Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168351.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_572, 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: 22689
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Found at i:1079 original size:18 final size:18
Alignment explanation
Indices: 1042--1080 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1032 AGAAAATTTT
*
1042 AAAACAAAGAAAAAAGTG
1 AAAACAAAGAAAAAAATG
1060 AAAACAAA-AAAAAATATG
1 AAAACAAAGAAAAAA-ATG
1078 AAA
1 AAA
1081 GCACATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.77, C:0.05, G:0.10, T:0.08
Consensus pattern (18 bp):
AAAACAAAGAAAAAAATG
Found at i:1217 original size:8 final size:8
Alignment explanation
Indices: 1176--1376 Score: 52
Period size: 8 Copynumber: 23.1 Consensus size: 8
1166 ACCAACAACG
1176 ATAAATAAA
1 ATAAA-AAA
1185 A-AAGAAAA
1 ATAA-AAAA
*
1193 GATAAAAAG
1 -ATAAAAAA
1202 ATAAAAAA
1 ATAAAAAA
1210 ATAAAAAA
1 ATAAAAAA
*
1218 ATCCAAAACATT
1 AT--AAAA-A-A
*
1230 ATAAAAATTT
1 ATAAAAA--A
* *
1240 ATGAAAAT
1 ATAAAAAA
*
1248 ATAAATAA
1 ATAAAAAA
* *
1256 AGAAAGAA
1 ATAAAAAA
1264 AT-AAAAA
1 ATAAAAAA
1271 ATAAAAATA
1 ATAAAAA-A
*
1280 AGAAAAAA
1 ATAAAAAA
*
1288 ATATAAAAT
1 ATA-AAAAA
*
1297 GTAAATAAA
1 ATAAA-AAA
1306 CA-AAAATACA
1 -ATAAAA-A-A
1316 AT-AAAAA
1 ATAAAAAA
1323 ATATAAAAA
1 ATA-AAAAA
* *
1332 GTAAGAAA
1 ATAAAAAA
1340 ATCAAAAATA
1 AT-AAAAA-A
1350 ATGAATCAAAA
1 AT-AA--AAAA
*
1361 A-CAAAAA
1 ATAAAAAA
1368 ATAAAAAA
1 ATAAAAAA
1376 A
1 A
1377 GACAAAAATT
Statistics
Matches: 145, Mismatches: 24, Indels: 47
0.67 0.11 0.22
Matches are distributed among these distances:
7 14 0.10
8 57 0.39
9 42 0.29
10 24 0.17
11 3 0.02
12 5 0.03
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.17
Consensus pattern (8 bp):
ATAAAAAA
Found at i:1272 original size:19 final size:19
Alignment explanation
Indices: 1250--1384 Score: 61
Period size: 20 Copynumber: 7.0 Consensus size: 19
1240 ATGAAAATAT
*
1250 AAATAAAGA-AAGAAATAAA
1 AAATAAAAATAAGAAA-AAA
1269 AAATAAAAATAAGAAAAAA
1 AAATAAAAATAAGAAAAAA
* * *
1288 ATAT-AAAAT--G-TAAAT
1 AAATAAAAATAAGAAAAAA
*
1303 AAACAAAAATACA-ATAAAAA
1 AAATAAAAATA-AGA-AAAAA
*
1323 ATATAAAAAGTAAGAAAATCAA
1 AAATAAAAA-TAAGAAAA--AA
*
1345 AAATAATGAATCAA-AAACAAA
1 AAATAA-AAAT-AAGAAA-AAA
1366 AAATAAAAA-AAGACAAAAA
1 AAATAAAAATAAGA-AAAAA
1385 TTGAATAAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 32
0.66 0.10 0.24
Matches are distributed among these distances:
15 5 0.06
16 6 0.07
18 7 0.08
19 18 0.21
20 24 0.28
21 11 0.13
22 11 0.13
23 5 0.06
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (19 bp):
AAATAAAAATAAGAAAAAA
Found at i:1278 original size:25 final size:25
Alignment explanation
Indices: 1243--1375 Score: 101
Period size: 24 Copynumber: 5.2 Consensus size: 25
1233 AAAATTTATG
*
1243 AAAATATAAATAAAGAAAGAAATAA
1 AAAATATAAATAAAGAAAAAAATAA
* *
1268 AAAATAAAAAT-AAGAAAAAAATAT
1 AAAATATAAATAAAGAAAAAAATAA
* *
1292 AAAATGTAAATAAACAAAAATACAATAA
1 AAAATATAAATAAA-GAAAA-A-AATAA
* *
1320 AAAATAT-AA-AAAGTAAGAAAATCA
1 AAAATATAAATAAAG-AAAAAAATAA
* *
1344 AAAATAATGAATCAAAAACAAAAAATAA
1 AAAAT-ATAAAT-AAAGA-AAAAAATAA
1372 AAAA
1 AAAA
1376 AGACAAAAAT
Statistics
Matches: 84, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
24 29 0.35
25 15 0.18
26 12 0.14
27 4 0.05
28 24 0.29
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (25 bp):
AAAATATAAATAAAGAAAAAAATAA
Found at i:2079 original size:24 final size:24
Alignment explanation
Indices: 2052--2125 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
2042 AACGCAAATA
2052 AGAAATAAAAAGAAAAGCAAGAAT
1 AGAAATAAAAAGAAAAGCAAGAAT
*
2076 AG-AATAAAAATGAAAAGACAAAAGATT
1 AGAAATAAAAA-GAAAAG-C--AAGAAT
*
2103 TGAAATAAAAAAGAAAA-CAAGAA
1 AGAAAT-AAAAAGAAAAGCAAGAA
2126 AGTAAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
23 8 0.20
24 12 0.29
25 1 0.02
26 1 0.02
27 6 0.15
28 8 0.20
29 5 0.12
ACGTcount: A:0.70, C:0.04, G:0.15, T:0.11
Consensus pattern (24 bp):
AGAAATAAAAAGAAAAGCAAGAAT
Found at i:2396 original size:6 final size:6
Alignment explanation
Indices: 2297--2380 Score: 50
Period size: 6 Copynumber: 13.8 Consensus size: 6
2287 AAAAAGATTC
**
2297 AAAAAT -AAAAT AAAAAT --AAAT GAAAAAT AAATTAAT AAAAAT ATTAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAA--AAT AAAAAT AAAAAT
* * *
2345 ATAAAAG AAAAA- AATAAAC AAAAAC AAAAAT AAAAA
1 A-AAAAT AAAAAT AA-AAAT AAAAAT AAAAAT AAAAA
2381 AGGAAAAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
4 4 0.06
5 7 0.11
6 37 0.59
7 9 0.14
8 6 0.10
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:2398 original size:8 final size:8
Alignment explanation
Indices: 2265--2422 Score: 79
Period size: 8 Copynumber: 19.4 Consensus size: 8
2255 AAAAAAAGAC
*
2265 AAAATAAG
1 AAAATAAA
*
2273 AAAATGAA
1 AAAATAAA
2281 AAAATAAA
1 AAAATAAA
**
2289 AAAGATTCA
1 AAA-ATAAA
2298 AAAATAAA
1 AAAATAAA
*
2306 ATAA-AAA
1 AAAATAAA
* *
2313 TAAAT-GA
1 AAAATAAA
2320 AAAATAAA
1 AAAATAAA
**
2328 TTAATAAA
1 AAAATAAA
*
2336 AATATTAATA
1 AA-AATAA-A
*
2346 TAAAAGAAA
1 -AAAATAAA
2355 AAAATAAA
1 AAAATAAA
*
2363 CAAAA-ACA
1 -AAAATAAA
2371 AAAATAAA
1 AAAATAAA
**
2379 AAAGGAAA
1 AAAATAAA
2387 AAAATAAA
1 AAAATAAA
* *
2395 AAAATTAG
1 AAAATAAA
**
2403 CTAATAAA
1 AAAATAAA
2411 AAAATATAA
1 AAAATA-AA
2420 AAA
1 AAA
2423 GACAAAATGA
Statistics
Matches: 106, Mismatches: 35, Indels: 17
0.67 0.22 0.11
Matches are distributed among these distances:
7 14 0.13
8 66 0.62
9 20 0.19
10 4 0.04
11 2 0.02
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (8 bp):
AAAATAAA
Found at i:3461 original size:17 final size:17
Alignment explanation
Indices: 3426--3476 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
3416 AGAAAATTTT
*
3426 AAAACAAAGAAAAAGTG
1 AAAACAAAGAAAAAATG
3443 AAAACAAA-AAAAATATG
1 AAAACAAAGAAAAA-ATG
* *
3460 AAAGCACATGAAAAAAT
1 AAAACA-AAGAAAAAAT
3477 AAGTAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 5 0.18
17 15 0.54
18 3 0.11
19 5 0.18
ACGTcount: A:0.71, C:0.08, G:0.12, T:0.10
Consensus pattern (17 bp):
AAAACAAAGAAAAAATG
Found at i:3654 original size:21 final size:21
Alignment explanation
Indices: 3621--3672 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3611 AAAACTTTAT
3621 GAAAATAATAAATAAAAGAAAA
1 GAAAATAATAAATAAAA-AAAA
* *
3643 GAAATTAA-AAATAAAAATAA
1 GAAAATAATAAATAAAAAAAA
*
3663 GAAAAAAATA
1 GAAAATAATA
3673 TTAAAAAGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 9 0.36
21 9 0.36
22 7 0.28
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (21 bp):
GAAAATAATAAATAAAAAAAA
Found at i:3664 original size:25 final size:26
Alignment explanation
Indices: 3627--3697 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 26
3617 TTATGAAAAT
*
3627 AATAAATAAAAGAAAAGAA-ATTAAA
1 AATAAATAAAAGAAAAAAATATTAAA
3652 AATAAA-AATAAGAAAAAAATATTAAA
1 AATAAATAA-AAGAAAAAAATATTAAA
* * *
3678 AAGCAAAAAAAAAAAAAAAA
1 AA-TAAATAAAAGAAAAAAA
3698 ACAAAAATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
24 2 0.05
25 15 0.38
26 8 0.21
27 12 0.31
28 2 0.05
ACGTcount: A:0.80, C:0.01, G:0.06, T:0.13
Consensus pattern (26 bp):
AATAAATAAAAGAAAAAAATATTAAA
Found at i:3675 original size:26 final size:23
Alignment explanation
Indices: 3627--3738 Score: 68
Period size: 25 Copynumber: 4.6 Consensus size: 23
3617 TTATGAAAAT
*
3627 AATAAATAAAAGAAAAGAAATTAAA
1 AATAAA-AAAA-AAAAAAAATTAAA
3652 AATAAAAATAAGAAAAAAATATTAAA
1 AATAAAAA-AA-AAAAAAA-ATTAAA
*
3678 AAGCAAAAAAAAAAAAAAA--AACA
1 AA-TAAAAAAAAAAAAAAATTAA-A
* * *
3701 AA-AATACAAATAAAAAATATAAA
1 AATAAAAAAAAAAAAAAAT-TAAA
*
3724 AAGTAAGAAAAAAAA
1 AA-TAAAAAAAAAAA
3739 GACAAAAATT
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
21 12 0.17
22 2 0.03
23 6 0.09
24 5 0.07
25 30 0.43
26 10 0.14
27 5 0.07
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.12
Consensus pattern (23 bp):
AATAAAAAAAAAAAAAAATTAAA
Found at i:3698 original size:45 final size:48
Alignment explanation
Indices: 3649--3747 Score: 125
Period size: 47 Copynumber: 2.1 Consensus size: 48
3639 AAAAGAAATT
*
3649 AAAAATAAAAATA-AGA-AAAAAATATTAAAAAGCAA-AAAAAAAA-AA
1 AAAAATAAAAATACAAATAAAAAATA-TAAAAAGCAAGAAAAAAAAGAA
* * *
3694 AAAAACAAAAATACAAATAAAAAATATAAAAAGTAAGAAAAAAAAGAC
1 AAAAATAAAAATACAAATAAAAAATATAAAAAGCAAGAAAAAAAAGAA
3742 AAAAAT
1 AAAAAT
3748 TGAATAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
45 12 0.27
46 11 0.24
47 16 0.36
48 6 0.13
ACGTcount: A:0.80, C:0.04, G:0.05, T:0.11
Consensus pattern (48 bp):
AAAAATAAAAATACAAATAAAAAATATAAAAAGCAAGAAAAAAAAGAA
Found at i:3726 original size:46 final size:45
Alignment explanation
Indices: 3649--3738 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 45
3639 AAAAGAAATT
* *
3649 AAAAATAAAAATAAGAAAAAAATATTAAAAAGCAAAAAAAAAAAA
1 AAAAACAAAAATAAAAAAAAAATATTAAAAAGCAAAAAAAAAAAA
* *
3694 AAAAACAAAAATACAAATAAAAAATA-TAAAAAGTAAGAAAAAAAA
1 AAAAACAAAAATA-AAA-AAAAAATATTAAAAAGCAAAAAAAAAAA
3739 GACAAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
45 12 0.31
46 19 0.49
47 8 0.21
ACGTcount: A:0.81, C:0.03, G:0.04, T:0.11
Consensus pattern (45 bp):
AAAAACAAAAATAAAAAAAAAATATTAAAAAGCAAAAAAAAAAAA
Found at i:4270 original size:21 final size:20
Alignment explanation
Indices: 4236--4344 Score: 67
Period size: 22 Copynumber: 5.1 Consensus size: 20
4226 AAAAAATTTT
* *
4236 AATATAAATGAAAAAATAAA
1 AATAAAAATAAAAAAATAAA
*
4256 AATAAATACT-AAAAAATAACA
1 AATAAA-AATAAAAAAATAA-A
* *
4277 ATTAAAAATAAACAAAACAAA
1 AATAAAAATAAA-AAAATAAA
* *
4298 AAGTAAAAGTAAGAAAATAAAA
1 AA-TAAAAATAAAAAAAT-AAA
*
4320 AATTAGAGAATAAAAAAATATAA
1 AA-TA-AAAATAAAAAAATA-AA
4343 AA
1 AA
4345 CGATAAAATG
Statistics
Matches: 68, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
20 16 0.24
21 16 0.24
22 22 0.32
23 14 0.21
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (20 bp):
AATAAAAATAAAAAAATAAA
Found at i:4475 original size:24 final size:23
Alignment explanation
Indices: 4448--4502 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
4438 AAAAGACATA
4448 AAAATCAAAGACAAAAAATAAAAT
1 AAAATCAAAGACAAAAAAT-AAAT
* *
4472 AAAAGTC-AATACAAAATATAAAT
1 AAAA-TCAAAGACAAAAAATAAAT
4495 AAAATCAA
1 AAAATCAA
4503 CAGGAAGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 2 0.07
23 9 0.33
24 14 0.52
25 2 0.07
ACGTcount: A:0.71, C:0.09, G:0.04, T:0.16
Consensus pattern (23 bp):
AAAATCAAAGACAAAAAATAAAT
Found at i:5022 original size:65 final size:66
Alignment explanation
Indices: 4899--5022 Score: 148
Period size: 65 Copynumber: 1.9 Consensus size: 66
4889 TAAGTACTAA
* ** *
4899 AAAAGAGAAAAATTAAAAATAAACAAAAACGCAATTAAAAAAAGTAAGAAAATTAAAAAATGAGT
1 AAAAGAGAAAAATTAAAAATAAACAAAAACGCAATAAAAAAAAAAAAGAAAATGAAAAAATGAGT
4964 T
66 T
*
4965 AAAAGA-AAAAATTAAAAA-AATACAAAAAC-TAATAAAAATGAAAAAAAGAAAA-GAAAAA
1 AAAAGAGAAAAATTAAAAATAA-ACAAAAACGCAATAAAAA--AAAAAAAGAAAATGAAAAA
5023 GACAATAGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
64 9 0.18
65 25 0.50
66 16 0.32
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.14
Consensus pattern (66 bp):
AAAAGAGAAAAATTAAAAATAAACAAAAACGCAATAAAAAAAAAAAAGAAAATGAAAAAATGAGT
T
Found at i:6276 original size:18 final size:19
Alignment explanation
Indices: 6255--6297 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
6245 AAATTTAGTT
6255 ATAAAATACAAA-CAAATA
1 ATAAAATACAAACCAAATA
*
6273 ATAAAAAATATAAACCAAATA
1 AT--AAAATACAAACCAAATA
6294 ATAA
1 ATAA
6298 GATAAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 2 0.10
19 2 0.10
20 9 0.43
21 8 0.38
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (19 bp):
ATAAAATACAAACCAAATA
Found at i:6282 original size:20 final size:21
Alignment explanation
Indices: 6257--6297 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6247 ATTTAGTTAT
6257 AAAATACAAA-CAAATAATAA
1 AAAATACAAACCAAATAATAA
*
6277 AAAATATAAACCAAATAATAA
1 AAAATACAAACCAAATAATAA
6298 GATAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAATACAAACCAAATAATAA
Found at i:6675 original size:18 final size:19
Alignment explanation
Indices: 6635--6675 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
6625 GAAAATTTTT
*
6635 AAAACAAAGAAAAAAGTGA
1 AAAACAAAGAAAAAAATGA
6654 AAAACAAA-AAAAAATATGA
1 AAAACAAAGAAAAAA-ATGA
6673 AAA
1 AAA
6676 GCGACATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07
Consensus pattern (19 bp):
AAAACAAAGAAAAAAATGA
Found at i:6866 original size:18 final size:17
Alignment explanation
Indices: 6838--6923 Score: 57
Period size: 18 Copynumber: 4.7 Consensus size: 17
6828 AAATTTATGA
6838 AAAATAATAAAAAGAAAAT
1 AAAA-AATAAAAA-AAAAT
6857 AAAAAATAAAAAATAAGA-
1 AAAAAATAAAAAA-AA-AT
* **
6875 AAAAAATATAAAAATGT
1 AAAAAATAAAAAAAAAT
* *
6892 AAATAAACAAAAATACAAT
1 AAA-AAATAAAAA-AAAAT
6911 AAAAAATATAAAA
1 AAAAAATA-AAAA
6924 GTAAGAAATC
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
17 5 0.10
18 33 0.63
19 14 0.27
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAAAATAAAAAAAAAT
Found at i:6939 original size:35 final size:34
Alignment explanation
Indices: 6858--6942 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
6848 AAAGAAAATA
6858 AAAAAT-AAAAAATAAGAAAAAAATATAAAAATGT
1 AAAAATCAAAAAATAAGAAAAAAATATAAAAA-GT
*
6892 AAATAAAC-AAAAATACA-ATAAAAAATAT-AAAAGT
1 AAA-AATCAAAAAATA-AGA-AAAAAATATAAAAAGT
6926 AAGAAATCAAAAAATAA
1 AA-AAATCAAAAAATAA
6943 TGAATCAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
34 11 0.26
35 22 0.51
36 10 0.23
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (34 bp):
AAAAATCAAAAAATAAGAAAAAAATATAAAAAGT
Found at i:7867 original size:12 final size:12
Alignment explanation
Indices: 7850--7885 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
7840 AAAAAATTAT
7850 AAAAATAGAACA
1 AAAAATAGAACA
7862 AAAAATAGAA-A
1 AAAAATAGAACA
7873 AAAAA-AG-ACA
1 AAAAATAGAACA
7883 AAA
1 AAA
7886 TAAAAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.04
10 6 0.26
11 6 0.26
12 10 0.43
ACGTcount: A:0.81, C:0.06, G:0.08, T:0.06
Consensus pattern (12 bp):
AAAAATAGAACA
Found at i:7890 original size:14 final size:14
Alignment explanation
Indices: 7861--7929 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
7851 AAAATAGAAC
*
7861 AAAAAAT-AGAAA-
1 AAAAAATGAAAAAT
7873 AAAAAA-GACAAAAT
1 AAAAAATGA-AAAAT
7887 AAAAAATGAAAAAT
1 AAAAAATGAAAAAT
*
7901 AAAACCA--AAAAAT
1 AAAA-AATGAAAAAT
*
7914 -AAAAATAAAAAAT
1 AAAAAATGAAAAAT
7927 AAA
1 AAA
7930 TGAAAAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
11 1 0.02
12 10 0.22
13 15 0.33
14 17 0.37
15 3 0.07
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.10
Consensus pattern (14 bp):
AAAAAATGAAAAAT
Found at i:7890 original size:25 final size:26
Alignment explanation
Indices: 7862--7954 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 26
7852 AAATAGAACA
*
7862 AAAAATAGAAAAA-AAAAGACAAAAT
1 AAAAATAGAAAAATAAAAGAAAAAAT
*
7887 AAAAA-ATGAAAAATAAAACCAAAAAAT
1 AAAAATA-GAAAAATAAAA-GAAAAAAT
*
7914 AAAAATA-AAAAATAAATGAAAAAAT
1 AAAAATAGAAAAATAAAAGAAAAAAT
7939 AAATTAATA-AAAAATA
1 AAA--AATAGAAAAATA
7955 TTAATATAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
24 1 0.02
25 21 0.36
26 13 0.22
27 22 0.38
28 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.14
Consensus pattern (26 bp):
AAAAATAGAAAAATAAAAGAAAAAAT
Found at i:7899 original size:26 final size:25
Alignment explanation
Indices: 7861--7952 Score: 78
Period size: 26 Copynumber: 3.5 Consensus size: 25
7851 AAAATAGAAC
7861 AAAAAATAGAAAAAAAAAGACAAAAT
1 AAAAAATA-AAAAAAAAAGACAAAAT
* * *
7887 AAAAAATGAAAAATAAAA-CCAAAAA
1 AAAAAAT-AAAAAAAAAAGACAAAAT
* *
7912 ATAAAAATAAAAAATAAATGAAAAAAT
1 A-AAAAATAAAAAA-AAAAGACAAAAT
*
7939 AAATTAATAAAAAA
1 AAA-AAATAAAAAA
7953 TATTAATATA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
25 11 0.21
26 26 0.50
27 15 0.29
ACGTcount: A:0.79, C:0.03, G:0.04, T:0.13
Consensus pattern (25 bp):
AAAAAATAAAAAAAAAAGACAAAAT
Found at i:7899 original size:33 final size:32
Alignment explanation
Indices: 7862--8025 Score: 90
Period size: 33 Copynumber: 4.9 Consensus size: 32
7852 AAATAGAACA
7862 AAAAATAGAAA-AAAAAAGACAAAATAAAAAATG
1 AAAAATA-AAACAAAAAAGA-AAAATAAAAAATG
*
7895 AAAAATAAAACCAAAAAATAAAAATAAAAAAT-
1 AAAAATAAAA-CAAAAAAGAAAAATAAAAAATG
* *
7927 AAATGAA-AAAATAAATTAATAAAAAATATTAATATAAATG
1 AAA--AATAAAACAAA--AA-AGAAAA-A-TAA-A-AAATG
* *
7967 AAAAAAATAAACAAAGAAG-AAAATAAAAAA-G
1 AAAAATA-AAACAAAAAAGAAAAATAAAAAATG
*
7998 AAGAAA-AATA-AAAAAAGAAGAAATAAAA
1 AA-AAATAAAACAAAAAAGAA-AAATAAAA
8026 TAAAAAAAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 36
0.71 0.05 0.24
Matches are distributed among these distances:
29 6 0.06
30 3 0.03
31 12 0.11
32 15 0.14
33 24 0.23
34 14 0.13
35 6 0.06
36 4 0.04
37 4 0.04
38 4 0.04
39 5 0.05
40 9 0.08
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.13
Consensus pattern (32 bp):
AAAAATAAAACAAAAAAGAAAAATAAAAAATG
Found at i:7975 original size:15 final size:15
Alignment explanation
Indices: 7966--8035 Score: 72
Period size: 16 Copynumber: 4.5 Consensus size: 15
7956 TAATATAAAT
7966 GAAAAAAATAAACAAA
1 GAAAAAAATAAA-AAA
*
7982 GAAGAAAATAAAAAA
1 GAAAAAAATAAAAAA
7997 GAAGAAAAATAAAAAA
1 GAA-AAAAATAAAAAA
*
8013 -AGAAGAAATAAAATAA
1 GA-AAAAAATAAAA-AA
8029 -AAAAAAA
1 GAAAAAAA
8036 AGACAAGTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
15 21 0.45
16 26 0.55
ACGTcount: A:0.81, C:0.01, G:0.10, T:0.07
Consensus pattern (15 bp):
GAAAAAAATAAAAAA
Found at i:7976 original size:13 final size:12
Alignment explanation
Indices: 7907--7996 Score: 58
Period size: 12 Copynumber: 7.4 Consensus size: 12
7897 AAATAAAACC
*
7907 AAAAAATAAAAA
1 AAAAAATAAATA
*
7919 TAAAAAATAAATG
1 -AAAAAATAAATA
*
7932 AAAAAATAAATT
1 AAAAAATAAATA
*
7944 AATAAA-AAATA
1 AAAAAATAAATA
** *
7955 TTAATATAAATGA
1 AAAAAATAAAT-A
*
7968 AAAAAATAAACA
1 AAAAAATAAATA
*
7980 AAGAAGA-AAATA
1 AA-AAAATAAATA
7992 AAAAA
1 AAAAA
7997 GAAGAAAAAT
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
11 8 0.14
12 29 0.50
13 21 0.36
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (12 bp):
AAAAAATAAATA
Found at i:7991 original size:16 final size:15
Alignment explanation
Indices: 7970--8025 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 15
7960 ATAAATGAAA
7970 AAAATAAACAAAGAAG
1 AAAATAAA-AAAGAAG
7986 AAAATAAAAAAGAAG
1 AAAATAAAAAAGAAG
8001 AAAAATAAAAAAAGAAG
1 -AAAAT-AAAAAAGAAG
8018 -AAATAAAA
1 AAAATAAAA
8026 TAAAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.11
15 11 0.29
16 13 0.34
17 10 0.26
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (15 bp):
AAAATAAAAAAGAAG
Found at i:8025 original size:20 final size:18
Alignment explanation
Indices: 7848--8038 Score: 82
Period size: 19 Copynumber: 10.8 Consensus size: 18
7838 TGAAAAAATT
* *
7848 ATAAAAATAGAACAAAAA
1 ATAAAAAAAGAAGAAAAA
* *
7866 ATAGAAAAAAAAAGACAAA
1 ATA-AAAAAAGAAGAAAAA
*
7885 ATAAAAAATGAA-AAATAA
1 ATAAAAAAAGAAGAAA-AA
** *
7903 A-ACCAAAA-AA-TAAAA
1 ATAAAAAAAGAAGAAAAA
7918 ATAAAAAATA-AATGAAAAA
1 ATAAAAAA-AGAA-GAAAAA
** *
7937 ATAAATTAATAA-AAAATA
1 ATAAAAAAAGAAGAAAA-A
* *
7955 TTAATATAAATG-A-AAAAA
1 ATAA-A-AAAAGAAGAAAAA
*
7973 ATAAACAAAGAAG--AAA
1 ATAAAAAAAGAAGAAAAA
7989 AT-AAAAAAGAAG-AAAA
1 ATAAAAAAAGAAGAAAAA
8005 ATAAAAAAAGAAGAAATAAA
1 ATAAAAAAAGAAG-AA-AAA
*
8025 ATAAAAAAAAAAGA
1 ATAAAAAAAGAAGA
8039 CAAGTGAAAA
Statistics
Matches: 130, Mismatches: 26, Indels: 33
0.69 0.14 0.17
Matches are distributed among these distances:
15 12 0.09
16 21 0.16
17 25 0.19
18 22 0.17
19 34 0.26
20 16 0.12
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (18 bp):
ATAAAAAAAGAAGAAAAA
Found at i:8033 original size:38 final size:38
Alignment explanation
Indices: 7991--8072 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
7981 AGAAGAAAAT
*
7991 AAAAAAGAAGAAAAAT-AAAAAAAGAAGAAATAAAATA-
1 AAAAAAAAAGAAAAATGAAAAAAAGAA-AAATAAAATAG
* * *
8028 AAAAAAAAAGACAAGTGAAAAAAAGAAATATAAAATAG
1 AAAAAAAAAGAAAAATGAAAAAAAGAAAAATAAAATAG
8066 AAAAAAA
1 AAAAAAA
8073 CTTTTAGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
37 22 0.56
38 17 0.44
ACGTcount: A:0.79, C:0.01, G:0.11, T:0.09
Consensus pattern (38 bp):
AAAAAAAAAGAAAAATGAAAAAAAGAAAAATAAAATAG
Found at i:8129 original size:23 final size:22
Alignment explanation
Indices: 8091--8155 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
8081 TTAAATATAC
*
8091 AAGAGAAAAAAAGAAAAGATAGCA
1 AAGA-AAAAAAAGAAAAAAT-GCA
8115 AA-AAAAAAAAGGAAAAAATGCA
1 AAGAAAAAAAA-GAAAAAATGCA
8137 AAGAAATAAAAA-AAAAAAT
1 AAGAAA-AAAAAGAAAAAAT
8156 AAAAAGTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
22 19 0.51
23 11 0.30
24 7 0.19
ACGTcount: A:0.77, C:0.03, G:0.14, T:0.06
Consensus pattern (22 bp):
AAGAAAAAAAAGAAAAAATGCA
Found at i:8130 original size:31 final size:30
Alignment explanation
Indices: 8095--8154 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
8085 ATATACAAGA
*
8095 GAAAAAAAGAAAAGATAGCAAAAAAAAAAAG
1 GAAAAAAAGAAAAGA-AACAAAAAAAAAAAG
* * *
8126 GAAAAAATGCAAAGAAATAAAAAAAAAAA
1 GAAAAAAAGAAAAGAAACAAAAAAAAAAA
8155 TAAAAAGTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.78, C:0.03, G:0.13, T:0.05
Consensus pattern (30 bp):
GAAAAAAAGAAAAGAAACAAAAAAAAAAAG
Found at i:8333 original size:12 final size:12
Alignment explanation
Indices: 8294--8322 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
8284 AAAGGCAAGA
8294 AAAAAAAAAATT
1 AAAAAAAAAATT
8306 AAAAAAAAAATT
1 AAAAAAAAAATT
8318 AAAAA
1 AAAAA
8323 TTAAACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAAAATT
Found at i:8633 original size:34 final size:34
Alignment explanation
Indices: 8589--8653 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
8579 AAGCAAAAGG
*
8589 AAAAAGATAAATAAGTAATAAAAAAGAAAAAAAAT
1 AAAAAGATAAAGAAGTAA-AAAAAAGAAAAAAAAT
**
8624 AAAAA-ATAAAGAAGTAAGGAAAAGAAAAAA
1 AAAAAGATAAAGAAGTAAAAAAAAGAAAAAA
8654 TGAGTCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 11 0.41
34 11 0.41
35 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (34 bp):
AAAAAGATAAAGAAGTAAAAAAAAGAAAAAAAAT
Found at i:9091 original size:19 final size:19
Alignment explanation
Indices: 9077--9116 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
9067 AGAAAATTTT
*
9077 AAAACAAAGAAAAAA-GTG
1 AAAACAAAAAAAAAATGTG
*
9095 AAAACAAAAAAAAAATATG
1 AAAACAAAAAAAAAATGTG
9114 AAA
1 AAA
9117 GCACATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07
Consensus pattern (19 bp):
AAAACAAAAAAAAAATGTG
Found at i:9311 original size:25 final size:24
Alignment explanation
Indices: 9276--9356 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 24
9266 AAAATTTATG
*
9276 AAAATATAAATAAAGAAAGAAATTA
1 AAAATAAAAATAAAGAAA-AAATTA
*
9301 AAAATAAAAATAAGAAAAAAATATTA
1 AAAATAAAAATAA-AGAAAAA-ATTA
*
9327 AAGAA-AAAAATACAATAAAAAATATA
1 AA-AATAAAAATA-AAGAAAAAAT-TA
9353 AAAA
1 AAAA
9357 GTAAGAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
25 18 0.38
26 27 0.56
27 3 0.06
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (24 bp):
AAAATAAAAATAAAGAAAAAATTA
Found at i:9335 original size:26 final size:27
Alignment explanation
Indices: 9276--9356 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 27
9266 AAAATTTATG
* * *
9276 AAAATATAAATA-AAGAAAGAA-ATTA
1 AAAATAAAAATACAATAAAAAATATTA
9301 AAAATAAAAATA-AGA-AAAAAATATTA
1 AAAATAAAAATACA-ATAAAAAATATTA
9327 AAGAA-AAAAATACAATAAAAAATA-TA
1 AA-AATAAAAATACAATAAAAAATATTA
9353 AAAA
1 AAAA
9357 GTAAGAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
25 19 0.39
26 19 0.39
27 11 0.22
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (27 bp):
AAAATAAAAATACAATAAAAAATATTA
Found at i:9371 original size:14 final size:14
Alignment explanation
Indices: 9300--9370 Score: 54
Period size: 15 Copynumber: 4.6 Consensus size: 14
9290 GAAAGAAATT
9300 AAAAATAAAAATAAG
1 AAAAA-AAAAATAAG
* *
9315 AAAAAAATATTAAAG
1 AAAAAAAAAAT-AAG
9330 AAAAAAATACAATAA-
1 AAAAAAA-A-AATAAG
9345 AAAATATAAAAAGTAAG
1 AAAA-A-AAAAA-TAAG
9362 AAAAAAAAA
1 AAAAAAAAA
9371 GGCAAAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
14 4 0.09
15 25 0.56
16 8 0.18
17 8 0.18
ACGTcount: A:0.79, C:0.01, G:0.06, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAATAAG
Found at i:9749 original size:40 final size:39
Alignment explanation
Indices: 9704--9785 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
9694 TATGAAATTT
*
9704 AAATAAAGAAAGA-AATA-AAAAATAAACCAAAATAAAAATA
1 AAAT-AAGAAA-ACAATATAAAAATAAAACAAAA-AAAAATA
* *
9744 AAATAAGAAAACAATATTAAAGTAAAACAAAAAAAAATA
1 AAATAAGAAAACAATATAAAAATAAAACAAAAAAAAATA
9783 AAA
1 AAA
9786 GAAACAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
38 1 0.03
39 20 0.54
40 16 0.43
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (39 bp):
AAATAAGAAAACAATATAAAAATAAAACAAAAAAAAATA
Found at i:9794 original size:15 final size:14
Alignment explanation
Indices: 9773--9815 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
9763 AAGTAAAACA
9773 AAAAAAAATAAAAG
1 AAAAAAAATAAAAG
* *
9787 AAACAAAAATACAAT
1 AAA-AAAAATAAAAG
*
9802 AAAAAATATAAAAG
1 AAAAAAAATAAAAG
9816 GTAAGATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.12
Consensus pattern (14 bp):
AAAAAAAATAAAAG
Found at i:9795 original size:20 final size:19
Alignment explanation
Indices: 9768--9805 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
9758 TATTAAAGTA
9768 AAACAAAAAAAAATAAAAG
1 AAACAAAAAAAAATAAAAG
*
9787 AAACAAAAATACAATAAAA
1 AAACAAAAA-AAAATAAAA
9806 AATATAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.82, C:0.08, G:0.03, T:0.08
Consensus pattern (19 bp):
AAACAAAAAAAAATAAAAG
Found at i:9805 original size:35 final size:35
Alignment explanation
Indices: 9721--9805 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 35
9711 GAAAGAAATA
** * *
9721 AAAAATAAACCAAAATAAAAATAAAATAAGAAAAC
1 AAAAATAAAGTAAAACAAAAATAAAATAAAAAAAC
* *
9756 AATATTAAAGTAAAACAAAAA-AAAATAAAAGAAAC
1 AAAAATAAAGTAAAACAAAAATAAAATAAAA-AAAC
9791 AAAAATACAA-TAAAA
1 AAAAATA-AAGTAAAA
9806 AATATAAAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
34 8 0.20
35 30 0.75
36 2 0.05
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.13
Consensus pattern (35 bp):
AAAAATAAAGTAAAACAAAAATAAAATAAAAAAAC
Found at i:9966 original size:17 final size:16
Alignment explanation
Indices: 9931--9974 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
9921 AACAAAAACA
9931 AAAAGTAAAAAAGTAAG
1 AAAA-TAAAAAAGTAAG
*
9948 AAAATAAAAAA-TTAG
1 AAAATAAAAAAGTAAG
9963 AGAAATAAAAAA
1 A-AAATAAAAAA
9975 AATATAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 4 0.16
16 17 0.68
17 4 0.16
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (16 bp):
AAAATAAAAAAGTAAG
Found at i:9975 original size:24 final size:22
Alignment explanation
Indices: 9874--9975 Score: 61
Period size: 24 Copynumber: 4.5 Consensus size: 22
9864 ATTTTAATAT
*
9874 AAATGAAAAAAT--AAAA-TAA
1 AAATAAAAAAATAAAAAATTAA
*
9893 AATACTAAAAAAAT-AACAATTAA
1 AA-A-TAAAAAAATAAAAAATTAA
*
9916 AAATAAACAAAA-ACAAAAAGTAAA
1 AAATAAA-AAAATA-AAAAA-TTAA
*
9940 AAAGTAAGAAAATAAAAAATTAGA
1 AAA-TAAAAAAATAAAAAATTA-A
9964 GAAATAAAAAAA
1 -AAATAAAAAAA
9976 ATATAAAACG
Statistics
Matches: 64, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
19 2 0.03
20 1 0.02
21 12 0.19
22 8 0.12
23 11 0.17
24 23 0.36
25 7 0.11
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (22 bp):
AAATAAAAAAATAAAAAATTAA
Found at i:10773 original size:18 final size:16
Alignment explanation
Indices: 10742--10803 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 16
10732 AAATAATAAG
10742 AAAAAATAAAGATTATA
1 AAAAAATAAAGATTA-A
*
10759 AAAAAATCAATGATTAA
1 AAAAAAT-AAAGATTAA
*
10776 AAAAAGA-AAAAAGTTAA
1 AAAAA-ATAAAGA-TTAA
10793 TAAAAAATAAA
1 -AAAAAATAAA
10804 AACAAAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 3 0.08
17 18 0.49
18 16 0.43
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAAAATAAAGATTAA
Found at i:11471 original size:37 final size:37
Alignment explanation
Indices: 11419--11491 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
11409 TATCTCTTAA
11419 CAAATTGTATCAAATAAAAGATAAATATTATACAATC
1 CAAATTGTATCAAATAAAAGATAAATATTATACAATC
* *
11456 CAAATTTTATTAAATAAAAGATAAATATTATACAAT
1 CAAATTGTATCAAATAAAAGATAAATATTATACAAT
11492 ATAATTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (37 bp):
CAAATTGTATCAAATAAAAGATAAATATTATACAATC
Found at i:11492 original size:21 final size:21
Alignment explanation
Indices: 11431--11492 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
11421 AATTGTATCA
11431 AATAAAAGATAAATATTATAC
1 AATAAAAGATAAATATTATAC
**
11452 AATCCAA-AT---T-TTATTA-
1 AATAAAAGATAAATATTA-TAC
11468 AATAAAAGATAAATATTATAC
1 AATAAAAGATAAATATTATAC
11489 AATA
1 AATA
11493 TAATTTTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
16 8 0.27
17 5 0.17
20 5 0.17
21 12 0.40
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (21 bp):
AATAAAAGATAAATATTATAC
Found at i:11700 original size:13 final size:13
Alignment explanation
Indices: 11667--11711 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
11657 TAAAATTTTT
*
11667 ATAAAAAA-CAAA
1 ATAAAAAATAAAA
11679 ATAACAAAATTAAAA
1 ATAA-AAAA-TAAAA
11694 ATAAAAAATAAAA
1 ATAAAAAATAAAA
11707 ATAAA
1 ATAAA
11712 GGAAAAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.14
13 14 0.48
14 4 0.14
15 7 0.24
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
ATAAAAAATAAAA
Found at i:12262 original size:19 final size:18
Alignment explanation
Indices: 12224--12263 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12214 AGAAAATTTT
* *
12224 AAAACAAAGAAAAAAGTG
1 AAAACAAAAAAAAAAATG
12242 AAAACAAAAAAAAAATATG
1 AAAACAAAAAAAAAA-ATG
12261 AAA
1 AAA
12264 GCACATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAACAAAAAAAAAAATG
Found at i:12387 original size:9 final size:9
Alignment explanation
Indices: 12373--12401 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
12363 AATAAAAAAG
12373 AAAGATAAA
1 AAAGATAAA
12382 AAAGATAAA
1 AAAGATAAA
12391 AAA-ATAAA
1 AAAGATAAA
12399 AAA
1 AAA
12402 TCCAAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (9 bp):
AAAGATAAA
Found at i:12397 original size:8 final size:8
Alignment explanation
Indices: 12377--12554 Score: 54
Period size: 8 Copynumber: 20.1 Consensus size: 8
12367 AAAAAGAAAG
12377 ATAAAAAA
1 ATAAAAAA
12385 GATAAAAAA
1 -ATAAAAAA
12394 AT-AAAAA
1 ATAAAAAA
*
12401 ATCCAAAACATT
1 AT--AAAA-A-A
12413 ATAAAAAA
1 ATAAAAAA
* *
12421 TTTATGAAAAT
1 ---ATAAAAAA
*
12432 ATAAATAA
1 ATAAAAAA
* *
12440 AGAAAGAA
1 ATAAAAAA
12448 ATAAAAAA
1 ATAAAAAA
*
12456 ATAAAATA
1 ATAAAAAA
*
12464 AGAAAAAA
1 ATAAAAAA
12472 TATAAAATGTAA
1 -ATAAAA---AA
12484 ATAAACAAA
1 ATAAA-AAA
12493 ATACAATAAAA
1 AT--AA-AAAA
12504 ATATAAAAA
1 ATA-AAAAA
* *
12513 GTAAGAAA
1 ATAAAAAA
12521 ATAAAAATA
1 ATAAAAA-A
**
12530 ATGAATCAA
1 AT-AAAAAA
*
12539 A-ACAAAA
1 ATAAAAAA
12546 ATAAAAAA
1 ATAAAAAA
12554 A
1 A
12555 GACAAAAATT
Statistics
Matches: 124, Mismatches: 25, Indels: 41
0.65 0.13 0.22
Matches are distributed among these distances:
7 11 0.09
8 47 0.38
9 30 0.24
10 11 0.09
11 19 0.15
12 6 0.05
ACGTcount: A:0.73, C:0.04, G:0.05, T:0.18
Consensus pattern (8 bp):
ATAAAAAA
Found at i:12459 original size:24 final size:23
Alignment explanation
Indices: 12427--12554 Score: 82
Period size: 24 Copynumber: 5.3 Consensus size: 23
12417 AAAATTTATG
*
12427 AAAATATAAATAAAGAAAGAAATA
1 AAAAAATAAATAAAGAAA-AAATA
12451 AAAAAATAAA-ATAAGAAAAAATA
1 AAAAAATAAATA-AAGAAAAAATA
** * * *
12474 TAAAATGTAAATAAACAAAATACA
1 -AAAAAATAAATAAAGAAAAAATA
12498 ATAAAAATATAA-AAAGTAAGAAAATA
1 A-AAAAATA-AATAAAG-AA-AAAATA
*
12524 AAAATAATGAATCAAA-ACAAAAATA
1 AAAA-AATAAAT-AAAGA-AAAAATA
12549 AAAAAA
1 AAAAAA
12555 GACAAAAATT
Statistics
Matches: 81, Mismatches: 12, Indels: 22
0.70 0.10 0.19
Matches are distributed among these distances:
23 7 0.09
24 41 0.51
25 21 0.26
26 9 0.11
27 3 0.04
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (23 bp):
AAAAAATAAATAAAGAAAAAATA
Found at i:12462 original size:25 final size:24
Alignment explanation
Indices: 12427--12554 Score: 86
Period size: 25 Copynumber: 5.2 Consensus size: 24
12417 AAAATTTATG
12427 AAAATATAAATAAAGAAAGAAATAAA
1 AAAATATAAAT-AAGAAA-AAATAAA
*
12453 AAAATA-AAATAAGAAAAAAT-AT
1 AAAATATAAATAAGAAAAAATAAA
* *
12475 AAAATGTAAATAA-ACAAAATACAATA
1 AAAATATAAATAAGA-AAAA-ATAA-A
12501 AAAATATAAA-AAGTAAGAAAATAAA
1 AAAATATAAATAAG-AA-AAAATAAA
* * *
12526 AATA-ATGAATCAAAACAAAAATAAA
1 AAAATATAAAT-AAGA-AAAAATAAA
12551 AAAA
1 AAAA
12555 GACAAAAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
22 7 0.09
23 14 0.17
24 11 0.14
25 23 0.28
26 22 0.27
27 4 0.05
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (24 bp):
AAAATATAAATAAGAAAAAATAAA
Found at i:12466 original size:20 final size:20
Alignment explanation
Indices: 12434--12512 Score: 55
Period size: 20 Copynumber: 4.1 Consensus size: 20
12424 ATGAAAATAT
12434 AAATAAAGA-AAGAAATAAAA
1 AAATAAA-ATAAGAAATAAAA
12454 AAATAAAATAAG--A-AAAA
1 AAATAAAATAAGAAATAAAA
*
12471 ATATAAAAT--GTAAATAAACA
1 AAATAAAATAAG-AAATAAA-A
*
12491 AAATACAATAA-AAATATAAA
1 AAATAAAATAAGAAATA-AAA
12511 AA
1 AA
12513 GTAAGAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 18
0.69 0.04 0.26
Matches are distributed among these distances:
15 1 0.02
17 12 0.26
18 2 0.04
19 4 0.09
20 26 0.55
21 2 0.04
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (20 bp):
AAATAAAATAAGAAATAAAA
Found at i:12554 original size:50 final size:46
Alignment explanation
Indices: 12427--12554 Score: 116
Period size: 48 Copynumber: 2.6 Consensus size: 46
12417 AAAATTTATG
*
12427 AAAATATAAATAAAGAAAGAAATAAAAAAATAAAATAAGAAAAAATAT
1 AAAATATAAATAAA-CAA-AAATAAAAAAATAAAATAAGAAAAAATAT
* *
12475 AAAATGTAAATAAACAAAATACAATAAAAATATAAA-AAGTAAGAAAATA-
1 AAAATATAAATAAACAAAA-ATAA-AAAAATA-AAATAAG-AA-AAAATAT
*
12524 AAAATAATGAATCAAAACAAAAATAAAAAAA
1 AAAAT-ATAAAT--AAACAAAAATAAAAAAA
12555 GACAAAAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
46 2 0.03
47 5 0.08
48 23 0.35
49 10 0.15
50 15 0.23
51 3 0.05
52 8 0.12
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (46 bp):
AAAATATAAATAAACAAAAATAAAAAAATAAAATAAGAAAAAATAT
Found at i:13457 original size:23 final size:22
Alignment explanation
Indices: 13419--13577 Score: 61
Period size: 23 Copynumber: 6.7 Consensus size: 22
13409 AAAAAATAGG
* * *
13419 AAAAAAAAAGACAAAATAAGAA
1 AAAAAAAAATAAAAAATAACAA
* * *
13441 AATGAAAAAATAAAAAAGATTCAA
1 AA-AAAAAAATAAAAAATA-ACAA
13465 AAAAAAAAATAAAAAATAA-ATGA
1 AAAAAAAAATAAAAAATAACA--A
* **
13488 AAAAATAAATTAAGTAAAAATATTAA
1 AAAAA-AAAAT-A--AAAAATAACAA
* * *
13514 TATAAAAGA-AAAAAATAAACAA
1 AAAAAAAAATAAAAAAT-AACAA
* *
13536 AAACAAAAAATAAAAAAGGAAGAA
1 AAA-AAAAAATAAAAAA-TAACAA
13560 AATAAAAAAATATAAAAA
1 AA-AAAAAAATA-AAAAA
13578 GACGAAGTGA
Statistics
Matches: 100, Mismatches: 22, Indels: 27
0.67 0.15 0.18
Matches are distributed among these distances:
21 7 0.07
22 6 0.06
23 38 0.38
24 28 0.28
25 9 0.09
26 4 0.04
27 7 0.07
28 1 0.01
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (22 bp):
AAAAAAAAATAAAAAATAACAA
Found at i:13458 original size:30 final size:29
Alignment explanation
Indices: 13409--13484 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
13399 AAAATAGAAC
**
13409 AAAAAATAGGAAA-AAAAAAGA-CAAAATA
1 AAAAAATAAAAAATAAAAAAGATCAAAA-A
*
13437 AGAAAATGAAAAAATAAAAAAGATTCAAAAA
1 AAAAAAT-AAAAAATAAAAAAGA-TCAAAAA
13468 AAAAAATAAAAAATAAA
1 AAAAAATAAAAAATAAA
13485 TGAAAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 6 0.15
29 4 0.10
30 18 0.45
31 7 0.17
32 5 0.12
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.11
Consensus pattern (29 bp):
AAAAAATAAAAAATAAAAAAGATCAAAAA
Found at i:13490 original size:24 final size:23
Alignment explanation
Indices: 13419--13577 Score: 74
Period size: 24 Copynumber: 6.7 Consensus size: 23
13409 AAAAAATAGG
* *
13419 AAAAAAAAAGACAAAAT-AAGAA
1 AAAAAAAAATAAAAAATAAAGAA
* * ***
13441 AATGAAAAAATAAAAAAGATTCAA
1 AA-AAAAAAATAAAAAATAAAGAA
13465 AAAAAAAAATAAAAAATAAATGAA
1 AAAAAAAAATAAAAAATAAA-GAA
**
13489 AAAATAAATTAAGT-AAAAAT-ATTAA
1 AAAA-AAA--AA-TAAAAAATAAAGAA
* * * *
13514 TATAAAAGA-AAAAAATAAACAA
1 AAAAAAAAATAAAAAATAAAGAA
**
13536 AAACAAAAAATAAAAAAGGAAGAA
1 AAA-AAAAAATAAAAAATAAAGAA
13560 AATAAAAAAATATAAAAA
1 AA-AAAAAAATA-AAAAA
13578 GACGAAGTGA
Statistics
Matches: 99, Mismatches: 25, Indels: 23
0.67 0.17 0.16
Matches are distributed among these distances:
21 6 0.06
22 7 0.07
23 30 0.30
24 33 0.33
25 13 0.13
26 1 0.01
27 8 0.08
28 1 0.01
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (23 bp):
AAAAAAAAATAAAAAATAAAGAA
Found at i:13849 original size:26 final size:26
Alignment explanation
Indices: 13830--13882 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
13820 AAAAAGCAAG
13830 AAAAAAT-AAAAAAATTAAAATACAA
1 AAAAAATAAAAAAAATTAAAATACAA
* *
13855 AATATATAAAAAAAATT-AAA-ACAA
1 AAAAAATAAAAAAAATTAAAATACAA
13879 AAAA
1 AAAA
13883 GAGAAAGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
24 7 0.29
25 8 0.33
26 9 0.38
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (26 bp):
AAAAAATAAAAAAAATTAAAATACAA
Found at i:14138 original size:1 final size:1
Alignment explanation
Indices: 14134--14166 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
14124 GGAAAAAGAT
*
14134 AAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14167 TAAAGAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:14792 original size:19 final size:17
Alignment explanation
Indices: 14770--14830 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 17
14760 ATGAAAATAT
14770 AAATAAAGAAAGAAATTAA
1 AAATAAAGAAAGAAA--AA
14789 AAATAAA-ATAAGAAAAA
1 AAATAAAGA-AAGAAAAA
14806 AATATTAAAGAAA-AAAAA
1 AA-A-TAAAGAAAGAAAAA
14824 AAATAAA
1 AAATAAA
14831 AATAAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
16 4 0.11
17 5 0.13
18 9 0.24
19 19 0.50
20 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.15
Consensus pattern (17 bp):
AAATAAAGAAAGAAAAA
Found at i:14801 original size:23 final size:25
Alignment explanation
Indices: 14763--14808 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
14753 AAAATTTATG
*
14763 AAAATATAAATAAAGAAAGAAATTA
1 AAAATATAAATAAAGAAAAAAATTA
14788 AAAATA-AAAT-AAGAAAAAAAT
1 AAAATATAAATAAAGAAAAAAAT
14809 ATTAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 4 0.20
25 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (25 bp):
AAAATATAAATAAAGAAAAAAATTA
Found at i:14808 original size:41 final size:40
Alignment explanation
Indices: 14763--14844 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 40
14753 AAAATTTATG
* * *
14763 AAAATA-TAAATAAAGAAAGAAATTAAAAATAAAATAAGAAA
1 AAAATATTAAAGAAA-AAAAAAAATAAAAAT-AAATAAGAAA
*
14804 AAAATATTAAAGAAAAAAAAAAATAAAAATAAATAATAAA
1 AAAATATTAAAGAAAAAAAAAAATAAAAATAAATAAGAAA
14844 A
1 A
14845 TATAAAAGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
40 10 0.28
41 19 0.53
42 7 0.19
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (40 bp):
AAAATATTAAAGAAAAAAAAAAATAAAAATAAATAAGAAA
Found at i:14821 original size:30 final size:29
Alignment explanation
Indices: 14787--14843 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
14777 GAAAGAAATT
* *
14787 AAAAATAAAATAAGAAAAAAATATTAAAGA
1 AAAAAAAAAATAA-AAAAAAATAATAAAGA
*
14817 AAAAAAAAAATAAAAATAAATAATAAA
1 AAAAAAAAAATAAAAAAAAATAATAAA
14844 ATATAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.16
Consensus pattern (29 bp):
AAAAAAAAAATAAAAAAAAATAATAAAGA
Found at i:14861 original size:37 final size:35
Alignment explanation
Indices: 14787--14862 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 35
14777 GAAAGAAATT
*
14787 AAAAATAAAATAAGAAAAAAATATTAAAGAAAAAA
1 AAAAATAAAATAAGAAAAAAATATAAAAGAAAAAA
* *
14822 AAAAATAAAAATAA-ATAATAAAATATAAAAGTAAGAA
1 AAAAAT-AAAATAAGA-AA-AAAATATAAAAGAAAAAA
14859 AAAA
1 AAAA
14863 GGCAAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 7 0.20
36 9 0.26
37 19 0.54
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (35 bp):
AAAAATAAAATAAGAAAAAAATATAAAAGAAAAAA
Found at i:15270 original size:17 final size:19
Alignment explanation
Indices: 15244--15281 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
15234 ATATTAAAGT
15244 AAAACAAAAA-A-AATAAA
1 AAAACAAAAATACAATAAA
*
15261 AAAACGAAAATACAATAAA
1 AAAACAAAAATACAATAAA
15280 AA
1 AA
15282 TATAAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 1 0.06
19 8 0.44
ACGTcount: A:0.82, C:0.08, G:0.03, T:0.08
Consensus pattern (19 bp):
AAAACAAAAATACAATAAA
Found at i:15288 original size:41 final size:39
Alignment explanation
Indices: 15180--15288 Score: 98
Period size: 39 Copynumber: 2.7 Consensus size: 39
15170 TATGAAAATT
* *
15180 TAAATAAAGAAAGA-AATAAAAAATAAACCAAAATAAAAA
1 TAAAAAAAGAAA-ACAATAAAAAATAAAACAAAATAAAAA
* * *
15219 TAAAATAAGAAAACAATATTAAAGTAAAAC-AAA-AAAAA
1 TAAAAAAAGAAAACAATA-AAAAATAAAACAAAATAAAAA
15257 TAAAAAAACGAAAATACAATAAAAATATAAAA
1 TAAAAAAA-G-AAA-ACAATAAAAA-ATAAAA
15289 GGTAAGATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
38 13 0.23
39 18 0.32
40 14 0.25
41 11 0.20
ACGTcount: A:0.75, C:0.06, G:0.05, T:0.15
Consensus pattern (39 bp):
TAAAAAAAGAAAACAATAAAAAATAAAACAAAATAAAAA
Found at i:15585 original size:25 final size:23
Alignment explanation
Indices: 15557--15602 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
15547 AAAATAAAAG
15557 ACCAAAAAATAAAATAAAGTCAATC
1 ACCAAAAAAT-AAATAAA-TCAATC
*
15582 ACCAAAATATAAATAAATCAA
1 ACCAAAAAATAAATAAATCAA
15603 AAGGAAGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 7 0.35
25 9 0.45
ACGTcount: A:0.65, C:0.15, G:0.02, T:0.17
Consensus pattern (23 bp):
ACCAAAAAATAAATAAATCAATC
Found at i:16135 original size:17 final size:17
Alignment explanation
Indices: 16091--16136 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
16081 AAAAATGAGT
*
16091 TAAAA-GAAAAAATTAA
1 TAAAATGAAAAAACTAA
*
16107 AAAAAT-ACAAAAACTAA
1 TAAAATGA-AAAAACTAA
16124 TAAAATGAAAAAA
1 TAAAATGAAAAAA
16137 GGAAAAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
16 5 0.21
17 18 0.75
18 1 0.04
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (17 bp):
TAAAATGAAAAAACTAA
Found at i:16997 original size:22 final size:22
Alignment explanation
Indices: 16969--17030 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
16959 CAAATTTTAT
*
16969 TAAATAAAGATAAATTACACGA
1 TAAATAAAGATAAATTACAAGA
* *
16991 TAAATAAAAATAAATTTCAAGA
1 TAAATAAAGATAAATTACAAGA
*
17013 TAAAATACAAGATGAATT
1 T-AAATA-AAGATAAATT
17031 TAATTAGATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 20 0.61
23 5 0.15
24 8 0.24
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (22 bp):
TAAATAAAGATAAATTACAAGA
Found at i:17922 original size:24 final size:23
Alignment explanation
Indices: 17895--17942 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
17885 AATAAAGAAG
17895 ATAAAATAAAAATAAAGAAAAAAT
1 ATAAAATAAAAAT-AAGAAAAAAT
** *
17919 ATAAAATGTAAATAAGCAAAAAT
1 ATAAAATAAAAATAAGAAAAAAT
17942 A
1 A
17943 CATAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (23 bp):
ATAAAATAAAAATAAGAAAAAAT
Found at i:17974 original size:34 final size:33
Alignment explanation
Indices: 17897--17974 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
17887 TAAAGAAGAT
*
17897 AAAAT-AAAAATAAAGAAAAAATATAAAATGTA
1 AAAATGAAAAATAAAGAAAAAATATAAAAAGTA
* *
17929 AATAA-GCAAAAATACATAAAAAATATAAAAAGTA
1 AA-AATG-AAAAATAAAGAAAAAATATAAAAAGTA
17963 AGAAATGAAAAA
1 A-AAATGAAAAA
17975 ATAATGAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
32 2 0.05
33 2 0.05
34 32 0.84
35 2 0.05
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.17
Consensus pattern (33 bp):
AAAATGAAAAATAAAGAAAAAATATAAAAAGTA
Found at i:18475 original size:28 final size:26
Alignment explanation
Indices: 18405--18477 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 26
18395 CAAATAAAAT
* *
18405 AAAATA-AAAAAGAATATTAAAAAGA
1 AAAATACAAAAAGAATATAAAAAACA
*
18430 TAAA-ACAAAAA-AA-ATAAAAACACA
1 AAAATACAAAAAGAATATAAAAA-ACA
18454 AAAATACAATAAAGAATATAAAAA
1 AAAATACAA-AAAGAATATAAAAA
18478 GTAAGAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
23 6 0.16
24 8 0.21
25 12 0.32
26 3 0.08
27 2 0.05
28 7 0.18
ACGTcount: A:0.77, C:0.05, G:0.04, T:0.14
Consensus pattern (26 bp):
AAAATACAAAAAGAATATAAAAAACA
Found at i:18949 original size:8 final size:7
Alignment explanation
Indices: 18938--19064 Score: 69
Period size: 7 Copynumber: 16.6 Consensus size: 7
18928 AAAAAAAGAC
18938 AAAATAA
1 AAAATAA
18945 GAAAATGAA
1 -AAAAT-AA
18954 AAAATAAA
1 AAAAT-AA
18962 AAAGATTCAA
1 AAA-A-T-AA
18972 AAAAT-A
1 AAAATAA
18978 AAAATAA
1 AAAATAA
18985 AAAATAA
1 AAAATAA
*
18992 ATTAATAA
1 A-AAATAA
*
19000 AAAATATT
1 AAAATA-A
*
19008 AATATAA
1 AAAATAA
19015 AAGAA-AA
1 AA-AATAA
*
19022 AAATAAACA
1 AAA-ATA-A
*
19031 AAAACAA
1 AAAATAA
19038 AAAATAA
1 AAAATAA
*
19045 AAAAGGAA
1 AAAA-TAA
19053 GAAAATAA
1 -AAAATAA
19061 AAAA
1 AAAA
19065 ATTAGCTAAT
Statistics
Matches: 95, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
6 7 0.07
7 35 0.37
8 35 0.37
9 12 0.13
10 6 0.06
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:18998 original size:15 final size:13
Alignment explanation
Indices: 18970--19047 Score: 68
Period size: 13 Copynumber: 5.9 Consensus size: 13
18960 AAAAAGATTC
18970 AAAAAATAAAAAT
1 AAAAAATAAAAAT
18983 AAAAAATAAATTAAT
1 AAAAAATAAA--AAT
**
18998 AAAAAATATTAAT
1 AAAAAATAAAAAT
* *
19011 ATAAAAGAAAAA-
1 AAAAAATAAAAAT
* * *
19023 AATAAACAAAAAC
1 AAAAAATAAAAAT
19036 AAAAAATAAAAA
1 AAAAAATAAAAA
19048 AGGAAGAAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
12 9 0.18
13 31 0.61
15 11 0.22
ACGTcount: A:0.79, C:0.03, G:0.01, T:0.17
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:19834 original size:111 final size:107
Alignment explanation
Indices: 19737--19944 Score: 235
Period size: 112 Copynumber: 1.9 Consensus size: 107
19727 AAAAACTAAT
19737 AAAAATGAAAA-AAATG-GCAAAATAGAAAAAAA-TTAAGTTTACAAAATACAAACAAAAAATAA
1 AAAAATGAAAAGAAATGAG-AAAATAGAAAAAAATTTAA-TTTACAAAATACAAAC-AAAAATAA
* * *
19799 TAAG-ATATAAAGATATAAAAAATCAAAGATAAAAAATTAAAAGAAGTTC
63 T--GTA-AT-AAGAAAAAAAAAATCAAAGATAAAAAA-TAAAAGAACTTC
** * * *
19848 AAAAATGAAAAGGGATGAGAAAGTAGAAAAAAATTTAATTTAGAAAATACAAGCAAAAATAATGT
1 AAAAATGAAAAGAAATGAGAAAATAGAAAAAAATTTAATTTACAAAATACAAACAAAAATAATGT
19913 AATAAGAAAAAAAAAATCAAAGATACAAAAAT
66 AATAAGAAAAAAAAAATCAAAGATA-AAAAAT
19945 TAACAGAGGG
Statistics
Matches: 85, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
108 21 0.25
109 8 0.09
110 1 0.01
111 20 0.24
112 30 0.35
113 5 0.06
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (107 bp):
AAAAATGAAAAGAAATGAGAAAATAGAAAAAAATTTAATTTACAAAATACAAACAAAAATAATGT
AATAAGAAAAAAAAAATCAAAGATAAAAAATAAAAGAACTTC
Found at i:20153 original size:22 final size:23
Alignment explanation
Indices: 20110--20153 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
20100 AGAAAATTTT
*
20110 AAAACAAAGAAAAAAGTGAAAAC
1 AAAACAAAGAAAAAAGTAAAAAC
20133 AAAA-AAA-AAAATAAGTAAAAA
1 AAAACAAAGAAAA-AAGTAAAAA
20154 AAGGAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.80, C:0.05, G:0.09, T:0.07
Consensus pattern (23 bp):
AAAACAAAGAAAAAAGTAAAAAC
Found at i:20314 original size:10 final size:9
Alignment explanation
Indices: 20293--20376 Score: 60
Period size: 10 Copynumber: 8.6 Consensus size: 9
20283 TAAAGAAATT
20293 AAAAATAAA
1 AAAAATAAA
* *
20302 AATAAGAAA
1 AAAAATAAA
*
20311 AAATATTAAA
1 AAA-AATAAA
20321 GAAAAATAAA
1 -AAAAATAAA
20331 ATAAAATAAA
1 A-AAAATAAA
20341 CAAAAATACAA
1 -AAAAATA-AA
*
20352 TAAAAATATA
1 -AAAAATAAA
*
20362 AAAAGTAAGA
1 AAAAATAA-A
20372 AAAAA
1 AAAAA
20377 AAAGGCAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
9 16 0.28
10 29 0.50
11 13 0.22
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.15
Consensus pattern (9 bp):
AAAAATAAA
Found at i:20336 original size:25 final size:23
Alignment explanation
Indices: 20273--20376 Score: 59
Period size: 25 Copynumber: 4.2 Consensus size: 23
20263 AAAATTTATG
*
20273 AAAATATAAATAAAGAAATTAAAA
1 AAAATA-AAATAAAAAAATTAAAA
*
20297 ATAAA-AATAAGAAAAAATATTAAAGA
1 A-AAATAA-AATAAAAAA-ATTAAA-A
*
20323 AAAATAAAATAAAATAAA-CAAAA
1 AAAATAAAATAAAA-AAATTAAAA
* *
20346 ATACAATAAAAATATAAAAAGTAAGAA
1 A-A-AAT-AAAATAAAAAAATTAA-AA
20373 AAAA
1 AAAA
20377 AAAGGCAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
23 3 0.05
24 13 0.21
25 27 0.43
26 17 0.27
27 3 0.05
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (23 bp):
AAAATAAAATAAAAAAATTAAAA
Found at i:20379 original size:33 final size:31
Alignment explanation
Indices: 20293--20379 Score: 81
Period size: 30 Copynumber: 2.8 Consensus size: 31
20283 TAAAGAAATT
* *
20293 AAAA-ATAAAAATAAGAAAAAATATTAAAGA
1 AAAATATAAAAATAAGAAAAAAAAATAAAGA
* * *
20323 AAAATA-AAATAA-AATAAACAAAAATACAATA
1 AAAATATAAA-AATAAGAAAAAAAAATA-AAGA
20354 AAAATATAAAAAGTAAGAAAAAAAAA
1 AAAATATAAAAA-TAAGAAAAAAAAA
20380 GGCAAAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
30 17 0.39
31 14 0.32
32 3 0.07
33 10 0.23
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (31 bp):
AAAATATAAAAATAAGAAAAAAAAATAAAGA
Found at i:20776 original size:8 final size:8
Alignment explanation
Indices: 20765--20950 Score: 50
Period size: 8 Copynumber: 23.6 Consensus size: 8
20755 AAGTAAAACA
20765 AAAAAAAT
1 AAAAAAAT
*
20773 AAAAAAACG
1 AAAAAAA-T
20782 AAAATACAAT
1 AAAA-A-AAT
*
20792 AAAAATAT
1 AAAAAAAT
**
20800 -AAAAGGT
1 AAAAAAAT
* *
20807 AAGATAAT
1 AAAAAAAT
20815 AAAAAAAT
1 AAAAAAAT
**
20823 -AATTAAT
1 AAAAAAAT
*
20830 -CAAAAAT
1 AAAAAAAT
*
20837 ACAAAAATT
1 A-AAAAAAT
*
20846 GAAAAAA-
1 AAAAAAAT
*
20853 AATAAAAT
1 AAAAAAAT
* *
20861 AAAATACT
1 AAAAAAAT
20869 AAAAAAAT
1 AAAAAAAT
*
20877 --AACAAT
1 AAAAAAAT
*
20883 -TAAAAAT
1 AAAAAAAT
20890 AAACAAAA-
1 AAA-AAAAT
*
20898 ACAAAAAGT
1 A-AAAAAAT
*
20907 AAAAAAGT
1 AAAAAAAT
*
20915 AAGAAAAT
1 AAAAAAAT
20923 -AAAAAAT
1 AAAAAAAT
* *
20930 -AGAGAAT
1 AAAAAAAT
20937 AAAAAAAT
1 AAAAAAAT
20945 ATAAAA
1 A-AAAA
20951 CGATAAAATG
Statistics
Matches: 126, Mismatches: 38, Indels: 27
0.66 0.20 0.14
Matches are distributed among these distances:
6 5 0.04
7 35 0.28
8 58 0.46
9 21 0.17
10 5 0.04
11 2 0.02
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.16
Consensus pattern (8 bp):
AAAAAAAT
Found at i:20785 original size:17 final size:19
Alignment explanation
Indices: 20759--20796 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
20749 ATATTAAAGT
20759 AAAACAAAAA-A-AATAAA
1 AAAACAAAAATACAATAAA
*
20776 AAAACGAAAATACAATAAA
1 AAAACAAAAATACAATAAA
20795 AA
1 AA
20797 TATAAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 1 0.06
19 8 0.44
ACGTcount: A:0.82, C:0.08, G:0.03, T:0.08
Consensus pattern (19 bp):
AAAACAAAAATACAATAAA
Found at i:20937 original size:14 final size:16
Alignment explanation
Indices: 20901--20942 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
20891 AACAAAAACA
20901 AAAAGTAAAAAAGTAAG
1 AAAA-TAAAAAAGTAAG
20918 AAAATAAAAAA-T-AG
1 AAAATAAAAAAGTAAG
*
20932 AGAATAAAAAA
1 AAAATAAAAAA
20943 ATATAAAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 12 0.50
15 1 0.04
16 7 0.29
17 4 0.17
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAATAAAAAAGTAAG
Found at i:21081 original size:23 final size:23
Alignment explanation
Indices: 21010--21109 Score: 69
Period size: 23 Copynumber: 4.2 Consensus size: 23
21000 TTAGAATATA
* *
21010 CAAAGA-AAAACAAAAAAAAAAAA
1 CAAAGACAAAA-AAAAAATAAAAT
* *
21033 CAAATGTAGAAAAAAAGACATAAAAAT
1 CAAA-G-ACAAAAAAA-AAAT-AAAAT
21060 CAAAGACAAAAAAAAAATAAAAGT
1 CAAAGACAAAAAAAAAATAAAA-T
* * *
21084 C-AATACAAAATATAAATAAAAT
1 CAAAGACAAAAAAAAAATAAAAT
21106 CAAA
1 CAAA
21110 AGGAAGTTCA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
22 2 0.03
23 27 0.44
24 6 0.10
25 12 0.19
26 7 0.11
27 8 0.13
ACGTcount: A:0.74, C:0.09, G:0.06, T:0.11
Consensus pattern (23 bp):
CAAAGACAAAAAAAAAATAAAAT
Found at i:22107 original size:18 final size:18
Alignment explanation
Indices: 22071--22121 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
22061 TATAAAAAGT
**
22071 AAAAAAAAAAAAACAAAA
1 AAAAAAAAAAAAATTAAA
22089 AAAAAAAAAAAAATTAAA
1 AAAAAAAAAAAAATTAAA
* **
22107 AGAAATTAAAAAATT
1 AAAAAAAAAAAAATT
22122 CTACAAAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.12
Consensus pattern (18 bp):
AAAAAAAAAAAAATTAAA
Found at i:22119 original size:1 final size:1
Alignment explanation
Indices: 22071--22101 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
22061 TATAAAAAGT
*
22071 AAAAAAAAAAAAACAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22102 TTAAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22475 original size:22 final size:23
Alignment explanation
Indices: 22437--22498 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
22427 CAAATTTTAT
*
22437 TAAATAAAAGATAAATTACACGA
1 TAAATAAAAGATAAATTACAAGA
*
22460 TAAATAAAA-ATAAATTTCAAGA
1 TAAATAAAAGATAAATTACAAGA
*
22482 TAAA-AACAAGATGAATT
1 TAAATAA-AAGATAAATT
22499 TAATTAGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.06
22 17 0.50
23 15 0.44
ACGTcount: A:0.61, C:0.06, G:0.08, T:0.24
Consensus pattern (23 bp):
TAAATAAAAGATAAATTACAAGA
Done.