Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1095
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: 34467
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:81 original size:18 final size:19
Alignment explanation
Indices: 58--116 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
48 ATTAAAGTTA
58 ATAAAAATA-ATACTATAT
1 ATAAAAATATATACTATAT
*
76 AT-AAAATATATA-TATAC
1 ATAAAAATATATACTATAT
*
93 ATAAAAATATACACTAATAT
1 ATAAAAATATATACT-ATAT
113 ATAA
1 ATAA
117 TAGTAATAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 12 0.35
18 14 0.41
19 1 0.03
20 7 0.21
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAAAAATATATACTATAT
Found at i:83 original size:17 final size:17
Alignment explanation
Indices: 61--103 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
51 AAAGTTAATA
*
61 AAAATA-ATACTATATAT
1 AAAATATATA-TATACAT
78 AAAATATATATATACAT
1 AAAATATATATATACAT
95 AAAA-ATATA
1 AAAATATATA
104 CACTAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 16 0.67
18 3 0.12
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATATATATATACAT
Found at i:348 original size:27 final size:28
Alignment explanation
Indices: 318--404 Score: 72
Period size: 30 Copynumber: 3.0 Consensus size: 28
308 GAGAGGGCAT
318 ATATAATAT-AAAATAATATAAAAAATA
1 ATATAATATAAAAATAATATAAAAAATA
* * *
345 ATATATACATGAGAAATAATAATAATAATATA
1 ATATA-ATAT-AAAAATAAT-ATAA-AAAATA
*
377 A-ATAATAGTAAAAATAATA-AAATAATA
1 ATATAATA-TAAAAATAATATAAAAAATA
404 A
1 A
405 AACAAAGCTC
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
27 10 0.21
28 5 0.11
29 1 0.02
30 17 0.36
31 8 0.17
32 6 0.13
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (28 bp):
ATATAATATAAAAATAATATAAAAAATA
Found at i:373 original size:9 final size:9
Alignment explanation
Indices: 359--404 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
349 ATACATGAGA
359 AATAATAAT
1 AATAATAAT
368 AATAAT-AT
1 AATAATAAT
*
376 AAATAATAGT
1 -AATAATAAT
*
386 AAAAATAAT
1 AATAATAAT
395 AA-AATAAT
1 AATAATAAT
403 AA
1 AA
405 AACAAAGCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 10 0.31
9 21 0.66
10 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (9 bp):
AATAATAAT
Found at i:380 original size:12 final size:12
Alignment explanation
Indices: 320--401 Score: 55
Period size: 12 Copynumber: 6.8 Consensus size: 12
310 GAGGGCATAT
320 ATAATAT-AA-A
1 ATAATATAAATA
*
330 ATAATATAAAAA
1 ATAATATAAATA
342 ATAATATATACATGA
1 ATAATATA-A-AT-A
357 GA-AATA-ATAATA
1 -ATAATATA-AATA
369 ATAATATAAATA
1 ATAATATAAATA
* *
381 ATAGTAAAAATA
1 ATAATATAAATA
*
393 ATAAAATAA
1 ATAATATAA
402 TAAAACAAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
10 7 0.12
11 3 0.05
12 34 0.59
13 4 0.07
14 4 0.07
15 5 0.09
16 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:405 original size:27 final size:29
Alignment explanation
Indices: 328--405 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 29
318 ATATAATATA
* *
328 AAATAATATAAAAAATAATATATACATGAG
1 AAATAATA-ATAAAATAATAAATACATGAG
358 AAATAATAATAATAAT-ATAAATA-AT-AG
1 AAATAATAATAA-AATAATAAATACATGAG
385 TAAA-AATAATAAAATAATAAA
1 -AAATAATAATAAAATAATAAA
406 ACAAAGCTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
26 3 0.07
27 15 0.35
28 5 0.12
29 9 0.21
30 11 0.26
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (29 bp):
AAATAATAATAAAATAATAAATACATGAG
Found at i:761 original size:25 final size:25
Alignment explanation
Indices: 733--793 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
723 CCTTTTTTCC
733 AAAAAAACAAAAAAACACCTCCAAA
1 AAAAAAACAAAAAAACACCTCCAAA
* *
758 AAAAACAA-AAAAAACCTCCTCCAAA
1 AAAAA-AACAAAAAAACACCTCCAAA
*
783 ACAAAGAACAA
1 A-AAAAAACAA
794 TCCTTCTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 23 0.77
26 7 0.23
ACGTcount: A:0.69, C:0.25, G:0.02, T:0.05
Consensus pattern (25 bp):
AAAAAAACAAAAAAACACCTCCAAA
Found at i:763 original size:23 final size:22
Alignment explanation
Indices: 733--776 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
723 CCTTTTTTCC
733 AAAAAAACAAAAAAACACCTCCA
1 AAAAAAACAAAAAAA-ACCTCCA
756 AAAAAAACAAAAAAAACCTCC
1 AAAAAAACAAAAAAAACCTCC
777 TCCAAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.70, C:0.25, G:0.00, T:0.05
Consensus pattern (22 bp):
AAAAAAACAAAAAAAACCTCCA
Found at i:783 original size:23 final size:23
Alignment explanation
Indices: 734--814 Score: 69
Period size: 23 Copynumber: 3.5 Consensus size: 23
724 CTTTTTTCCA
**
734 AAAAAACAAAAAAACACCTCC-AA
1 AAAAAACAAAAAAA-ACCTCCTCC
757 AAAAAACAAAAAAAACCTCCTCC
1 AAAAAACAAAAAAAACCTCCTCC
* *
780 --AAAACAAAGAACAATCCTTCTCC
1 AAAAAACAAA-AA-AAACCTCCTCC
*
803 AAAAACCAAAAA
1 AAAAAACAAAAA
815 CCCACCCTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 8 0.17
22 8 0.17
23 23 0.48
24 2 0.04
25 7 0.15
ACGTcount: A:0.63, C:0.27, G:0.01, T:0.09
Consensus pattern (23 bp):
AAAAAACAAAAAAAACCTCCTCC
Found at i:1316 original size:40 final size:40
Alignment explanation
Indices: 1272--1422 Score: 187
Period size: 40 Copynumber: 3.8 Consensus size: 40
1262 GTGTTTTTAG
*
1272 TCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* * * * ***
1312 TCTGCTTCACTATTGCTTAGGGAAATAAGATCTATGGTTTTA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGCGA
*
1354 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
*
1394 TCTACTCCACTACTGCTTA-GGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
1423 TTGTAATCTT
Statistics
Matches: 92, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 10 0.11
40 47 0.51
41 4 0.04
42 31 0.34
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:1363 original size:82 final size:82
Alignment explanation
Indices: 1266--1423 Score: 246
Period size: 82 Copynumber: 1.9 Consensus size: 82
1256 AGATTTGTGT
* * * *
1266 TTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCGATCTGCTTCACTATTGCTTA
1 TTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCACTACTGCTTA
1331 GGGAAATAAGATCTATGG
66 -GGAAATAAGATCTATGG
*
1349 TTTTA-TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGCGATCTACTCCACTACTGCTTA
1 TTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCACTACTGCTTA
*
1413 GGAGATAAGAT
66 GGAAATAAGAT
1424 TGTAATCTTC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
81 10 0.14
82 54 0.78
83 5 0.07
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (82 bp):
TTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCACTACTGCTTA
GGAAATAAGATCTATGG
Found at i:1445 original size:82 final size:82
Alignment explanation
Indices: 1276--1446 Score: 202
Period size: 82 Copynumber: 2.1 Consensus size: 82
1266 TTTTAGTCTG
* * * *
1276 CTCCACTACTACTTAGGGAGATAAGACTTGATGCGATCTGCTTCACTATTGCTTAGGGAAATAAG
1 CTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCACTACTGCTTAGGGAAATAAG
* ** *
1341 ATCTATGGTTTTATCTG
66 ATCTATGCTTCGATCTA
* *
1358 CTCCACTACTGCTTAGGGAGATAAGACTTAATGCGATCTACTCCACTACTGCTTA-GGAGATAAG
1 CTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCACTACTGCTTAGGGAAATAAG
*
1422 ATTGTAAT-CTTCGATCTA
66 A-TCT-ATGCTTCGATCTA
*
1440 TTCCACT
1 CTCCACT
1447 GTTGCCAAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
81 9 0.12
82 64 0.85
83 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (82 bp):
CTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCACTACTGCTTAGGGAAATAAG
ATCTATGCTTCGATCTA
Found at i:1881 original size:133 final size:133
Alignment explanation
Indices: 1583--2552 Score: 1604
Period size: 133 Copynumber: 7.3 Consensus size: 133
1573 ACTTCCTACC
* *
1583 AATATAGGAAGGCAGGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAG-T
*
1648 ATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATC-TCGATCTGCTTCG
65 ATCGGCTTCAATGTACTCCACTGTGGT--CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCG
*
1712 CTGCCT
128 CTGCCG
*
1718 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGATAGAGTA
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTA
*
1783 TCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTG
66 TCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTG
1848 CCG
131 CCG
*
1851 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAG-T
*
1916 ATCGGCTTCAATGTACTCCACTGTGGTCA-GGAGGTAAAATCTGCCATCTTCAATCTGCTTCGCT
65 ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
1980 GCCG
130 GCCG
*
1984 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAG-T
*
2049 ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCT
65 ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
*
2114 GCCA
130 GCCG
* * *
2118 AATATAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACA-GGAGATAGAATT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAG-AGT
*
2182 ATCGGCTTCAGTGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
65 ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
*
2247 GCCT
130 GCCG
* *
2251 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGATAGATTA
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTA
* *
2316 TCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCACTG
66 TCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTG
2381 CCG
131 CCG
* * * *
2384 AATACAGGAAGGTAAGATCTGCAATATTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAG-AGT
* **
2449 ATCGGCTTCAGTGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTAATCTGCTTCGCT
65 ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
*
2514 GCCA
130 GCCG
2518 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
2553 CTTTACCACC
Statistics
Matches: 792, Mismatches: 37, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
132 22 0.03
133 461 0.58
134 249 0.31
135 60 0.08
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (133 bp):
AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTA
TCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTG
CCG
Found at i:2132 original size:267 final size:268
Alignment explanation
Indices: 1583--2552 Score: 1671
Period size: 267 Copynumber: 3.6 Consensus size: 268
1573 ACTTCCTACC
* * * * *
1583 AATATAGGAAGGCAGGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATT
* *
1648 ATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATC-TCGATCTGCTTCG
66 ATCGGCTTCAATGTACTCCACTGTGGT--CAGGGAGGTAAAATCTGCCATCTTCAATCTGCTTCG
1712 CTGCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGAT
129 CTGCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGAT
1777 AGAG-TATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGC
194 AGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGC
1841 TTCGCTGCCG
259 TTCGCTGCCG
* *
1851 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATT
1916 ATCGGCTTCAATGTACTCCACTGTGGTCA-GGAGGTAAAATCTGCCATCTTCAATCTGCTTCGCT
66 ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCAATCTGCTTCGCT
* * *
1980 GCCGAATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGAGATAG
131 GCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGATAG
* *
2045 AGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTT
196 AGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT
*
2110 CGCTGCCA
261 CGCTGCCG
* *
2118 AATATAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACA-GGAGATAGAATT
1 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATT
* *
2182 ATCGGCTTCAGTGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCT
66 ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCAATCTGCTTCGCT
2247 GCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGATAG
131 GCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGATAG
2312 A-TTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT
196 AGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT
*
2376 CACTGCCG
261 CGCTGCCG
*
2384 AATACAGGAAGGTAAGATCTGCAATATTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATT
1 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATT
* *
2449 ATCGGCTTCAGTGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTAATCTGCTTCGCT
66 ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCAATCTGCTTCGCT
*
2514 GCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
131 GCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
2553 CTTTACCACC
Statistics
Matches: 668, Mismatches: 30, Indels: 9
0.94 0.04 0.01
Matches are distributed among these distances:
265 19 0.03
266 235 0.35
267 326 0.49
268 88 0.13
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (268 bp):
AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATT
ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCAATCTGCTTCGCT
GCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGATAG
AGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT
CGCTGCCG
Found at i:2199 original size:400 final size:400
Alignment explanation
Indices: 1583--2552 Score: 1685
Period size: 400 Copynumber: 2.4 Consensus size: 400
1573 ACTTCCTACC
* * *
1583 AATATAGGAAGGCAGGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
* *
1648 ATCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATC-TCGATCTGCTTCG
66 ATCGGCTTCAATGTACTCCACTGTGGT--CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCG
* *
1712 CTGCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGAT
129 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGTGAGAT
1777 AGAGTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCT
194 AGAGTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCT
1842 TCGCTGCCGAATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGA
259 TCGCTGCCGAATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGA
*
1907 GATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCA-GGAGGTAAAATCTGCCATCTTCAATC
324 GATAGA-TTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCAATC
*
1971 TGCTTCGCTGCCG
388 TGCTTCACTGCCG
1984 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
2049 ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCT
66 ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCT
*
2114 GCCAAATATAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAG-GAGATAG
131 GCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGTGAGATAG
* * *
2178 AATTATCGGCTTCAGTGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT
196 -AGTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT
* * *
2243 CGCTGCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAG
260 CGCTGCCGAATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGAG
*
2308 ATAGATTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTG
325 ATAGATTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCAATCTG
2373 CTTCACTGCCG
390 CTTCACTGCCG
* * *
2384 AATACAGGAAGGTAAGATCTGCAATATTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATT
1 AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
* *
2449 ATCGGCTTCAGTGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTAATCTGCTTCGCT
66 ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCT
2514 GCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
131 GCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
2553 CTTTACCACC
Statistics
Matches: 543, Mismatches: 23, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
399 59 0.11
400 396 0.73
401 88 0.16
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (400 bp):
AATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTT
ATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCT
GCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGTGAGATAG
AGTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTC
GCTGCCGAATACAGGAAGGCAAGATCTGCAATATTCAATCTATTCCACTGCCAGATACAGGGAGA
TAGATTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCAATCTGC
TTCACTGCCG
Found at i:2643 original size:44 final size:45
Alignment explanation
Indices: 2518--3064 Score: 436
Period size: 44 Copynumber: 12.4 Consensus size: 45
2508 TTCGCTGCCA
* * * * * *
2518 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTACTTTACCACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * *
2563 AGTAT-GGAAGACAAGATCTGC-ATCTTGGATCGACTTC-CTATC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * *
2605 AATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC-GCC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * * * *
2649 AATACATGAAGACAAGATCTGCTTTCTGCGATCTATTTCGCCACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * *
2694 AATATGGGAAGACAAGATCTGC-ATATTGGATCCACTTC-CTATC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * *
2737 AATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC-GCC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * * * *
2781 AATACATGAAGACAAGATCTACTTTCTGCGATCTACTTCGCCACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* *
2826 AATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * *
2869 AATATAGAAAGATAGGATCTGCTACCTTCGATCTACTTCAC-GCC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * * *
2913 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * *
2958 AATATGGGAAGACAAGATCTGC-ATCCTGGATCCACTTC-CTATC
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* * * * * *
3001 AATATAGGAAGATAGGACCTGCTATCTTCGATCTGCTTCAC-GCT
1 AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
* *
3045 AATACATGAAGACAAGATCT
1 AATATAGGAAGACAAGATCT
3065 ACTTTAATGA
Statistics
Matches: 382, Mismatches: 108, Indels: 25
0.74 0.21 0.05
Matches are distributed among these distances:
42 7 0.02
43 89 0.23
44 217 0.57
45 69 0.18
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (45 bp):
AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACC
Found at i:2751 original size:132 final size:132
Alignment explanation
Indices: 2518--3069 Score: 899
Period size: 132 Copynumber: 4.2 Consensus size: 132
2508 TTCGCTGCCA
* * ** * * ** *
2518 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTACTTTACCACCAGTAT-GGAAGACAAGATCT
1 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
*
2582 GCATCTTGGATCGACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
66 GCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
2647 CC
131 CC
*
2649 AATACATGAAGACAAGATCTGCTTTCTGCGATCTATTTCGCCACCAATATGGGAAGACAAGATCT
1 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
*
2714 GCATATTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
66 GCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
2779 CC
131 CC
*
2781 AATACATGAAGACAAGATCTACTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
1 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
* * * * *
2846 GCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGATCTGCTACCTTCGATCTACTTCACG
66 GCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
2911 CC
131 CC
2913 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
1 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
* *
2978 GCATCCTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTGCTTCACG
66 GCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
*
3043 CT
131 CC
*
3045 AATACATGAAGACAAGATCTACTTT
1 AATACATGAAGACAAGATCTGCTTT
3070 AATGACTTTA
Statistics
Matches: 390, Mismatches: 30, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
131 40 0.10
132 350 0.90
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (132 bp):
AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
GCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
CC
Found at i:13985 original size:12 final size:12
Alignment explanation
Indices: 13970--13999 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
13960 ACAATAATAC
13970 TATATATAAATG
1 TATATATAAATG
*
13982 TATATATATATG
1 TATATATAAATG
13994 TATATA
1 TATATA
14000 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATATAAATG
Found at i:14106 original size:17 final size:17
Alignment explanation
Indices: 14084--14126 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
14074 TAAAGTAATA
*
14084 AAAATA-ATACTATATAT
1 AAAATATATA-TATACAT
14101 AAAATATATATATACAT
1 AAAATATATATATACAT
14118 AAAA-ATATA
1 AAAATATATA
14127 CACTAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 16 0.67
18 3 0.12
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATATATATATACAT
Found at i:14126 original size:18 final size:19
Alignment explanation
Indices: 14081--14131 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
14071 AATTAAAGTA
*
14081 ATAAAAATA-ATACTATAT
1 ATAAAAATATATACTATAC
14099 AT-AAAATATATA-TATAC
1 ATAAAAATATATACTATAC
*
14116 ATAAAAATATACACTA
1 ATAAAAATATATACTA
14132 ATATATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 12 0.43
18 14 0.50
19 2 0.07
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAAAATATATACTATAC
Found at i:14358 original size:3 final size:3
Alignment explanation
Indices: 14345--14427 Score: 54
Period size: 3 Copynumber: 28.3 Consensus size: 3
14335 GAGGGCATAT
14345 ATA AT- ATA ATA AT- ATA A-A A-A ATA ATA TATA CATGA GA-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA ATA
* *
14389 ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
14428 AACAAAGCTC
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
2 13 0.20
3 43 0.66
4 7 0.11
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:14403 original size:12 final size:12
Alignment explanation
Indices: 14343--14424 Score: 60
Period size: 12 Copynumber: 6.5 Consensus size: 12
14333 GAGAGGGCAT
14343 ATATAATATAATA
1 ATATAA-ATAATA
*
14356 ATATAAAAAATA
1 ATATAAATAATA
14368 ATATATACATGAGA-A
1 ATATA-A-AT-A-ATA
14383 ATA-ATAATAATA
1 ATATA-AATAATA
14395 ATATAAATAATA
1 ATATAAATAATA
* *
14407 GTAAAAATAATA
1 ATATAAATAATA
*
14419 AAATAA
1 ATATAA
14425 TAAAACAAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
11 1 0.02
12 35 0.62
13 10 0.18
14 4 0.07
15 5 0.09
16 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (12 bp):
ATATAAATAATA
Found at i:18698 original size:17 final size:19
Alignment explanation
Indices: 18662--18699 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
18652 AAATAATGGT
18662 AAAATATATTGTAATCTTA
1 AAAATATATTGTAATCTTA
*
18681 AAAATA-ATT-TAATTTTA
1 AAAATATATTGTAATCTTA
18698 AA
1 AA
18700 TTTTAAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 3 0.17
19 6 0.33
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (19 bp):
AAAATATATTGTAATCTTA
Found at i:22100 original size:26 final size:28
Alignment explanation
Indices: 22053--22106 Score: 94
Period size: 26 Copynumber: 2.0 Consensus size: 28
22043 CCCCCAACTC
22053 TTCTCTTCAATTTTTTTTTACTTTCCCT
1 TTCTCTTCAATTTTTTTTTACTTTCCCT
22081 TTCTCTTC-A-TTTTTTTTACTTTCCCT
1 TTCTCTTCAATTTTTTTTTACTTTCCCT
22107 CCCCTTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 17 0.65
27 1 0.04
28 8 0.31
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.65
Consensus pattern (28 bp):
TTCTCTTCAATTTTTTTTTACTTTCCCT
Found at i:24079 original size:35 final size:35
Alignment explanation
Indices: 24021--24088 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
24011 AGATTCACAA
* * *
24021 TCGGGCCTGGGCCCATATCAGATATAGATACAGAT
1 TCGGGCCTGAGCCCATATCAGATACAAATACAGAT
* *
24056 TCGGGCCTGAGCCCATTTTAGATACAAATACAG
1 TCGGGCCTGAGCCCATATCAGATACAAATACAG
24089 TTACAGATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (35 bp):
TCGGGCCTGAGCCCATATCAGATACAAATACAGAT
Found at i:29288 original size:18 final size:18
Alignment explanation
Indices: 29265--29300 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29255 TCAGAAAAGT
29265 ATGAATAAAAGTTTATGA
1 ATGAATAAAAGTTTATGA
29283 ATGAATAAAAGTTTATGA
1 ATGAATAAAAGTTTATGA
29301 TACATATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (18 bp):
ATGAATAAAAGTTTATGA
Done.