Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015197.1 Corchorus olitorius cultivar O-4 contig15230, 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: 60122
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:980 original size:12 final size:12
Alignment explanation
Indices: 959--992 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
949 GATATAGTAA
959 AAGAAAATGAAG
1 AAGAAAATGAAG
*
971 AAGAATATGAAG
1 AAGAAAATGAAG
*
983 AGGAAAATGA
1 AAGAAAATGA
993 GGAATTGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (12 bp):
AAGAAAATGAAG
Found at i:6827 original size:29 final size:25
Alignment explanation
Indices: 6769--6820 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
6759 AGGCTTCCAA
6769 CAAAATAAGACAGGAAGAAGAAATT
1 CAAAATAAGACAGGAAGAAGAAATT
*
6794 CAAAATAAGATAGGAAGAAGAAATT
1 CAAAATAAGACAGGAAGAAGAAATT
6819 CA
1 CA
6821 TTCAAAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.60, C:0.08, G:0.19, T:0.13
Consensus pattern (25 bp):
CAAAATAAGACAGGAAGAAGAAATT
Found at i:8048 original size:8 final size:8
Alignment explanation
Indices: 8026--8054 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
8016 TTTCAAAACA
8026 AATAAATT
1 AATAAATT
8034 AAT-AATT
1 AATAAATT
8041 AATAAATT
1 AATAAATT
8049 AATAAA
1 AATAAA
8055 CAAAAGCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AATAAATT
Found at i:20399 original size:29 final size:29
Alignment explanation
Indices: 20360--20419 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
20350 TTCAATAACC
* * *
20360 TTACATCTTTTGTGATTTTGGTTATCTTA
1 TTACATCTTTTGTAATTTTGATTATCATA
*
20389 TTACATTTTTTGTAATTTTGATTATCATA
1 TTACATCTTTTGTAATTTTGATTATCATA
20418 TT
1 TT
20420 TCTCCAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.08, G:0.10, T:0.60
Consensus pattern (29 bp):
TTACATCTTTTGTAATTTTGATTATCATA
Found at i:21319 original size:209 final size:206
Alignment explanation
Indices: 20950--21352 Score: 727
Period size: 209 Copynumber: 1.9 Consensus size: 206
20940 ATCAATGGTG
*
20950 AATGTTATTAATTTTTTAAGTCTAAGATTTCTAACAAAGTTGTAGTGAATAAGATACAACACATT
1 AATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATT
*
21015 ATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAATTA
66 ACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAATTA
*
21080 AATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT-CCGATTTATTTAT
131 AATCAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCCCGATTTATTTAT
21144 CAATGGTGAATT
195 CAATGGTGAATT
21156 AATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACAT
1 AATGTTATTAA-TTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACAT
*
21221 TACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGATTTATTAAA
65 TACTATTATATATA-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAA
21286 TTAAATCAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCCGATTTATTT
128 TTAAATCAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCCGATTTATTT
21351 AT
193 AT
21353 TATTAAGGAA
Statistics
Matches: 189, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
206 11 0.06
207 65 0.34
208 6 0.03
209 107 0.57
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (206 bp):
AATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATT
ACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTATTAAATTA
AATCAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCCGATTTATTTATC
AATGGTGAATT
Found at i:21495 original size:17 final size:17
Alignment explanation
Indices: 21475--21536 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
21465 AATTAATGTA
21475 AGTATTTCAGTTATTAT
1 AGTATTTCAGTTATTAT
* *
21492 AGTATTACATTTAATTAATGT
1 AGTATTTCAGTT-ATT-A--T
21513 AAGTATTTCAGTTATTAT
1 -AGTATTTCAGTTATTAT
21531 AGTATT
1 AGTATT
21537 ACATTTAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
17 16 0.44
18 4 0.11
19 1 0.03
20 1 0.03
21 4 0.11
22 10 0.28
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (17 bp):
AGTATTTCAGTTATTAT
Found at i:21503 original size:22 final size:22
Alignment explanation
Indices: 21478--21542 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
21468 TAATGTAAGT
21478 ATTTCAGTTATTATAGTATTAC
1 ATTTCAGTTATTATAGTATTAC
* *
21500 ATTT-AATTA--AT-GTA--AGT
1 ATTTCAGTTATTATAGTATTA-C
21517 ATTTCAGTTATTATAGTATTAC
1 ATTTCAGTTATTATAGTATTAC
21539 ATTT
1 ATTT
21543 AATTAATGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
16 1 0.03
17 4 0.12
18 7 0.22
19 2 0.06
20 2 0.06
21 7 0.22
22 8 0.25
23 1 0.03
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (22 bp):
ATTTCAGTTATTATAGTATTAC
Found at i:21515 original size:39 final size:39
Alignment explanation
Indices: 21461--21580 Score: 213
Period size: 39 Copynumber: 3.1 Consensus size: 39
21451 ATACCTAAGA
21461 ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTAC
21500 ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTAC
* *
21539 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
21579 AT
1 AT
21581 AGGAATTAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
39 70 0.90
40 8 0.10
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (39 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTAC
Found at i:24935 original size:30 final size:30
Alignment explanation
Indices: 24899--25018 Score: 168
Period size: 30 Copynumber: 4.0 Consensus size: 30
24889 GCCGTCCGAC
24899 GTGGCATGCCACGTGTACCAAAAATGACAT
1 GTGGCATGCCACGTGTACCAAAAATGACAT
* *
24929 GTGGCATGCCATGTGTACAAAAAATGACAT
1 GTGGCATGCCACGTGTACCAAAAATGACAT
* * * *
24959 GTGACATACCACGTGTACCAAAAGTGATAT
1 GTGGCATGCCACGTGTACCAAAAATGACAT
*
24989 GTGGCATGCCACGTTTACACAAAAATGACA
1 GTGGCATGCCACGTGTAC-CAAAAATGACA
25019 CATGGCACGC
Statistics
Matches: 76, Mismatches: 13, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
30 67 0.88
31 9 0.12
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (30 bp):
GTGGCATGCCACGTGTACCAAAAATGACAT
Found at i:29795 original size:13 final size:13
Alignment explanation
Indices: 29759--29806 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
29749 CTATTTAATA
29759 ATCTTACTATCTT
1 ATCTTACTATCTT
*
29772 ATGTTACTATCTT
1 ATCTTACTATCTT
29785 A-C-TATCTTATCTT
1 ATCTTA-C-TATCTT
29798 ATCTTACTA
1 ATCTTACTA
29807 CTATATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
11 2 0.07
12 1 0.03
13 22 0.76
14 2 0.07
15 2 0.07
ACGTcount: A:0.25, C:0.21, G:0.02, T:0.52
Consensus pattern (13 bp):
ATCTTACTATCTT
Found at i:29810 original size:21 final size:21
Alignment explanation
Indices: 29759--29798 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29749 CTATTTAATA
*
29759 ATCTTACTATCTTATGTTACT
1 ATCTTACTATCTTATCTTACT
29780 ATCTTACTATCTTATCTTA
1 ATCTTACTATCTTATCTTA
29799 TCTTACTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.20, G:0.03, T:0.53
Consensus pattern (21 bp):
ATCTTACTATCTTATCTTACT
Found at i:31122 original size:62 final size:61
Alignment explanation
Indices: 31046--31192 Score: 181
Period size: 61 Copynumber: 2.4 Consensus size: 61
31036 TTTTTTCCAT
* * * *
31046 CGTTTGCGAAAATGCTTAAATAAGGGCTCAAATAAAAAAAAAATGCTTAAATCAGGGCTCAA
1 CGTTTGCGAAAATGCTCAAATAAGGGCCCAAA-AAAAAAAAAATGCTCAAATAAGGGCTCAA
* *
31108 CGTTTGCGAAAATGCTCAAATAAGTGCCCAAAGAAAAAAAAATGCTCAAATAAGGG-TCCAA
1 CGTTTGCGAAAATGCTCAAATAAGGGCCCAAAAAAAAAAAAATGCTCAAATAAGGGCT-CAA
**
31169 C-TTTTAGAAAATTGCTCAAATAAG
1 CGTTTGCGAAAA-TGCTCAAATAAG
31193 TCCCTGCTGT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
60 9 0.12
61 37 0.49
62 29 0.39
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (61 bp):
CGTTTGCGAAAATGCTCAAATAAGGGCCCAAAAAAAAAAAAATGCTCAAATAAGGGCTCAA
Found at i:31242 original size:21 final size:21
Alignment explanation
Indices: 31213--31266 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
31203 CATTGTGTGG
31213 TTATGCAAATTCCATAAT-AAGA
1 TTAT-CAAATTCCAT-ATGAAGA
* *
31235 TTATCAAAATTTCATATGGAGA
1 TTATC-AAATTCCATATGAAGA
31257 TTATCAAATT
1 TTATCAAATT
31267 TTCATTGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (21 bp):
TTATCAAATTCCATATGAAGA
Found at i:31244 original size:22 final size:22
Alignment explanation
Indices: 31219--31264 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
31209 GTGGTTATGC
31219 AAATTCCATAAT-AAGATTATCA
1 AAATTCCAT-ATGAAGATTATCA
* *
31241 AAATTTCATATGGAGATTATCA
1 AAATTCCATATGAAGATTATCA
31263 AA
1 AA
31265 TTTTCATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.33
Consensus pattern (22 bp):
AAATTCCATATGAAGATTATCA
Found at i:33295 original size:39 final size:40
Alignment explanation
Indices: 33239--33319 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
33229 TTTAATTCCT
*
33239 ATGTAATATATATAATAACTAAAATATTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
33279 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
33318 AT
1 AT
33320 TTTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:33346 original size:23 final size:23
Alignment explanation
Indices: 33310--33355 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
33300 AATACTTACA
33310 TTAATTAAATTTTTAGGTATTTT
1 TTAATTAAATTTTTAGGTATTTT
33333 TTAATTTAAATTTTTAGGTATTT
1 TTAA-TTAAATTTTTAGGTATTT
33356 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (23 bp):
TTAATTAAATTTTTAGGTATTTT
Found at i:33780 original size:201 final size:203
Alignment explanation
Indices: 33426--33834 Score: 668
Period size: 202 Copynumber: 2.0 Consensus size: 203
33416 TTCCTTAATA
33426 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
* *
33491 ATTTAATAAACCAACCACTAATGTTCAACTAATTTTTTTTTGGATAGTTCTATATATATAATAGT
66 ATTTAATAAACCAACCACTAATGTTCAACTAACTTTTTTTTGGATAGTTCTATATATATAATAAT
*
33556 AATCTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAA-ATT-ATAACATT
131 AATCTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAGATTAACAACATT
33619 CACCATTG
196 CACCATTG
*
33627 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTCG-TTGATATTGATCTAATT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTT-GTTTGACATTGATCTAATT
**
33691 TAATTTAATAAATTAACCACTAATGTTCAACT-ACTTTTTTTTGGATAG-T-TATATATATAATA
64 TAATTTAATAAACCAACCACTAATGTTCAACTAACTTTTTTTTGGATAGTTCTATATATATAATA
*
33753 ATAATGTCGTTAGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAGATTAACAA
129 ATAATCT-GTT-GTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAGATTAACAA
*
33818 CATTCATCATTG
192 CATTCACCATTG
33830 ATAAA
1 ATAAA
33835 GTTATTAAGC
Statistics
Matches: 194, Mismatches: 8, Indels: 10
0.92 0.04 0.05
Matches are distributed among these distances:
199 18 0.09
200 4 0.02
201 75 0.39
202 77 0.40
203 20 0.10
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.44
Consensus pattern (203 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAACCAACCACTAATGTTCAACTAACTTTTTTTTGGATAGTTCTATATATATAATAAT
AATCTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAGATTAACAACATT
CACCATTG
Found at i:33999 original size:25 final size:25
Alignment explanation
Indices: 33952--33999 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
33942 TAAGGTTATT
*
33952 AAATTAGTTGAAAGTTATCTAATAA
1 AAATTAGTTGAAAGTTATATAATAA
33977 AAATTAGTTGAAAG-TAGTATAAT
1 AAATTAGTTGAAAGTTA-TATAAT
34000 GTCTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (25 bp):
AAATTAGTTGAAAGTTATATAATAA
Found at i:42404 original size:64 final size:64
Alignment explanation
Indices: 42303--42495 Score: 386
Period size: 64 Copynumber: 3.0 Consensus size: 64
42293 GTATGGTAAT
42303 AAAATAAATAAAACAGAGATCAATGTAGCTTCATTAATTGGCAACTTGTTGATTTTATAATACA
1 AAAATAAATAAAACAGAGATCAATGTAGCTTCATTAATTGGCAACTTGTTGATTTTATAATACA
42367 AAAATAAATAAAACAGAGATCAATGTAGCTTCATTAATTGGCAACTTGTTGATTTTATAATACA
1 AAAATAAATAAAACAGAGATCAATGTAGCTTCATTAATTGGCAACTTGTTGATTTTATAATACA
42431 AAAATAAATAAAACAGAGATCAATGTAGCTTCATTAATTGGCAACTTGTTGATTTTATAATACA
1 AAAATAAATAAAACAGAGATCAATGTAGCTTCATTAATTGGCAACTTGTTGATTTTATAATACA
42495 A
1 A
42496 TTGTATAATT
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 129 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (64 bp):
AAAATAAATAAAACAGAGATCAATGTAGCTTCATTAATTGGCAACTTGTTGATTTTATAATACA
Found at i:42965 original size:38 final size:38
Alignment explanation
Indices: 42914--42994 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 38
42904 TTTGTCATGT
*
42914 TAACAAAATCATTATATTACAAAAGTGAAAATATGAGA
1 TAACAAAACCATTATATTACAAAAGTGAAAATATGAGA
*
42952 TAACAAAACCATTATATTACAAAAGTGAAAATATGAGC
1 TAACAAAACCATTATATTACAAAAGTGAAAATATGAGA
42990 TAACA
1 TAACA
42995 TTAGGGGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.54, C:0.11, G:0.10, T:0.25
Consensus pattern (38 bp):
TAACAAAACCATTATATTACAAAAGTGAAAATATGAGA
Found at i:44023 original size:3 final size:3
Alignment explanation
Indices: 44015--44047 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
44005 AATTAGAAAT
44015 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
44048 ATTAATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:48489 original size:333 final size:330
Alignment explanation
Indices: 47324--50133 Score: 2666
Period size: 333 Copynumber: 8.5 Consensus size: 330
47314 TCATGATGGT
* * * * * *
47324 AAAAA-TGACCCGAATGATTTATCCTTAATTTTTGGCAAAAATACTCAT-AAATATAAATAATTC
1 AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
* * *
47387 AACGCCAAAAGGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTA
66 AACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTA
* *
47452 ATTTCTAATTAAATCGAAACAAGAGTT-AGATGCACATAAAAACAAATCCTTAAATCCAATGTGC
130 ATTTCTAATTAAATCGAAACAAGA-TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGC
* * * *
47516 CTAAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCGAAA-T
194 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACT
* * * *
47580 AGAGTCGTGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCTGTTA
259 -GAGCCG-GGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTA
*
47645 AAATTTTAC
322 AAATTTTGC
* * * *
47654 AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGTTAAAATTCTCATAAAAAATATATAATTA
1 AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
** * * * * * * * *
47719 AACATAAAAAAGACTGAAGGGCTTTTAACGCTTCTAATATTG-TTTTCCTGTTTTT-TCAAATTA
66 AACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCT-GAATTA
* * ** *
47782 ATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATTTAATGTGGC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGCC
* * * * * * *
47847 TAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTTGACACAAAAAATCATGCAAAACTG
195 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTG
* * * * *
47912 ATCCGGG-CCCAGAACGCGGTTTTAGCCGAAAA-TCGTGATGATTAGTACACGATTTCGGCTAAA
260 AGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACT-GTGATGGTTAGTACACGATTTCGGCTAAA
47975 ATTTTGC
324 ATTTTGC
* * * * * *
47982 AAAATTTGACCCGAAAGATTTTTCCTCGATTTCTAGCGAAAATACTCAATAAAATATATATAATT
1 AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGGCTAAAATACTC-ATAAAAAATATATAATT
*** * *
48047 CAACTTGAAAAGGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTA
65 CAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTA
* * * * * ** **
48112 ATTTTTAATTAAATCGAAATAAGATTCAGATTCACATAAAAACAAATCCTTAAATTTAATACGCC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGCC
* * * * * *
48177 TGAGATTTGATTAGATGAATAAAGATATTTTAAGGAGTCTCAGCGTCAAAAATCATGTAAAACAG
195 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTG
** * *
48242 AGCCGTGGCCATGGAACGCGTATTTAGCCAAAAACTGTGATGGTTAGTATACGATTTCGGCTAAA
260 AGCCG-GGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAA
*
48307 ATTTTAC
324 ATTTTGC
* * *
48314 AAAAATTGATCCGAAAGATATTTCCTCAATTTTTGGATAAAATACTCATAAAAAATATATAATTC
1 AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
* * * * * * * *
48379 GACATCAAAAAGATTGTAGGGCTTTTAACGCTTCTAATATTGTTTTTCTTATATTTTT-TCAAAT
66 AACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTC--ATATTTTTCT-GAAT
* * * *
48443 TAATTTCTTATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAACCCTTAAATCTAATGT-
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * ** *
48507 CGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTTGGTACAAAAAATCATGCAAAA
193 C-CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA
* * * * ** * * * *
48572 TTGTGCCGGGCCCTGGAACGCGGTTTTAG-C-TGAA----GAGGGTCAGTATATGATTTCGGCTA
257 CTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTA
48631 AAATTTTGC
322 AAATTTTGC
* * * * * * * *
48640 AAGAATTGACTCGAAATATTTTTACTCGATTTCTAGCGAAAATACTCATAAAAAATATATAATTC
1 AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
* * * * * *
48705 AACACCAAAAAAACTGAAAGCCTTTTTCATGATTTTAATATCGTTTTTCATATTTTTCTGAATTA
66 AACACCAAAAAGATTGAAGGAC-TTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTA
*
48770 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGCC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGCC
* *
48835 TGAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGGCACCAAAAATCATGCAAAACTG
195 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTG
* * ** * * * *
48900 AGTCGGGCCCCGGAATGCGTTTTTATTCGAAAACCGTGATGGTTAGTACAGGATTTCGGCTACAA
260 AGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA
*
48965 TTTTGT
325 TTTTGC
* * *
48971 AAATATTTGACCCGAAAGATTTTTCCTGTCAATTTTTGCCTAAAATACTCATAAAATATATATAA
1 AAA-AATTGACCCGAAAGATTTTTCC--TCAATTTTTGGCTAAAATACTCATAAAAAATATATAA
* * * *
49036 -TCTAACGCCAAAAAGATTGGAGGACTTTTAACGCTTTTAATATCATTTTTCATATTTTTCTGAA
63 TTC-AACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAA
* * ** * *
49100 TTAATTTCTAGTTAAATCGAAATAAGATTCAGATGCTTATAAAAACAAATTCTTCAATCCAATGT
127 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * * * * * *
49165 AG-CTGAGATTAGATTAAATGAATATGGATATCTCAAAGAGTCTTGGTGCCAAAAATCACGCAAA
192 -GCCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAA
* * * * *
49229 ACTTAGCCGGGGCCGCGGAACGCGTTTTTAGCCAAAAACAGTGATTGATTA-TCACACGATTTGG
256 ACTGAGCC-GGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGA-TGGTTAGT-ACACGATTTCG
49293 GCTAGAAA-TTTGC
318 GCTA-AAATTTTGC
* ** * * *
49306 AAAAATTGACTCG-AA-ATTTATATCCTCAATTTTTATCCACAATACTCATAAAAATTATATAAT
1 AAAAATTGACCCGAAAGATTT-T-TCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAAT
* * ** ** * * * * *
49369 TGAACGCCCGAAAGATTGAAGGGTTTTTCATGCTTCTAATTTCGTTTTTCCTATTATTTTCCGAA
64 TCAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-T-TTTTCTGAA
* * ***
49434 -T-ATTTCTAATTAAATCGAAACATGATTCAGATGCTTGT-TTTACAAATCCTTAAATCCAATGT
127 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * * *
49496 GGCTGAGATTTGATTAGATGAATGTAGATGTTTCAAGGAGTCTCGGCGCAAAAAATCATGCAACA
192 GCCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA
* ** * * * *
49561 CTGAACCGAAACCCCGGAACACGTTTTTAGCCAAAAACCT-TGATTTCGACTAACGTGCACGATT
257 CTGAGCCG-GGCCCCGGAACGCGTTTTTAGCCAAAAA-CTGTGA--T-G-GTTA-GTACACGATT
* * *
49625 TCAGCTAATATTTTGA
315 TCGGCTAAAATTTTGC
* * * * ** * *
49641 AAAAATTGACCGGAAATATTTTTTCTTAATTTTTCTCTAAAATACT--TATAATATATATAATTC
1 AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
* * * *
49704 AACTCGAAAAAGATTTG-AGGACTTTTCTCGCTTTTAATATTGTTTTTCATATTTTTCTGAATTA
66 AACACCAAAAAGA-TTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTA
* * * * *
49768 AATTCTAATTAAATCAAAACAAGATTCAGATACTCGT-AAAACGAAATCCTTAAATGCAATGTGG
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC-AAATCCTTAAATCCAATGTGC
* ** *
49832 CT--GA---GATT---T-AATATAGATATTTCGAGGAGTCTCGATGCCAAAAATCATGTAAAACT
194 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACT
* ** * * * * * * * * *
49888 AAGTTAGGGCTCCGAAACGCATTTTTA-ACAAAAACCGTGTTGGTTAGTAGACGATTTAGCCTAA
259 GAG-CCGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAA
*
49952 AATTTTAC
323 AATTTTGC
* * * * * * *
49960 AAAAAGTGACCAC-AAA-AATATTCTCTCAATTTTTAGCCACAATACTTA-AAAAAATATATAAT
1 AAAAATTGACC-CGAAAGATTTTTC-CTCAATTTTTGGCTAAAATACTCATAAAAAATATATAAT
* * * * * * *
50022 TCAACTCCAAATAA-ATTCAAAGACTTTTCACGCTTCTGATATCGTTTATCCTATTTTTTCTGAA
64 TCAACACCAAA-AAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAA
* * * *
50086 TTAATTTCTAATTAAAACGAAACATGATTCAGATGTTTGTAAAAACAA
127 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
50134 TTGTTGAGAT
Statistics
Matches: 2012, Mismatches: 404, Indels: 137
0.79 0.16 0.05
Matches are distributed among these distances:
318 4 0.00
319 50 0.02
320 52 0.03
321 48 0.02
322 6 0.00
323 1 0.00
324 8 0.00
325 203 0.10
326 104 0.05
327 23 0.01
328 93 0.05
329 58 0.03
330 258 0.13
331 243 0.12
332 288 0.14
333 366 0.18
334 126 0.06
335 71 0.04
336 6 0.00
337 4 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (330 bp):
AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
AACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGCCT
GAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGA
GCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAAT
TTTGC
Found at i:48887 original size:658 final size:656
Alignment explanation
Indices: 47361--50120 Score: 2758
Period size: 660 Copynumber: 4.2 Consensus size: 656
47351 ATTTTTGGCA
* * * *
47361 AAAATACTCAT-AAATATAAATAATTCAACGCCAAAAGGATTGGAGGACTTTTCACGCTTTTAAT
1 AAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGGAAGACTTTTCACGCTTTTAAT
47425 ATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGAGTT-AGATGCACAT
66 ATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGA-TTCAGATGCACAT
*
47489 AAAAACAAATCCTTAAATCCAATGTGCCTAAGATTTGATTAGATGAATAAAGATATTTCAAGGAG
130 AAAAACAAATCCTTAAATCCAATGTGCCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAG
* * * *
47554 TCTCGGTGCCAAAAATCATGCGAAATAGAGTCGTGGCCCCGGAACGCGTTTTTAGCCAAAAACCG
195 TCTCGGCGCCAAAAATCATGCAAAACAGAGCCGTGGCCCCGGAACGCGTTTTTAGCCAAAAACCG
* *
47619 TGATGGTTAGTACACGATTTCTGTTAAAATTTTACAAAAATTGACCCGAAAGATATTTCCTCAAT
260 TGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAGATATTTCCTCAAT
* * * * * * *
47684 TTTTGGTTAAAATTCTCATAAAAAATATATAATTAAACATAAAAAAGACTGAAGGGCTTTTAACG
325 TTTTGGCTAAAATACTCATAAAAAATATATAATTCAACATCAAAAAGATTGTAGGACTTTTAACG
* * *
47749 CTTCTAATATTG-TTTTCCTGTTTTT-TCAAATTAATTTCTAATTAAATTGAAACAAGATTCAGA
390 CTTCTAATATTGTTTTTCATATTTTTCT-AAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
* * *
47812 TGCTCGTAAAAACAAATTCTTAAATTTAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTT
454 TGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTT
** * * *
47877 CAAGGAGTTTTGACACAAAAAATCATGCAAAACTGAT-CCGGGCCCAGAACGCGGTTTTAGCCGA
519 CAAGGAGTTTTGGTACAAAAAATCATGCAAAATTG-TGCCGGGCCCGGAACGCGGTTTTAGCAGA
* * * *
47941 AAATCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAATTTGACCCGAAAGATTTTTC
583 AAA--GTGA-G-TCAGTATACGATTTCGGCTAAAATTTTGCAAAA-TTGACTCGAAATATTTTTC
48006 CTCGATTTCTAGCG
643 CTCGATTTCTAGCG
* *** * *
48020 AAAATACTCAATAAAATATATATAATTCAACTTGAAAAGGATTGGAGGACTTTTCACGCTTTTAA
1 AAAATACTC-ATAAAAAATATATAATTCAACGCCAAAAAGATTGGAAGACTTTTCACGCTTTTAA
* * *
48085 TATCGTTTTTCATA-TTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATTCACAT
65 TATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACAT
** ** *
48149 AAAAACAAATCCTTAAATTTAATACGCCTGAGATTTGATTAGATGAATAAAGATATTTTAAGGAG
130 AAAAACAAATCCTTAAATCCAATGTGCCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAG
* * * ** * *
48214 TCTCAGCGTCAAAAATCATGTAAAACAGAGCCGTGGCCATGGAACGCGTATTTAGCCAAAAACTG
195 TCTCGGCGCCAAAAATCATGCAAAACAGAGCCGTGGCCCCGGAACGCGTTTTTAGCCAAAAACCG
* *
48279 TGATGGTTAGTATACGATTTCGGCTAAAATTTTACAAAAATTGATCCGAAAGATATTTCCTCAAT
260 TGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAGATATTTCCTCAAT
* * *
48344 TTTTGGATAAAATACTCATAAAAAATATATAATTCGACATCAAAAAGATTGTAGGGCTTTTAACG
325 TTTTGGCTAAAATACTCATAAAAAATATATAATTCAACATCAAAAAGATTGTAGGACTTTTAACG
* *
48409 CTTCTAATATTGTTTTTCTTATATTTTT-TCAAATTAATTTCTTATTAAATCGAAATAAGATTCA
390 CTTCTAATATTGTTTTTC--ATATTTTTCT-AAATTAATTTCTAATTAAATCGAAACAAGATTCA
* *
48473 GATGCTCGTAAAAACAAACCCTTAAATCTAATGTCGCTGAGATTTGGTTAGATGAATATAGATAT
452 GATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGGTTAGATGAATATAGATAT
*
48538 TTCAAGGAGTTTTGGTACAAAAAATCATGCAAAATTGTGCCGGGCCCTGGAACGCGGTTTTAGCT
517 TTCAAGGAGTTTTGGTACAAAAAATCATGCAAAATTGTGCCGGGCCC-GGAACGCGGTTTTAGCA
* * *
48603 GAAGAG-G-GTCAGTATATGATTTCGGCTAAAATTTTGCAAGAATTGACTCGAAATATTTTTACT
581 GAAAAGTGAGTCAGTATACGATTTCGGCTAAAATTTTGCAA-AATTGACTCGAAATATTTTTCCT
48666 CGATTTCTAGCG
645 CGATTTCTAGCG
* * * * * * *
48678 AAAATACTCATAAAAAATATATAATTCAACACCAAAAAAACTGAAAGCCTTTTTCATGATTTTAA
1 AAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGGAAGAC-TTTTCACGCTTTTAA
* *
48743 TATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
65 TATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACAT
* * *
48807 AAAAACAAATCCTTAAATTCAATGTGCCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAT
130 AAAAACAAATCCTTAAATCCAATGTGCCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAG
* * * * ** *
48872 TCTCGGCACCAAAAATCATGCAAAACTGAGTCG-GGCCCCGGAATGCGTTTTTATTCGAAAACCG
195 TCTCGGCGCCAAAAATCATGCAAAACAGAGCCGTGGCCCCGGAACGCGTTTTTAGCCAAAAACCG
* * ** * *
48936 TGATGGTTAGTACAGGATTTCGGCTACAATTTTGTAAATATTTGACCCGAAAGATTTTTCCTGTC
260 TGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAA-AATTGACCCGAAAGATATTTCC--TC
* * ** *
49001 AATTTTTGCCTAAAATACTCATAAAATATATATAA-TCTAACGCCAAAAAGATTGGAGGACTTTT
322 AATTTTTGGCTAAAATACTCATAAAAAATATATAATTC-AACATCAAAAAGATTGTAGGACTTTT
* ** * * *
49065 AACGCTTTTAATATCATTTTTCATATTTTTCTGAATTAATTTCTAGTTAAATCGAAATAAGATTC
386 AACGCTTCTAATATTGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTC
** * * * * * * * *
49130 AGATGCTTATAAAAACAAATTCTTCAATCCAATGTAGCTGAGATTAGATTAAATGAATATGGATA
451 AGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGGTTAGATGAATATAGATA
* * * * * * * *
49195 TCTCAAAGAGTCTTGGTGCCAAAAATCACGCAAAACTT-AGCCGGGGCCGCGGAACGCGTTTTTA
516 TTTCAAGGAGTTTTGGTACAAAAAATCATGCAAAA-TTGTGCC-GGGCC-CGGAACGCGGTTTTA
* * * * *
49259 GCCAAAAACAGTGATTGATTATCACACGATTTGGGCTAGAAA-TTTGCAAAAATTGACTCGAAAT
578 G-CAGAAA-AGTGAGTCAGTAT---ACGATTTCGGCTA-AAATTTTGC-AAAATTGACTCGAAAT
* * * * *
49323 -TTATATCCTCAATTTTTATCC
636 ATT-TTTCCTCGATTTCTAGCG
* * * ** ** * *
49344 ACAATACTCATAAAAATTATATAATTGAACGCCCGAAAGATT-GAAGGGTTTTTCATGCTTCTAA
1 AAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGGAA-GACTTTTCACGCTTTTAA
* * * * ***
49408 TTTCGTTTTTCCTATTATTTTCCGAA-T-ATTTCTAATTAAATCGAAACATGATTCAGATGCTTG
65 TATCGTTTTTCATATT-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACA
*** * ** *
49471 T-TTTACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATGTAGATGTTTCAAGGA
129 TAAAAACAAATCCTTAAATCCAATGTGCCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGA
* * * * *** *
49535 GTCTCGGCGCAAAAAATCATGCAACACTGAACCGAAACCCCGGAACACGTTTTTAGCCAAAAACC
194 GTCTCGGCGCCAAAAATCATGCAAAACAGAGCCGTGGCCCCGGAACGCGTTTTTAGCCAAAAACC
* * * * * * * * *
49600 TTGATTTCGACTAACGTGCACGATTTCAGCTAATATTTTGA-AAAAATTGACCGGAAATATTTTT
259 GTGA--T-G-GTTA-GTACACGATTTCGGCTAAAATTTT-ACAAAAATTGACCCGAAAGATATTT
* * ** * *
49664 TCTTAATTTTTCTCTAAAATACT--TATAATATATATAATTCAAC-TCGAAAAAGATT-TGAGGA
318 CCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACATC-AAAAAGATTGT-AGGA
** * * * *
49725 CTTTTCTCGCTTTTAATATTGTTTTTCATATTTTTCTGAATTAAATTCTAATTAAATCAAAACAA
381 CTTTTAACGCTTCTAATATTGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAA
*
49790 GATTCAGATACTCGT-AAAACGAAATCCTTAAATGC-AATGTGGCTGAGA-----TT---T-AAT
446 GATTCAGATGCTCGTAAAAAC-AAATCCTTAAAT-CTAATGTGGCTGAGATTTGGTTAGATGAAT
* * * * * * * * ** *
49844 ATAGATATTTCGAGGAGTCTCGATGCCAAAAATCATGTAAAACTAAGT-TAGGGCTCCGAAACGC
509 ATAGATATTTCAAGGAGTTTTGGTACAAAAAATCATGCAAAA-T-TGTGCCGGGC-CCGGAACGC
** * * * * * * * *
49908 ATTTTTAACA-AAAACCGTGTTGGTTAGTAGACGATTTAGCCTAAAATTTTACAAAAAGTGAC-C
571 GGTTTTAGCAGAAAA--GTG--AGTCAGTATACGATTTCGGCTAAAATTTTGC-AAAATTGACTC
* * * * * *
49971 -ACAAAAATATTCTCTCAATTTTTAGCC
631 GA-AATATTTTTC-CTCGATTTCTAGCG
* * * ** * *
49998 ACAATACTTA-AAAAAATATATAATTCAACTCCAAATAA-ATTCAAAGACTTTTCACGCTTCTGA
1 AAAATACTCATAAAAAATATATAATTCAACGCCAAA-AAGATTGGAAGACTTTTCACGCTTTTAA
* * * *
50061 TATCGTTTATCCTATTTTTTCTGAATTAATTTCTAATTAAAACGAAACATGATTCAGATG
65 TATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
50121 TTTGTAAAAA
Statistics
Matches: 1779, Mismatches: 264, Indels: 121
0.82 0.12 0.06
Matches are distributed among these distances:
652 9 0.01
653 61 0.03
654 85 0.05
655 5 0.00
656 56 0.03
657 92 0.05
658 368 0.21
659 38 0.02
660 370 0.21
661 70 0.04
662 3 0.00
663 146 0.08
664 109 0.06
665 210 0.12
666 82 0.05
667 32 0.02
668 1 0.00
669 20 0.01
670 22 0.01
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (656 bp):
AAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGGAAGACTTTTCACGCTTTTAAT
ATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACATA
AAAACAAATCCTTAAATCCAATGTGCCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGT
CTCGGCGCCAAAAATCATGCAAAACAGAGCCGTGGCCCCGGAACGCGTTTTTAGCCAAAAACCGT
GATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAGATATTTCCTCAATT
TTTGGCTAAAATACTCATAAAAAATATATAATTCAACATCAAAAAGATTGTAGGACTTTTAACGC
TTCTAATATTGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
CTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCA
AGGAGTTTTGGTACAAAAAATCATGCAAAATTGTGCCGGGCCCGGAACGCGGTTTTAGCAGAAAA
GTGAGTCAGTATACGATTTCGGCTAAAATTTTGCAAAATTGACTCGAAATATTTTTCCTCGATTT
CTAGCG
Found at i:50439 original size:15 final size:16
Alignment explanation
Indices: 50421--50450 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
50411 ATAAATAATG
50421 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
50436 ATATTATAATCTAAA
1 ATATTATAATCTAAA
50451 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:50917 original size:8 final size:8
Alignment explanation
Indices: 50904--50930 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
50894 TTTTATATAG
50904 TAGTAAGA
1 TAGTAAGA
50912 TAGTAAGA
1 TAGTAAGA
50920 TAGTAAGA
1 TAGTAAGA
50928 TAG
1 TAG
50931 GAACGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (8 bp):
TAGTAAGA
Found at i:54496 original size:17 final size:17
Alignment explanation
Indices: 54474--54507 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54464 GAGAAGAATC
54474 TAGTTATAGATAAGAAA
1 TAGTTATAGATAAGAAA
54491 TAGTTATAGATAAGAAA
1 TAGTTATAGATAAGAAA
54508 CATGAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (17 bp):
TAGTTATAGATAAGAAA
Found at i:55366 original size:21 final size:21
Alignment explanation
Indices: 55337--55433 Score: 105
Period size: 21 Copynumber: 4.6 Consensus size: 21
55327 TTATGAAGGG
55337 TATATATTTATTTTTTAA-GATA
1 TATA-ATTTATTTTTTAAGGA-A
*
55359 TACAATTTA-TTTTTAAGGAA
1 TATAATTTATTTTTTAAGGAA
55379 TATAA-TTATTTTTTTAA-GATA
1 TATAATTTA-TTTTTTAAGGA-A
55400 TATAATTTATTTTTTAAAGGAA
1 TATAATTTATTTTTT-AAGGAA
55422 TA-AATTTATTTT
1 TATAATTTATTTT
55434 AAAGGCATAT
Statistics
Matches: 66, Mismatches: 2, Indels: 15
0.80 0.02 0.18
Matches are distributed among these distances:
19 3 0.05
20 14 0.21
21 36 0.55
22 11 0.17
23 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (21 bp):
TATAATTTATTTTTTAAGGAA
Found at i:55401 original size:41 final size:43
Alignment explanation
Indices: 55338--55433 Score: 137
Period size: 41 Copynumber: 2.3 Consensus size: 43
55328 TATGAAGGGT
*
55338 ATATATTTA-TTTTTTAAGATATACAATTTA-TTTTT-AAGGA
1 ATATAATTATTTTTTTAAGATATACAATTTATTTTTTAAAGGA
*
55378 ATATAATTATTTTTTTAAGATATATAATTTATTTTTTAAAGGA
1 ATATAATTATTTTTTTAAGATATACAATTTATTTTTTAAAGGA
55421 ATA-AATTTATTTT
1 ATATAA-TTATTTT
55434 AAAGGCATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
40 8 0.16
41 20 0.40
42 7 0.14
43 15 0.30
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (43 bp):
ATATAATTATTTTTTTAAGATATACAATTTATTTTTTAAAGGA
Found at i:55444 original size:41 final size:41
Alignment explanation
Indices: 55338--55444 Score: 103
Period size: 41 Copynumber: 2.6 Consensus size: 41
55328 TATGAAGGGT
* * * *
55338 ATATATTTAT-TTTTTAAGATATACAATTTATTTTTAAGGA
1 ATATAATTATATTTTAAAGACATATAATTTATTTTTAAGGA
* * *
55378 ATATAATTATTTTTTTAAGATATATAATTTATTTTTTAAAGGA
1 ATATAATTATATTTTAAAGACATATAATTTA-TTTTT-AAGGA
*
55421 ATA-AATT-TATTTTAAAGGCATATA
1 ATATAATTATATTTTAAAGACATATA
55445 TGTAATTTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
40 9 0.16
41 32 0.55
42 9 0.16
43 8 0.14
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.50
Consensus pattern (41 bp):
ATATAATTATATTTTAAAGACATATAATTTATTTTTAAGGA
Found at i:55452 original size:20 final size:19
Alignment explanation
Indices: 55411--55453 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
55401 ATAATTTATT
*
55411 TTTTAAAGGAATAAATTTA
1 TTTTAAAGGAATAAATTAA
* *
55430 TTTTAAAGGCATATATGTAA
1 TTTTAAAGGAATAAAT-TAA
55450 TTTT
1 TTTT
55454 CAATCAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (19 bp):
TTTTAAAGGAATAAATTAA
Found at i:56980 original size:45 final size:45
Alignment explanation
Indices: 56916--57008 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
56906 AAGACTTGAC
56916 GGGTTGGGCCGCACGGGGGAGAGACCCGACTCACAAGTGAATCGG
1 GGGTTGGGCCGCACGGGGGAGAGACCCGACTCACAAGTGAATCGG
56961 GGGTTGGGCCGCACGGGGGAGAGACCCGACTCACAAGTGAATCGG
1 GGGTTGGGCCGCACGGGGGAGAGACCCGACTCACAAGTGAATCGG
57006 GGG
1 GGG
57009 AGATTGTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.22, C:0.24, G:0.44, T:0.11
Consensus pattern (45 bp):
GGGTTGGGCCGCACGGGGGAGAGACCCGACTCACAAGTGAATCGG
Found at i:60027 original size:6 final size:6
Alignment explanation
Indices: 60016--60072 Score: 73
Period size: 6 Copynumber: 9.5 Consensus size: 6
60006 TTCAATTTTC
*
60016 AAAAAG AAAAAG -AAAAG AAAAGG AAAAAG AAAAAG -AAAAG AAAAGAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA-AG
60063 AAAAGAG AAA
1 AAAA-AG AAA
60073 TAGATTAGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
5 10 0.22
6 24 0.52
7 12 0.26
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:60031 original size:5 final size:5
Alignment explanation
Indices: 60017--60061 Score: 54
Period size: 5 Copynumber: 8.2 Consensus size: 5
60007 TCAATTTTCA
60017 AAAAG AAAAAG AAAAG AAAAGG AAAAAG AAAAAG AAAAG AAAAG A
1 AAAAG -AAAAG AAAAG AAAA-G -AAAAG -AAAAG AAAAG AAAAG A
60062 GAAAAGAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 20 0.54
6 13 0.35
7 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:60046 original size:23 final size:24
Alignment explanation
Indices: 60016--60072 Score: 98
Period size: 23 Copynumber: 2.4 Consensus size: 24
60006 TTCAATTTTC
60016 AAAAAGAAAAAGAAAAGAAAAG-G
1 AAAAAGAAAAAGAAAAGAAAAGAG
60039 AAAAAGAAAAAGAAAAGAAAAGAG
1 AAAAAGAAAAAGAAAAGAAAAGAG
60063 AAAAGAGAAA
1 AAAA-AGAAA
60073 TAGATTAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 22 0.69
24 5 0.16
25 5 0.16
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (24 bp):
AAAAAGAAAAAGAAAAGAAAAGAG
Done.