Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1526
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: 39871
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Found at i:3528 original size:21 final size:21
Alignment explanation
Indices: 3487--3536 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3477 TAGCCTTTGA
**
3487 CCATGCATTTTTTTACTATGT
1 CCATGCATTTTTAAACTATGT
3508 CCATGCATTTTTAAAAC-ATGT
1 CCATGCATTTTT-AAACTATGT
3529 CCA-GCATT
1 CCATGCATT
3537 CTCATTGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 19 0.73
22 2 0.08
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (21 bp):
CCATGCATTTTTAAACTATGT
Found at i:4977 original size:19 final size:19
Alignment explanation
Indices: 4950--5003 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
4940 AGTATTTATA
*
4950 AAATAATATATATTTAATT
1 AAATGATATATATTTAATT
*
4969 AAATGATATGATTTTTAA-T
1 AAATGATAT-ATATTTAATT
4988 AAA-GATAT-TA-TTAATT
1 AAATGATATATATTTAATT
5004 TACTTAGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
15 4 0.13
16 2 0.07
18 5 0.17
19 12 0.40
20 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (19 bp):
AAATGATATATATTTAATT
Found at i:5005 original size:20 final size:21
Alignment explanation
Indices: 4960--5005 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
4950 AAATAATATA
4960 TATTTAATTAAATGATATGAT
1 TATTTAATTAAATGATATGAT
*
4981 T-TTTAA-TAAA-GATATTAT
1 TATTTAATTAAATGATATGAT
4999 TAATTTA
1 T-ATTTA
5006 CTTAGGTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 8 0.36
19 4 0.18
20 9 0.41
21 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TATTTAATTAAATGATATGAT
Found at i:5055 original size:49 final size:49
Alignment explanation
Indices: 4998--5131 Score: 250
Period size: 49 Copynumber: 2.7 Consensus size: 49
4988 AAAGATATTA
*
4998 TTAATTTACTTAGGTTAGCTAAAATCATACAAGCTTTTTTTATATTTTT
1 TTAATTTACTTAGGTTAGCTAAAATCATATAAGCTTTTTTTATATTTTT
*
5047 TTAATTTACTTAGGTTACCTAAAATCATATAAGCTTTTTTTATATTTTT
1 TTAATTTACTTAGGTTAGCTAAAATCATATAAGCTTTTTTTATATTTTT
5096 TTAATTTACTTAGGTTAGCTAAAATCATATAAGCTT
1 TTAATTTACTTAGGTTAGCTAAAATCATATAAGCTT
5132 ATATTAAAAT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 82 1.00
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.49
Consensus pattern (49 bp):
TTAATTTACTTAGGTTAGCTAAAATCATATAAGCTTTTTTTATATTTTT
Found at i:7474 original size:18 final size:19
Alignment explanation
Indices: 7442--7513 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 19
7432 CGATCAAATC
*
7442 AATTAAATTAA-ATTATTT
1 AATTAAATAAATATTATTT
*
7460 AATTAAA-AAATATTA-TA
1 AATTAAATAAATATTATTT
7477 ATATTAAATAAATATT-TTT
1 A-ATTAAATAAATATTATTT
*
7496 AATATTAAATAAAAATTA
1 -A-ATTAAATAAATATTA
7514 AATATATAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 4 0.09
18 17 0.39
19 8 0.18
20 15 0.34
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTAAATAAATATTATTT
Found at i:7500 original size:20 final size:19
Alignment explanation
Indices: 7461--7518 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
7451 AAATTATTTA
7461 ATTAAA-AAATATTATAAT
1 ATTAAATAAATATTATAAT
*
7479 ATTAAATAAATATTTTTAAT
1 ATTAAATAAATA-TTATAAT
*
7499 ATTAAATAAAAATTA-AAT
1 ATTAAATAAATATTATAAT
7517 AT
1 AT
7519 ATAAGTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.31
19 7 0.20
20 17 0.49
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTAAATAAATATTATAAT
Found at i:8495 original size:13 final size:13
Alignment explanation
Indices: 8477--8502 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8467 ACATTTTGGG
8477 ATGTATCGATACA
1 ATGTATCGATACA
8490 ATGTATCGATACA
1 ATGTATCGATACA
8503 TAATGTGTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:8497 original size:33 final size:32
Alignment explanation
Indices: 8455--8522 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
8445 CGTTACAAGC
**
8455 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATAATGGG-TGTATCGATA
*
8488 CAATGTATCGATACATAATGTGTGTATCGATA
1 CAATGTATCGATACATAATGGGTGTATCGATA
8520 CAA
1 CAA
8523 ACAGTTAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (32 bp):
CAATGTATCGATACATAATGGGTGTATCGATA
Found at i:11104 original size:13 final size:13
Alignment explanation
Indices: 11086--11122 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
11076 AAACCCTTTG
*
11086 TATCGATACACTA
1 TATCGATACAATA
*
11099 TATCGATACAATG
1 TATCGATACAATA
11112 TATCGATACAA
1 TATCGATACAA
11123 AGAATGTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:17101 original size:73 final size:73
Alignment explanation
Indices: 17010--17195 Score: 354
Period size: 73 Copynumber: 2.5 Consensus size: 73
17000 ATCCCGTGTA
17010 AATGTATCGATACATTTTGGGATGTATCGATACATGTATTTGAAAATATAGCCATTACTAGCCGT
1 AATGTATCGATACATTTTGGGATGTATCGATACATGTATTTGAAAATATAGCCATTACTAGCCGT
17075 TACAAGCC
66 TACAAGCC
*
17083 AATGTATCGATACATTTTGGGATGTATCGATACATGTATTTGAAAATATAGCCATTACTAGCTGT
1 AATGTATCGATACATTTTGGGATGTATCGATACATGTATTTGAAAATATAGCCATTACTAGCCGT
17148 TACAAGCC
66 TACAAGCC
17156 AATGTATCGATACATTTTGGGATGTATCGATACAATGTAT
1 AATGTATCGATACATTTTGGGATGTATCGATAC-ATGTAT
17196 CGATACATAA
Statistics
Matches: 111, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
73 105 0.95
74 6 0.05
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (73 bp):
AATGTATCGATACATTTTGGGATGTATCGATACATGTATTTGAAAATATAGCCATTACTAGCCGT
TACAAGCC
Found at i:17195 original size:13 final size:13
Alignment explanation
Indices: 17177--17202 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17167 ACATTTTGGG
17177 ATGTATCGATACA
1 ATGTATCGATACA
17190 ATGTATCGATACA
1 ATGTATCGATACA
17203 TAATGTGTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:17197 original size:33 final size:32
Alignment explanation
Indices: 17155--17222 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
17145 TGTTACAAGC
**
17155 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATAATGGG-TGTATCGATA
*
17188 CAATGTATCGATACATAATGTGTGTATCGATA
1 CAATGTATCGATACATAATGGGTGTATCGATA
17220 CAA
1 CAA
17223 ACAGTTAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (32 bp):
CAATGTATCGATACATAATGGGTGTATCGATA
Found at i:18809 original size:65 final size:65
Alignment explanation
Indices: 18697--18823 Score: 173
Period size: 65 Copynumber: 2.0 Consensus size: 65
18687 CATTTCACAC
* * * *
18697 TTTCAAAGCTCAATAATTTCATTATGTATTGTCAAAAAACATCAATTAAGAATGGCTAACTCTTA
1 TTTCAAAGCTCAATAATTTCATTACGTACTATCAAAAAACATCAATTAAGAATGGCCAACTCTTA
* * * * *
18762 TTTCAAAGCTCAATAATTTCATTGCGTACTATCGAAAAATATTAATTAAGAATTGCCAACTC
1 TTTCAAAGCTCAATAATTTCATTACGTACTATCAAAAAACATCAATTAAGAATGGCCAACTC
18824 ATATCAAGTG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (65 bp):
TTTCAAAGCTCAATAATTTCATTACGTACTATCAAAAAACATCAATTAAGAATGGCCAACTCTTA
Found at i:19773 original size:21 final size:20
Alignment explanation
Indices: 19744--19795 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
19734 ATTAAATTAT
*
19744 TTAATTAAAAAGATTTTAATA
1 TTAAATAAAAA-ATTTTAATA
* *
19765 TTAAATAAATAATTTTAGTA
1 TTAAATAAAAAATTTTAATA
19785 TTAAATAAAAA
1 TTAAATAAAAA
19796 TTAAATATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (20 bp):
TTAAATAAAAAATTTTAATA
Found at i:20990 original size:17 final size:18
Alignment explanation
Indices: 20947--20992 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
20937 GTTATATTAA
*
20947 AATAAATTAGGTTTAATAT
1 AATAAATTA-TTTTAATAT
*
20966 ATTAAATTATTTTAA-AT
1 AATAAATTATTTTAATAT
20983 AATAAATTAT
1 AATAAATTAT
20993 GCAAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 11 0.46
18 5 0.21
19 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (18 bp):
AATAAATTATTTTAATAT
Found at i:21139 original size:65 final size:65
Alignment explanation
Indices: 21058--21184 Score: 182
Period size: 65 Copynumber: 2.0 Consensus size: 65
21048 TATTTCAGAT
** * *
21058 TTTCAAAGCTCAATAATTTCATTATATACTGCCAAAAAACATCAATTAAGAATGGCGAACTCTTA
1 TTTCAAAGCTCAATAATTTCACCACATACTGCCAAAAAACATCAATTAAGAATGGCCAACTCTTA
* * * *
21123 TTTCAAAGCTCAATAATTTCACCACGTACTGCCCAAAAATATTAATTAAGAATGGCCAACTC
1 TTTCAAAGCTCAATAATTTCACCACATACTGCCAAAAAACATCAATTAAGAATGGCCAACTC
21185 ATATCAAGTG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.29
Consensus pattern (65 bp):
TTTCAAAGCTCAATAATTTCACCACATACTGCCAAAAAACATCAATTAAGAATGGCCAACTCTTA
Found at i:22162 original size:20 final size:19
Alignment explanation
Indices: 22130--22176 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
22120 ATTATTTAAT
*
22130 TAAAAAATTTAATATAAAA
1 TAAAAATTTTAATATAAAA
*
22149 TAAATAATTTTAATATTAAA
1 TAAA-AATTTTAATATAAAA
22169 TAAAAATT
1 TAAAAATT
22177 AAATATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAATTTTAATATAAAA
Found at i:22192 original size:27 final size:27
Alignment explanation
Indices: 22126--22192 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
22116 TTAAATTATT
* * *
22126 TAATTAAAAAATTTAATATAAAATAAA
1 TAATTATAATATTAAATATAAAATAAA
*
22153 TAATTTTAATATTAAATA-AAAATTAAA
1 TAATTATAATATTAAATATAAAA-TAAA
22180 T-ATTATAAGTATT
1 TAATTATAA-TATT
22193 TACAAAAGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (27 bp):
TAATTATAATATTAAATATAAAATAAA
Found at i:23253 original size:70 final size:70
Alignment explanation
Indices: 23168--23308 Score: 246
Period size: 70 Copynumber: 2.0 Consensus size: 70
23158 ACCAAATATA
* *
23168 TGGTAGAAGCTGTCATTGTTGAATCAACAGAGAAAAAGACAAGGACAAAAGCTGCTCCAACTCTT
1 TGGTAGAAGCTGTCATTGTTGAATCAACAGAGAAAAACACAAGGACAAAAGCTGCTCCAACTCTG
23233 ATTTC
66 ATTTC
* *
23238 TGGTAGAAGCTGTCATTGTTGAATCAACAGAGAAAAACACAAGGGCAAAAGCTGCTTCAACTCTG
1 TGGTAGAAGCTGTCATTGTTGAATCAACAGAGAAAAACACAAGGACAAAAGCTGCTCCAACTCTG
23303 ATTTC
66 ATTTC
23308 T
1 T
23309 TCTCTCTTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (70 bp):
TGGTAGAAGCTGTCATTGTTGAATCAACAGAGAAAAACACAAGGACAAAAGCTGCTCCAACTCTG
ATTTC
Found at i:24594 original size:20 final size:18
Alignment explanation
Indices: 24553--24606 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
24543 TTTTAAATAT
24553 TAAATATAATATATATTTA
1 TAAA-ATAATATATATTTA
24572 TAAAATAATATATATTTA
1 TAAAATAATATATATTTA
*
24590 AATAAATAATATA-ATTT
1 TA-AAATAATATATATTT
24607 TTAATCTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 19 0.58
19 14 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATAATATATATTTA
Found at i:25935 original size:16 final size:16
Alignment explanation
Indices: 25892--25955 Score: 51
Period size: 20 Copynumber: 3.7 Consensus size: 16
25882 AATTTAATTA
25892 ATTAAATTAAATTATT-T
1 ATTAAA-TAAATT-TTAT
25909 ATTTAAA-AAATTTTAT
1 A-TTAAATAAATTTTAT
25925 ATTAAATAAATAATTTTAAT
1 ATTAAAT--A-AATTTT-AT
25945 ATTAAATAAAT
1 ATTAAATAAAT
25956 ATTAAATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
15 7 0.17
16 7 0.17
17 4 0.10
18 7 0.17
19 6 0.15
20 9 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAAATAAATTTTAT
Found at i:25939 original size:19 final size:20
Alignment explanation
Indices: 25912--25956 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
25902 ATTATTTATT
*
25912 TAAAAAATTTT-ATATTAAA
1 TAAATAATTTTAATATTAAA
25931 TAAATAATTTTAATATTAAA
1 TAAATAATTTTAATATTAAA
25951 TAAATA
1 TAAATA
25957 TTAAATATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATAATTTTAATATTAAA
Found at i:27034 original size:15 final size:16
Alignment explanation
Indices: 27007--27039 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
26997 CTCTTTTTTC
27007 TTCTTTCTTTTATCTT
1 TTCTTTCTTTTATCTT
27023 TTCTTT-TTTTATCTT
1 TTCTTTCTTTTATCTT
27038 TT
1 TT
27040 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (16 bp):
TTCTTTCTTTTATCTT
Found at i:27037 original size:26 final size:25
Alignment explanation
Indices: 26998--27049 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
26988 CTGCTCCAAC
26998 TCTTTTTTCTTCTTTCTTTTATCTTT
1 TCTTTTTTCTTCTTT-TTTTATCTTT
*
27024 TCTTTTTT-TATCTTTTTTTATTTTT
1 TCTTTTTTCT-TCTTTTTTTATCTTT
27049 T
1 T
27050 AAAATTTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (25 bp):
TCTTTTTTCTTCTTTTTTTATCTTT
Found at i:27109 original size:21 final size:20
Alignment explanation
Indices: 27084--27127 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
27074 CAATCATAAC
*
27084 TAAAATCAAACAAATTTATAT
1 TAAAATAAAACAAATTTA-AT
*
27105 TAAAATAAAATAAATTTAAT
1 TAAAATAAAACAAATTTAAT
27125 TAA
1 TAA
27128 TTAAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAATAAAACAAATTTAAT
Found at i:28436 original size:19 final size:18
Alignment explanation
Indices: 28403--28446 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
28393 CACAAAACAA
28403 AAAATAACATAAACACATC
1 AAAAT-ACATAAACACATC
* *
28422 ATAAATACATGAACATATC
1 A-AAATACATAAACACATC
28441 AAAATA
1 AAAATA
28447 TATATAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 13 0.59
20 4 0.18
ACGTcount: A:0.61, C:0.16, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAATACATAAACACATC
Found at i:29689 original size:17 final size:18
Alignment explanation
Indices: 29662--29697 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
29652 AAAAAATTTA
29662 AATTTTGAAAAATAAAAT
1 AATTTTGAAAAATAAAAT
29680 AATTTT-AAAAATAAAAT
1 AATTTTGAAAAATAAAAT
29697 A
1 A
29698 TTAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
AATTTTGAAAAATAAAAT
Found at i:30915 original size:2 final size:2
Alignment explanation
Indices: 30908--30937 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30898 CATTGCAATA
30908 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
30938 TTGTTCAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:34485 original size:4 final size:4
Alignment explanation
Indices: 34478--34502 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
34468 TTTTTGTTTG
34478 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
34503 TTGAATTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:34696 original size:22 final size:22
Alignment explanation
Indices: 34662--34704 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
34652 CATATAATCG
*
34662 AATATATTTATGAATAATTAAA
1 AATATATTCATGAATAATTAAA
*
34684 AATATGTTCATGAATAATTAA
1 AATATATTCATGAATAATTAA
34705 CAAGCAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (22 bp):
AATATATTCATGAATAATTAAA
Found at i:38074 original size:13 final size:13
Alignment explanation
Indices: 38056--38081 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38046 TACACCAAGT
38056 ATGTATCGATACA
1 ATGTATCGATACA
38069 ATGTATCGATACA
1 ATGTATCGATACA
38082 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:38079 original size:32 final size:33
Alignment explanation
Indices: 38038--38101 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
38028 TAGCCAAACT
* **
38038 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
38070 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
38102 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Done.