Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold310
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: 19589
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:1321 original size:15 final size:15
Alignment explanation
Indices: 1303--1349 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1293 GATGTGAATA
1303 ATAAAATATATAAAT
1 ATAAAATATATAAAT
1318 ATAAAATAT-TAAAAT
1 ATAAAATATAT-AAAT
1333 ATCAAAA-ATATAGAAT
1 AT-AAAATATATA-AAT
1349 A
1 A
1350 ATAATAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 1 0.04
15 18 0.64
16 9 0.32
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (15 bp):
ATAAAATATATAAAT
Found at i:1556 original size:22 final size:22
Alignment explanation
Indices: 1503--1560 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
1493 ATAATATTAA
*
1503 AAATATGTACATAATATAGTGTT
1 AAATATATACATAATATAG-GTT
*
1526 AAA-AAATACATAATATA-GTT
1 AAATATATACATAATATAGGTT
1546 AAGATATATACATAA
1 AA-ATATATACATAA
1561 GATAACATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 5 0.17
21 1 0.03
22 21 0.70
23 3 0.10
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (22 bp):
AAATATATACATAATATAGGTT
Found at i:1607 original size:25 final size:25
Alignment explanation
Indices: 1579--1712 Score: 77
Period size: 25 Copynumber: 5.6 Consensus size: 25
1569 GTAAAAAAAT
1579 ATATATAAATAATATAATATTAAAG
1 ATATATAAATAATATAATATTAAAG
* * * * *
1604 ATATATACATAAAATAGTATAAAAT
1 ATATATAAATAATATAATATTAAAG
* *
1629 ATATATATACGTAATATAGA-ATTTAA-
1 ATATATA-A-ATAATATA-ATATTAAAG
** *
1655 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATAAATAATATAATATTAAAG
*
1677 A-ATATATATAATATAATATT-AAG
1 ATATATAAATAATATAATATTAAAG
*
1700 AAATAT-AATAATA
1 ATATATAAATAATA
1713 ACAAAAAAGA
Statistics
Matches: 82, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
21 4 0.05
22 12 0.15
23 18 0.22
24 5 0.06
25 32 0.39
26 1 0.01
27 10 0.12
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATAAATAATATAATATTAAAG
Found at i:1634 original size:27 final size:27
Alignment explanation
Indices: 1531--1647 Score: 91
Period size: 25 Copynumber: 4.5 Consensus size: 27
1521 GTGTTAAAAA
* *
1531 ATACATAATATAGT-TAAGATATATAC
1 ATACATAATATAGTATAAAATATATAT
* * *
1557 ATAAGATAACAT-GTA-AAAAAATATAT
1 AT-ACATAATATAGTATAAAATATATAT
* * * *
1583 ATAAATAATATAATAT-TAA-AGATAT
1 ATACATAATATAGTATAAAATATATAT
*
1608 ATACATAAAATAGTATAAAATATATAT
1 ATACATAATATAGTATAAAATATATAT
*
1635 ATACGTAATATAG
1 ATACATAATATAG
1648 AATTTAAAAT
Statistics
Matches: 68, Mismatches: 17, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
25 25 0.37
26 20 0.29
27 23 0.34
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.32
Consensus pattern (27 bp):
ATACATAATATAGTATAAAATATATAT
Found at i:1659 original size:27 final size:27
Alignment explanation
Indices: 1574--1660 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 27
1564 AACATGTAAA
*
1574 AAAATATATATAAATAATAT--AATATT
1 AAAATATATATACATAATATAGAAT-TT
* * * *
1600 -AAAGATATATACATAAAATAGTA-TA
1 AAAATATATATACATAATATAGAATTT
*
1625 AAATATATATATACGTAATATAGAATTT
1 AAA-ATATATATACATAATATAGAATTT
1653 AAAATATA
1 AAAATATA
1661 CCTAATATAT
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
25 17 0.37
26 2 0.04
27 23 0.50
28 4 0.09
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (27 bp):
AAAATATATATACATAATATAGAATTT
Found at i:2272 original size:28 final size:29
Alignment explanation
Indices: 2195--2388 Score: 283
Period size: 28 Copynumber: 6.8 Consensus size: 29
2185 TAGGTACAAG
* *
2195 TGGTGGTGGAGAAGGTGTGGCTAGT-GAG-
1 TGGTGGTGGA-AAAGAGTGGCTAGTGGAGT
2223 TGGTGGTGG-AAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGAGTGGCTAGTGGAGT
*
2251 T-GTGGTGGAAAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGAGTGGCTAGTGGAGT
2279 TGGTGGTGGAAAAG-GTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGAGTGGCTAGTGGAGT
2307 TGGTGGTGGAAAAGAGTGGCTAGTGGAG-
1 TGGTGGTGGAAAAGAGTGGCTAGTGGAGT
* *
2335 TGGTGGTGGAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGAGTGGCTAGTGGAGT
2364 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAA-GAGTGGCTAGT
2389 TGAGAAAAAG
Statistics
Matches: 152, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
26 12 0.08
27 10 0.07
28 83 0.55
29 37 0.24
30 10 0.07
ACGTcount: A:0.21, C:0.04, G:0.50, T:0.25
Consensus pattern (29 bp):
TGGTGGTGGAAAAGAGTGGCTAGTGGAGT
Found at i:2345 original size:85 final size:83
Alignment explanation
Indices: 2195--2388 Score: 300
Period size: 85 Copynumber: 2.3 Consensus size: 83
2185 TAGGTACAAG
* * *
2195 TGGTGGTGGAGAAGGTGTGGCTAGTGAGTGGTGGTGGAAAGAGTGGCTAGTGGAGTTGTGGTGGA
1 TGGTGGTGGA-AAAGAGTGGCTAGTGAGTGGTGGTGGAAAGAGTGGCTAGTGGAGTGGTGGTGGA
2260 AAAGTGTGGCTAGTGGAGT
65 AAAGTGTGGCTAGTGGAGT
2279 TGGTGGTGGAAAAG-GTGGCTAGTGGAGTTGGTGGTGGAAAAGAGTGGCTAGTGGAGTGGTGGTG
1 TGGTGGTGGAAAAGAGTGGCTAGT-GAG-TGGTGGTGG-AAAGAGTGGCTAGTGGAGTGGTGGTG
*
2343 GAAAGGTGTGGCTAGTGGAGT
63 GAAAAGTGTGGCTAGTGGAGT
2364 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAA-GAGTGGCTAGT
2389 TGAGAAAAAG
Statistics
Matches: 102, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
82 9 0.09
83 6 0.06
84 19 0.19
85 58 0.57
86 1 0.01
87 9 0.09
ACGTcount: A:0.21, C:0.04, G:0.50, T:0.25
Consensus pattern (83 bp):
TGGTGGTGGAAAAGAGTGGCTAGTGAGTGGTGGTGGAAAGAGTGGCTAGTGGAGTGGTGGTGGAA
AAGTGTGGCTAGTGGAGT
Found at i:2354 original size:57 final size:55
Alignment explanation
Indices: 2195--2388 Score: 284
Period size: 57 Copynumber: 3.4 Consensus size: 55
2185 TAGGTACAAG
* *
2195 TGGTGGTGGAGAAGGTGTGGCTAGT-GAGTGGTGGTGGAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGA-AAAGAGTGGCTAGTGGAGTGGTGGTGGAAAG-GTGGCTAGTGGAGT
*
2251 T-GTGGTGGAAAAGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGAGTGGCTAGTGGAG-TGGTGGTGG-AAAGGTGGCTAGTGGAGT
2307 TGGTGGTGGAAAAGAGTGGCTAGTGGAGTGGTGGTGGAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGAGTGGCTAGTGGAGTGGTGGTGGAAA-G-GTGGCTAGTGGAGT
2364 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAA-GAGTGGCTAGT
2389 TGAGAAAAAG
Statistics
Matches: 129, Mismatches: 2, Indels: 12
0.90 0.01 0.08
Matches are distributed among these distances:
54 13 0.10
55 14 0.11
56 35 0.27
57 56 0.43
58 11 0.09
ACGTcount: A:0.21, C:0.04, G:0.50, T:0.25
Consensus pattern (55 bp):
TGGTGGTGGAAAAGAGTGGCTAGTGGAGTGGTGGTGGAAAGGTGGCTAGTGGAGT
Found at i:3142 original size:14 final size:14
Alignment explanation
Indices: 3123--3172 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
3113 GAGTTGATTT
* *
3123 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
3137 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
3152 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
3166 TT-AAAAA
1 TTGAAAAA
3173 AGACCTCAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:3174 original size:15 final size:15
Alignment explanation
Indices: 3134--3174 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3124 TGAAAAATAT
3134 AAATTGAAAAAA-CAG
1 AAATT-AAAAAAGCAG
*
3149 AAATT-GAAAAGCAG
1 AAATTAAAAAAGCAG
3163 AAATTAAAAAAG
1 AAATTAAAAAAG
3175 ACCTCAGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.18
14 8 0.36
15 10 0.45
ACGTcount: A:0.66, C:0.05, G:0.15, T:0.15
Consensus pattern (15 bp):
AAATTAAAAAAGCAG
Found at i:3283 original size:72 final size:71
Alignment explanation
Indices: 3175--3319 Score: 175
Period size: 72 Copynumber: 2.0 Consensus size: 71
3165 ATTAAAAAAG
* * * *
3175 ACCTCAGCATGTAGCCGAGACTC-ACTCAACTCTCGCAATATGAGTTAATTTTTGGACAAACAGA
1 ACCTCAGCGTGT--CCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTT-GAAAAACAGA
3239 AATTGAATT
63 AATTGAATT
* *
3248 ACCTCAGCGTGTCCGAGGCTCAACTCACCTTTCGCAATATGAAGTTGATTTTTTTGAAAAACAGA
1 ACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATG-AGTT-A-ATTTTTGAAAAACAGA
3313 AATTGAA
63 AATTGAA
3320 GAACAGAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
71 8 0.13
72 17 0.27
73 15 0.24
74 17 0.27
75 5 0.08
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (71 bp):
ACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAACAGAAAT
TGAATT
Found at i:3324 original size:14 final size:14
Alignment explanation
Indices: 3301--3335 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3291 GTTGATTTTT
3301 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
*
3315 TTGAAGAACAGAAA
1 TTGAAAAACAGAAA
3329 TTGAAAA
1 TTGAAAA
3336 GACCTCAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:3458 original size:71 final size:73
Alignment explanation
Indices: 3315--3530 Score: 284
Period size: 72 Copynumber: 3.0 Consensus size: 73
3305 AAAACAGAAA
* * *
3315 TTGAAGAACAGAAATTGAAAAGACCTCAGCTGTGAGC-CGA-GCTCACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAATACCTCAGC-GTGACCTCGAGGCTCACTCACCTCTCGCAATATG
*
3378 AGTTAATTT
65 AGTTGATTT
* *
3387 TTGACAAACAGAAATTGAAATTACCTCAGCGTG-CCTCGAGGCTC-CTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCTCGAGGCTCACTCACCTCTCGCAATATGA
*
3450 GTCGATTT
66 GTTGATTT
*
3458 TTGAAAAACAGAAATT-AAAATA-CTCAAGCGTGTCCT-GAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTC-AGCGTGACCTCGAGGCTC-ACTCACCTCTCGCAATAT
3520 GAGTTGATTT
64 GAGTTGATTT
3530 T
1 T
3531 ATTTTACGAA
Statistics
Matches: 128, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
69 3 0.02
70 19 0.15
71 49 0.38
72 57 0.45
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (73 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCTCGAGGCTCACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:3460 original size:232 final size:233
Alignment explanation
Indices: 3190--4155 Score: 1181
Period size: 232 Copynumber: 4.2 Consensus size: 233
3180 AGCATGTAGC
* * *
3190 CGAGACTCACTCAACTCTCGCAATATGAGTTAATTTTTGGACAAACAGAAATTG-AATTACCTCA
1 CGAGGCTCACTCACCTCTCGCAATATGAGTTGATTTTT-GACAAACAGAAATTGAAATTACCTCA
*
3254 GCGTGTCCGAGGCTCAACTCACCTTTCGCAATATGAAGTTGATTTTTTTGAAAAACAGAAATTGA
65 GCGTGTCCGAGGCTCAACTCACCTCTCGCAATATG-AGTTGATTTTTTTGAAAAACAGAAATT-A
*
3319 AGAACAGAAATTGAAAAGACCTCAGCTGTGAGCCGA-GCTC-ACTCACCTCTCGCAATATGAGTT
128 AAAACAGAAATTGAAAAGACCTCAGCTGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
3382 AATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGCCT
193 AATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGCCT
* * *
3423 CGAGGCTC-CTCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAGAAATT-AAAATA-CTCAA
1 CGAGGCTCACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTC-A
* **
3485 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTATTTTACGAACAGAAATTG
65 GCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TTTGAAAAACAGAAATT-
* *
3550 AAAAATAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCATCTCACCTCTCGCAATATGAG
127 AAAAACAGAAATTGAAAAGACCTCAGC-TGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAG
* *
3615 TTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCT
191 TTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGCCT
* *
3658 TGAGGCTCAACTCA-CTCTCGCAATATGAGTTGA-TTTTGA-GAACAGAAATTGAAATTACCTCA
1 CGAGGCTC-ACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCA
* *
3720 GCGTGTCTGAGGCTCAACTCACCTCTCGCCAATATGAGTTGA----TTTAAAAAACAGAAATTAA
65 GCGTGTCCGAGGCTCAACTCACCTCTCG-CAATATGAGTTGATTTTTTTGAAAAACAGAAATTAA
* * * *
3781 AAACCAGAAATTTGAAAATTACCTCAGTGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGA
129 AAA-CAGAAA-TTGAAAA-GACCTCAG-CTGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGA
* ** * * **
3846 GCTAATTTTTGATGAACATAAATTAAAACCACCTCAGCGTGCCT
190 GTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGCCT
*
3890 -GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCA
1 CGAGGCTC-ACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCA
* *
3954 GCGT-T-TGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTTTTG--AAACATAAATTAA
65 GCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAAATTAA
* * *
4014 AAAAACGAAAATTGAAAATACCTCAGC-GTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAG
129 AAACA-G-AAATTGAAAAGACCTCAGCTGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAG
* * * *
4077 TTGAA--ATT-AAAACACAAAAATTGAAAATACCTCAGCGTGCC-
191 TT-AATTTTTGACAA-ACAGAAATTGAAATTACCTCAGCGTGCCT
* *
4118 CGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTT
1 CGAGGCTC-ACTCACCTCTCGCAATATGAGTTGATTTT
4156 GAAAAAGTAG
Statistics
Matches: 646, Mismatches: 57, Indels: 64
0.84 0.07 0.08
Matches are distributed among these distances:
228 2 0.00
229 68 0.11
230 66 0.10
231 64 0.10
232 209 0.32
233 47 0.07
234 62 0.10
235 103 0.16
236 21 0.03
237 4 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (233 bp):
CGAGGCTCACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAG
CGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAA
ACAGAAATTGAAAAGACCTCAGCTGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAAT
TTTTGACAAACAGAAATTGAAATTACCTCAGCGTGCCT
Found at i:3716 original size:70 final size:70
Alignment explanation
Indices: 3586--3778 Score: 307
Period size: 70 Copynumber: 2.7 Consensus size: 70
3576 CATGTGAGCC
*
3586 GAGGCTCATCTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGA-AAACAGAAATTGAAATTACCTCAG
3651 CGTGTCTT
64 CGTGTC-T
*
3659 GAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTGAGAACAGAAATTGAAATTACCTCAGCG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTGAAATTACCTCAGCG
3723 TGTCT
66 TGTCT
**
3728 GAGGCTCAACTCACCTCTCGCCAATATGAGTTGATTTAAAAAACAGAAATT
1 GAGGCTCAACTCACCTCTCG-CAATATGAGTTGATTTTGAAAACAGAAATT
3779 AAAAACCAGA
Statistics
Matches: 113, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
69 14 0.12
70 35 0.31
71 33 0.29
72 19 0.17
73 12 0.11
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (70 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTGAAATTACCTCAGCG
TGTCT
Found at i:3798 original size:15 final size:15
Alignment explanation
Indices: 3761--3798 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
3751 ATATGAGTTG
3761 ATTTAAAAAACAGAA
1 ATTTAAAAAACAGAA
*
3776 A-TTAAAAACCAGAA
1 ATTTAAAAAACAGAA
3790 ATTTGAAAA
1 ATTT-AAAA
3799 TTACCTCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 13 0.65
15 3 0.15
16 4 0.20
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (15 bp):
ATTTAAAAAACAGAA
Found at i:4005 original size:70 final size:72
Alignment explanation
Indices: 3819--4015 Score: 249
Period size: 72 Copynumber: 2.8 Consensus size: 72
3809 GTGTGAGCCA
* * * *
3819 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGATG-AACATAAATTAAAACCACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTATGAAACATAAATTAAAACCACCTCAG
3883 CGTGCCTG
66 CGT-CCTG
* * * * **
3891 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA-CAAACAAAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTATGAAACATAAATTAAAACCACCTCAG
*
3955 CGT-TTG
66 CGTCCTG
*
3961 AGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTTTTGAAACATAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTATGAAACATAAATTAAAA
4016 AAACGAAAAT
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
69 24 0.22
70 27 0.25
72 58 0.53
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (72 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTATGAAACATAAATTAAAACCACCTCAG
CGTCCTG
Found at i:4090 original size:85 final size:82
Alignment explanation
Indices: 3931--4090 Score: 205
Period size: 85 Copynumber: 1.9 Consensus size: 82
3921 GATTTTTGAC
*
3931 AAACAAAAATTGAAATTACCTCAGCGTTTGAGGCTCAACTCACTCTCGCAATATGAGTTGATTTT
1 AAACAAAAATTGAAAATACCTCAGCGTTTGAGGCTCAACTCACTCTCGCAATATGAGTTGA---T
** *
3996 TTTTGAAACATAAATTAAAA
63 AATTAAAACATAAATTAAAA
*
4016 AAACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACAAAAATTGAAAATACCTCAGCGT-T--TGAGGCTCAACTCA-CTCTCGCAATATGAGTTGA
4081 -AATTAAAACA
62 TAATTAAAACA
4091 CAAAAATTGA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
85 32 0.48
86 1 0.02
88 14 0.21
89 19 0.29
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (82 bp):
AAACAAAAATTGAAAATACCTCAGCGTTTGAGGCTCAACTCACTCTCGCAATATGAGTTGATAAT
TAAAACATAAATTAAAA
Found at i:4142 original size:71 final size:73
Alignment explanation
Indices: 4007--4147 Score: 232
Period size: 71 Copynumber: 2.0 Consensus size: 73
3997 TTTGAAACAT
* *
4007 AAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
1 AAATTAAAAAAACAAAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAAT
4072 ATGAGTTG
66 ATGAGTTG
* *
4080 AAATT-AAAACACAAAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTTGCAAT
1 AAATTAAAAAAACAAAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAAT
4143 ATGAG
66 ATGAG
4148 CTGATTTTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 30 0.47
72 29 0.45
73 5 0.08
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (73 bp):
AAATTAAAAAAACAAAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTG
Found at i:4263 original size:69 final size:69
Alignment explanation
Indices: 4177--4615 Score: 384
Period size: 69 Copynumber: 6.4 Consensus size: 69
4167 AATTAAAAGT
*
4177 TCAACTCACCTCTCGCAATATGAGTTGATTTGACAAACAGAAATTG-AAATACCTCATGTGTCCT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTGA-AAACAGAAATTGAAAATACCTCACGTGTCCT
4241 GAGGC
65 GAGGC
* ** * * ** *
4246 TCAACTCACCTCTCGCAATAT-A----AATTGAAAA-A-AAA-T-ACCACA-GT-GTGTAAT-CT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTGAAAACAGAAATTGAAAATACCTCACGT-GTCCT
4299 GA-GC
65 GAGGC
* *
4303 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAACAGAAATTGAAAATACCTCAGCATG
1 TCAACTCACCTCTCGCAATATGAGTTGA----TTTGAAAACAGAAATTGAAAATACCTCA-CGTG
4368 TGCC-GAGGC
61 T-CCTGAGGC
*
4377 TCAACTCACCTCTCGCAATAT-A-TTGATTTTTTG-AAACA-AAATTGAAAATACCTCAAGTGTC
1 TCAACTCACCTCTCGCAATATGAGTTGA---TTTGAAAACAGAAATTGAAAATACCTCACGTGTC
*
4438 TTGAGGC
63 CTGAGGC
** *
4445 TCAACTCATTTCTCGCAATATAAGTTGAATTTGAAAACAGAAATTG-AAATACCTCAGCGTGTCC
1 TCAACTCACCTCTCGCAATATGAGTTG-ATTTGAAAACAGAAATTGAAAATACCTCA-CGTGTCC
4509 TGA-GC
64 TGAGGC
** *
4514 TCAACTCATTTCTCGCAATATGAGTTGATTTTTTAAAACAGAAATTGAAAATTACCTCAGCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGA--TTTGAAAACAGAAATTGAAAA-TACCTCA-CGTGT
4579 CCTGAGGC
62 CCTGAGGC
*
4587 TCAACTCATC-CT-GCAATATGAGTTGATTT
1 TCAACTCACCTCTCGCAATATGAGTTGATTT
4616 TTGAAAAAAA
Statistics
Matches: 309, Mismatches: 28, Indels: 66
0.77 0.07 0.16
Matches are distributed among these distances:
57 23 0.07
58 8 0.03
59 2 0.01
60 3 0.01
61 3 0.01
62 2 0.01
63 3 0.01
64 5 0.02
66 6 0.02
67 2 0.01
68 36 0.12
69 86 0.28
70 41 0.13
71 25 0.08
72 25 0.08
73 15 0.05
74 24 0.08
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (69 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTGAAAACAGAAATTGAAAATACCTCACGTGTCCTG
AGGC
Found at i:4432 original size:126 final size:124
Alignment explanation
Indices: 4052--4432 Score: 322
Period size: 122 Copynumber: 3.0 Consensus size: 124
4042 TGTCCTGAGG
* *
4052 CTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGC--GT
1 CTCAACTCACCTCTCGCAATATGAGTTG-ATTTAAAA-ACAGAAATTGAAAATACCTCAGCATGT
* ** * **
4115 GCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGT-
64 GCCCGAGGCTCAACTCACCTCTCGCAATAT-AATTGATTTTAAAAAACCA-AAATTGAAAA-TA
*
4177 -TCAACTCACCTCTCGCAATATGAGTTGATTTGACAAACAGAAATTG-AAATACCT---CATGTG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTT-AAAAACAGAAATTGAAAATACCTCAGCATGTG
* ** * * **
4237 TCCTGAGGCTCAACTCACCTCTCGCAATATAAATTGA--AAAAAAATACCACAGTGTGTAATCTG
65 -CCCGAGGCTCAACTCACCTCTCGCAATAT-AATTGATTTTAAAAA-ACCAAAAT-TG-AAAAT-
4300 A
124 A
*
4301 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAACAGAAATTGAAAATACCTCAGCA
1 -CTCAACTCACCTCTCGCAATATGAGTTGA----TTTAAAAACAGAAATTGAAAATACCTCAGCA
***
4366 TGTG-CCGAGGCTCAACTCACCTCTCGCAATAT-ATTGATTTTTTGAAA-CAAAATTGAAAATA
61 TGTGCCCGAGGCTCAACTCACCTCTCGCAATATAATTGATTTTAAAAAACCAAAATTGAAAATA
4427 CCTCAA
1 -CTCAA
4433 GTGTCTTGAG
Statistics
Matches: 204, Mismatches: 30, Indels: 43
0.74 0.11 0.16
Matches are distributed among these distances:
119 1 0.00
120 6 0.03
121 6 0.03
122 40 0.20
123 14 0.07
124 30 0.15
126 34 0.17
127 3 0.01
128 2 0.01
129 21 0.10
130 12 0.06
131 29 0.14
133 6 0.03
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (124 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTAAAAACAGAAATTGAAAATACCTCAGCATGTGC
CCGAGGCTCAACTCACCTCTCGCAATATAATTGATTTTAAAAAACCAAAATTGAAAATA
Found at i:4557 original size:70 final size:72
Alignment explanation
Indices: 4297--4622 Score: 422
Period size: 69 Copynumber: 4.6 Consensus size: 72
4287 AGTGTGTAAT
*
4297 CTGA-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAACAGAAATTGAAAATACCT
1 CTGAGGCTCAACTCACTTCTCGCAATATGAGTTGA--TTTTTTAAAACAGAAATTGAAAATACCT
*
4361 CAGCATGTGC
64 CAGCGTGT-C
* *
4371 C-GAGGCTCAACTCACCTCTCGCAATAT-A-TTGATTTTTTGAAACA-AAATTGAAAATACCTCA
1 CTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTAAAACAGAAATTGAAAATACCTCA
*
4432 -AGTGTC
66 GCGTGTC
* * * * *
4438 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA-ATTTGAAAACAGAAATTG-AAATACCTCA
1 CTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTAAAACAGAAATTGAAAATACCTCA
4501 GCGTGTC
66 GCGTGTC
*
4508 CTGA-GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTAAAACAGAAATTGAAAATTACCTC
1 CTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTAAAACAGAAATTGAAAA-TACCTC
4572 AGCGTGTC
65 AGCGTGTC
* *
4580 CTGAGGCTCAACTCA-TCCT-GCAATATGAGTTGATTTTTGAAAA
1 CTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTAAAA
4623 AAAAAATTAA
Statistics
Matches: 226, Mismatches: 16, Indels: 23
0.85 0.06 0.09
Matches are distributed among these distances:
67 1 0.00
68 27 0.12
69 65 0.29
70 45 0.20
71 26 0.12
72 25 0.11
73 13 0.06
74 24 0.11
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (72 bp):
CTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTAAAACAGAAATTGAAAATACCTCA
GCGTGTC
Found at i:4579 original size:142 final size:139
Alignment explanation
Indices: 4297--4622 Score: 421
Period size: 142 Copynumber: 2.3 Consensus size: 139
4287 AGTGTGTAAT
* *
4297 CTGA-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAACAGAAATTGAAAATACCT
1 CTGAGGCTCAACTCA-TTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAATTGAAAATACCT
*
4361 CAGCATGTGCCGAGGCTCAACTCACCTCTCGCAATATATTGATTTTTTGAAACAAAATTGAAAAT
63 CAGCATGTGCCGAGGCTCAACTCACCTCTCGCAATATATTGATTTTTTAAAACAAAATTGAAAAT
4426 ACCTCAAGTGTC
128 ACCTCAAGTGTC
* * *
4438 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA-ATTTGAAAACAGAAATTG-AAATACCTCA
1 CTGAGGCTCAACTCA-TTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCA
* **
4501 GCGTGT-CCTGA-GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTAAAACAGAAATTGAAA
65 GCATGTGCC-GAGGCTCAACTCACCTCTCGCAATAT-A-TTGATTTTTTAAAACA-AAATTGAAA
*
4564 ATTACCTCAGCGTGTC
126 A-TACCTCA-AGTGTC
*
4580 CTGAGGCTCAACTCATCCT-GCAATATGAGTTGATTTTTGAAAA
1 CTGAGGCTCAACTCATTCTCGCAATATGAGTTGATTTTTGAAAA
4623 AAAAAATTAA
Statistics
Matches: 162, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
137 23 0.14
138 18 0.11
139 31 0.19
140 23 0.14
141 21 0.13
142 46 0.28
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (139 bp):
CTGAGGCTCAACTCATTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCAG
CATGTGCCGAGGCTCAACTCACCTCTCGCAATATATTGATTTTTTAAAACAAAATTGAAAATACC
TCAAGTGTC
Found at i:4847 original size:69 final size:69
Alignment explanation
Indices: 4639--4876 Score: 285
Period size: 68 Copynumber: 3.6 Consensus size: 69
4629 TTAAAAGCTT
* * * * *
4639 AACTCACCTCTCGCAATATGAG-TCA-ATTTAAAAAAAAATTAAAATACCTC-GCGTG-C-CGAG
1 AACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAAAATTAAAATACCTCAACGTGACTTGAG
4699 GCTC
66 GCTC
* * *
4703 AACTCACTTCTCGCAATATGAGTTGA-TTTTGAAAAAAAATTAAAATACCTCAACGTGTCTTGAG
1 AACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAAAATTAAAATACCTCAACGTGACTTGAG
*
4767 GTTC
66 GCTC
* * * *
4771 AACTCACCTCTCGCAATATGAGTTGATTTTTTTAGATAAATTGAAAATACCTCAATG-GACTTGA
1 AACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAAAATT-AAAATACCTCAACGTGACTTGA
4835 GGCTC
65 GGCTC
*
4840 AACTCACCTCTC-CAATATGAGTTGATTTTTTGAAAAA
1 AACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAA
4877 CAGAAATTGA
Statistics
Matches: 150, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
64 21 0.14
65 25 0.17
66 4 0.03
67 1 0.01
68 53 0.35
69 33 0.22
70 13 0.09
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (69 bp):
AACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAAAATTAAAATACCTCAACGTGACTTGAG
GCTC
Found at i:5241 original size:69 final size:70
Alignment explanation
Indices: 5007--5255 Score: 371
Period size: 70 Copynumber: 3.5 Consensus size: 70
4997 ACGTGTGCCC
5007 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTAAAAACAAAATTGAAAATACCTCAGCG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAAAATTGAAAATACCTCAGCG
*
5071 ATGTCC
66 -TGTCT
* *
5077 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAATAGAATTTGAAAATACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTAAAAACA-AAATTGAAAATACCTCA
5142 GCGTGTCT
63 GCGTGTCT
* *
5150 GAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTGACAAACAAAATTGAAATTACCTCAGC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAAACAAAATTGAAAATACCTCAGC
*
5214 GTCT-T
65 GTGTCT
5219 GAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
5256 TTGAAACATA
Statistics
Matches: 166, Mismatches: 8, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
69 38 0.23
70 58 0.35
71 5 0.03
72 19 0.11
73 27 0.16
74 19 0.11
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (70 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAAAATTGAAAATACCTCAGCG
TGTCT
Found at i:5346 original size:83 final size:80
Alignment explanation
Indices: 5190--5346 Score: 208
Period size: 83 Copynumber: 1.9 Consensus size: 80
5180 GATTTTTGAC
* * *
5190 AAACAAAATTGAAATTACCTCAGCGTCTTGAGGCTCAACTCACTCTCGCAATATGAGTTGATTTT
1 AAACAAAATTGAAAATACCTCAGCGTCCTGAGGCTCAACTCACTCTCGCAATATGAGTTGA--TA
* *
5255 TTTGAAACATAAATTAA
64 ATTAAAACATAAATTAA
5272 AAACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAAC-AAAATTGAAAATACCTCAGC--GTCCTGAGGCTCAACTCA-CTCTCGCAATATGAGTTGA
5337 -AATTAAAACA
62 TAATTAAAACA
5347 CAAAAATTGA
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
82 4 0.06
83 26 0.39
85 17 0.26
86 19 0.29
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (80 bp):
AAACAAAATTGAAAATACCTCAGCGTCCTGAGGCTCAACTCACTCTCGCAATATGAGTTGATAAT
TAAAACATAAATTAA
Found at i:5425 original size:71 final size:72
Alignment explanation
Indices: 5265--5407 Score: 236
Period size: 71 Copynumber: 2.0 Consensus size: 72
5255 TTTGAAACAT
* *
5265 AAATTAAAA-ACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
1 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATA
*
5329 TGAGTTG
66 TGAGCTG
*
5336 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTTGCAATA
1 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATA
5400 TGAGCTG
66 TGAGCTG
5407 A
1 A
5408 TTTTGAAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 42 0.63
72 25 0.37
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (72 bp):
AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATA
TGAGCTG
Found at i:5755 original size:75 final size:74
Alignment explanation
Indices: 5550--5893 Score: 368
Period size: 75 Copynumber: 4.7 Consensus size: 74
5540 ACAGTGTAAT
* * ** *
5550 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAA-AACAGAAATTGAAAATAC
1 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA-TTTTTGAAAACAAAAGAAATTG-AAATAC
*
5614 CTCAGCATGTGAC
64 CTCAGC--GTGTC
5627 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAAC---AGAAATTGAAATAC
1 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA--TTTTTGAAAACAAAAGAAATTGAAATAC
*
5688 CTCAACGTGTC
64 CTCAGCGTGTC
* *
5699 TTGAGGCTCAACTCA-TTCTCGCAATATAAGTTGA-TTTTGAAAAC---AGAAATTGAAATTACC
1 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAACAAAAGAAATTGAAA-TACC
5759 TCAGCGTGTC
65 TCAGCGTGTC
** * *** *
5769 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAACAAAAGAAATTGAAA-TACC
5834 TCAGCGTGTC
65 TCAGCGTGTC
* *
5844 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTG-AAAACAAAA
5894 ATTAAAAGGC
Statistics
Matches: 236, Mismatches: 21, Indels: 22
0.85 0.08 0.08
Matches are distributed among these distances:
69 21 0.09
70 27 0.11
71 18 0.08
72 29 0.12
73 13 0.06
74 15 0.06
75 72 0.31
76 31 0.13
77 10 0.04
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (74 bp):
CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAACAAAAGAAATTGAAATACCT
CAGCGTGTC
Found at i:5819 original size:144 final size:145
Alignment explanation
Indices: 5550--5900 Score: 476
Period size: 144 Copynumber: 2.4 Consensus size: 145
5540 ACAGTGTAAT
* *
5550 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAAACAGAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTGAAAACAGAAATTGAAAATACC
5615 TCAGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAAT
62 TCAGCA-GTGACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAAT
5680 TGAAA-TACCTCAACGTGTC
126 TGAAATTACCTCAACGTGTC
* * * *
5699 TTGAGGCTCAACTCA-TTCTCGCAATATAAGTTGATTTTGAAAACAGAAATTGAAATTACCTCAG
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTGAAAATACCTCAG
* ** * *
5763 C-GTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGA
66 CAGTGACC-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAA-AACAGAAATTGA
*
5827 AATTACCTCAGCGTGTC
129 AATTACCTCAACGTGTC
* *
5844 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATT-AAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAGAAATTGAAAA
5901 GGCTTAACTC
Statistics
Matches: 179, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
142 5 0.03
143 39 0.22
144 43 0.24
145 27 0.15
146 24 0.13
147 11 0.06
148 17 0.09
149 13 0.07
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (145 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTGAAAATACCTCAG
CAGTGACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAATTGAAA
TTACCTCAACGTGTC
Found at i:6056 original size:70 final size:68
Alignment explanation
Indices: 5900--6073 Score: 208
Period size: 70 Copynumber: 2.5 Consensus size: 68
5890 AAAAATTAAA
* * * * **
5900 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
5964 CCCG
65 CCCG
*
5968 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAA-AAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCAC-TCTCGCAATATGAGTTGATTTT-AAAACAAAAACTAAAAATACCTCAACGT
**
6032 GTCTTG
64 G-CCCG
6038 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTT
6074 CCTTGGAAAG
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
67 1 0.01
68 25 0.27
69 25 0.27
70 40 0.43
71 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (68 bp):
AGGCTCAACTCACTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTGC
CCG
Found at i:14375 original size:16 final size:15
Alignment explanation
Indices: 14354--14396 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 15
14344 GATGTGAATA
14354 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
14370 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
14385 ATCAAAATATTA
1 AT-AAAATATTA
14397 GGATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:14384 original size:8 final size:8
Alignment explanation
Indices: 14350--14396 Score: 60
Period size: 8 Copynumber: 5.9 Consensus size: 8
14340 TAATGATGTG
*
14350 AATAATAA
1 AATATTAA
14358 AATATATAA
1 AATAT-TAA
14367 AATA-TAA
1 AATATTAA
14374 AATATTAA
1 AATATTAA
*
14382 AATATCAA
1 AATATTAA
14390 AATATTA
1 AATATTA
14397 GGATAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 7 0.21
8 20 0.59
9 7 0.21
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (8 bp):
AATATTAA
Found at i:14648 original size:15 final size:14
Alignment explanation
Indices: 14627--14693 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
14617 ATAACATGTA
14627 AAAAATATATATAT
1 AAAAATATATATAT
14641 AAATAATATA-ATATT
1 AAA-AATATATATA-T
* *
14656 AAAGATATATACAT
1 AAAAATATATATAT
*
14670 -AAAATA-GTATA-
1 AAAAATATATATAT
*
14681 AAATATATATATA
1 AAAAATATATATA
14694 CGTAATATAG
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
12 8 0.20
13 9 0.22
14 12 0.29
15 12 0.29
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (14 bp):
AAAAATATATATAT
Found at i:14666 original size:31 final size:31
Alignment explanation
Indices: 14604--14681 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
14594 TATAGTTAAG
* *
14604 ATATATACATAAGATAACATGTAAAAAATAT
1 ATATATAAATAATATAACATGTAAAAAATAT
* *
14635 ATATATAAATAATATAATAT-T-AAAGATAT
1 ATATATAAATAATATAACATGTAAAAAATAT
* *
14664 ATACATAAAATAGTATAA
1 ATATAT-AAATAATATAA
14682 AATATATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 12 0.30
30 11 0.28
31 17 0.43
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (31 bp):
ATATATAAATAATATAACATGTAAAAAATAT
Found at i:14671 original size:25 final size:25
Alignment explanation
Indices: 14545--14768 Score: 101
Period size: 25 Copynumber: 9.0 Consensus size: 25
14535 TAAATACGTG
* *
14545 ATAATATTAAAAATATGTACATAAT
1 ATAATATTAAAGATATATACATAAT
* * * *
14570 ATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAAGATATATACATAAT
* *
14595 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAGATATATACATAAT
* * *
14617 ATAACATGTAAAAAATATATATATAAATAAT
1 ATAATAT-T----AA-AGATATATACATAAT
*
14648 ATAATATTAAAGATATATACATAAA
1 ATAATATTAAAGATATATACATAAT
* * * *
14673 ATAGTATAAAATATATATATACGTAAT
1 ATAATAT-TAA-AGATATATACATAAT
* *
14700 ATAGA-ATTTAA-A-ATATACCTAAT
1 ATA-ATATTAAAGATATATACATAAT
* *
14723 AT-AT-TAAAAGA-ATATATATAAT
1 ATAATATTAAAGATATATACATAAT
*
14745 ATAATATT-AAGAAATATA-ATAAT
1 ATAATATTAAAGATATATACATAAT
14768 A
1 A
14769 ACAAAAAAAG
Statistics
Matches: 152, Mismatches: 30, Indels: 36
0.70 0.14 0.17
Matches are distributed among these distances:
21 4 0.03
22 27 0.18
23 28 0.18
24 8 0.05
25 43 0.28
26 5 0.03
27 17 0.11
30 2 0.01
31 18 0.12
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (25 bp):
ATAATATTAAAGATATATACATAAT
Found at i:14690 original size:27 final size:27
Alignment explanation
Indices: 14557--14703 Score: 108
Period size: 27 Copynumber: 5.6 Consensus size: 27
14547 AATATTAAAA
* * *
14557 ATATGTACATAATATAGTGTTAAA-A-
1 ATATATACATAATATAGTATAAAATAT
* *
14582 ATACATACATAATATAGT-TAAGATAT
1 ATATATACATAATATAGTATAAAATAT
* * * *
14608 ATACATAAGATAACAT-GTAAAAAATAT
1 ATATAT-ACATAATATAGTATAAAATAT
* * * *
14635 ATATATAAATAATATAATAT-TAA-AG
1 ATATATACATAATATAGTATAAAATAT
*
14660 ATATATACATAAAATAGTATAAAATAT
1 ATATATACATAATATAGTATAAAATAT
*
14687 ATATATACGTAATATAG
1 ATATATACATAATATAG
14704 AATTTAAAAT
Statistics
Matches: 93, Mismatches: 22, Indels: 12
0.73 0.17 0.09
Matches are distributed among these distances:
24 3 0.03
25 35 0.38
26 19 0.20
27 36 0.39
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.33
Consensus pattern (27 bp):
ATATATACATAATATAGTATAAAATAT
Found at i:15281 original size:30 final size:30
Alignment explanation
Indices: 15245--15417 Score: 287
Period size: 30 Copynumber: 5.8 Consensus size: 30
15235 TAGGTACAAG
* *
15245 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
15275 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
15305 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
15335 TGGTGGTGGAAAA-GAGT-GCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
15363 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
15393 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGT
15418 TGAGAAAAGT
Statistics
Matches: 133, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
28 24 0.18
29 6 0.05
30 103 0.77
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:15383 original size:58 final size:59
Alignment explanation
Indices: 15245--15417 Score: 312
Period size: 58 Copynumber: 2.9 Consensus size: 59
15235 TAGGTACAAG
*
15245 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGG-AAAAGAGTGGCTAGTGGAGT
15305 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGAGT-GCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGAGTGGCTAGTGGAGT
15363 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAA-GAGTGGCTAGT
15418 TGAGAAAAGT
Statistics
Matches: 110, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
58 54 0.49
59 12 0.11
60 44 0.40
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.25
Consensus pattern (59 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGAGTGGCTAGTGGAGT
Found at i:15396 original size:88 final size:90
Alignment explanation
Indices: 15245--15417 Score: 287
Period size: 88 Copynumber: 1.9 Consensus size: 90
15235 TAGGTACAAG
* *
15245 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGTTGGTG
1 TGGTGGTGGAGAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGTTGGTG
*
15310 GTGGAAAAGGTGTGGCTAGTGGAGT
66 GTGGAAAAGGAGTGGCTAGTGGAGT
* *
15335 TGGTGGTGGA-AAAGAGT-GCTAGTGGAGTTGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTG
1 TGGTGGTGGAGAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGTTGGTG
15398 GTGGAAAAGGAGTGGCTAGT
66 GTGGAAAAGGAGTGGCTAGT
15418 TGAGAAAAGT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
88 63 0.81
89 5 0.06
90 10 0.13
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.25
Consensus pattern (90 bp):
TGGTGGTGGAGAAAGAGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGTTGGTG
GTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:15962 original size:16 final size:16
Alignment explanation
Indices: 15893--15960 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
15883 TTTGGTTCGC
15893 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
15909 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
15925 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
15941 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
15957 TGTA
1 TGTA
15961 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:15995 original size:45 final size:44
Alignment explanation
Indices: 15941--16035 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
15931 GGATTAGAGG
* *
15941 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
15986 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
16030 TGTAAT
1 TGTAAT
16036 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:16205 original size:25 final size:25
Alignment explanation
Indices: 16173--16227 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
16163 TAATTTAATC
*
16173 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
16197 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
16222 ATATAT
1 ATATAT
16228 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:16409 original size:47 final size:46
Alignment explanation
Indices: 16358--16506 Score: 132
Period size: 47 Copynumber: 3.3 Consensus size: 46
16348 GATTTAATAA
16358 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
16405 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
16446 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
16493 AATTTAAAATAATT
1 AATTTAAAATAATT
16507 TAGGAAATGG
Statistics
Matches: 78, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.17
42 11 0.14
43 5 0.06
44 4 0.05
45 5 0.06
46 10 0.13
47 29 0.37
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Done.