Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2039
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: 245426
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
File 1 of 2
Found at i:965 original size:2 final size:2
Alignment explanation
Indices: 958--999 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
948 GAGTAGAGCC
958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1000 TAAGACTACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1278 original size:27 final size:27
Alignment explanation
Indices: 1236--1319 Score: 72
Period size: 27 Copynumber: 3.1 Consensus size: 27
1226 AAAAAAATTA
1236 AAATATTTATTT--TTAAATTAATATTT
1 AAATATTT-TTTAATTAAATTAATATTT
1262 AAATATTTTTTAATTAAATTTAA-A--T
1 AAATATTTTTTAATTAAA-TTAATATTT
*
1287 AAATTTTTTTATTAATTAAA-TAATAATTT
1 AAA-TATTTT-TTAATTAAATTAAT-ATTT
1316 AAAT
1 AAAT
1320 TAAGTTGATA
Statistics
Matches: 48, Mismatches: 1, Indels: 16
0.74 0.02 0.25
Matches are distributed among these distances:
25 10 0.21
26 13 0.27
27 16 0.33
28 5 0.10
29 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
AAATATTTTTTAATTAAATTAATATTT
Found at i:1282 original size:21 final size:21
Alignment explanation
Indices: 1243--1308 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
1233 TTAAAATATT
*
1243 TATTTTTAAATTAATATTTAAA
1 TATTTTTTAATTAA-ATTTAAA
1265 TATTTTTTAATTAAATTTAAA
1 TATTTTTTAATTAAATTTAAA
*
1286 TAAATTTTTTTATT-AA-TTAAA
1 T--ATTTTTTAATTAAATTTAAA
1307 TA
1 TA
1309 ATAATTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.03
21 14 0.35
22 15 0.38
23 10 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTTTTAATTAAATTTAAA
Found at i:1315 original size:23 final size:23
Alignment explanation
Indices: 1244--1309 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 23
1234 TAAAATATTT
*
1244 ATTTTTAAATTAATATTTAAAT--
1 ATTTTTTAATTAA-ATTTAAATAA
1266 ATTTTTTAATTAAATTTAAATAA
1 ATTTTTTAATTAAATTTAAATAA
*
1289 ATTTTTTTATT-AA-TTAAATAA
1 ATTTTTTAATTAAATTTAAATAA
1310 TAATTTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
21 16 0.40
22 14 0.35
23 10 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTTTTAATTAAATTTAAATAA
Found at i:2032 original size:24 final size:24
Alignment explanation
Indices: 2005--2101 Score: 79
Period size: 24 Copynumber: 3.9 Consensus size: 24
1995 TCATAGTATA
*
2005 TAAATATATATATTATTATTACAT
1 TAAATATAAATATTATTATTACAT
* **
2029 TAAATATAAATGCATTTTTATTTTTATT
1 TAAATATAAAT--ATTATTA-TTACA-T
* *
2057 ATAAATATATATATGATTATTACAT
1 -TAAATATAAATATTATTATTACAT
*
2082 CAAATATAAATATT-TTATTA
1 TAAATATAAATATTATTATTA
2102 TATTTATTAT
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
23 6 0.11
24 21 0.38
25 1 0.02
26 9 0.16
27 8 0.14
28 1 0.02
29 10 0.18
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
TAAATATAAATATTATTATTACAT
Found at i:2108 original size:53 final size:52
Alignment explanation
Indices: 2003--2111 Score: 157
Period size: 53 Copynumber: 2.1 Consensus size: 52
1993 ATTCATAGTA
* * *
2003 TATAAATATATATATTATTATTACATTAAATATAAATGCATTTTTATTTTTAT
1 TATAAATATATATATGATTATTACATCAAATATAAAT-CATTTTTATATTTAT
2056 TATAAATATATATATGATTATTACATCAAATATAAAT-ATTTTATTATATTTAT
1 TATAAATATATATATGATTATTACATCAAATATAAATCA-TTT-TTATATTTAT
2109 TAT
1 TAT
2112 TTTTAAAATG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
51 1 0.02
52 3 0.06
53 47 0.92
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (52 bp):
TATAAATATATATATGATTATTACATCAAATATAAATCATTTTTATATTTAT
Found at i:2655 original size:3 final size:3
Alignment explanation
Indices: 2641--2683 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
2631 ACAAGAATTG
*
2641 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2684 AGTAGTAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2904 original size:20 final size:18
Alignment explanation
Indices: 2865--2913 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
2855 TAACTTTATA
* **
2865 ATTACTATTTAATAGGTT
1 ATTATTATTTAATAAATT
2883 ATTTATATATTTAATAAATT
1 A-TTAT-TATTTAATAAATT
2903 ATTATTATTTA
1 ATTATTATTTA
2914 TTTTATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 7 0.27
19 7 0.27
20 12 0.46
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (18 bp):
ATTATTATTTAATAAATT
Found at i:4622 original size:8 final size:8
Alignment explanation
Indices: 4596--4633 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
4586 TATTTACTAC
4596 AAAATAA-
1 AAAATAAG
4603 AAAATCAAG
1 AAAAT-AAG
4612 AAAATAAG
1 AAAATAAG
*
4620 AAAATAAA
1 AAAATAAG
4628 AAAATA
1 AAAATA
4634 TAATCACCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 5 0.18
8 18 0.64
9 5 0.18
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (8 bp):
AAAATAAG
Found at i:7112 original size:20 final size:20
Alignment explanation
Indices: 7075--7113 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7065 GGTTAACTTG
*
7075 TTTTTTATTTTTCAATTTAT
1 TTTTTTATTTATCAATTTAT
*
7095 TTTTTTATTTATCTATTTA
1 TTTTTTATTTATCAATTTA
7114 AACTTTAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTTATTTATCAATTTAT
Found at i:9505 original size:12 final size:12
Alignment explanation
Indices: 9488--9513 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9478 TTATATTTAC
9488 ATAATTAATTAA
1 ATAATTAATTAA
9500 ATAATTAATTAA
1 ATAATTAATTAA
9512 AT
1 AT
9514 TATCATTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATTAATTAA
Found at i:10423 original size:17 final size:17
Alignment explanation
Indices: 10397--10432 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
10387 TTTTTTGTAC
*
10397 ATATTAAAATATGAAAT
1 ATATTAAAATATCAAAT
*
10414 ATATTTAAATATCAAAT
1 ATATTAAAATATCAAAT
10431 AT
1 AT
10433 TGATGTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (17 bp):
ATATTAAAATATCAAAT
Found at i:11916 original size:18 final size:18
Alignment explanation
Indices: 11894--11953 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
11884 ACTCAAATTC
*
11894 ATGATTTTTAGAAAATCT
1 ATGATTTCTAGAAAATCT
*
11912 TTGATTTCTAGAAAATCT
1 ATGATTTCTAGAAAATCT
* *
11930 ATGATTTCTAAAAAATTT
1 ATGATTTCTAGAAAATCT
11948 ATGATT
1 ATGATT
11954 CTTAAAATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (18 bp):
ATGATTTCTAGAAAATCT
Found at i:13542 original size:24 final size:23
Alignment explanation
Indices: 13487--13539 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
13477 CTTATAAGTA
13487 TTATTTAATAAATAATTTATATAT
1 TTATTTAAT-AATAATTTATATAT
* *
13511 TTAATTAATAATAATTCTTTAT-T
1 TTATTTAATAATAATT-TATATAT
13534 TTATTT
1 TTATTT
13540 TAAAATATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATTTAATAATAATTTATATAT
Found at i:15038 original size:34 final size:34
Alignment explanation
Indices: 14992--15209 Score: 273
Period size: 34 Copynumber: 6.5 Consensus size: 34
14982 GTAAAAACCA
*
14992 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
15026 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
15060 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
15094 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
15127 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
15161 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
15194 CCATTTAATTAACAAT
1 CCATTTAATCAACAAT
15210 TCTCCCACTT
Statistics
Matches: 161, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 44 0.27
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:15106 original size:68 final size:67
Alignment explanation
Indices: 14990--15209 Score: 314
Period size: 67 Copynumber: 3.3 Consensus size: 67
14980 TGGTAAAAAC
* * *
14990 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
15055 AT
66 AT
* * *
15057 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
15122 AAT
65 AAT
* * * * * *
15125 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
15190 AT
66 AT
*
15192 CACCATTTAATTAACAAT
1 CACCATTTAATCAACAAT
15210 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 74 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:19303 original size:19 final size:19
Alignment explanation
Indices: 19276--19338 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
19266 TCACGTGTAC
* *
19276 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
19295 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
19314 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
19333 AGTACC
1 AGTACC
19339 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:19686 original size:34 final size:34
Alignment explanation
Indices: 19640--19855 Score: 269
Period size: 34 Copynumber: 6.4 Consensus size: 34
19630 GTAAAAACCA
*
19640 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
19674 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
19708 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
19742 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
19775 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
19809 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
19842 CCATTTAATTAACA
1 CCATTTAATCAACA
19856 GCTTGGAGCT
Statistics
Matches: 159, Mismatches: 18, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
33 42 0.26
34 115 0.72
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:19754 original size:68 final size:67
Alignment explanation
Indices: 19638--19855 Score: 310
Period size: 67 Copynumber: 3.2 Consensus size: 67
19628 TGGTAAAAAC
* * *
19638 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
19703 AT
66 AT
* * *
19705 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
19770 AAT
65 AAT
* * * * * *
19773 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
19838 AT
66 AT
*
19840 CACCATTTAATTAACA
1 CACCATTTAATCAACA
19856 GCTTGGAGCT
Statistics
Matches: 133, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 72 0.54
68 61 0.46
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:20611 original size:4 final size:4
Alignment explanation
Indices: 20604--20631 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
20594 ATACATACAA
20604 GCAG GCAG GCAG GCAG GCAG GCAG GCAG
1 GCAG GCAG GCAG GCAG GCAG GCAG GCAG
20632 ACTGAGTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.50, T:0.00
Consensus pattern (4 bp):
GCAG
Found at i:23329 original size:30 final size:30
Alignment explanation
Indices: 23254--23331 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 30
23244 CAACCTACTA
*
23254 TTTAAATAATAAATATTTTATTTAAATTAAT
1 TTTAAATAAAAAATA-TTTATTTAAATTAAT
*
23285 ATTAATATAAAAAATATTT-TTTAATATT-AT
1 TTTAA-ATAAAAAATATTTATTTAA-ATTAAT
23315 TTTAAATAACAAAATAT
1 TTTAAATAA-AAAATAT
23332 GGTTTCAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 4 0.10
30 18 0.44
31 10 0.24
32 9 0.22
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
TTTAAATAAAAAATATTTATTTAAATTAAT
Found at i:23525 original size:2 final size:2
Alignment explanation
Indices: 23518--23556 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
23508 AAATAGAACA
23518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23557 AATTTACTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23788 original size:24 final size:25
Alignment explanation
Indices: 23733--23791 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
23723 ATTTTAATAT
* * *
23733 ATATTTTGAATTTATTAAATTTTAA
1 ATATTTTTAATTTATTAAATATAAA
*
23758 ATATTTTTAATTTA-TATATATAAA
1 ATATTTTTAATTTATTAAATATAAA
23782 ATATTTTTAA
1 ATATTTTTAA
23792 ATATGAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 17 0.57
25 13 0.43
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
ATATTTTTAATTTATTAAATATAAA
Found at i:26284 original size:23 final size:23
Alignment explanation
Indices: 26258--26314 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
26248 TGGGCATGTT
26258 AAAAATGCATGAAACATAACAAA
1 AAAAATGCATGAAACATAACAAA
*
26281 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAACAAA
26304 AAAAATGCATG
1 AAAAATGCATG
26315 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.16
Consensus pattern (23 bp):
AAAAATGCATGAAACATAACAAA
Found at i:27273 original size:20 final size:20
Alignment explanation
Indices: 27226--27300 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
27216 AAAAAGACAT
*
27226 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
27245 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
27266 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
27286 AATGTATCGATACAT
1 AATGTATCGATACAT
27301 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:27294 original size:40 final size:39
Alignment explanation
Indices: 27223--27300 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
27213 GGTAAAAAGA
* *
27223 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
27262 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
27301 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:27680 original size:27 final size:25
Alignment explanation
Indices: 27636--27687 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
27626 ATACGATCGA
27636 TATTAAAATTAAAATAATACTAAAAAT
1 TATTAAAATTAAAATAAT--TAAAAAT
**
27663 TATTAAAATTAATTTAATTAAAAAT
1 TATTAAAATTAAAATAATTAAAAAT
27688 CAATATCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
27 16 0.70
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
TATTAAAATTAAAATAATTAAAAAT
Found at i:28190 original size:27 final size:26
Alignment explanation
Indices: 28160--28238 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 26
28150 TATAATTATA
28160 TTTAAAATATTTTATATTTATATAAAT
1 TTTAAAATATTTTATA-TTATATAAAT
* *
28187 TTTATTAATAATTTATATTATATAAAT
1 TTTA-AAATATTTTATATTATATAAAT
*
28214 TTTAAAATA-TTTATATAATA-AAAT
1 TTTAAAATATTTTATATTATATAAAT
28238 T
1 T
28239 ATTTTTATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
24 5 0.11
25 10 0.21
26 4 0.09
27 18 0.38
28 10 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTAAAATATTTTATATTATATAAAT
Found at i:28217 original size:16 final size:15
Alignment explanation
Indices: 28170--28215 Score: 62
Period size: 13 Copynumber: 3.2 Consensus size: 15
28160 TTTAAAATAT
28170 TTTATATTTATATAAA
1 TTTATA-TTATATAAA
28186 TTT-TATTA-AT-AA
1 TTTATATTATATAAA
28198 TTTATATTATATAAA
1 TTTATATTATATAAA
28213 TTT
1 TTT
28216 TAAAATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.19
13 7 0.26
14 5 0.19
15 7 0.26
16 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTATATTATATAAA
Found at i:28242 original size:27 final size:27
Alignment explanation
Indices: 28144--28243 Score: 86
Period size: 25 Copynumber: 3.7 Consensus size: 27
28134 TATATTTTTA
28144 TTATATTAT--AATTATATTTAAAATATT
1 TTATATTATAAAATTAT-TTTAAAATA-T
*
28171 TTATATTTATATAAATT-TTATTAATA-AT
1 TTATA-TTATA-AAATTATT-TTAAAATAT
*
28199 TTATATTATATAA--ATTTTAAAATAT
1 TTATATTATAAAATTATTTTAAAATAT
*
28224 TTATATAATAAAATTATTTT
1 TTATATTATAAAATTATTTT
28244 TATATTATAA
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
24 5 0.08
25 15 0.25
26 2 0.03
27 15 0.25
28 10 0.17
29 2 0.03
30 6 0.10
31 4 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTATATTATAAAATTATTTTAAAATAT
Found at i:29382 original size:13 final size:13
Alignment explanation
Indices: 29366--29391 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29356 TAGGTACAGC
29366 AGTTAGCTTGTCT
1 AGTTAGCTTGTCT
29379 AGTTAGCTTGTCT
1 AGTTAGCTTGTCT
29392 TATATTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
AGTTAGCTTGTCT
Found at i:37330 original size:3 final size:3
Alignment explanation
Indices: 37324--37355 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
37314 GCCGCCACCA
*
37324 CCT CCT CCT CCT CCT TCT CCT CCT CCT CCT CC
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CC
37356 ACCACCACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CCT
Found at i:37369 original size:12 final size:12
Alignment explanation
Indices: 37354--37394 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
37344 TCCTCCTCCT
*
37354 CCACCACCACCA
1 CCACTACCACCA
*
37366 CCACTACCTCCA
1 CCACTACCACCA
*
37378 CCTCTACCACCA
1 CCACTACCACCA
37390 CCACT
1 CCACT
37395 TCCATATCCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.27, C:0.61, G:0.00, T:0.12
Consensus pattern (12 bp):
CCACTACCACCA
Found at i:37476 original size:12 final size:12
Alignment explanation
Indices: 37461--37512 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
37451 CACCTCCATT
*
37461 GCCTCCACCTCC
1 GCCTCCACCACC
37473 GCCTCCACCACC
1 GCCTCCACCACC
* *
37485 TCCTCTACCACC
1 GCCTCCACCACC
*
37497 GCCCCCACCACC
1 GCCTCCACCACC
37509 GCCT
1 GCCT
37513 ATCCCATTGC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.13, C:0.65, G:0.08, T:0.13
Consensus pattern (12 bp):
GCCTCCACCACC
Found at i:37550 original size:126 final size:126
Alignment explanation
Indices: 37420--37667 Score: 388
Period size: 126 Copynumber: 2.0 Consensus size: 126
37410 GCTTCCGTAA
* * * *
37420 CCGTATCCAGATCCATAGCCTGAGCCATGTCCACCTCCATTGCCTCCACCTCCGCCTCCACCACC
1 CCGTATCCAGATCCATAACCTGAGCCATGTCCACCTCCATTGCCACCACCTCCACCACCACCACC
*
37485 TCCTCTACCACCGCCCCCACCACCGCCTATCCCATTGCCAGACCCATACCCTGACCCCGAC
66 TCCTCTACCACCGCCCCCACCACCGCCTATCCCACTGCCAGACCCATACCCTGACCCCGAC
* *
37546 CCGTATCCGGATCCATAACCTGAGCCATGTCCGCCTCCATTGCCACCACCTCCACCACCACCACC
1 CCGTATCCAGATCCATAACCTGAGCCATGTCCACCTCCATTGCCACCACCTCCACCACCACCACC
* * * * *
37611 TCCTCTACCCCCGCCTCCACCACCTCCTATCCCGCTGCCAGACCCATTCCCTGACCC
66 TCCTCTACCACCGCCCCCACCACCGCCTATCCCACTGCCAGACCCATACCCTGACCC
37668 GTATCCAGAC
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 110 1.00
ACGTcount: A:0.19, C:0.53, G:0.11, T:0.18
Consensus pattern (126 bp):
CCGTATCCAGATCCATAACCTGAGCCATGTCCACCTCCATTGCCACCACCTCCACCACCACCACC
TCCTCTACCACCGCCCCCACCACCGCCTATCCCACTGCCAGACCCATACCCTGACCCCGAC
Found at i:37599 original size:15 final size:15
Alignment explanation
Indices: 37588--37634 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
37578 GCCTCCATTG
37588 CCACCACCTCCACCA
1 CCACCACCTCCACCA
* *
37603 CCACCACCTCCTCTA
1 CCACCACCTCCACCA
* *
37618 CCCCCGCCTCCACCA
1 CCACCACCTCCACCA
37633 CC
1 CC
37635 TCCTATCCCG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.19, C:0.68, G:0.02, T:0.11
Consensus pattern (15 bp):
CCACCACCTCCACCA
Found at i:37678 original size:12 final size:12
Alignment explanation
Indices: 37648--37694 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
37638 TATCCCGCTG
37648 CCAGACCCAT-T
1 CCAGACCCATAT
* *
37659 CCCTGACCCGTAT
1 -CCAGACCCATAT
37672 CCAGACCCATAT
1 CCAGACCCATAT
37684 CCAGACCCATA
1 CCAGACCCATA
37695 CCCATTGCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 29 0.97
13 1 0.03
ACGTcount: A:0.28, C:0.45, G:0.11, T:0.17
Consensus pattern (12 bp):
CCAGACCCATAT
Found at i:37739 original size:24 final size:24
Alignment explanation
Indices: 37707--37757 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
37697 CATTGCCTGA
*
37707 TCCTTCGCCACCTCCACCACCACC
1 TCCTTCGCCACCACCACCACCACC
*
37731 TCCTTCGCCACCACCACCACCAGC
1 TCCTTCGCCACCACCACCACCACC
37755 TCC
1 TCC
37758 ACTACCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.61, G:0.06, T:0.16
Consensus pattern (24 bp):
TCCTTCGCCACCACCACCACCACC
Found at i:37870 original size:21 final size:21
Alignment explanation
Indices: 37846--37898 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
37836 ACCATTCCCA
*
37846 CCACCTCCACCACTTCCTCCT
1 CCACCTCCACCACCTCCTCCT
* *
37867 CCACCACCACCGCCTCCTCCT
1 CCACCTCCACCACCTCCTCCT
* *
37888 CTACCTACACC
1 CCACCTCCACC
37899 CTTAAGTAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.62, G:0.02, T:0.19
Consensus pattern (21 bp):
CCACCTCCACCACCTCCTCCT
Found at i:38891 original size:32 final size:30
Alignment explanation
Indices: 38844--38911 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 30
38834 TCGGATTTGG
38844 ATATTTTAGATTT-AAATATTTTAAAATTTAGT
1 ATATTTTAGATTTAAAAT-TTTTAAAATTT--T
38876 ATATTTTA-ATATTAAAATTTTTAAAATTTT
1 ATATTTTAGAT-TTAAAATTTTTAAAATTTT
38906 ATATTT
1 ATATTT
38912 GGATTTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 7 0.21
31 2 0.06
32 21 0.62
33 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (30 bp):
ATATTTTAGATTTAAAATTTTTAAAATTTT
Found at i:39748 original size:18 final size:19
Alignment explanation
Indices: 39725--39770 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
39715 TCTATTAAAA
39725 ATATTAAAAATTAT-TTTT
1 ATATTAAAAATTATATTTT
* *
39743 ATATTAATATTTATATTTT
1 ATATTAAAAATTATATTTT
39762 ATAATTAAA
1 AT-ATTAAA
39771 TTTATATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 12 0.52
19 6 0.26
20 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTAAAAATTATATTTT
Found at i:40183 original size:34 final size:33
Alignment explanation
Indices: 40135--40355 Score: 230
Period size: 34 Copynumber: 6.5 Consensus size: 33
40125 TGGTAAAAAC
* *
40135 CACCATTTAATCAACAATAGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
40168 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
40202 CACCTATTTAATCAATAATGGTAAGCTACCAAAT
1 CACC-ATTTAATCAACAATGGTAACCTACCAAAT
** *
40236 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * * *
40270 CTCCCATTTAGTCAACAATGGCAA-ATCACCAAAT
1 C-ACCATTTAATCAACAATGGTAACCT-ACCAAAT
* * *
40304 CACCGATTTAATCAATAATAGTAAACTACCAAAT
1 CACC-ATTTAATCAACAATGGTAACCTACCAAAT
40338 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
40356 TCTCCCACTT
Statistics
Matches: 158, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
33 21 0.13
34 132 0.84
35 5 0.03
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:40314 original size:102 final size:101
Alignment explanation
Indices: 40135--40355 Score: 325
Period size: 102 Copynumber: 2.2 Consensus size: 101
40125 TGGTAAAAAC
* *
40135 CACCATTTAATCAACAATAGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATAGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* * *
40200 ATCACCTATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCGATTTAATCAATAATAGTAAACTACCAAAT
** * * * * *
40236 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAATCACCA
1 CAC-CATTTAATCAACAATAGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
40301 AATCACCGATTTAATCAATAATAGTAAACTACCAAAT
65 AATCACCGATTTAATCAATAATAGTAAACTACCAAAT
40338 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
40356 TCTCCCACTT
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
101 16 0.15
102 89 0.85
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATAGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCGATTTAATCAATAATAGTAAACTACCAAAT
Found at i:44225 original size:34 final size:33
Alignment explanation
Indices: 44177--44395 Score: 262
Period size: 34 Copynumber: 6.5 Consensus size: 33
44167 TGGTAAAAAC
44177 CACCATTTAATCAACAATGGTAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* *
44210 CTACCATTTAGTCAACAATGGTAA-GTCACCAAAT
1 C-ACCATTTAATCAACAATGGTAACCT-ACCAAAT
* *
44244 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
44278 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* *
44312 CTCCCATTTAGTCAACAATGGTAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGGT-AACCTACCAAAT
* *
44346 CACACATTTAATCAATAATGGTAAACTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
44380 CACCATTTAATCAACA
1 CACCATTTAATCAACA
44396 GTCCATAACA
Statistics
Matches: 160, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 20 0.12
34 135 0.84
35 5 0.03
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:44356 original size:102 final size:101
Alignment explanation
Indices: 44177--44395 Score: 357
Period size: 102 Copynumber: 2.2 Consensus size: 101
44167 TGGTAAAAAC
**
44177 CACCATTTAATCAACAATGGTAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGTCACCAA
1 CACCATTTAATCAACAATGGTAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCAA
* *
44242 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACACATTTAATCAATAATGGTAAACTACCAAAT
** * *
44278 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCA
1 CAC-CATTTAATCAACAATGGTAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCA
44343 AATCACACATTTAATCAATAATGGTAAACTACCAAAT
65 AATCACACATTTAATCAATAATGGTAAACTACCAAAT
44380 CACCATTTAATCAACA
1 CACCATTTAATCAACA
44396 GTCCATAACA
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 14 0.13
102 93 0.87
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGTAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCAA
ATCACACATTTAATCAATAATGGTAAACTACCAAAT
Found at i:46205 original size:60 final size:60
Alignment explanation
Indices: 46087--46205 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
46077 GATAAATTTA
* ** *
46087 ATCAATATAAAAGCAATTAGTTTTACATATTATATTTTTACCAAGGAGGTCATCGTTTGG
1 ATCAATATAAAAGCAATTAGTTTTACATATTATATATTTACCAAAAAGGTCATAGTTTGG
** ** *
46147 ATCAATATAAAATTAATTAGTTTTATGTATTATATATTTACTAAAAAGG-CTATAGTTTG
1 ATCAATATAAAAGCAATTAGTTTTACATATTATATATTTACCAAAAAGGTC-ATAGTTTG
46206 AAGATAGAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (60 bp):
ATCAATATAAAAGCAATTAGTTTTACATATTATATATTTACCAAAAAGGTCATAGTTTGG
Found at i:48784 original size:20 final size:20
Alignment explanation
Indices: 48761--48801 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
48751 AAAAATTATT
* *
48761 TAAATTTAATTATAAATATA
1 TAAATGTAAATATAAATATA
*
48781 TAAATGTAAATATTAATATA
1 TAAATGTAAATATAAATATA
48801 T
1 T
48802 TTTTTAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TAAATGTAAATATAAATATA
Found at i:49393 original size:16 final size:17
Alignment explanation
Indices: 49374--49415 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
49364 TTCAAACTAC
49374 TTCAA-TTTAGAGTTAT
1 TTCAAGTTTAGAGTTAT
49390 TTCAAGTTT-GAGTTAT
1 TTCAAGTTTAGAGTTAT
*
49406 TTTAAGTTTA
1 TTCAAGTTTA
49416 AGTCAGTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (17 bp):
TTCAAGTTTAGAGTTAT
Found at i:50181 original size:13 final size:13
Alignment explanation
Indices: 50163--50196 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
50153 TTCATACACG
50163 ATATAATTATAAA
1 ATATAATTATAAA
50176 ATATAA-TATAAA
1 ATATAATTATAAA
*
50188 AAATAATTA
1 ATATAATTA
50197 AAATATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAATTATAAA
Found at i:50343 original size:19 final size:19
Alignment explanation
Indices: 50319--50356 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
50309 AATATGATCA
50319 TAATACGATAAAAATATAT
1 TAATACGATAAAAATATAT
*
50338 TAATACGATACAAATATAT
1 TAATACGATAAAAATATAT
50357 GGATTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (19 bp):
TAATACGATAAAAATATAT
Found at i:54219 original size:2 final size:2
Alignment explanation
Indices: 54212--54243 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54202 TCTGTACGTC
54212 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54244 CTAAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58471 original size:18 final size:19
Alignment explanation
Indices: 58436--58475 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
58426 AGTTTTGACA
58436 ATTCGTATATTCTTATTAT
1 ATTCGTATATTCTTATTAT
58455 ATTCGTATATT-TTATTAT
1 ATTCGTATATTCTTATTAT
58473 ATT
1 ATT
58476 ATAATCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTCGTATATTCTTATTAT
Found at i:58518 original size:25 final size:25
Alignment explanation
Indices: 58490--58551 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
58480 TCATATTAAA
*
58490 AATATTTTATATTTATATAGATTTT
1 AATAATTTATATTTATATAGATTTT
*
58515 AATACGTTTA-ATTTATATAGATTTT
1 AATA-ATTTATATTTATATAGATTTT
58540 AA-AATTTATATT
1 AATAATTTATATT
58552 CGTATTATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 4 0.12
24 4 0.12
25 21 0.64
26 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (25 bp):
AATAATTTATATTTATATAGATTTT
Found at i:58804 original size:17 final size:15
Alignment explanation
Indices: 58757--58810 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 15
58747 ATTCATAATC
58757 ATATTTAATATATTTT
1 ATATTTAATA-ATTTT
58773 ATATTTATATAAATTTT
1 ATATTTA-AT-AATTTT
58790 GATATATTAATAA-TTT
1 -ATAT-TTAATAATTTT
58806 ATATT
1 ATATT
58811 ATATAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.03
15 4 0.12
16 10 0.29
17 9 0.26
18 7 0.21
19 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
ATATTTAATAATTTT
Found at i:58816 original size:32 final size:34
Alignment explanation
Indices: 58757--58820 Score: 98
Period size: 32 Copynumber: 1.9 Consensus size: 34
58747 ATTCATAATC
58757 ATATTTAATATATTTTATATTTATATAAATTTTG
1 ATATTTAATATATTTTATATTTATATAAATTTTG
58791 ATATATTAATA-A-TTTATA-TTATATAAATTT
1 ATAT-TTAATATATTTTATATTTATATAAATTT
58821 CAAAATATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 12 0.41
33 6 0.21
34 5 0.17
35 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (34 bp):
ATATTTAATATATTTTATATTTATATAAATTTTG
Found at i:58829 original size:32 final size:34
Alignment explanation
Indices: 58761--58838 Score: 97
Period size: 32 Copynumber: 2.3 Consensus size: 34
58751 ATAATCATAT
** *
58761 TTAATATATTTTATATTTATATAAATTTTGATATA
1 TTAATATA-TTTATATTTATATAAATTTCAAAATA
58796 TTAATA-ATTTATA-TTATATAAATTTCAAAATA
1 TTAATATATTTATATTTATATAAATTTCAAAATA
*
58828 TTCATATATTT
1 TTAATATATTT
58839 GTATCGTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 21 0.55
33 10 0.26
34 1 0.03
35 6 0.16
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (34 bp):
TTAATATATTTATATTTATATAAATTTCAAAATA
Found at i:59730 original size:26 final size:27
Alignment explanation
Indices: 59690--59742 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
59680 TACATAAATT
*
59690 TATTAAAATTTATATAAA-AAATAATA
1 TATTAAAATTCATATAAATAAATAATA
* *
59716 TATTAATATTCATATAAATATATAATA
1 TATTAAAATTCATATAAATAAATAATA
59743 CTTTATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TATTAAAATTCATATAAATAAATAATA
Found at i:60119 original size:28 final size:27
Alignment explanation
Indices: 60061--60127 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
60051 TGCTTATTAA
*
60061 TTTTTTTTTCTCCTTGCTTTACCTTTT
1 TTTTTTTTTCTCCTTGCCTTACCTTTT
* *
60088 TTTTTTTTTC-CTCTTTCCTTATCTTTT
1 TTTTTTTTTCTC-CTTGCCTTACCTTTT
60115 CTTTTTTTCTTCT
1 -TTTTTTT-TTCT
60128 AATGACAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 1 0.03
27 22 0.67
28 7 0.21
29 3 0.09
ACGTcount: A:0.03, C:0.22, G:0.01, T:0.73
Consensus pattern (27 bp):
TTTTTTTTTCTCCTTGCCTTACCTTTT
Found at i:61162 original size:18 final size:18
Alignment explanation
Indices: 61139--61174 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
61129 TATAACAATT
61139 TTTTAACTAATTAATTAA
1 TTTTAACTAATTAATTAA
*
61157 TTTTAATTAATTAATTAA
1 TTTTAACTAATTAATTAA
61175 ATAAAAATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTAACTAATTAATTAA
Found at i:61165 original size:14 final size:14
Alignment explanation
Indices: 61146--61172 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
61136 ATTTTTTAAC
61146 TAATTAATTAATTT
1 TAATTAATTAATTT
61160 TAATTAATTAATT
1 TAATTAATTAATT
61173 AAATAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTAATTAATTT
Found at i:65540 original size:20 final size:20
Alignment explanation
Indices: 65486--65541 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
65476 CTTTAAAAGT
65486 TTTAAAGCAAAAATTAGAAAA
1 TTTAAA-CAAAAATTAGAAAA
* * *
65507 TTTAACCCAAAATTAG-GAA
1 TTTAAACAAAAATTAGAAAA
65526 TTTAAACAAATAATTA
1 TTTAAACAAA-AATTA
65542 ACCAAGAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 10 0.34
20 14 0.48
21 5 0.17
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.29
Consensus pattern (20 bp):
TTTAAACAAAAATTAGAAAA
Found at i:66611 original size:21 final size:21
Alignment explanation
Indices: 66577--66616 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
66567 TATATTTATT
66577 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
66598 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
66617 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:66751 original size:15 final size:17
Alignment explanation
Indices: 66733--66765 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
66723 TAATTAAATT
66733 TAAA-TAAAT-TTTTTA
1 TAAATTAAATATTTTTA
66748 TAAATTAAATATTTTTA
1 TAAATTAAATATTTTTA
66765 T
1 T
66766 TTAAGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 5 0.31
17 7 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TAAATTAAATATTTTTA
Found at i:66960 original size:19 final size:20
Alignment explanation
Indices: 66923--66961 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
66913 TGGTTTCTTA
66923 ATAAAATTATATATAATTAT
1 ATAAAATTATATATAATTAT
66943 ATAAAA-TAT-TACTAATTAT
1 ATAAAATTATATA-TAATTAT
66962 TTATGCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 10 0.56
20 6 0.33
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAAATTATATATAATTAT
Found at i:66998 original size:27 final size:27
Alignment explanation
Indices: 66927--66998 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
66917 TTCTTAATAA
66927 AATTATATATAATTATATAAAATATTACT
1 AATTATATATAA--ATATAAAATATTACT
* **
66956 AATTATTTATGCATATAAAATATTA-T
1 AATTATATATAAATATAAAATATTACT
*
66982 CAATTACATATAAATAT
1 -AATTATATATAAATAT
66999 TATTAGTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
26 1 0.03
27 25 0.71
29 9 0.26
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (27 bp):
AATTATATATAAATATAAAATATTACT
Found at i:67566 original size:28 final size:27
Alignment explanation
Indices: 67530--67584 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
67520 CTTAAGTTGC
* * *
67530 TATTGTAAATTAAACTTTTAAAATATAT
1 TATTGTAAAATAAA-ATTAAAAATATAT
*
67558 TATTTTAAAATAAAATTAAAAATATAT
1 TATTGTAAAATAAAATTAAAAATATAT
67585 AAAATAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
TATTGTAAAATAAAATTAAAAATATAT
Found at i:67640 original size:13 final size:12
Alignment explanation
Indices: 67624--67667 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
67614 ACGAATCAAT
67624 TTTAAATATAATA
1 TTTAAATATAA-A
*
67637 TTTAAAAATAAAA
1 TTTAAATAT-AAA
*
67650 TTTAAATTTAAA
1 TTTAAATATAAA
67662 TTTAAA
1 TTTAAA
67668 CTTTAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 9 0.33
13 16 0.59
14 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TTTAAATATAAA
Found at i:67667 original size:19 final size:19
Alignment explanation
Indices: 67621--67674 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
67611 TGTACGAATC
* *
67621 AATTTTAAATATAATATTTA
1 AATTTAAAATTTAA-ATTTA
**
67641 AAAATAAAATTTAAATTTA
1 AATTTAAAATTTAAATTTA
*
67660 AATTTAAACTTTAAA
1 AATTTAAAATTTAAA
67675 AAAATTAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTTAAAATTTAAATTTA
Found at i:67977 original size:19 final size:19
Alignment explanation
Indices: 67945--67993 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
67935 TTATCACTAA
67945 AAATTATTAAAATTATAAAT
1 AAATTATTAAAATT-TAAAT
* *
67965 AAA-TATTATAATTTATAT
1 AAATTATTAAAATTTAAAT
67983 AAATTATTAAA
1 AAATTATTAAA
67994 GTATAGATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 7 0.28
19 15 0.60
20 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATTATTAAAATTTAAAT
Found at i:68624 original size:19 final size:20
Alignment explanation
Indices: 68584--68629 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
68574 ATTGAGTTTT
*
68584 ATAATATAATTAATTATAAA
1 ATAATATAATTAATAATAAA
* *
68604 ATTATATAA-TAATAATTAA
1 ATAATATAATTAATAATAAA
68623 ATAATAT
1 ATAATAT
68630 TATTTTTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAATATAATTAATAATAAA
Found at i:69138 original size:22 final size:25
Alignment explanation
Indices: 69101--69148 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
69091 TAGTAATTAA
69101 TTTAATATTTATATTTAAAT-ATAT
1 TTTAATATTTATATTTAAATAATAT
69125 TTTAAT-TTTA-ATTTAAATAATAT
1 TTTAATATTTATATTTAAATAATAT
69148 T
1 T
69149 AAATAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.35
23 9 0.39
24 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTAATATTTATATTTAAATAATAT
Found at i:69752 original size:25 final size:23
Alignment explanation
Indices: 69707--69752 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
69697 ACTTATATAA
*
69707 ATAATAAATTTAAATATTTAAAT
1 ATAATAAATTTAAATAATTAAAT
*
69730 ATAATAATTATTTATATAATTAA
1 ATAATAA--ATTTAAATAATTAA
69753 TTTTTATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
25 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATAATAAATTTAAATAATTAAAT
Found at i:69829 original size:26 final size:25
Alignment explanation
Indices: 69785--69833 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
69775 TATTTAAATA
* *
69785 ATAAATAAATAATTTTAAATATTAT
1 ATAAATAAAAAATTATAAATATTAT
69810 ATAAATTAAAAAATTATAAATATT
1 ATAAA-TAAAAAATTATAAATATT
69834 TGATTCCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAAATAAAAAATTATAAATATTAT
Found at i:70272 original size:16 final size:17
Alignment explanation
Indices: 70251--70290 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
70241 AAAATAATTA
*
70251 AAATATGATA-AAAAAT
1 AAATATAATATAAAAAT
70267 AAATATAATATAAAAAT
1 AAATATAATATAAAAAT
70284 -AATATAA
1 AAATATAA
70291 ATTATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
AAATATAATATAAAAAT
Found at i:70774 original size:20 final size:19
Alignment explanation
Indices: 70707--70775 Score: 54
Period size: 20 Copynumber: 3.6 Consensus size: 19
70697 TTTGTATCCT
*
70707 TTTATATATT-TTTTAT-C
1 TTTATATATTATTTAATAC
*
70724 TTTATCAT-TATATTTAAATAT
1 TTTAT-ATAT-TATTT-AATAC
*
70745 TTTTTATATTATTTAATAC
1 TTTATATATTATTTAATAC
70764 TTTATATTATTA
1 TTTATA-TATTA
70776 AAATTTATCT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
17 6 0.15
18 3 0.08
19 12 0.30
20 14 0.35
21 5 0.12
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATATATTATTTAATAC
Found at i:70791 original size:39 final size:39
Alignment explanation
Indices: 70748--70835 Score: 98
Period size: 38 Copynumber: 2.3 Consensus size: 39
70738 TAAATATTTT
*
70748 TTATATTATTTAA-TACT-TTATAT-TATTAAAATTTATCTA
1 TTATATTATTTAATTA-TATTATATCTATT--AATTTATATA
70787 TTATATT-TTTAATTATATTATATCTATTAATTTATATA
1 TTATATTATTTAATTATATTATATCTATTAATTTATATA
70825 TT-TA-TATTTAA
1 TTATATTATTTAA
70836 AATTATCTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
36 1 0.02
37 7 0.16
38 17 0.39
39 15 0.34
40 4 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (39 bp):
TTATATTATTTAATTATATTATATCTATTAATTTATATA
Found at i:71416 original size:18 final size:20
Alignment explanation
Indices: 71374--71417 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
71364 GTTTAAAATA
71374 AATTAAATTTAAATATAATTT
1 AATT-AATTTAAATATAATTT
71395 --TTAATTTAAAT-T-ATTT
1 AATTAATTTAAATATAATTT
71411 AATTAAT
1 AATTAAT
71418 AAAAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
16 4 0.19
17 1 0.05
18 14 0.67
19 2 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AATTAATTTAAATATAATTT
Found at i:71439 original size:22 final size:22
Alignment explanation
Indices: 71411--71482 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
71401 TAAATTATTT
*
71411 AATTAATAAAAAATTTTAAAAA
1 AATTAATATAAAATTTTAAAAA
*
71433 AATTAATTATAAAA-TTTATAAA
1 AATTAA-TATAAAATTTTAAAAA
* *
71455 TATTAATATAAAATTATTTAAAA
1 AATTAATATAAAATT-TTAAAAA
71478 AATTA
1 AATTA
71483 TTTTTAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
21 7 0.17
22 19 0.46
23 15 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAATATAAAATTTTAAAAA
Found at i:71446 original size:12 final size:12
Alignment explanation
Indices: 71431--71513 Score: 54
Period size: 12 Copynumber: 7.2 Consensus size: 12
71421 AAATTTTAAA
71431 AAAATTAATTAT
1 AAAATTAATTAT
71443 AAAA-T--TTAT
1 AAAATTAATTAT
71452 AAATATTAA-TAT
1 AAA-ATTAATTAT
* *
71464 AAAATTATTTAA
1 AAAATTAATTAT
* *
71476 AAAATTATTTTT
1 AAAATTAATTAT
71488 AAAATAATAATT-T
1 AAAAT--TAATTAT
71501 -AAATTAATT-T
1 AAAATTAATTAT
71511 AAA
1 AAA
71514 TAAATTTAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
9 7 0.12
10 7 0.12
11 8 0.14
12 31 0.53
13 1 0.02
14 4 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AAAATTAATTAT
Found at i:71511 original size:37 final size:39
Alignment explanation
Indices: 71447--71519 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 39
71437 AATTATAAAA
*
71447 TTTATAAATATTAATATAAAATTATTTAAA-AAATTATT
1 TTTATAAATAATAATATAAAATTATTTAAATAAATTATT
*
71485 TTTA-AAATAATAAT-TTAAATTAATTTAAATAAATT
1 TTTATAAATAATAATATAAAATT-ATTTAAATAAATT
71520 TAATTCACGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 6 0.19
37 16 0.52
38 9 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (39 bp):
TTTATAAATAATAATATAAAATTATTTAAATAAATTATT
Found at i:72173 original size:29 final size:30
Alignment explanation
Indices: 72113--72180 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
72103 TTAGTTTAAA
* * *
72113 AAATATTTTTATATATAATATATTATTTTTAT
1 AAAT-TTTTTAAAAATAATATATTA-TATTAT
*
72145 AATTTTTTTAAAAATAATATATTA-ATTAT
1 AAATTTTTTAAAAATAATATATTATATTAT
72174 AAATTTT
1 AAATTTT
72181 CAGAGTTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 10 0.32
31 18 0.58
32 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
AAATTTTTTAAAAATAATATATTATATTAT
Found at i:72409 original size:27 final size:28
Alignment explanation
Indices: 72356--72410 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
72346 TCGACTATCA
** *
72356 TTAATTAATAAAAAAATATTATTTAAAT
1 TTAATTAATAAAAAAATAAAATATAAAT
*
72384 TTAATT-ATAATAAAATAAAATATAAAT
1 TTAATTAATAAAAAAATAAAATATAAAT
72411 AAAAAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TTAATTAATAAAAAAATAAAATATAAAT
Found at i:73500 original size:25 final size:25
Alignment explanation
Indices: 73472--73522 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
73462 TTGAATGTGT
* * *
73472 CAATATTCGATTTATTTGAAAATTA
1 CAATATTAGATCTATTTAAAAATTA
73497 CAATATTAGATCTATTTAAAAATTA
1 CAATATTAGATCTATTTAAAAATTA
73522 C
1 C
73523 GTAACTTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (25 bp):
CAATATTAGATCTATTTAAAAATTA
Found at i:73592 original size:20 final size:18
Alignment explanation
Indices: 73569--73614 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
73559 TAACTTGATC
73569 TAATTTAAATAATTATTTAT
1 TAATTTAAATAA-TATTT-T
73589 TAA-TTAAATAATATTTT
1 TAATTTAAATAATATTTT
73606 T-ATTTAAAT
1 TAATTTAAAT
73615 TTAATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.04
17 8 0.32
18 5 0.20
19 8 0.32
20 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATTTAAATAATATTTT
Found at i:73927 original size:31 final size:30
Alignment explanation
Indices: 73892--73961 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
73882 ACACGATATG
*
73892 AATATAAATATAAAAATCTCAAAATTTAGAT
1 AATATAAAT-TAAAAATATCAAAATTTAGAT
* * * *
73923 AATATGAATTTAATATATCAAAATTTATAT
1 AATATAAATTAAAAATATCAAAATTTAGAT
73953 AGATATAAA
1 A-ATATAAA
73962 ATACTTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (30 bp):
AATATAAATTAAAAATATCAAAATTTAGAT
Found at i:81331 original size:23 final size:21
Alignment explanation
Indices: 81305--81375 Score: 54
Period size: 23 Copynumber: 3.2 Consensus size: 21
81295 TTAAAAATTT
81305 TAAAATTTTAAAATATTTAATAA
1 TAAAATTTTAAAA-ATTTAAT-A
* * *
81328 TAAATTTTTATTTAAATTTAATT
1 TAAAATTTTA--AAAATTTAATA
* *
81351 TAAAATTTTAAATA-CTAATA
1 TAAAATTTTAAAAATTTAATA
81371 TAAAA
1 TAAAA
81376 ATAATATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
20 9 0.24
21 2 0.05
23 18 0.47
24 7 0.18
25 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAATTTTAAAAATTTAATA
Found at i:81569 original size:23 final size:23
Alignment explanation
Indices: 81528--81571 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
81518 CGAGATAAAT
*
81528 TATTTTACTTTTTTAAATTTTCG
1 TATTTTAATTTTTTAAATTTTCG
81551 TATTTTAATTATTTT-AATTTT
1 TATTTTAATT-TTTTAAATTTT
81572 GAATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (23 bp):
TATTTTAATTTTTTAAATTTTCG
Found at i:81719 original size:28 final size:26
Alignment explanation
Indices: 81681--81746 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
81671 ATTTCAACTT
81681 AATT-ATTTAAATAATTTAAAATTAA
1 AATTAATTTAAATAATTTAAAATTAA
* **
81706 TAATTAAATTTAAATTATTTTCAATTAA
1 -AATT-AATTTAAATAATTTAAAATTAA
*
81734 AATTATTTTAAAT
1 AATTAATTTAAAT
81747 TTAAATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 12 0.35
27 4 0.12
28 18 0.53
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATTAATTTAAATAATTTAAAATTAA
Found at i:81736 original size:16 final size:16
Alignment explanation
Indices: 81712--81772 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
81702 TTAATAATTA
*
81712 AATTTAAATTATTTTC
1 AATTAAAATTATTTTC
*
81728 AATTAAAATTATTTTA
1 AATTAAAATTATTTTC
* *
81744 AATTTAAA-TA-ATTC
1 AATTAAAATTATTTTC
81758 AATTAAAATTATTTT
1 AATTAAAATTATTTT
81773 TAAATTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
14 9 0.25
15 4 0.11
16 23 0.64
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTAAAATTATTTTC
Found at i:81761 original size:30 final size:33
Alignment explanation
Indices: 81709--81780 Score: 114
Period size: 30 Copynumber: 2.3 Consensus size: 33
81699 AAATTAATAA
*
81709 TTAAATTTAAATTATTTTCAATTAAAATTA-TT
1 TTAAATTTAAATTATATTCAATTAAAATTATTT
81741 TTAAATTTAAA-TA-ATTCAATTAAAATTATTT
1 TTAAATTTAAATTATATTCAATTAAAATTATTT
81772 TTAAATTTA
1 TTAAATTTA
81781 TTCTAATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
30 14 0.37
31 13 0.34
32 11 0.29
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (33 bp):
TTAAATTTAAATTATATTCAATTAAAATTATTT
Found at i:84419 original size:50 final size:50
Alignment explanation
Indices: 84362--84463 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 50
84352 GCTCAAGCTC
* *
84362 AAGTTCAGGTTGAACTAAGTTCGGTTCAAGCTTGATTAAATTTTACTTTT
1 AAGTTCAGGTTGAACTAAGATCAGTTCAAGCTTGATTAAATTTTACTTTT
*
84412 AAGTTCAGGTTGAACTAAGATCAGTTCAAGTTTGATTAAATTTTACTTTT
1 AAGTTCAGGTTGAACTAAGATCAGTTCAAGCTTGATTAAATTTTACTTTT
84462 AA
1 AA
84464 ATTGATTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (50 bp):
AAGTTCAGGTTGAACTAAGATCAGTTCAAGCTTGATTAAATTTTACTTTT
Found at i:84471 original size:22 final size:22
Alignment explanation
Indices: 84443--84486 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
84433 CAGTTCAAGT
*
84443 TTGATTAAATTTTACTTTTAAA
1 TTGATTAAATTTCACTTTTAAA
84465 TTGATTAAATTTCACTTTTAAA
1 TTGATTAAATTTCACTTTTAAA
84487 ATTAAAGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (22 bp):
TTGATTAAATTTCACTTTTAAA
Found at i:84761 original size:26 final size:27
Alignment explanation
Indices: 84715--84768 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
84705 TATTTTATAG
*
84715 TTTGAACTCGATTTAACAATAATTAAA
1 TTTGAACTCGATTTAACAATAATCAAA
* *
84742 TTTGAACT-TATTTAATAATAATCAAA
1 TTTGAACTCGATTTAACAATAATCAAA
84768 T
1 T
84769 GAAATTGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (27 bp):
TTTGAACTCGATTTAACAATAATCAAA
Found at i:85100 original size:18 final size:18
Alignment explanation
Indices: 85056--85100 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
85046 ATAAAATTGA
*
85056 TTATATATTTATATATTT
1 TTATATATTTAAATATTT
* *
85074 GTATCTATTTAAATATTT
1 TTATATATTTAAATATTT
85092 TTATATATT
1 TTATATATT
85101 ATAATCGTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTATATATTTAAATATTT
Found at i:88427 original size:13 final size:14
Alignment explanation
Indices: 88394--88430 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
88384 ATTCGAATTA
88394 AATTTT-ATATTTT
1 AATTTTAATATTTT
88407 AATATTTAAT-TTTT
1 AAT-TTTAATATTTT
88421 AATTTTAATA
1 AATTTTAATA
88431 ATATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 9 0.43
14 10 0.48
15 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AATTTTAATATTTT
Found at i:89433 original size:52 final size:52
Alignment explanation
Indices: 89347--89444 Score: 155
Period size: 51 Copynumber: 1.9 Consensus size: 52
89337 ATAATAAATT
*
89347 TTTAAATTTAAATTAATATAACATAAATTATTTTTTAATAATAAAATTTTTA
1 TTTAAATTTAAATTAATATAACATAAAATATTTTTTAATAATAAAATTTTTA
*
89399 TTTAAATTT-AATT-ATATAGATATAAAATATTTTTTAATAATAAAAT
1 TTTAAATTTAAATTAATATA-ACATAAAATATTTTTTAATAATAAAAT
89445 AGATTGGTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 5 0.12
51 29 0.67
52 9 0.21
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
TTTAAATTTAAATTAATATAACATAAAATATTTTTTAATAATAAAATTTTTA
Found at i:91643 original size:22 final size:23
Alignment explanation
Indices: 91599--91646 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
91589 TCATCGGTTT
*
91599 AATTGATTTAATTAACTAAATTA
1 AATTGATTTAATTAACAAAATTA
91622 AATT-ATTTAATTAA-AAAGATTA
1 AATTGATTTAATTAACAAA-ATTA
91644 AAT
1 AAT
91647 ATTAATATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 2 0.09
22 17 0.74
23 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (23 bp):
AATTGATTTAATTAACAAAATTA
Found at i:92156 original size:21 final size:21
Alignment explanation
Indices: 92130--92172 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
92120 AATTGGTAAG
92130 TCTGGTTGAAATACGAGTTCT
1 TCTGGTTGAAATACGAGTTCT
**
92151 TCTGGTTGAAATATTAGTTCT
1 TCTGGTTGAAATACGAGTTCT
92172 T
1 T
92173 ACTTCAACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (21 bp):
TCTGGTTGAAATACGAGTTCT
Found at i:92472 original size:18 final size:18
Alignment explanation
Indices: 92449--92483 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
92439 AATGCCCCAA
92449 CACCAGCACCTGCACCAG
1 CACCAGCACCTGCACCAG
*
92467 CACCAGCACCTGGACCA
1 CACCAGCACCTGCACCA
92484 TGGAGATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.49, G:0.17, T:0.06
Consensus pattern (18 bp):
CACCAGCACCTGCACCAG
Found at i:93525 original size:22 final size:23
Alignment explanation
Indices: 93500--93569 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 23
93490 TATATTCGTA
**
93500 TTAT-TTTATATATTTTATTATG
1 TTATATTTATATATTAAATTATG
*
93522 TTATATTTATAT-TTAAATTATT
1 TTATATTTATATATTAAATTATG
93544 TTATATTTATATA-TAAATT-T-
1 TTATATTTATATATTAAATTATG
93564 TTATAT
1 TTATAT
93570 ATTAATAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
20 6 0.14
21 1 0.02
22 29 0.67
23 7 0.16
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (23 bp):
TTATATTTATATATTAAATTATG
Found at i:93568 original size:14 final size:14
Alignment explanation
Indices: 93549--93596 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
93539 TTATTTTATA
93549 TTTATATATAAATT
1 TTTATATATAAATT
93563 TTTATATATTAATAATT
1 TTTATATA-T-A-AATT
*
93580 TATATTATATAAATT
1 TTTA-TATATAAATT
93595 TT
1 TT
93597 AAAATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 8 0.29
15 6 0.21
16 2 0.07
17 8 0.29
18 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTATATATAAATT
Found at i:93570 original size:22 final size:22
Alignment explanation
Indices: 93516--93572 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
93506 TATATATTTT
* *
93516 ATTATGTTATATTTATATTTAA
1 ATTATTTTATATTTATATATAA
93538 ATTATTTTATATTTATATATAA
1 ATTATTTTATATTTATATATAA
93560 ATT-TTTATATATT
1 ATTATTT-TATATT
93573 AATAATTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 3 0.09
22 29 0.91
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTATTTTATATTTATATATAA
Found at i:99856 original size:16 final size:16
Alignment explanation
Indices: 99813--99859 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
99803 ATAAACGAAT
*
99813 TATTAACATATCAAAATT
1 TATTAA-ATAT-AAAATA
99831 TATATAAATATAAAATA
1 TAT-TAAATATAAAATA
99848 TATTAAATATAA
1 TATTAAATATAA
99860 TTATGATCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 9 0.33
17 8 0.30
18 7 0.26
19 3 0.11
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (16 bp):
TATTAAATATAAAATA
Found at i:100465 original size:22 final size:21
Alignment explanation
Indices: 100427--100476 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
100417 TATTTTTACT
*
100427 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAAAATA
*
100448 TAAATATTAA-TATAAAAAAATT
1 TAAAT-TTAATTAT-AAAAAATA
100470 TAAATTT
1 TAAATTT
100477 TTGGACTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTTAATTATAAAAAATA
Found at i:101964 original size:2 final size:2
Alignment explanation
Indices: 101957--101983 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
101947 ATAAATTATG
101957 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
101984 GGTTTGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:103554 original size:2 final size:2
Alignment explanation
Indices: 103547--103585 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
103537 ACCGCACAAA
103547 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
103586 AATGCAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:104280 original size:2 final size:2
Alignment explanation
Indices: 104273--104303 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
104263 AAGCAACATC
104273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
104304 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:104308 original size:2 final size:2
Alignment explanation
Indices: 104303--104334 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
104293 TATATATATA
104303 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
104335 CATTTCCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:104638 original size:25 final size:25
Alignment explanation
Indices: 104583--104639 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
104573 CCCAAATTAC
*
104583 AATTTAATAATAATTAATTTTTTTA
1 AATTTAATAATAATAAATTTTTTTA
*
104608 ATTTTAAT-ATAA-AAATATTTTTTA
1 AATTTAATAATAATAAAT-TTTTTTA
104632 ACATTTAA
1 A-ATTTAA
104640 ATATTATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.11
24 12 0.44
25 12 0.44
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
AATTTAATAATAATAAATTTTTTTA
Found at i:104658 original size:18 final size:19
Alignment explanation
Indices: 104610--104658 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
104600 TTTTTTTAAT
* *
104610 TTTAATATAA-AAATATTT
1 TTTAACATAATAAATATTA
*
104628 TTTAACAT-TTAAATATTA
1 TTTAACATAATAAATATTA
104646 TTTAA-ATAATAAA
1 TTTAACATAATAAA
104659 ACAAAACATC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAACATAATAAATATTA
Found at i:105367 original size:34 final size:35
Alignment explanation
Indices: 105329--105406 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 35
105319 ATATATTTAA
* *
105329 ATAAAATTTGATATGTTAAT-AATTTAAATTATGT
1 ATAAAATTTAATATATTAATGAATTTAAATTATGT
* * *
105363 ATAAATTTTAATATATTTATGTATTTAAATTATGT
1 ATAAAATTTAATATATTAATGAATTTAAATTATGT
*
105398 -TAAATTTTA
1 ATAAAATTTA
105407 TATTATGTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
34 25 0.66
35 13 0.34
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.51
Consensus pattern (35 bp):
ATAAAATTTAATATATTAATGAATTTAAATTATGT
Found at i:105390 original size:35 final size:33
Alignment explanation
Indices: 105350--105422 Score: 103
Period size: 35 Copynumber: 2.2 Consensus size: 33
105340 TATGTTAATA
*
105350 ATTTAAATTATGTATAAATTTTA-ATATATTTATGT
1 ATTTAAATTATGT-TAAATTTTATAT-TATGT-TGT
105385 ATTTAAATTATGTTAAATTTTATATTATGTTGT
1 ATTTAAATTATGTTAAATTTTATATTATGTTGT
105418 ATTTA
1 ATTTA
105423 TTTTTCGACG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
33 8 0.22
34 13 0.36
35 15 0.42
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (33 bp):
ATTTAAATTATGTTAAATTTTATATTATGTTGT
Found at i:105406 original size:17 final size:17
Alignment explanation
Indices: 105340--105415 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 17
105330 TAAAATTTGA
*
105340 TATGTTAATAATTTAAAT
1 TATGTTAA-ATTTTAAAT
105358 TATGTATAAATTTT-AAT
1 TATGT-TAAATTTTAAAT
**
105375 ATAT-TTATGTATTTAAAT
1 -TATGTTAAAT-TTTAAAT
*
105393 TATGTTAAATTTTATAT
1 TATGTTAAATTTTAAAT
105410 TATGTT
1 TATGTT
105416 GTATTTATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
16 3 0.06
17 22 0.47
18 19 0.40
19 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (17 bp):
TATGTTAAATTTTAAAT
Found at i:106226 original size:2 final size:2
Alignment explanation
Indices: 106221--106252 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
106211 AACTAATTTC
106221 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
106253 GATTAACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:108083 original size:17 final size:17
Alignment explanation
Indices: 108047--108086 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
108037 GAATATGAGC
* * *
108047 ATATGTTTGATATGATT
1 ATATATTTGATATAAAT
108064 ATATATTTGATATAAAT
1 ATATATTTGATATAAAT
108081 ATATAT
1 ATATAT
108087 AATATATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (17 bp):
ATATATTTGATATAAAT
Found at i:109119 original size:2 final size:2
Alignment explanation
Indices: 109112--109144 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
109102 CTCCATGATC
109112 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
109145 TGTTTGATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:109335 original size:14 final size:14
Alignment explanation
Indices: 109311--109343 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
109301 TGTTTTACGA
109311 TTTAAATTTAAAAAT
1 TTTAAATTT-AAAAT
109326 TTTAAA-TTAAAAT
1 TTTAAATTTAAAAT
109339 TTTAA
1 TTTAA
109344 TATATCGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 2 0.11
15 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTAAATTTAAAAT
Found at i:110748 original size:16 final size:17
Alignment explanation
Indices: 110727--110809 Score: 57
Period size: 17 Copynumber: 4.8 Consensus size: 17
110717 TAATATTATC
110727 AAATTA-ATATTTAA-TT
1 AAATTATAT-TTTAATTT
110743 AAATTATATTTTAATTT
1 AAATTATATTTTAATTT
* * * *
110760 AAATAGAAATTAAATATTTT
1 AAAT-TATATT--TTAATTT
110780 AAA-TATATTTTTAATTT
1 AAATTATA-TTTTAATTT
110797 AAA-TATATTTTAA
1 AAATTATATTTTAA
110810 ACCTTAACAA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
16 17 0.32
17 20 0.38
18 6 0.11
19 2 0.04
20 8 0.15
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (17 bp):
AAATTATATTTTAATTT
Found at i:111206 original size:27 final size:28
Alignment explanation
Indices: 111173--111243 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 28
111163 GCCACCCATT
111173 TATTTGTCAAAAATGGTGGTTAT-TTTG
1 TATTTGTCAAAAATGGTGGTTATCTTTG
* *
111200 TGTTTGTCAAAAATGGTGGTTTTCTTTG
1 TATTTGTCAAAAATGGTGGTTATCTTTG
*
111228 TATTTGTCAAATATGG
1 TATTTGTCAAAAATGG
111244 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.24, C:0.06, G:0.23, T:0.48
Consensus pattern (28 bp):
TATTTGTCAAAAATGGTGGTTATCTTTG
Found at i:111363 original size:20 final size:20
Alignment explanation
Indices: 111340--111379 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
111330 AGGCTCCCAA
111340 ATCCATCTCTAGCATCCCTC
1 ATCCATCTCTAGCATCCCTC
* * *
111360 ATCCTTCTCTTGTATCCCTC
1 ATCCATCTCTAGCATCCCTC
111380 TTCAATTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.42, G:0.05, T:0.38
Consensus pattern (20 bp):
ATCCATCTCTAGCATCCCTC
Done.