTTTC
311 ATCTGAATCTTGTTTC
* * * *
107543 GATTTAATTAGAAATAAATTTG-GATAAAACTATGAAAAACGTTATTAGAAGAGTGAAAACCGTT
1 GATTTAATTAGAAATTAA-TTGAGA-AAAA-TATGAAAAACGATATTAGAAGCGTGAAAACCCTT
* * * * * * *
107607 CAAT-TTTTTGGTGTTGAATTTTAGAT-TTTTTTTAGTATTATGG-AAAAGAATTGA-GAAACCA
63 CAATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAA-AATTGAGGAAA--A
* * ** * * * *
107668 TTTTTTCAGGTCTGTTTTTGCAAAATCTTAGTCGAAATCGT-T--TACTCGTCACAGTTTTTGGC
125 -ATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGTAC-CATCACGGTTTTTGGC
* * *
107730 TAAAAACGCGTTCCAGGGACCCTGCTCAGTTTTGCATGATTTTTGGCG-TAGAGACTCCTTGAAA
188 TAAAAACGCGTTCC-GGG-CCCCGATCAGTTTTGCATGATTTTTGGCGCCA-AGACTCCTTGAAA
* * * * * * * *
107794 TATCCATATTCATCGAACCAAATCCCAGTCACATTCGATTTAACGATTTGTTTTTACGAGCATTT
250 TATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
107859 GAATCTTGTTTC
315 GAATCTTGTTTC
* * * *
107871 GATTTATTTAGAAATTAATTCTG-GAAAAAT-GGAAAAACGATATTGGAAGCGTGAAAAACTCTT
1 GATTTAATTAGAAATTAA-T-TGAGAAAAATATGAAAAACGATATTAGAAGCGTG-AAAACCCTT
* * * *
107934 CAATATTTTTGACGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAAT
63 CAATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAG-GAAAAAT
* * * *
107999 TTTCGGGTC-A--GTT-C-----TTT-GCCGAAATCGTATACTAACCATCACGGTTTTTGTCTAA
127 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGT-ACCATCACGGTTTTTGGCTAA
* * * * * * * *** * * *
108054 AAACACGTTTCGGGGCCTCGACACAGTTTTGCGTGGTTTTTGACATAAAGGCTTCATGAAATATC
191 AAACGCG-TTCCGGGCCCCGA-TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATC
* * * *
108119 TATATTTATCTAA-CAAAATATCAACCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAA
254 TATATTCATCTAATC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
108183 TCTTGTTTC
318 TCTTGTTTC
* ** * * * *
108192 GATTTAATAAGAAAAAAATTCGGAAAAAAATATGAAAAACGATATTATAAGCATTAAAAACCCTT
1 GATTTAATTAGAAATTAATT--GAGAAAAATATGAAAAACGATATTAGAAGC-GTGAAAACCCTT
* * ** *
108257 CAACT-TTTTTGGCATTGAATTATATAT-TTCTTCTGAGTATTGCAGCAAAAAATTGAGGAAAAA
63 CAA-TATTTTTGGCGTTGAATTATATATATT-TTATGAGTATTGTGGCTAAAAATTGAGGAAAAA
* * * * * **
108320 CTTTCCGAGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACTATCATAGTTTTTGGC
126 -TTTTCGGGTCA-ATTTTTGCAAAATTTTAGCCGAAATCGTGTAGT-ACCATCACGGTTTTTGGC
* * * * * * * *
108385 TAAAAACGCGTTCCGAAGCCCGGCTCAATTTTGCATGACTTTTGGCGCAAAAACTCCTTGAAAAA
188 TAAAAACGCGTTCCG-GGCCCCGATCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATA
* * *
108450 TCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGA
252 TCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGA
*
108515 ATCTTATTTC
317 ATCTTGTTTC
* * * * *
108525 GATTTAATTAGAAATTGATTCGGGAAAAAT-GGAAAAATGATATTAGAAGCGTGAAAAGCCCATC
1 GATTTAATTAGAAATTAATT-GAGAAAAATATGAAAAACGATATTAGAAGCGTGAAAA-CCCTTC
* * * * *
108589 AAAATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGG-TAAAAAATTGAGAGGAAACT
64 AATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCT-AAAAATTGAG-GAAAAAT
* * *
108653 TTTCGGGTC-A-----G----TTTTTAGCCGAAATCGTGTACTAACCAT--CGGTTTTTGACTAA
127 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGT-ACCATCACGGTTTTTGGCTAA
* * * * * * **
108706 AAATGCGTTCTTGGGCACTGCTCTGTTTTGCATGATTTTTGGCGCCGTGACTCCTTGAAATATCT
191 AAACGCGTTC-CGGGCCCCGATCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCT
* * * * * *
108771 TTATTCATCTAATCAAATATAAGCCACATTGGATTTAAGAATTTGTTTTTACGTGCATCTAAATC
255 ATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
*
108836 TAGTTTC
320 TTGTTTC
* ** ** * * *
108843 GATTT-ATTTGAAAATTCGTTTTGAAAAATATGAAAAATGATATTAAAAGCGTGAAAAGTCCTTC
1 GATTTAATTAG-AAATTAATTGAGAAAAATATGAAAAACGATATTAGAAGCGTGAAAA-CCCTTC
** * * *
108907 AATCCTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTTGCGAAAAATTGAGGAAAAATCT
64 AATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAAT-T
*
108972 ATCGGGTC-ATTTTT
128 TTCGGGTCAATTTTT
108986 ATCATCATGG
Statistics
Matches: 3857, Mismatches: 707, Indels: 473
0.77 0.14 0.09
Matches are distributed among these distances:
317 16 0.00
318 230 0.06
319 9 0.00
320 41 0.01
321 133 0.03
322 47 0.01
323 91 0.02
324 46 0.01
325 251 0.07
326 40 0.01
327 70 0.02
328 215 0.06
329 139 0.04
330 154 0.04
331 170 0.04
332 160 0.04
333 520 0.13
334 364 0.09
335 257 0.07
336 88 0.02
337 55 0.01
338 146 0.04
339 66 0.02
340 50 0.01
341 1 0.00
342 9 0.00
343 141 0.04
344 4 0.00
345 43 0.01
346 20 0.01
347 8 0.00
349 7 0.00
350 72 0.02
351 14 0.00
352 42 0.01
353 2 0.00
354 76 0.02
355 6 0.00
356 4 0.00
357 13 0.00
358 6 0.00
359 31 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (326 bp):
GATTTAATTAGAAATTAATTGAGAAAAATATGAAAAACGATATTAGAAGCGTGAAAACCCTTCAA
TATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATTTTC
GGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGTACCATCACGGTTTTTGGCTAAAAACG
CGTTCCGGGCCCCGATCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTC
ATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTT
C
Found at i:114684 original size:14 final size:14
Alignment explanation
Indices: 114665--114694 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
114655 TTCAAGTAGT
114665 AAGCGATTTGTTCC
1 AAGCGATTTGTTCC
114679 AAGCGATTTGTTCC
1 AAGCGATTTGTTCC
114693 AA
1 AA
114695 CTTATGCAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (14 bp):
AAGCGATTTGTTCC
Found at i:118249 original size:186 final size:182
Alignment explanation
Indices: 117939--118306 Score: 603
Period size: 186 Copynumber: 2.0 Consensus size: 182
117929 ACCTCCTACT
** *
117939 TCATTTCCTGCAATGATCGAATTTAGAATTAAATGAAGCCTCTTAACCACAATGTCAAATTCGAT
1 TCATTTCCTGCAATGATCGAATTTAGAATTAAACCAAGCCTCTAAACCACAATGTCAAATTCGAT
*
118004 CTATAGTGACAAATGGCTATTCAAAATGGAATGACACTTCATAAATAGCTAATCAATGCAGTAAT
66 CTATAGTGACAAATGGCTATTCAAAATGCAATGACACTTCATAAATAGCTAATCAATGCAGTAAT
* *
118069 CAATGTAGCTAACGAGATTATGGGACATTAATTATAGGAAACAGAACTATTG
131 CAATGTAGCTAACGAGATTATGGGACATGAATTATAGAAAACAGAACTATTG
118121 TCATTTCCTGCAATGATCGAATTTAGAATTAAACCAAGCCTCTAAACCACAAT-TCCAAATTCGA
1 TCATTTCCTGCAATGATCGAATTTAGAATTAAACCAAGCCTCTAAACCACAATGT-CAAATTCG-
*
118185 AAAATCTATAGTGACAAATGGCTATTCAAAATGCAATGACACTTTATAAATAGCTAATCAATGCA
64 ---ATCTATAGTGACAAATGGCTATTCAAAATGCAATGACACTTCATAAATAGCTAATCAATGCA
* *
118250 GTAGTCAATGTAGCTAACGAGATTATGGGACATGAATTATAGAAAACAGACCTATTG
126 GTAATCAATGTAGCTAACGAGATTATGGGACATGAATTATAGAAAACAGAACTATTG
118307 GCAGAGCCCA
Statistics
Matches: 172, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
181 1 0.01
182 58 0.34
186 113 0.66
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (182 bp):
TCATTTCCTGCAATGATCGAATTTAGAATTAAACCAAGCCTCTAAACCACAATGTCAAATTCGAT
CTATAGTGACAAATGGCTATTCAAAATGCAATGACACTTCATAAATAGCTAATCAATGCAGTAAT
CAATGTAGCTAACGAGATTATGGGACATGAATTATAGAAAACAGAACTATTG
Found at i:120985 original size:62 final size:62
Alignment explanation
Indices: 120880--121000 Score: 156
Period size: 62 Copynumber: 2.0 Consensus size: 62
120870 AGTACCCACT
* * ** *
120880 CTTTTGAAGATTTTCGGATTCATTGGGCTTTCATTTGATGATTTTTCAA-GCTTATAGATCGC
1 CTTTTGAAGATTTGCGGATCCATTGGGCTTTCACCTGAGGATTTTT-AAGGCTTATAGATCGC
*
120942 CTTTTGAAGATTTGGGGATCCATTGGGCTTTCACCT-ACGGATTTTTAAGGCTTATAGAT
1 CTTTTGAAGATTTGCGGATCCATTGGGCTTTCACCTGA-GGATTTTTAAGGCTTATAGAT
121001 AACTTATCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
61 3 0.06
62 48 0.94
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.42
Consensus pattern (62 bp):
CTTTTGAAGATTTGCGGATCCATTGGGCTTTCACCTGAGGATTTTTAAGGCTTATAGATCGC
Found at i:123167 original size:13 final size:13
Alignment explanation
Indices: 123149--123189 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
123139 ATTGACCCCA
123149 ATCTTATCTTACT
1 ATCTTATCTTACT
123162 ATCTTATCTTATCT
1 ATCTTATCTTA-CT
*
123176 -TATTATCTTACT
1 ATCTTATCTTACT
123188 AT
1 AT
123190 TATATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 2 0.08
13 21 0.84
14 2 0.08
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (13 bp):
ATCTTATCTTACT
Found at i:123172 original size:18 final size:18
Alignment explanation
Indices: 123149--123185 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
123139 ATTGACCCCA
123149 ATCTTATCTTACTATCTT
1 ATCTTATCTTACTATCTT
*
123167 ATCTTATCTTATTATCTT
1 ATCTTATCTTACTATCTT
123185 A
1 A
123186 CTATTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.19, G:0.00, T:0.57
Consensus pattern (18 bp):
ATCTTATCTTACTATCTT
Found at i:125264 original size:333 final size:327
Alignment explanation
Indices: 124600--125827 Score: 1518
Period size: 333 Copynumber: 3.8 Consensus size: 327
124590 CTCCACTCAG
* * *
124600 TTTTGGCATTGAATTATATA-TTTTTCTGAGTATAGTGGCAAAAAATTGAGGAACAATTTTTTGG
1 TTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAATTTTTCGG
* * *
124664 TTTAGTTTTTTTGCAAAATTTTAGCCGAAATCGTGTATATTACGGTTTTTGGCTAAAAACGCGTT
66 GTCAG-TTTTTTGCAAAATTTTAGCCGAAATCGTGTATATCACGGTTTTTGGCTAAAAACGCGTT
124729 CCAGAGT-CACGACTCAATTTTACATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCA
130 CCAGAGTCCACGACTCAATTTTACATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCA
* *
124793 TCGAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTAAATCTTGTTTT
195 TCGAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTT
*
124858 GATTTTATTAAAAATAAATTAAGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCA
260 GATTTTATTAGAAATAAATTAAGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCA
124923 ATTT
325 A-TT
124927 TTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAATTTTTCGG
1 TTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAATTTTTCGG
* *
124992 GTTAGTTTTTTTGCAAAATATTT-GCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAA
66 GTCAG-TTTTTTGCAAAAT-TTTAGCCGAAATCGTGTA-T----ATCACGGTTTTTGGCTAAAAA
* *
125056 CGCGTTCCAGAGT-CACGGCTCAATTTTACATGATTTTTGGCGCAAAGACTCCTTGAAATATCTT
124 CGCGTTCCAGAGTCCACGACTCAATTTTACATGATTTTTGGCGCAAAGACTCCTTGAAATATCTA
**
125120 TATTCATCGAACCAAATCTTAGCCACATTAAAATTTAAGGATTTGTTTTTACGAGCATCTGAATC
189 TATTCATCGAACCAAATCTTAGCCACATT-GGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
125185 TTGTTTTGATTTTATTAGAAATAAATTAAGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAA
253 TTGTTTTGATTTTATTAGAAATAAATTAAGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAA
125250 CCCTTCAATT
318 CCCTTCAATT
* * *
125260 TTTTGGCATTGAATTATATATTTTTTATGAGTATTCTGGCAAAAAATTGAGGAAAAACTTTTTTG
1 TTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAA-TTTTTCG
* * * *
125325 GG-CA-ATTTTTGCAAAATTTTAGCTGAAATCGTG--TATCACGGGTTTTGGCAAAAAACGCGTT
65 GGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTATATCACGGTTTTTGGCTAAAAACGCGTT
* * * * * * *
125386 CCGGAGTGC-CGATTCAATTTTGCAAGATTTTTGGCACAAAGGCTCCTT-AAAGTATCTATATTC
130 CCAGAGTCCACGACTCAATTTTACATGATTTTTGGCGCAAAGACTCCTTGAAA-TATCTATATTC
* * * * * * * *
125449 ATTGAACCAAATATCAGCCACATTGGATATAAGAATTTGTATTTACGAGAATCTCAATCTTGTTT
194 ATCGAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTT
* * * * * *
125514 TGATTTAATTAGAAATTAATT-CGAAAACAAATGGAAAAACGATATTAGAAGGGTGAAAAGCCCG
259 TGATTTTATTAGAAATAAATTAAGAAAA-AAA-GGAAAAACGATATTAGAAGCGTGAAAAACCCT
125578 TCAATCT
322 TCAAT-T
* * * * *
125585 TTTTGGCATTGAATTATATAATTTTTCTAAATATT-TCGCAAAAAAAATTGA-GAAAAACTTTTC
1 TTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGC--AAAAAATTGAGGAAAAATTTTTC
*
125648 GGGTCAG-----T------TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGGCTAAAAA
64 GGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTA-T----ATCACGGTTTTTGGCTAAAAA
** * * * * * *
125702 CGCGTT-TTGGGTCCCCGATTTAGTTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCT
124 CGCGTTCCAGAGTCCACGACTCAATTTTACATGATTTTTGGC-GCAAAGACTCCTTGAAATATCT
* * * *
125765 ATATTCATCTAACCAAATCTAAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAA
188 ATATTCATCGAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
125828 AATTGAGGAA
Statistics
Matches: 795, Mismatches: 77, Indels: 63
0.85 0.08 0.07
Matches are distributed among these distances:
315 16 0.02
318 1 0.00
321 5 0.01
322 119 0.15
323 62 0.08
324 138 0.17
325 41 0.05
326 10 0.01
327 20 0.03
328 74 0.09
329 4 0.01
330 3 0.00
331 23 0.03
333 168 0.21
334 111 0.14
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (327 bp):
TTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAATTTTTCGG
GTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTATATCACGGTTTTTGGCTAAAAACGCGTTC
CAGAGTCCACGACTCAATTTTACATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCAT
CGAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTG
ATTTTATTAGAAATAAATTAAGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA
TT
Done.