Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1271
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: 52245
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1178 original size:29 final size:29
Alignment explanation
Indices: 1044--2728 Score: 2081
Period size: 29 Copynumber: 58.5 Consensus size: 29
1034 TGTTCATCCC
*
1044 TTTCAAAGCCCCACAAATCAGTGGCACTCT
1 TTTCAAAG-CCCACAAGTCAGTGGCACTCT
*
1074 TTTCAAA-ACCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1102 TTTCAAAGCCCACAAATCAGT-GCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1129 TTTC-AAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * * *
1157 TTTCAAAGCCTATAAATAAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
1186 TTTCAAAGCCTACGAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1214 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1243 TTTCAAAGCCCATAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1272 TTTCAAAGCCCACGAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1300 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1329 TTTCAAAGCCTACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
1358 TTTCAAAGCCCACGAGTTAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
1387 TTCCAAAGCCCACAAGTTAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1416 TTCCAAAGCCCACAAGTCAATGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1445 TTTCAAAGCCTACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1474 TTTCAAAGCCCACAAGTCGGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * * *
1503 TTTCAAAGCCCATAAATTAGGGGCACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1532 TTTCAAAGCCCACGAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1560 TTTCAAAACCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1589 TTTCAAAGCCCATAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1618 TTTCAAAGCCCACAAGTTAGTGACACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1647 TTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
1676 TTCCAAAACCCACAAGTGAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1705 TTTCAAAGCCCACGAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1734 TTCCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1763 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1792 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1821 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1850 TTTCAAAGCCCACAAATCGGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1879 TTTCAAAGCCCATAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
1908 TTTCAAAGCCCACGAGTCAGTGACAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1936 TTTCAAAGCCCAGAAGTCAGTGGCA-TCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACT-CT
* *
1965 TTCCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1994 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
2023 TTTCAAAGCCCACAAGTCAATGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * **
2052 TTTCAAAGCCTATACGAGTTGGTGGCAACTCT
1 TTTCAAAGCC--CACAAGTCAGTGGC-ACTCT
* *
2084 TTCCAAAGCTCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
2113 TTTCAAAGCTCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
2141 TTTAAAAGCCCACAAGTCAGTGGCA-TCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
2169 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
2197 TTTCAAAGACCATGCAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
*
2227 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
2256 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
2284 TTTCAAAGCCAACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
2313 TTTCAAAGCCCACAAGTTAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
2341 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
2369 TTTCAAAGCCCATAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
2397 TTTCAAAGCCCATGTAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
* * *
2427 TTTCAAAGCTCATAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
2456 TTTCAAAACCCACAAGTCAATGGCACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
2485 TTTCGAAGCCCAAAAGTTAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
2513 TTTCAATGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
**
2541 TTTCAAAGCCCACGTAAGTTGGTGGCACTC-
1 TTTCAAAGCCCAC--AAGTCAGTGGCACTCT
* *
2571 TTTCAAA-ACCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
2599 TTTCAAAGCCCATAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
2627 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
2655 TTTCAAAGCCCATAAGGT-AGTGGCACTC-
1 TTTCAAAGCCCACAA-GTCAGTGGCACTCT
**
2683 TTTCAAAGCCCACACGAGTTGGTGGCAACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGC-ACTCT
2715 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
2729 CAAGTAGTGG
Statistics
Matches: 1448, Mismatches: 171, Indels: 70
0.86 0.10 0.04
Matches are distributed among these distances:
26 15 0.01
27 24 0.02
28 419 0.29
29 853 0.59
30 96 0.07
31 14 0.01
32 27 0.02
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:3331 original size:20 final size:20
Alignment explanation
Indices: 3303--3377 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
3293 TTTTACCTAG
3303 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
3323 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
3343 ATGTATTGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
3363 ATGTATCGATACATT
1 ATGTATCGATACATT
3378 ATATCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:9936 original size:210 final size:208
Alignment explanation
Indices: 9568--9954 Score: 612
Period size: 210 Copynumber: 1.9 Consensus size: 208
9558 ATTACTAACC
*
9568 TGGCTGTTGATTGTATGGACAGATTGCAATACCATTATGTTTTCTTATCGTAACCTGGAAAGTAT
1 TGGCTGTTGATTGTATGGACAGATTGCAATACCATTATGGTTTCTTATCGTAACCTGGAAAGTAT
9633 TGAATTTCATTTTTGGGACTTGGAGCTTCATTCCTTAACCCAAAAGAATAGACCATAATTTCACA
66 TGAATTTCATTTTTGGGACTTGGAGCTTCATTCCTTAACCCAAAAGAATAGACCATAATTTCACA
*
9698 TCCACTTTAAATCTTATGAGAATAAACAACTAAACAAATTGTTTATGTTCTAAAGATGTCTTAAT
131 TCCACTTTAAATCTTATCAGAATAAACAACTAAACAAATTGTTTATGTTCTAAAGATGTCTTAAT
9763 GATTGGATTGTCT
196 GATTGGATTGTCT
* * **
9776 TGGCTGTTGATTGTATGGACAGATTGCAATACTATTATGGTTTCTTATCGTAACCTAAGTATTGT
1 TGGCTGTTGATTGTATGGACAGATTGCAATACCATTATGGTTTCTTATCGTAACCT--GGAAAGT
* ** * *
9841 GTTTCATTTCATTTTTGGGAGTTGGAGCTTTATTCCTTAACCCAAAAGAATAGACCATAATTTCA
64 ATTGAATTTCATTTTTGGGACTTGGAGCTTCATTCCTTAACCCAAAAGAATAGACCATAATTTCA
* * * * *
9906 CTTCCACTTTGAATCTTATCCGAGTAAACAACTAAGCAAATTGTTTATG
129 CATCCACTTTAAATCTTATCAGAATAAACAACTAAACAAATTGTTTATG
9955 AGCATTTATA
Statistics
Matches: 161, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
208 54 0.34
210 107 0.66
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (208 bp):
TGGCTGTTGATTGTATGGACAGATTGCAATACCATTATGGTTTCTTATCGTAACCTGGAAAGTAT
TGAATTTCATTTTTGGGACTTGGAGCTTCATTCCTTAACCCAAAAGAATAGACCATAATTTCACA
TCCACTTTAAATCTTATCAGAATAAACAACTAAACAAATTGTTTATGTTCTAAAGATGTCTTAAT
GATTGGATTGTCT
Found at i:10979 original size:17 final size:18
Alignment explanation
Indices: 10951--10986 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
10941 AATTTCTTAT
10951 TCATGCATTTTTCCCCTC
1 TCATGCATTTTTCCCCTC
10969 TCATGCA-TTTTCCCCTC
1 TCATGCATTTTTCCCCTC
10986 T
1 T
10987 TTTGCGTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.11, C:0.39, G:0.06, T:0.44
Consensus pattern (18 bp):
TCATGCATTTTTCCCCTC
Found at i:13515 original size:23 final size:22
Alignment explanation
Indices: 13488--13533 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
13478 AATAAGAATT
13488 TCATATCAAAATATTTTAATATA
1 TCATATCAAAAT-TTTTAATATA
* *
13511 TCATATTATAATTTTTAATATA
1 TCATATCAAAATTTTTAATATA
13533 T
1 T
13534 TAAATTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
TCATATCAAAATTTTTAATATA
Found at i:14354 original size:23 final size:23
Alignment explanation
Indices: 14324--14367 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
14314 TAAGTCAAAT
14324 TATTATATTTAATATAATAATAA
1 TATTATATTTAATATAATAATAA
* *
14347 TATTATATTTAGTATATTAAT
1 TATTATATTTAATATAATAAT
14368 TAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTATATTTAATATAATAATAA
Found at i:15352 original size:7 final size:6
Alignment explanation
Indices: 15320--15369 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
15310 TGATTACTAA
*
15320 TTTAAT TTTAAT TTT-CT TTTAAT TTTGAATT TTTAAT TTT-AT TTT-AT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTT-AA-T TTTAAT TTTAAT TTTAAT
15367 TTT
1 TTT
15370 TTACTAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 14 0.36
6 17 0.44
7 4 0.10
8 4 0.10
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (6 bp):
TTTAAT
Found at i:15370 original size:11 final size:11
Alignment explanation
Indices: 15317--15369 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
15307 TTATGATTAC
*
15317 TAATTTAATTT
1 TAATTTTATTT
*
15328 TAATTTTCTTT
1 TAATTTTATTT
15339 TAATTTTGAATTTT
1 TAATTTT--A-TTT
15353 TAATTTTATTT
1 TAATTTTATTT
15364 T-ATTTT
1 TAATTTT
15370 TTACTAGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
10 5 0.14
11 20 0.56
12 1 0.03
14 10 0.28
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (11 bp):
TAATTTTATTT
Found at i:15923 original size:20 final size:21
Alignment explanation
Indices: 15891--15929 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
15881 TAGATGTTAT
15891 ATTTAATTTTTCTTAATAATA
1 ATTTAATTTTTCTTAATAATA
*
15912 ATTTAA-TTTTCTTCATAA
1 ATTTAATTTTTCTTAATAA
15930 AAATATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTAATTTTTCTTAATAATA
Found at i:18963 original size:16 final size:15
Alignment explanation
Indices: 18944--18995 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
18934 CTTGAAATTT
18944 AAATGATTTAAACTAA
1 AAATGATTTAAACT-A
*
18960 AAATGATATGAAACTA
1 AAATGAT-TTAAACTA
*
18976 AAATAATTTAAACTTA
1 AAATGATTTAAAC-TA
18992 AAAT
1 AAAT
18996 TTTAAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 5 0.16
16 20 0.65
17 6 0.19
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (15 bp):
AAATGATTTAAACTA
Found at i:18975 original size:17 final size:16
Alignment explanation
Indices: 18944--18978 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
18934 CTTGAAATTT
*
18944 AAATGATTTAAACTAA
1 AAATGATTGAAACTAA
18960 AAATGATATGAAACTAA
1 AAATGAT-TGAAACTAA
18977 AA
1 AA
18979 TAATTTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.60, C:0.06, G:0.09, T:0.26
Consensus pattern (16 bp):
AAATGATTGAAACTAA
Found at i:22140 original size:3 final size:3
Alignment explanation
Indices: 22132--22161 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
22122 TTTTGCTGTT
22132 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
22162 AAAAACACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:22669 original size:5 final size:5
Alignment explanation
Indices: 22659--22770 Score: 114
Period size: 5 Copynumber: 23.6 Consensus size: 5
22649 TAATATGATT
*
22659 ATATA ATATA A-A-A AT-TA AT-TA AGATATA ATATA ATATT ATA-A ATATA
1 ATATA ATATA ATATA ATATA ATATA A--TATA ATATA ATATA ATATA ATATA
* * *
22706 ATATA ATATT ATA-A ATATA ATATA ATATT ATA-A ATATA ATATA ATATT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
22754 ATA-A ATATA ATATA ATA
1 ATATA ATATA ATATA ATA
22771 ATAAAAAAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 18
0.78 0.07 0.16
Matches are distributed among these distances:
3 2 0.02
4 19 0.21
5 65 0.72
6 1 0.01
7 3 0.03
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:22705 original size:14 final size:14
Alignment explanation
Indices: 22705--22771 Score: 79
Period size: 14 Copynumber: 5.1 Consensus size: 14
22695 TTATAAATAT
22705 AATATAATATTATA
1 AATATAATATTATA
*
22719 AATATAATATAAT-
1 AATATAATATTATA
*
22732 ATTATAA-A-TAT-
1 AATATAATATTATA
22743 AATATAATATTATA
1 AATATAATATTATA
*
22757 AATATAATATAATA
1 AATATAATATTATA
22771 A
1 A
22772 TAAAAAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
11 8 0.18
12 2 0.04
13 9 0.20
14 26 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATATTATA
Found at i:22706 original size:19 final size:19
Alignment explanation
Indices: 22659--22770 Score: 179
Period size: 19 Copynumber: 5.7 Consensus size: 19
22649 TAATATGATT
*
22659 ATATAATATAAAAATTAATTAA
1 ATATAATAT-AATATT-A-TAA
22681 GATATAATATAATATTATAA
1 -ATATAATATAATATTATAA
22701 ATATAATATAATATTATAA
1 ATATAATATAATATTATAA
22720 ATATAATATAATATTATAA
1 ATATAATATAATATTATAA
22739 ATATAATATAATATTATAA
1 ATATAATATAATATTATAA
22758 ATATAATATAATA
1 ATATAATATAATA
22771 ATAAAAAAAA
Statistics
Matches: 88, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
19 70 0.80
20 3 0.03
21 1 0.01
22 5 0.06
23 9 0.10
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (19 bp):
ATATAATATAATATTATAA
Found at i:22856 original size:16 final size:16
Alignment explanation
Indices: 22804--22859 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
22794 AATAATTAAA
* *
22804 TATATCAAAATTTATG
1 TATATTAAAATTTATT
22820 TA-ATATAAAA-TTATT
1 TATAT-TAAAATTTATT
22835 AATATATTAAAATTTATT
1 --TATATTAAAATTTATT
22853 TATATTA
1 TATATTA
22860 TATATAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
15 6 0.18
16 13 0.39
17 7 0.21
18 7 0.21
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
TATATTAAAATTTATT
Found at i:23483 original size:38 final size:36
Alignment explanation
Indices: 23391--23487 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 36
23381 TATATATAAT
*
23391 AAATAATTAAAAATTATA-TTAATGTTAAATAATAAA
1 AAATAATT-AAAATTATATTTAATGTTAAATAAAAAA
* * *
23427 ATATATGTTAAAATTATATTTTATGTTAAATAAAAATGA
1 AAATA-ATTAAAATTATATTTAATGTTAAATAAAAA--A
*
23466 AAATAATTAAAGTTATATTTAA
1 AAATAATTAAAATTATATTTAA
23488 ATTAAAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
36 13 0.27
37 17 0.35
38 14 0.29
39 5 0.10
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (36 bp):
AAATAATTAAAATTATATTTAATGTTAAATAAAAAA
Found at i:23500 original size:12 final size:13
Alignment explanation
Indices: 23485--23513 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
23475 AAGTTATATT
23485 TAAATTAA-AAAA
1 TAAATTAATAAAA
23497 TAAATTAATAAAA
1 TAAATTAATAAAA
23510 TAAA
1 TAAA
23514 ACTAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAATTAATAAAA
Found at i:23657 original size:23 final size:21
Alignment explanation
Indices: 23606--23679 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 21
23596 AAATATATTT
*
23606 TTATTAATTTATTATATAATAAA
1 TTATTAATTT-TTAAATAA-AAA
*
23629 CTTTATTAATTATATTAAATAAAAG
1 --TTATTAATT-T-TTAAATAAAAA
*
23654 TTATTTCATTTTTAAATAAAAA
1 TTA-TTAATTTTTAAATAAAAA
23676 TTAT
1 TTAT
23680 AATAAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 1 0.02
22 13 0.30
23 4 0.09
24 5 0.12
25 11 0.26
26 9 0.21
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (21 bp):
TTATTAATTTTTAAATAAAAA
Found at i:23924 original size:2 final size:2
Alignment explanation
Indices: 23917--23953 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
23907 TTAAAAGTTC
23917 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 A
23954 CACACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24420 original size:32 final size:32
Alignment explanation
Indices: 24379--24442 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
24369 TAATAATTTT
* *
24379 CAAACTTAAGACCACGCACTTTGTTAAGTTAA
1 CAAACTTAAGACCACGCACTTTGCTAAATTAA
*
24411 CAAACTTAAGACCACGCGCTTTGCTAAATTAA
1 CAAACTTAAGACCACGCACTTTGCTAAATTAA
24443 AATCTAAGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (32 bp):
CAAACTTAAGACCACGCACTTTGCTAAATTAA
Found at i:26488 original size:13 final size:13
Alignment explanation
Indices: 26470--26572 Score: 89
Period size: 13 Copynumber: 7.0 Consensus size: 13
26460 TTTAGCGATT
26470 TGTATCGATACAA
1 TGTATCGATACAA
26483 TGTATCGATACAA
1 TGTATCGATACAA
26496 TGTATCGATACATAAGTGA
1 TGTATCGATAC---A---A
26515 TGTATCGATACAA
1 TGTATCGATACAA
26528 TGTATCGATACATAAGTGA
1 TGTATCGATAC---A---A
26547 TGTATCGATACAA
1 TGTATCGATACAA
*
26560 TGTATCGCTACAA
1 TGTATCGATACAA
26573 AGCTACTGCC
Statistics
Matches: 77, Mismatches: 1, Indels: 24
0.75 0.01 0.24
Matches are distributed among these distances:
13 49 0.64
16 4 0.05
19 24 0.31
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:26519 original size:19 final size:19
Alignment explanation
Indices: 26495--26558 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
26485 TATCGATACA
26495 ATGTATCGATACATAAGTG
1 ATGTATCGATACATAAGTG
26514 ATGTATCGATAC---A---
1 ATGTATCGATACATAAGTG
26527 ATGTATCGATACATAAGTG
1 ATGTATCGATACATAAGTG
26546 ATGTATCGATACA
1 ATGTATCGATACA
26559 ATGTATCGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 12 0.31
16 2 0.05
19 25 0.64
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACATAAGTG
Found at i:26523 original size:32 final size:32
Alignment explanation
Indices: 26482--26571 Score: 171
Period size: 32 Copynumber: 2.8 Consensus size: 32
26472 TATCGATACA
26482 ATGTATCGATACAATGTATCGATACATAAGTG
1 ATGTATCGATACAATGTATCGATACATAAGTG
26514 ATGTATCGATACAATGTATCGATACATAAGTG
1 ATGTATCGATACAATGTATCGATACATAAGTG
*
26546 ATGTATCGATACAATGTATCGCTACA
1 ATGTATCGATACAATGTATCGATACA
26572 AAGCTACTGC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (32 bp):
ATGTATCGATACAATGTATCGATACATAAGTG
Found at i:29021 original size:53 final size:51
Alignment explanation
Indices: 28898--29026 Score: 127
Period size: 51 Copynumber: 2.5 Consensus size: 51
28888 TTGCGTTTCT
* * * * **
28898 CAATTCTTCGCAATCGGGGGTA-TCCCAACTCCGATTTTATTTTTAAAACAC
1 CAATTTTTCACAATCGGGGATACT-CAAACTCCGATTTTATTTAAAAAACAC
* * *
28949 TAA-TTTTCTATAATTGGGGATACTCAAACTCCGATTTTATTTCCAAAAAACAC
1 CAATTTTTC-ACAATCGGGGATACTCAAACTCCGATTTTATTT--AAAAAACAC
29002 CAATTTTTCACAATCGGGGATACTC
1 CAATTTTTCACAATCGGGGATACTC
29027 CAACCCCGTT
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
50 4 0.07
51 28 0.46
52 1 0.02
53 23 0.38
54 5 0.08
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (51 bp):
CAATTTTTCACAATCGGGGATACTCAAACTCCGATTTTATTTAAAAAACAC
Found at i:29149 original size:52 final size:52
Alignment explanation
Indices: 29040--29162 Score: 144
Period size: 52 Copynumber: 2.4 Consensus size: 52
29030 CCCCGTTAAT
* * *
29040 CATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCCTTTA
1 CATCGAGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTT-CTTTA
** *
29093 -ATCGAGGATACTCCGGCTCCGATTTTATTTCCAAAAACACCAA-TTT-TTTA
1 CATCGAGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTCTTTA
29143 CCATCGAGGATACTCCAACC
1 -CATCGAGGATACTCCAACC
29163 TCGTTATTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
50 4 0.07
52 45 0.78
53 9 0.16
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (52 bp):
CATCGAGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCTTTA
Found at i:29154 original size:131 final size:132
Alignment explanation
Indices: 28922--29193 Score: 404
Period size: 131 Copynumber: 2.1 Consensus size: 132
28912 CGGGGGTATC
* * * *
28922 CCAACTCCGATTTTATTTTTAAAACACTAATTTTCTATAATTGGGGATACTCAAACTCCGATTTT
1 CCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGAGGATACTCAAACTCCGATTTT
*
28987 ATTTCCAAAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTA-ATCATCGGGGATA
66 ATTTCCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTATATCATCGGGGATA
29051 CT
131 CT
* ***
29053 CCAACCCCGATTTTATTTTCAAAACACTAATTTTCCTTTAATCGAGGATACTCCGGCTCCGATTT
1 CCAACCCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGAGGATACTCAAACTCCGATTT
* * * *
29118 TATTTCC-AAAAACACCAATTTTTTACCATCGAGGATACTCCAACCTCGTTATTTCATCGGGGAT
65 TATTTCCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTATATCATCGGGGAT
29182 ACT
130 ACT
29185 CCAACCCCG
1 CCAACCCCG
29194 TTACCTCCGA
Statistics
Matches: 126, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
131 72 0.57
132 54 0.43
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.32
Consensus pattern (132 bp):
CCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGAGGATACTCAAACTCCGATTTT
ATTTCCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTATATCATCGGGGATA
CT
Found at i:29324 original size:79 final size:79
Alignment explanation
Indices: 29175--29379 Score: 259
Period size: 79 Copynumber: 2.6 Consensus size: 79
29165 GTTATTTCAT
** *
29175 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTCTCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCTCAAAATAT
* * *
29240 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * * *
29254 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCTCAAAAT-A
29318 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * *
29333 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGGACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
29380 TTATTATCTC
Statistics
Matches: 108, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 3 0.03
79 105 0.97
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCTCAAAATAT
CGATTTCTCACAAC
Found at i:41804 original size:9 final size:9
Alignment explanation
Indices: 41781--41823 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
41771 ACCTTCTCTT
41781 AAAAAAAAGC
1 AAAAAAAA-C
41791 GAAAAAAAAC
1 -AAAAAAAAC
41801 AAAAAAAAC
1 AAAAAAAAC
* *
41810 AAAACAAAG
1 AAAAAAAAC
41819 AAAAA
1 AAAAA
41824 GAGAGAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 20 0.69
10 1 0.03
11 8 0.28
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:43093 original size:28 final size:28
Alignment explanation
Indices: 43007--43093 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
42997 CGCCTTCTCC
43007 TTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAAAGCCCACACAAGTTGGTGGCAT
* * * * ** *
43035 TTTC-TAGTCCTCAAAGAGCAGGAT-GCCT
1 TTTCAAAGCCCACACA-AGTTGG-TGGCAT
43063 TTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAAAGCCCACACAAGTTGGTGGCAT
43091 TTT
1 TTT
43094 TTAGTCCTCA
Statistics
Matches: 41, Mismatches: 14, Indels: 8
0.65 0.22 0.13
Matches are distributed among these distances:
27 8 0.20
28 25 0.61
29 8 0.20
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (28 bp):
TTTCAAAGCCCACACAAGTTGGTGGCAT
Found at i:43215 original size:55 final size:55
Alignment explanation
Indices: 42825--43565 Score: 787
Period size: 55 Copynumber: 13.0 Consensus size: 55
42815 GATGCCTGTT
* * * *
42825 CCTTTTAAAGCTCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGATGCTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA--C----A
* * *
42885 CTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCCCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* *
42940 CCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCAC-CTTCAGTCCTCAAAGAGCAGGACGCCTTC
1 CC-TTTC----AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA------C
*
43004 T
55 A
**
43005 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACA
* * ***
43060 CCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCATGATGTTTTTT
1 CC-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCA-G--G---ACA
* * * *
43122 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAGGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
43177 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* *
43232 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTT
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA--C----A
* * *
43293 CTTTTCAAAGCCTACACGAGTTGGTGGCACTTTTCAGTCC-CTAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTC-AAAGAGCAGGACA
43348 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* * *
43403 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* * * *
43458 TCTTTCAAAGCCCATACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* *
43513 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
43566 TACACTTTAT
Statistics
Matches: 591, Mismatches: 52, Indels: 81
0.82 0.07 0.11
Matches are distributed among these distances:
54 7 0.01
55 288 0.49
56 55 0.09
57 6 0.01
58 1 0.00
59 21 0.04
60 81 0.14
61 123 0.21
62 2 0.00
64 4 0.01
65 3 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
Found at i:43301 original size:171 final size:172
Alignment explanation
Indices: 42825--43565 Score: 977
Period size: 171 Copynumber: 4.3 Consensus size: 172
42815 GATGCCTGTT
* * ** **
42825 CCTTTTAAAGCTCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGATGCTTTTTCTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C---ACCTTT
* * * *
42889 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCCCAAAGAGCAGGACGCCTTTTCTTTT-A
61 TCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCA
* * *
42952 AAGCCCACACAAGTTAGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGCCTTCT
125 AAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGA------CA
* **
43005 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCAAA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTTCAAA
** * * *
43070 GCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCATGATGTTTTTTCTTTTCAAAGCCC
66 GCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCC
*
43135 ACACAAGTTGGTGGCACCTTTCAGTCCCCAAGGAGCAGGACA
131 ACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
*
43177 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTTCAAA
*
43241 GCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCT
66 GCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCC
* * *
43306 ACACGAGTTGGTGGCACTTTTCAGTCCCTAAAGAGCAGGACA
131 ACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
43348 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTT-AAA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTTCAAA
*
43412 GCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA--C---GTC-TTTCAAAGCCC
66 GCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCC
* * *
43471 ATACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
131 ACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
* *
43513 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
43566 TACACTTTAT
Statistics
Matches: 513, Mismatches: 43, Indels: 25
0.88 0.07 0.04
Matches are distributed among these distances:
165 92 0.18
166 6 0.01
169 1 0.00
171 207 0.40
172 58 0.11
176 55 0.11
177 28 0.05
178 19 0.04
180 29 0.06
181 18 0.04
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (172 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTTCAAA
GCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCC
ACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
Found at i:43434 original size:29 final size:29
Alignment explanation
Indices: 43346--43436 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
43336 AAGAGCAGGA
*
43346 CACCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTTTAAAGCCCACACAAGTTGGTGG
** * * * **
43375 CA--TTTTCCAGTCCTCA-AAG-AGCAGG
1 CACCTTTTAAAGCCCACACAAGTTGGTGG
43400 ACACCTTTTAAAGCCCACACAAGTTGGTGG
1 -CACCTTTTAAAGCCCACACAAGTTGGTGG
43430 CACCTTT
1 CACCTTT
43437 CAGTCCTCAA
Statistics
Matches: 42, Mismatches: 15, Indels: 10
0.63 0.22 0.15
Matches are distributed among these distances:
25 3 0.07
26 5 0.12
27 9 0.21
28 10 0.24
29 12 0.29
30 3 0.07
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (29 bp):
CACCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:44380 original size:19 final size:18
Alignment explanation
Indices: 44356--44452 Score: 88
Period size: 19 Copynumber: 5.8 Consensus size: 18
44346 TTTCAGTGAT
44356 TTGTATCGATACATAAGTG
1 TTGTATCGATACA-AAGTG
44375 TTGTATCGATAC-AA---
1 TTGTATCGATACAAAGTG
44389 -TGTATCGATACACAAGTG
1 TTGTATCGATACA-AAGTG
44407 TTGTATCGATAC-AA---
1 TTGTATCGATACAAAGTG
44421 -TGTATCGATACACAAGTG
1 TTGTATCGATACA-AAGTG
*
44439 ATGTATCGATACAA
1 TTGTATCGATACAA
44453 TGTATCGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
18 1 0.02
19 35 0.53
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (18 bp):
TTGTATCGATACAAAGTG
Found at i:44394 original size:13 final size:13
Alignment explanation
Indices: 44376--44465 Score: 63
Period size: 13 Copynumber: 6.0 Consensus size: 13
44366 ACATAAGTGT
44376 TGTATCGATACAA
1 TGTATCGATACAA
44389 TGTATCGATACACAA
1 TGTATCGAT--ACAA
44404 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
44421 TGTATCGATACACAAGTGA
1 TGTATCGAT--AC-A---A
44440 TGTATCGATACAA
1 TGTATCGATACAA
*
44453 TGTATCGCTACAA
1 TGTATCGATACAA
44466 AGCTACTACC
Statistics
Matches: 64, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 31 0.48
15 6 0.09
16 2 0.03
17 6 0.09
19 19 0.30
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:44398 original size:32 final size:32
Alignment explanation
Indices: 44357--44464 Score: 189
Period size: 32 Copynumber: 3.4 Consensus size: 32
44347 TTCAGTGATT
*
44357 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACACAAGTGTTGTATCGATACAA
44389 TGTATCGATACACAAGTGTTGTATCGATACAA
1 TGTATCGATACACAAGTGTTGTATCGATACAA
*
44421 TGTATCGATACACAAGTGATGTATCGATACAA
1 TGTATCGATACACAAGTGTTGTATCGATACAA
*
44453 TGTATCGCTACA
1 TGTATCGATACA
44465 AAGCTACTAC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 73 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (32 bp):
TGTATCGATACACAAGTGTTGTATCGATACAA
Found at i:46936 original size:51 final size:52
Alignment explanation
Indices: 46879--47001 Score: 171
Period size: 51 Copynumber: 2.4 Consensus size: 52
46869 CAATTCTCCG
* *
46879 CAATCGGGGATA-TCCCAACTCCGATTTTATTTTC-AAAACACTAA-TTTTCTA
1 CAATCGGGGATACT-CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-A
*
46930 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTTTTCA
46983 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
47002 CCCGTTAATC
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
51 30 0.47
52 1 0.02
53 28 0.44
54 5 0.08
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (52 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCA
Found at i:46993 original size:53 final size:51
Alignment explanation
Indices: 46879--47001 Score: 169
Period size: 53 Copynumber: 2.4 Consensus size: 51
46869 CAATTCTCCG
* *
46879 CAATCGGGGATA-TCCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACT-CCAACTCCGATTTTATTTCCAAAACACCAATTTTCTA
*
46930 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTT-TCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACACCAATTTTCT-A
46983 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
47002 CCCGTTAATC
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
51 30 0.47
52 2 0.03
53 32 0.50
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTA
Found at i:47125 original size:52 final size:52
Alignment explanation
Indices: 47011--47136 Score: 148
Period size: 52 Copynumber: 2.4 Consensus size: 52
47001 CCCCGTTAAT
* * **
47011 CATCGGGGATACTCCAACCTCGATTTTATTTTCAAAACACTAATTTTCCTTT
1 CATCGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTCCTAC
* * *
47063 AATCGGGGATACTCCGA-CTCCGATTTTATTTCCAAAAACACCAATTTTTC-AC
1 CATCGGGGATACTCCAACCT-CGATTTTATTTCC-AAAACACCAATTTTCCTAC
*
47115 CATCGAGGATACTCCAACCTCG
1 CATCGGGGATACTCCAACCTCG
47137 TTATTTCATC
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
51 2 0.03
52 43 0.70
53 16 0.26
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.32
Consensus pattern (52 bp):
CATCGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTCCTAC
Found at i:47125 original size:131 final size:133
Alignment explanation
Indices: 46881--47161 Score: 455
Period size: 131 Copynumber: 2.1 Consensus size: 133
46871 ATTCTCCGCA
46881 ATCGGGGATA-TCCCAA-CTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
1 ATCGGGGATACT-CCAACCTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
*
46944 CCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTA
65 CCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTA
47009 -ATC
130 TATC
*
47012 ATCGGGGATACTCCAACCT-CGATTTTATTTTCAAAACACTAATTTTCCTTTAATCGGGGATACT
1 ATCGGGGATACTCCAACCTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGATACT
* * *
47076 CCGACTCCGATTTTATTTCC-AAAAACACCAATTTTTCACCATCGAGGATACTCCAACCTCGTTA
65 CCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTA
*
47140 TTTC
130 TATC
47144 ATCGGGGATACTCCAACC
1 ATCGGGGATACTCCAACC
47162 CCGTTACCTC
Statistics
Matches: 140, Mismatches: 6, Indels: 7
0.92 0.04 0.05
Matches are distributed among these distances:
131 82 0.59
132 58 0.41
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (133 bp):
ATCGGGGATACTCCAACCTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTC
CAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTAT
ATC
Found at i:47144 original size:31 final size:28
Alignment explanation
Indices: 47115--47192 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
47105 AATTTTTCAC
*
47115 CATCGAGGATACTCCAACCTCGTTATTT
1 CATCGAGGATACTCCAACCCCGTTATTT
* **
47143 CATCGGGGATACTCCAACCCCGTTACCT
1 CATCGAGGATACTCCAACCCCGTTATTT
47171 C--CGAGGGGATACTCCAACCCCG
1 CATCGA--GGATACTCCAACCCCG
47193 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 41 0.95
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (28 bp):
CATCGAGGATACTCCAACCCCGTTATTT
Found at i:47295 original size:79 final size:79
Alignment explanation
Indices: 47146--47350 Score: 216
Period size: 79 Copynumber: 2.6 Consensus size: 79
47136 GTTATTTCAT
**
47146 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAC
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAC
* *
47211 TGATTTCTCATAAT
66 TGATTTCTCACAAC
* * * ** * ** *
47225 TGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAAT-C
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAC
47288 ATCGATTTCTCACAAC
66 -T-GATTTCTCACAAC
* * * **
47304 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGGACCCTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG
47351 TTATTATCTC
Statistics
Matches: 103, Mismatches: 21, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
77 1 0.01
78 4 0.04
79 98 0.95
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.28
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAC
TGATTTCTCACAAC
Found at i:48462 original size:20 final size:19
Alignment explanation
Indices: 48437--48490 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
48427 CTACCACTGT
48437 TTGTATCGATACATG-GCATA
1 TTGTATCGATACATGAG-A-A
48457 TTGTATCGATACATGAAGAA
1 TTGTATCGATACATG-AGAA
48477 TTGTATCGATACAT
1 TTGTATCGATACAT
48491 TGTTCCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:50748 original size:19 final size:21
Alignment explanation
Indices: 50705--50756 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
50695 TTTCAATATT
*
50705 TGTATCGATACATTCAGTAAA
1 TGTATCGATACATTAAGTAAA
50726 TGTATCGATACA-TAAGT-AA
1 TGTATCGATACATTAAGTAAA
50745 TGTATCGATACA
1 TGTATCGATACA
50757 GTGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 14 0.47
20 4 0.13
21 12 0.40
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATTAAGTAAA
Found at i:50806 original size:13 final size:13
Alignment explanation
Indices: 50788--50813 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50778 GCCAAGGAAA
50788 TGTATCGATACAT
1 TGTATCGATACAT
50801 TGTATCGATACAT
1 TGTATCGATACAT
50814 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Done.