Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold235
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: 1667838
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 72548 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1587940 original size:26 final size:26
Alignment explanation
Indices: 1587911--1588075 Score: 159
Period size: 27 Copynumber: 6.2 Consensus size: 26
1587901 TATAGCAGTC
* *
1587911 ATTTTACCCTATGAGGTATTTCGGTT
1 ATTTTACCCTTTGGGGTATTTCGGTT
** *
1587937 ATTTTATACTTTGGGGGTATTTCAGTT
1 ATTTTACCCTTT-GGGGTATTTCGGTT
*
1587964 ATTTCACCCTTTGGGGTATTTCGGTT
1 ATTTTACCCTTTGGGGTATTTCGGTT
* * *
1587990 ATTTTACCCCTTGGGGTATTTCGATC
1 ATTTTACCCTTTGGGGTATTTCGGTT
* *
1588016 ATTTTACCCTTTTGGGGTATTTCAGTC
1 ATTTTACCC-TTTGGGGTATTTCGGTT
** * * *
1588043 ATTTTGTCTTTTGGGGGTATTTTGGTC
1 ATTTTACCCTTT-GGGGTATTTCGGTT
1588070 ATTTTA
1 ATTTTA
1588076 TTGACCCCAT
Statistics
Matches: 114, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
26 56 0.49
27 58 0.51
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.49
Consensus pattern (26 bp):
ATTTTACCCTTTGGGGTATTTCGGTT
Found at i:1587957 original size:27 final size:26
Alignment explanation
Indices: 1587908--1588075 Score: 165
Period size: 26 Copynumber: 6.3 Consensus size: 26
1587898 GGGTATAGCA
* *
1587908 GTCATTTTACCCTATGAGGTATTTCG
1 GTCATTTTACCCTTTGGGGTATTTCG
* ** *
1587934 GTTATTTTATACTTTGGGGGTATTTCA
1 GTCATTTTACCCTTT-GGGGTATTTCG
* *
1587961 GTTATTTCACCCTTTGGGGTATTTCG
1 GTCATTTTACCCTTTGGGGTATTTCG
* *
1587987 GTTATTTTACCCCTTGGGGTATTTCG
1 GTCATTTTACCCTTTGGGGTATTTCG
* *
1588013 ATCATTTTACCCTTTTGGGGTATTTCA
1 GTCATTTTACCC-TTTGGGGTATTTCG
** * *
1588040 GTCATTTTGTCTTTTGGGGGTATTTTG
1 GTCATTTTACCCTTT-GGGGTATTTCG
1588067 GTCATTTTA
1 GTCATTTTA
1588076 TTGACCCCAT
Statistics
Matches: 116, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
26 58 0.50
27 58 0.50
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.49
Consensus pattern (26 bp):
GTCATTTTACCCTTTGGGGTATTTCG
Found at i:1587982 original size:53 final size:52
Alignment explanation
Indices: 1587897--1588075 Score: 182
Period size: 53 Copynumber: 3.4 Consensus size: 52
1587887 TCGACTCCTA
** * *
1587897 GGGGTATAGCAGTCATTTTACCCTATGAGGTATTTCGGTTATTTTATACTTTG
1 GGGGTATTTCAGTCATTTTACCCTTTGGGGTATTTCGGTTATTTTAT-CTTTG
* * * *
1587950 GGGGTATTTCAGTTATTTCACCCTTTGGGGTATTTCGGTTATTTTACCCCTT-
1 GGGGTATTTCAGTCATTTTACCCTTTGGGGTATTTCGGTTATTTTA-TCTTTG
* * *
1588002 GGGGTATTTC-GATCATTTTACCCTTTTGGGGTATTTCAGTCATTTTGTCTTTTG
1 GGGGTATTTCAG-TCATTTTACCC-TTTGGGGTATTTCGGTTATTTTATC-TTTG
**
1588056 GGGGTATTTTGGTCATTTTA
1 GGGGTATTTCAGTCATTTTA
1588076 TTGACCCCAT
Statistics
Matches: 104, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
51 1 0.01
52 20 0.19
53 65 0.62
54 17 0.16
55 1 0.01
ACGTcount: A:0.16, C:0.15, G:0.23, T:0.47
Consensus pattern (52 bp):
GGGGTATTTCAGTCATTTTACCCTTTGGGGTATTTCGGTTATTTTATCTTTG
Found at i:1593497 original size:55 final size:57
Alignment explanation
Indices: 1593424--1593543 Score: 142
Period size: 55 Copynumber: 2.1 Consensus size: 57
1593414 AAAATCTGTC
* *
1593424 TAAAAAA-AGAAGAGAAGATAATCCTGGGATGTTAGTTTTTTATCCTAG-AAAAAA-AT
1 TAAAAAAGAGAAGAGAAGATAATCCTGGGATGTTAG--ATTTACCCTAGTAAAAAATAT
* *
1593480 TAAAAAAGAGAA-A-AAGATAATCTTGGGTTGTTAGATTTACCCTAGTAAAAAATAT
1 TAAAAAAGAGAAGAGAAGATAATCCTGGGATGTTAGATTTACCCTAGTAAAAAATAT
1593535 TATAAAAAG
1 TA-AAAAAG
1593544 TCAAAGGAGG
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
53 9 0.16
54 6 0.11
55 23 0.41
56 14 0.25
57 4 0.07
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (57 bp):
TAAAAAAGAGAAGAGAAGATAATCCTGGGATGTTAGATTTACCCTAGTAAAAAATAT
Found at i:1594346 original size:12 final size:11
Alignment explanation
Indices: 1594320--1594354 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1594310 TGCTATAGTA
*
1594320 TTATTAGTTAT
1 TTATTTGTTAT
1594331 TTATTTGTTCAT
1 TTATTTGTT-AT
1594343 TTATTTGTTAT
1 TTATTTGTTAT
1594354 T
1 T
1594355 CACATAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.20, C:0.03, G:0.09, T:0.69
Consensus pattern (11 bp):
TTATTTGTTAT
Found at i:1599206 original size:43 final size:44
Alignment explanation
Indices: 1599122--1599207 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
1599112 TTTTTATCCT
* * *
1599122 AGAAAAAAAATTTAAAAAGAGGAGAAGATAACCTTGGGTTGTTG
1 AGAAAAAAAATTTAAAAAGAGGAAAAAATAACCTTCGGTTGTTG
* *
1599166 AGAAAAAGAATTTAAAAAGAGGAAAAAAT-ATCTTCGGTTGTT
1 AGAAAAAAAATTTAAAAAGAGGAAAAAATAACCTTCGGTTGTT
1599208 AGATTTACCC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 11 0.30
44 26 0.70
ACGTcount: A:0.49, C:0.05, G:0.22, T:0.24
Consensus pattern (44 bp):
AGAAAAAAAATTTAAAAAGAGGAAAAAATAACCTTCGGTTGTTG
Found at i:1602955 original size:30 final size:30
Alignment explanation
Indices: 1602911--1603004 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
1602901 ATTTCTTATG
** *
1602911 CCAATATCTTGATACTTATATCTTTGATTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
1602942 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
1602972 CCATTATTTGATAACCATATATTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
1603002 CCA
1 CCA
1603005 TAAATACAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 50 0.88
31 7 0.12
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:1602981 original size:15 final size:16
Alignment explanation
Indices: 1602928--1603006 Score: 67
Period size: 15 Copynumber: 5.2 Consensus size: 16
1602918 CTTGATACTT
* *
1602928 ATATCTTTGATTTTCC
1 ATATATTTGACTTTCC
**
1602944 A-ATATTTGA-TACCC
1 ATATATTTGACTTTCC
*
1602958 ATATCTTTGACTTTCC
1 ATATATTTGACTTTCC
**
1602974 AT-TATTTGA-TAACC
1 ATATATTTGACTTTCC
1602988 ATATATTTGACTTTCC
1 ATATATTTGACTTTCC
1603004 ATA
1 ATA
1603007 AATACAGATG
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
14 9 0.19
15 27 0.56
16 12 0.25
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (16 bp):
ATATATTTGACTTTCC
Found at i:1604528 original size:21 final size:19
Alignment explanation
Indices: 1604502--1604540 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1604492 TGTACACTTT
1604502 CACTTTCGAATTGCCATTAAA
1 CACTTTCGAA-TGCC-TTAAA
*
1604523 CACTTTTGAATGCCTTAA
1 CACTTTCGAATGCCTTAA
1604541 CTTTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (19 bp):
CACTTTCGAATGCCTTAAA
Found at i:1608639 original size:30 final size:31
Alignment explanation
Indices: 1608603--1608664 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
1608593 TAGGGGTGTA
1608603 GGGTGA-TTTTATTTTGTTTATTTCAAGTCT
1 GGGTGATTTTTATTTTGTTTATTTCAAGTCT
*
1608633 GGGTGATTTTTTTTTTGTTTATTTCAAGTCT
1 GGGTGATTTTTATTTTGTTTATTTCAAGTCT
1608664 G
1 G
1608665 CTGTTAAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.15, C:0.06, G:0.21, T:0.58
Consensus pattern (31 bp):
GGGTGATTTTTATTTTGTTTATTTCAAGTCT
Found at i:1612203 original size:21 final size:22
Alignment explanation
Indices: 1612163--1612209 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
1612153 TTTCAATTTG
1612163 ATTTAAATTTATTTTATTTT-T
1 ATTTAAATTTATTTTATTTTCT
1612184 ATTTAAATTTATTTCT-TTTTCT
1 ATTTAAATTTATTT-TATTTTCT
1612206 ATTT
1 ATTT
1612210 TCAGGTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTTAAATTTATTTTATTTTCT
Found at i:1614607 original size:42 final size:42
Alignment explanation
Indices: 1614560--1614642 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1614550 TTGTGTGTGA
*
1614560 CACACGAACGTGTGACAGACCGTGTAACT-TTCTGACTTGAGT
1 CACACGAACGTGTGACAGACCATGTAACTCTT-TGACTTGAGT
** *
1614602 CACACGAGTGTGTGCCAGACCATGTAACTCTTTGACTTGAG
1 CACACGAACGTGTGACAGACCATGTAACTCTTTGACTTGAG
1614643 CTACATGGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (42 bp):
CACACGAACGTGTGACAGACCATGTAACTCTTTGACTTGAGT
Found at i:1614657 original size:42 final size:43
Alignment explanation
Indices: 1614560--1614658 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 43
1614550 TTGTGTGTGA
* * *
1614560 CACACGA-ACGTGTGACAGACCGTGTAACTTTCTGACTTGAGT
1 CACACGAGTCGTGTGCCAGACCATGTAACTTTCTGACTTGAGT
1614602 CACACGAGT-GTGTGCCAGACCATGTAACTCTT-TGACTTGAG-
1 CACACGAGTCGTGTGCCAGACCATGTAACT-TTCTGACTTGAGT
*
1614643 CTACATG-GTCGTGTGC
1 C-ACACGAGTCGTGTGC
1614659 TAGGTTGTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
41 3 0.06
42 44 0.90
43 2 0.04
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.27
Consensus pattern (43 bp):
CACACGAGTCGTGTGCCAGACCATGTAACTTTCTGACTTGAGT
Found at i:1615668 original size:52 final size:52
Alignment explanation
Indices: 1615603--1615701 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
1615593 GCATTCTCTA
* *
1615603 TTCTGTTTATATGATCATTATCAAAATCTCTGTGATACTCTGATTTGCTTTG
1 TTCTGTTTATATGATCATTACCAAAATCTCTGCGATACTCTGATTTGCTTTG
* *
1615655 TTCTGGTTT-TATGATCATTACCAAATTCTCTGCGTTACTCTGATTTG
1 TTCT-GTTTATATGATCATTACCAAAATCTCTGCGATACTCTGATTTG
1615702 TATATTATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 38 0.90
53 4 0.10
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.47
Consensus pattern (52 bp):
TTCTGTTTATATGATCATTACCAAAATCTCTGCGATACTCTGATTTGCTTTG
Found at i:1615720 original size:52 final size:52
Alignment explanation
Indices: 1615607--1615722 Score: 135
Period size: 52 Copynumber: 2.2 Consensus size: 52
1615597 TCTCTATTCT
* * * * *
1615607 GTTTATATGATCATTATCAAAATCTCTGTGATACTCTGATTTGCTTTGTTCTG
1 GTTT-TATGATCATTACCAAAATCTCTGCGATACTCTGATTTGCTATATTATG
* *
1615660 GTTTTATGATCATTACCAAATTCTCTGCGTTACTCTGATTTG-TATATTATG
1 GTTTTATGATCATTACCAAAATCTCTGCGATACTCTGATTTGCTATATTATG
*
1615711 TTTTGTATGATC
1 GTTT-TATGATC
1615723 TCTGTCTGAG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
51 9 0.17
52 41 0.76
53 4 0.07
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (52 bp):
GTTTTATGATCATTACCAAAATCTCTGCGATACTCTGATTTGCTATATTATG
Found at i:1619257 original size:15 final size:15
Alignment explanation
Indices: 1619237--1619269 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1619227 GATTTCTCAT
1619237 TTTTCATTTATTTAC
1 TTTTCATTTATTTAC
*
1619252 TTTTCATTTATTTCC
1 TTTTCATTTATTTAC
1619267 TTT
1 TTT
1619270 CTTATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCATTTATTTAC
Found at i:1624077 original size:20 final size:20
Alignment explanation
Indices: 1624052--1624095 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1624042 TAAGAATAAT
1624052 TTTCCTAACATTGATAGACC
1 TTTCCTAACATTGATAGACC
1624072 TTTCCTAACATTGATAGACC
1 TTTCCTAACATTGATAGACC
1624092 TTTC
1 TTTC
1624096 TGTCATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (20 bp):
TTTCCTAACATTGATAGACC
Found at i:1628266 original size:22 final size:20
Alignment explanation
Indices: 1628250--1628336 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
1628240 ATTTTAAAAT
*
1628250 CAAGTGAAAATGATTTTAAC
1 CAAGTCAAAATGATTTTAAC
* *
1628270 CAAGTCAAAATGATTTCAAT
1 CAAGTCAAAATGATTTTAAC
* * * *
1628290 TAAGTTAAAATCACTTTAA-
1 CAAGTCAAAATGATTTTAAC
*
1628309 CACA-TCAAAATGATTTTCAAA
1 CA-AGTCAAAATGATTTT-AAC
1628330 CAAGTCA
1 CAAGTCA
1628337 GAATTGCTCT
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
19 11 0.22
20 35 0.69
21 5 0.10
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (20 bp):
CAAGTCAAAATGATTTTAAC
Found at i:1638193 original size:22 final size:20
Alignment explanation
Indices: 1638177--1638253 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
1638167 ATTTTAAAAT
*
1638177 CAAGTGAAAATGATTTTAAC
1 CAAGTCAAAATGATTTTAAC
* *
1638197 CAAGTCAAAATGATTTCAAT
1 CAAGTCAAAATGATTTTAAC
* * *
1638217 TAAGTTAAAATCATTTTAA-
1 CAAGTCAAAATGATTTTAAC
1638236 CACA-TCAAAAATGATTTT
1 CA-AGTC-AAAATGATTTT
1638254 CAAATAAGTC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 2 0.04
20 43 0.96
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (20 bp):
CAAGTCAAAATGATTTTAAC
Found at i:1638247 original size:40 final size:41
Alignment explanation
Indices: 1638167--1638262 Score: 108
Period size: 40 Copynumber: 2.3 Consensus size: 41
1638157 TTTTGAAACA
* *
1638167 ATTTTAAAATCAAGTGAAAATGATTTTAACCAAGTCAAAATG
1 ATTTTCAAAT-AAGTGAAAATCATTTTAACCAAGTCAAAATG
* *
1638209 A-TTTCAATTAAGTTAAAATCATTTTAA-CACA-TCAAAAATG
1 ATTTTCAAATAAGTGAAAATCATTTTAACCA-AGTC-AAAATG
1638249 ATTTTCAAATAAGT
1 ATTTTCAAATAAGT
1638263 CAGAATTGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
39 4 0.09
40 24 0.52
41 17 0.37
42 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.34
Consensus pattern (41 bp):
ATTTTCAAATAAGTGAAAATCATTTTAACCAAGTCAAAATG
Found at i:1643167 original size:14 final size:14
Alignment explanation
Indices: 1643150--1643176 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1643140 CTATTTTTTA
1643150 TCAATAAAATTGGC
1 TCAATAAAATTGGC
1643164 TCAATAAAATTGG
1 TCAATAAAATTGG
1643177 GTTTTTTTTG
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:0.11, G:0.15, T:0.30
Consensus pattern (14 bp):
TCAATAAAATTGGC
Found at i:1643231 original size:16 final size:16
Alignment explanation
Indices: 1643206--1643238 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1643196 ACGGTATTCT
*
1643206 ATATTTTATAGTAGCA
1 ATATTCTATAGTAGCA
1643222 ATATTCTATAGTAGCA
1 ATATTCTATAGTAGCA
1643238 A
1 A
1643239 AGCAATAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (16 bp):
ATATTCTATAGTAGCA
Found at i:1644037 original size:28 final size:28
Alignment explanation
Indices: 1644006--1644186 Score: 134
Period size: 28 Copynumber: 6.3 Consensus size: 28
1643996 AAAAGGATGT
1644006 CTTTGTGGCAAATCTCTGAAAGGAAAGC
1 CTTTGTGGCAAATCTCTGAAAGGAAAGC
* * * *
1644034 CTTTGTGGAAAATATTTGAAATGAAAGC
1 CTTTGTGGCAAATCTCTGAAAGGAAAGC
* * * *
1644062 CCTTGTGGCGAGT-ACTGAAA-GAAAGGTTGC
1 CTTTGTGGCAAATCTCTGAAAGGAAA----GC
* *
1644092 CTTTGTGGCAAATATTTGAAAGGAAAGC
1 CTTTGTGGCAAATCTCTGAAAGGAAAGC
* * ** *
1644120 CTTTGTGGCGAGTACTAAAAGAAAGG-ATGC
1 CTTTGTGGCAAAT-CT--CTGAAAGGAAAGC
*
1644150 CTTTGTGGCAAACCTCTGAAAGGAAAGC
1 CTTTGTGGCAAATCTCTGAAAGGAAAGC
1644178 CTTTGTGGC
1 CTTTGTGGC
1644187 GAGTACTGAA
Statistics
Matches: 116, Mismatches: 27, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
26 4 0.03
27 11 0.09
28 58 0.50
29 3 0.03
30 25 0.22
31 11 0.09
32 4 0.03
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (28 bp):
CTTTGTGGCAAATCTCTGAAAGGAAAGC
Found at i:1644216 original size:31 final size:29
Alignment explanation
Indices: 1644064--1644216 Score: 113
Period size: 28 Copynumber: 5.2 Consensus size: 29
1644054 ATGAAAGCCC
1644064 TTGTGGCGAGTACTGAAAGAAAGGTTGCCT
1 TTGTGGCGAGTACTGAAAGAAAGG-TGCCT
* * *
1644094 TTGTGGCAAATATTTGAAAGGAAA---GCCT
1 TTGTGGCGAGTA-CTGAAA-GAAAGGTGCCT
*
1644122 TTGTGGCGAGTACTAAAAGAAAGGATGCCT
1 TTGTGGCGAGTACTGAAAGAAAGG-TGCCT
* *
1644152 TTGTGGCAAACCT-CTGAAAGGAAA---GCCT
1 TTGTGGC-GA-GTACTGAAA-GAAAGGTGCCT
*
1644180 TTGTGGCGAGTACTGAAAGAAAAGGTTGTCT
1 TTGTGGCGAGTACTGAAAG-AAAGG-TGCCT
1644211 TTGTGG
1 TTGTGG
1644217 AAAATATCTG
Statistics
Matches: 95, Mismatches: 13, Indels: 29
0.69 0.09 0.21
Matches are distributed among these distances:
26 6 0.06
27 14 0.15
28 25 0.26
30 21 0.22
31 20 0.21
32 9 0.09
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (29 bp):
TTGTGGCGAGTACTGAAAGAAAGGTGCCT
Found at i:1644233 original size:59 final size:59
Alignment explanation
Indices: 1644032--1644365 Score: 368
Period size: 59 Copynumber: 5.7 Consensus size: 59
1644022 TGAAAGGAAA
* * * *
1644032 GCCTTTGTGGAAAATATTTGAAATGAAAGCCCTTGTGGCGAGTACTGAAAG-AAAGGTT
1 GCCTTTGTGGAAAATATCTGAAAGGAAAGCCTTTGTGGCGAGTACTGAAAGAAAAGGAT
* * *
1644090 GCCTTTGTGGCAAATATTTGAAAGGAAAGCCTTTGTGGCGAGTACTAAAAG-AAAGGAT
1 GCCTTTGTGGAAAATATCTGAAAGGAAAGCCTTTGTGGCGAGTACTGAAAGAAAAGGAT
* ** *
1644148 GCCTTTGTGGCAAACCTCTGAAAGGAAAGCCTTTGTGGCGAGTACTGAAAGAAAAGGTT
1 GCCTTTGTGGAAAATATCTGAAAGGAAAGCCTTTGTGGCGAGTACTGAAAGAAAAGGAT
* ** * * *
1644207 GTCTTTGTGGAAAATATCTGAAAGGAAAATCTTTGTGGTGAGTACCGAATGAAAAGGAT
1 GCCTTTGTGGAAAATATCTGAAAGGAAAGCCTTTGTGGCGAGTACTGAAAGAAAAGGAT
* * * * * * ** * *
1644266 GTCTTTATGGCAAATCTTTAAAAATAAAGCCTTTGT-GCTGAGTACTGAATGAAAAAGAT
1 GCCTTTGTGGAAAATATCTGAAAGGAAAGCCTTTGTGGC-GAGTACTGAAAGAAAAGGAT
* * *
1644325 GCCTTTGTGGAAAATCTCTAAAAGGAAAGCCTTAGTGGCGA
1 GCCTTTGTGGAAAATATCTGAAAGGAAAGCCTTTGTGGCGA
1644366 CCTCTGTTAA
Statistics
Matches: 234, Mismatches: 39, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
58 101 0.43
59 131 0.56
60 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (59 bp):
GCCTTTGTGGAAAATATCTGAAAGGAAAGCCTTTGTGGCGAGTACTGAAAGAAAAGGAT
Found at i:1656060 original size:18 final size:19
Alignment explanation
Indices: 1656020--1656063 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
1656010 AAAAAAAACG
1656020 TTTTGAAATTGAATAATGA
1 TTTTGAAATTGAATAATGA
1656039 -TTTGTAAA-TGAATAAT-A
1 TTTTG-AAATTGAATAATGA
1656056 TTTTGAAA
1 TTTTGAAA
1656064 ACGAACGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.17
18 16 0.70
19 3 0.13
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (19 bp):
TTTTGAAATTGAATAATGA
Found at i:1658957 original size:20 final size:21
Alignment explanation
Indices: 1658921--1658962 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1658911 ACTTTTTACT
1658921 TTTTAATTTTATAATATAATA
1 TTTTAATTTTATAATATAATA
* *
1658942 TTTTATTTTTAT-ATATTATA
1 TTTTAATTTTATAATATAATA
1658962 T
1 T
1658963 NNNNNNNNNN
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTAATTTTATAATATAATA
Found at i:1659655 original size:19 final size:19
Alignment explanation
Indices: 1659623--1659664 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1659613 GCTATATTTC
*
1659623 AAATGGAATCTAATAGATA
1 AAATGGAATATAATAGATA
*
1659642 AAATGTAATATAATAGATA
1 AAATGGAATATAATAGATA
1659661 AAAT
1 AAAT
1659665 ATTAATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.02, G:0.12, T:0.29
Consensus pattern (19 bp):
AAATGGAATATAATAGATA
Found at i:1660658 original size:191 final size:191
Alignment explanation
Indices: 1660334--1660714 Score: 762
Period size: 191 Copynumber: 2.0 Consensus size: 191
1660324 CAAATTGAGT
1660334 CAAGTGAAATAAAATTCAAGTCGAGTAGAATCAAGTGAAATTGTTCGAGTCGAATTAAAAAAAGT
1 CAAGTGAAATAAAATTCAAGTCGAGTAGAATCAAGTGAAATTGTTCGAGTCGAATTAAAAAAAGT
1660399 AAACATGTCAAATTAAAATCTTGCTACAGTATAACTAATTTCGTGTTAGAACACATAAATTTGAA
66 AAACATGTCAAATTAAAATCTTGCTACAGTATAACTAATTTCGTGTTAGAACACATAAATTTGAA
1660464 ACCATATATACTTAAAAACTTTTTCAAAGCAGAATTAAAGATAAAATAAGATACTTTAGTG
131 ACCATATATACTTAAAAACTTTTTCAAAGCAGAATTAAAGATAAAATAAGATACTTTAGTG
1660525 CAAGTGAAATAAAATTCAAGTCGAGTAGAATCAAGTGAAATTGTTCGAGTCGAATTAAAAAAAGT
1 CAAGTGAAATAAAATTCAAGTCGAGTAGAATCAAGTGAAATTGTTCGAGTCGAATTAAAAAAAGT
1660590 AAACATGTCAAATTAAAATCTTGCTACAGTATAACTAATTTCGTGTTAGAACACATAAATTTGAA
66 AAACATGTCAAATTAAAATCTTGCTACAGTATAACTAATTTCGTGTTAGAACACATAAATTTGAA
1660655 ACCATATATACTTAAAAACTTTTTCAAAGCAGAATTAAAGATAAAATAAGATACTTTAGT
131 ACCATATATACTTAAAAACTTTTTCAAAGCAGAATTAAAGATAAAATAAGATACTTTAGT
1660715 ATGATAAACT
Statistics
Matches: 190, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
191 190 1.00
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (191 bp):
CAAGTGAAATAAAATTCAAGTCGAGTAGAATCAAGTGAAATTGTTCGAGTCGAATTAAAAAAAGT
AAACATGTCAAATTAAAATCTTGCTACAGTATAACTAATTTCGTGTTAGAACACATAAATTTGAA
ACCATATATACTTAAAAACTTTTTCAAAGCAGAATTAAAGATAAAATAAGATACTTTAGTG
Found at i:1663231 original size:25 final size:26
Alignment explanation
Indices: 1663203--1663251 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
1663193 TTTTTTAAAA
1663203 AAATTTTAAAATTTTTA-AAATATAT
1 AAATTTTAAAATTTTTATAAATATAT
**
1663228 AAATTTTGGAATTTTTATAAATAT
1 AAATTTTAAAATTTTTATAAATAT
1663252 TTTGAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (26 bp):
AAATTTTAAAATTTTTATAAATATAT
Found at i:1663253 original size:20 final size:21
Alignment explanation
Indices: 1663230--1663283 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
1663220 AAATATATAA
1663230 ATTTTGGAATTTTT-ATAAA-T
1 ATTTTGGAATTTTTGA-AAATT
1663250 ATTTT-GAATTTTTGAAAATT
1 ATTTTGGAATTTTTGAAAATT
1663270 ATTTTGGAATTTTT
1 ATTTTGGAATTTTT
1663284 TTTTTGTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.35
20 12 0.39
21 8 0.26
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (21 bp):
ATTTTGGAATTTTTGAAAATT
Found at i:1663260 original size:19 final size:19
Alignment explanation
Indices: 1663225--1663283 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
1663215 TTTTAAAATA
*
1663225 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
1663243 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
1663262 TGA-AAATTATTTTGGAATTTT
1 T-ATAAA-TATTTT-GAATTTT
1663283 T
1 T
1663284 TTTTTGTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 7 0.19
19 14 0.39
20 7 0.19
21 8 0.22
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:1665414 original size:18 final size:18
Alignment explanation
Indices: 1665366--1665451 Score: 50
Period size: 17 Copynumber: 4.6 Consensus size: 18
1665356 GGGTTGGCAT
* *
1665366 TTTTATTTTTTATTAAAAC
1 TTTTAATTTTT-TTAAAAA
**
1665385 TTTT-ATAATTTTAAAAA
1 TTTTAATTTTTTTAAAAA
*
1665402 TTTTAATTTTTTT-ATAA
1 TTTTAATTTTTTTAAAAA
*
1665419 TTTTTATGATTTTTTAAATTAA
1 TTTTAAT--TTTTTTAAA--AA
1665441 TTTTAAATTTT
1 TTTT-AATTTT
1665452 AAAAGGGCCT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
17 19 0.38
18 9 0.18
19 10 0.20
20 1 0.02
21 3 0.06
22 6 0.12
23 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTTAATTTTTTTAAAAA
Found at i:1666484 original size:39 final size:40
Alignment explanation
Indices: 1666441--1666517 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
1666431 AAACTGATAT
*
1666441 TTAGCAGCGTTTTCA-ATAGAACGCCGCAAAAAAAATGCA
1 TTAGCAGCGTTTTCACATAAAACGCCGCAAAAAAAATGCA
1666480 TTAGCAGCGTTTTCACATAAAACGCCGCAAAAAAAATG
1 TTAGCAGCGTTTTCACATAAAACGCCGCAAAAAAAATG
1666518 GTACGGCGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 15 0.42
40 21 0.58
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (40 bp):
TTAGCAGCGTTTTCACATAAAACGCCGCAAAAAAAATGCA
Found at i:1667071 original size:86 final size:84
Alignment explanation
Indices: 1666942--1667103 Score: 288
Period size: 86 Copynumber: 1.9 Consensus size: 84
1666932 TTTTATGTAT
*
1666942 GCGCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTCTGGTCAATCGCCACTAATGTTAAGGTATT
1 GCGCCGCTATTGATTGGGGGTGATAGTGGCGTGTTCTGGTCAATCGCCACTAATGTTAAGGTATT
1667007 TAGCGGCGTTTCTATCATA
66 TAGCGGCGTTTCTATCATA
*
1667026 GCGCCGCTATTTGATTGGTGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTA
1 GCGCCGCTA-TTGATTGG-GGGTGATAGTGGCGTGTTCTGGTCAATCGCCACTAATGTTAAGGTA
1667091 TTTAGCGGCGTTT
64 TTTAGCGGCGTTT
1667104 GGTTTTAAAG
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
84 9 0.12
85 7 0.09
86 58 0.78
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.35
Consensus pattern (84 bp):
GCGCCGCTATTGATTGGGGGTGATAGTGGCGTGTTCTGGTCAATCGCCACTAATGTTAAGGTATT
TAGCGGCGTTTCTATCATA
Found at i:1667740 original size:21 final size:21
Alignment explanation
Indices: 1667716--1667788 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
1667706 GGGTTAAGGA
1667716 TTTGGGATTTGGGGTTGGTGG
1 TTTGGGATTTGGGGTTGGTGG
* * * *
1667737 TTTGGGGTCTGGGGTTTGTGA
1 TTTGGGATTTGGGGTTGGTGG
1667758 TTTAGGG-TTTGGGGTTTTGG-GG
1 TTT-GGGATTTGGGG--TTGGTGG
1667780 TTTGGGATT
1 TTTGGGATT
1667789 AAGGTTTAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
21 29 0.71
22 9 0.22
23 3 0.07
ACGTcount: A:0.05, C:0.01, G:0.48, T:0.45
Consensus pattern (21 bp):
TTTGGGATTTGGGGTTGGTGG
Found at i:1667742 original size:14 final size:14
Alignment explanation
Indices: 1667718--1667785 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 14
1667708 GTTAAGGATT
*
1667718 TGGGATTTGGGGT-
1 TGGGGTTTGGGGTC
1667731 TGGTGGTTTGGGGTC
1 TGG-GGTTTGGGGTC
* * *
1667746 TGGGGTTTGTGATT
1 TGGGGTTTGGGGTC
* *
1667760 TAGGGTTTGGGGTTT
1 TGGGGTTTGGGG-TC
1667775 TGGGGTTTGGG
1 TGGGGTTTGGG
1667786 ATTAAGGTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
13 3 0.07
14 26 0.59
15 15 0.34
ACGTcount: A:0.04, C:0.01, G:0.51, T:0.43
Consensus pattern (14 bp):
TGGGGTTTGGGGTC
Found at i:1667801 original size:29 final size:29
Alignment explanation
Indices: 1667746--1667802 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1667736 GTTTGGGGTC
* * *
1667746 TGGGGTTTGTGATTTAGGGTTTGGGGTTT
1 TGGGGTTTGGGATTTAAGGTTTAGGGTTT
1667775 TGGGGTTTGGGA-TTAAGGTTTAAGGGTT
1 TGGGGTTTGGGATTTAAGGTTT-AGGGTT
1667803 AAGGACTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (29 bp):
TGGGGTTTGGGATTTAAGGTTTAGGGTTT
Done.