Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000023.1 Hibiscus syriacus cultivar Beakdansim tig00000040_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 75657
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:5376 original size:149 final size:148
Alignment explanation
Indices: 5090--5390 Score: 442
Period size: 149 Copynumber: 2.0 Consensus size: 148
5080 TAGATCGAGT
* * * *
5090 AGCTAGAGGGAGCTATCTACCAAGGAGACGATCCAGACATTTGCCTACTGAGGTAACAAGTTGGA
1 AGCTAGAGGGAGCTACCTACCAAGAAGACAATCCAAACATTTGCCTACTGAGGTAACAAGTTGGA
** * *
5155 CTCGAGACGATTCAACGCTGAAGCCAACAGTTGAAGATCACGAACCAGCTCGAAATTTTTTTTGA
66 CTCGAGACGATTCAACGCTGAAGCCAACAGTTGAAGATCACGAACCAGCTCGAAAGATTTCTGGA
* *
5220 AGTAGGAGATGAAGTAGG
131 AGCAGGAGATGAAGTAGA
* *
5238 AGCTAGAGGGAGTTTACCTACCAAGAAGACAATCTAAACATTTGCCTACTGAGGTAACAAGTTGG
1 AGCTAGAGGGAG-CTACCTACCAAGAAGACAATCCAAACATTTGCCTACTGAGGTAACAAGTTGG
* * *
5303 ACTCGAGACGATTCGACG-TCGAAGCCAACAGTTGAAGATTACGAGCCAGCTCGAAAGATTTCTG
65 ACTCGAGACGATTCAACGCT-GAAGCCAACAGTTGAAGATCACGAACCAGCTCGAAAGATTTCTG
5367 GAAGCAGGAGATGAAGTAGA
129 GAAGCAGGAGATGAAGTAGA
5387 AGCT
1 AGCT
5391 TTGAAGATGA
Statistics
Matches: 136, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
148 13 0.10
149 123 0.90
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (148 bp):
AGCTAGAGGGAGCTACCTACCAAGAAGACAATCCAAACATTTGCCTACTGAGGTAACAAGTTGGA
CTCGAGACGATTCAACGCTGAAGCCAACAGTTGAAGATCACGAACCAGCTCGAAAGATTTCTGGA
AGCAGGAGATGAAGTAGA
Found at i:6964 original size:44 final size:46
Alignment explanation
Indices: 6923--7089 Score: 188
Period size: 45 Copynumber: 3.8 Consensus size: 46
6913 TATAAAATCT
6923 TTACCATTT-ATCCCATAAGCTCGTAAGCTTA-TTTAC-CAAAATAC
1 TTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACAC-AAATAC
* * *
6967 TTACCATTTAAATTCCATAAG-TCATAAGC-TATTTTATACAAATAC
1 TTACCATTT-AATCCCATAAGCTCGTAAGCTTATTTTACACAAATAC
* *
7012 TTACCATTTAATCTCATAAGCTCGT-AGCTTATTTTACACATATAC
1 TTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACACAAATAC
* * *
7057 TTGCCA-TT-ATTCCAAAAGCTCGTAAGCTTATTT
1 TTACCATTTAATCCCATAAGCTCGTAAGCTTATTT
7090 GTATGCTTAC
Statistics
Matches: 104, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
43 12 0.12
44 34 0.33
45 48 0.46
46 10 0.10
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.38
Consensus pattern (46 bp):
TTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACACAAATAC
Found at i:9932 original size:12 final size:13
Alignment explanation
Indices: 9915--9963 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 13
9905 CAAGGATAAA
9915 AGCAAA-AAAAAG
1 AGCAAAGAAAAAG
*
9927 AGCAAAGAAAAAA
1 AGCAAAGAAAAAG
*
9940 ATCAAAG-AAAA-
1 AGCAAAGAAAAAG
9951 A-CAAAGAAAAAG
1 AGCAAAGAAAAAG
9963 A
1 A
9964 ACAAGAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 5 0.16
11 5 0.16
12 11 0.34
13 11 0.34
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.02
Consensus pattern (13 bp):
AGCAAAGAAAAAG
Found at i:9939 original size:14 final size:13
Alignment explanation
Indices: 9912--9951 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
9902 AACCAAGGAT
9912 AAAAGCAAA-AAA
1 AAAAGCAAAGAAA
*
9924 AAGAGCAAAGAAA
1 AAAAGCAAAGAAA
*
9937 AAAATCAAAGAAA
1 AAAAGCAAAGAAA
9950 AA
1 AA
9952 CAAAGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.78, C:0.07, G:0.12, T:0.03
Consensus pattern (13 bp):
AAAAGCAAAGAAA
Found at i:10952 original size:32 final size:32
Alignment explanation
Indices: 10910--10973 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
10900 AAGAAACGAT
*
10910 GAATGATGGGGCATCTTCGGAGATTCAACATC
1 GAATGATGGGGAATCTTCGGAGATTCAACATC
* * *
10942 GAATGTTGGGGAATCTTTGGGGATTCAACATC
1 GAATGATGGGGAATCTTCGGAGATTCAACATC
10974 CTGATATGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (32 bp):
GAATGATGGGGAATCTTCGGAGATTCAACATC
Found at i:11194 original size:37 final size:36
Alignment explanation
Indices: 11121--11219 Score: 144
Period size: 37 Copynumber: 2.7 Consensus size: 36
11111 GTTTTACTCA
**
11121 AGATAGTTTTTCTTAAAATAGATTTTATCTCCCTTG
1 AGATAGTTTCACTTAAAATAGATTTTATCTCCCTTG
* *
11157 AGATAGTTTCACTTAAAATATGTTTTTATCTCTCTTG
1 AGATAGTTTCACTTAAAATA-GATTTTATCTCCCTTG
*
11194 AGATAGTTTCACTTAAAACAGATTTT
1 AGATAGTTTCACTTAAAATAGATTTT
11220 TAGGGGTTTC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 23 0.41
37 33 0.59
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (36 bp):
AGATAGTTTCACTTAAAATAGATTTTATCTCCCTTG
Found at i:11349 original size:59 final size:61
Alignment explanation
Indices: 11215--11353 Score: 212
Period size: 61 Copynumber: 2.3 Consensus size: 61
11205 CTTAAAACAG
*
11215 ATTTTTAGGGGTTTCTTGATGAAGATTTTCAATGAATTTTTTTAAAAGGAATCTAAGCCTG
1 ATTTTTAGGGGTTTCTTGATGAAGATTTTCAATGAATTTTTTTAAAAGGAATCTAAGCCTA
* *
11276 ATTTTCAGGGGTTTCTTGATGAAGATTTTTAATGAA-TTTTTT-AAAGGAAGT-TAAGCCTA
1 ATTTTTAGGGGTTTCTTGATGAAGATTTTCAATGAATTTTTTTAAAAGGAA-TCTAAGCCTA
*
11335 ATTTTTAGGAGTTTCTTGA
1 ATTTTTAGGGGTTTCTTGA
11354 CAACTAAGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
59 31 0.43
60 7 0.10
61 34 0.47
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (61 bp):
ATTTTTAGGGGTTTCTTGATGAAGATTTTCAATGAATTTTTTTAAAAGGAATCTAAGCCTA
Found at i:11380 original size:98 final size:98
Alignment explanation
Indices: 11267--11492 Score: 328
Period size: 98 Copynumber: 2.3 Consensus size: 98
11257 TAAAAGGAAT
* * * * * *
11267 CTAAGCCTGATTTTCAGGGGTTTCTTGATGAAGATTTTTAATGAATTTTTTAAAGGAAGTTAAGC
1 CTAAGCTTGATTTTCAGGGGTTTCTTGATGAAGATTTTCAAAGAATTTTTAAAAGAAAGCTAAGC
* * *
11332 CTAATTTTTAGGAGTTTCTTGACAACTAAGAAA
66 CTAATTTTTAGGAGCTCCTTGACAAATAAGAAA
* *
11365 CTAAGCTTGATTTTCAGGGGTTTCTTGATGATGATTTTCAAAGAGTTTTTAAAAGAAAGCTAAGC
1 CTAAGCTTGATTTTCAGGGGTTTCTTGATGAAGATTTTCAAAGAATTTTTAAAAGAAAGCTAAGC
*
11430 CTAATTTTTAGGGGCTCCTTGACAAATAAGAAA
66 CTAATTTTTAGGAGCTCCTTGACAAATAAGAAA
*
11463 CTAAGCTTGATTTTCAAGGG-TTCTTGATGA
1 CTAAGCTTGATTTTCAGGGGTTTCTTGATGA
11493 GTAAGTCCTT
Statistics
Matches: 115, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
97 10 0.09
98 105 0.91
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (98 bp):
CTAAGCTTGATTTTCAGGGGTTTCTTGATGAAGATTTTCAAAGAATTTTTAAAAGAAAGCTAAGC
CTAATTTTTAGGAGCTCCTTGACAAATAAGAAA
Found at i:11604 original size:41 final size:41
Alignment explanation
Indices: 11502--11604 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 41
11492 AGTAAGTCCT
* * *
11502 TCCTTCGGGTCATCAGTAAGTCTTTCGAACGTGATGCGTAAA
1 TCCTTCGGGCCATCA-TAAGTCTTTCGAACATGATGCATAAA
* *
11544 TCCTTCGGGCCATCTATAAGTCTTTCGAGCATGATG-ATAAG
1 TCCTTCGGGCCATC-ATAAGTCTTTCGAACATGATGCATAAA
11585 TCCTTCGGGCCATGCATAAG
1 TCCTTCGGGCCAT-CATAAG
11605 ACCCTCGGGC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
41 21 0.39
42 32 0.59
43 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (41 bp):
TCCTTCGGGCCATCATAAGTCTTTCGAACATGATGCATAAA
Found at i:12050 original size:34 final size:35
Alignment explanation
Indices: 11983--12050 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
11973 AAAAAGAATT
*
11983 TTGTCTCACTTGAGACAATTTTTACTCAAAACAAG
1 TTGTCTCACTTGAGACAATTTCTACTCAAAACAAG
** *
12018 TTGTCTCTTTTGAGACAGTTTCT-CTCAAAACAA
1 TTGTCTCACTTGAGACAATTTCTACTCAAAACAA
12051 AAGCCCGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 10 0.34
35 19 0.66
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (35 bp):
TTGTCTCACTTGAGACAATTTCTACTCAAAACAAG
Found at i:12171 original size:37 final size:36
Alignment explanation
Indices: 12070--12188 Score: 159
Period size: 36 Copynumber: 3.3 Consensus size: 36
12060 TCTGTTTCTT
* * *
12070 TTGAAACAAAGTTTGTCTCACTTGAGACAACTTCTC
1 TTGAAACAAAGTTTGTCTCTCTTGAGACAATTTTTC
*
12106 TTGAAACAAAGTTTGTCTCTCTTAAGACAATTTTTC
1 TTGAAACAAAGTTTGTCTCTCTTGAGACAATTTTTC
* *
12142 TTGAAACAAAGTTTTGT-TCCTCTTGAGACAGTTTTCC
1 TTGAAACAAAG-TTTGTCT-CTCTTGAGACAATTTTTC
12179 TTGAAACAAA
1 TTGAAACAAA
12189 ATCTTTGAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
36 44 0.59
37 30 0.41
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.37
Consensus pattern (36 bp):
TTGAAACAAAGTTTGTCTCTCTTGAGACAATTTTTC
Found at i:12248 original size:65 final size:66
Alignment explanation
Indices: 12141--12315 Score: 198
Period size: 66 Copynumber: 2.7 Consensus size: 66
12131 GACAATTTTT
** * *
12141 CTTGAAACAAAGTTTTGT-TCCTCTTGAGACAGTTTTCCTTGAAACA-AAATCTTTGA-ATCTAT
1 CTTGAAAC-AAGTTTTGTCT-CTCTTGAGACAGACTTCCTTGAAACACAAACCATTGATATC-AT
12203 TTCC
63 TTCC
* *
12207 CTTGAAACATGTTTTGTCTCTCTTGAGACA-ACTTCCTTTGAAACACCAACCATTGATATCATTT
1 CTTGAAACAAGTTTTGTCTCTCTTGAGACAGACTTCC-TTGAAACACAAACCATTGATATCATTT
12271 CC
65 CC
**
12273 CTTGAAACGAA-TTTTGTCTCTCTTGAGACAGTTTTCCTTGAAA
1 CTTGAAAC-AAGTTTTGTCTCTCTTGAGACAGACTTCCTTGAAA
12316 TAAGAAATTT
Statistics
Matches: 94, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
64 4 0.04
65 27 0.29
66 55 0.59
67 8 0.09
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (66 bp):
CTTGAAACAAGTTTTGTCTCTCTTGAGACAGACTTCCTTGAAACACAAACCATTGATATCATTTC
C
Found at i:12346 original size:39 final size:39
Alignment explanation
Indices: 12282--12565 Score: 131
Period size: 39 Copynumber: 7.5 Consensus size: 39
12272 CCTTGAAACG
* * *
12282 AATTTTGTCTCTCTTGAGACAGTTTTCCTTGAAATAAGA
1 AATTTTATCTCACTTGAGATAGTTTTCCTTGAAATAAGA
* * * * *
12321 AATTTTATCTTACTTGAGATGGTTTTTCTTAAAATCAG-
1 AATTTTATCTCACTTGAGATAGTTTTCCTTGAAATAAGA
** * * * *
12359 --TTTCGTCTCAGTGGAGACAG-TTTCCTCTGAAACAAGA
1 AATTTTATCTCACTTGAGATAGTTTTCCT-TGAAATAAGA
* * * **
12396 AATTTTATCTCACTCGAGATGGTTTTTCTT--AA-AACC
1 AATTTTATCTCACTTGAGATAGTTTTCCTTGAAATAAGA
* ** * * * * * *
12432 AACTTCGTCTCGCTTAAGACAG-TTTCTGTTGAAACAATA
1 AATTTTATCTCACTTGAGATAGTTTTC-CTTGAAATAAGA
* * * **
12471 AATTTTATCTTACTTGAGATGGTTTTTCTT--AA-AACC
1 AATTTTATCTCACTTGAGATAGTTTTCCTTGAAATAAGA
* ** *
12507 AACTTCGTCTCGCTTGAGATAGTTTTCCCTTGAAATAAGA
1 AATTTTATCTCACTTGAGATAGTTTT-CCTTGAAATAAGA
12547 AATTTTATCTCACTTGAGA
1 AATTTTATCTCACTTGAGA
12566 GAGCTTATCT
Statistics
Matches: 166, Mismatches: 65, Indels: 27
0.64 0.25 0.10
Matches are distributed among these distances:
35 8 0.05
36 59 0.36
37 7 0.04
38 2 0.01
39 65 0.39
40 25 0.15
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (39 bp):
AATTTTATCTCACTTGAGATAGTTTTCCTTGAAATAAGA
Found at i:12415 original size:75 final size:76
Alignment explanation
Indices: 12288--12565 Score: 361
Period size: 75 Copynumber: 3.7 Consensus size: 76
12278 AACGAATTTT
* * *
12288 GTCTCTCTTGAGACAGTTTTCCT-TGAAATAAGAAATTTTATCTTACTTGAGATGGTTTTTCTTA
1 GTCTCGCTTGAGACAGTTTTCCTCTGAAACAAGAAATTTTATCTCACTTGAGATGGTTTTTCTTA
* **
12352 AAATCAGTTTC
66 AAACCAACTTC
* *
12363 GTCTCAG-TGGAGACAG-TTTCCTCTGAAACAAGAAATTTTATCTCACTCGAGATGGTTTTTCTT
1 GTCTC-GCTTGAGACAGTTTTCCTCTGAAACAAGAAATTTTATCTCACTTGAGATGGTTTTTCTT
12426 AAAACCAACTTC
65 AAAACCAACTTC
* * * *
12438 GTCTCGCTTAAGACAG-TTT-CTGTTGAAACAATAAATTTTATCTTACTTGAGATGGTTTTTCTT
1 GTCTCGCTTGAGACAGTTTTCCT-CTGAAACAAGAAATTTTATCTCACTTGAGATGGTTTTTCTT
12501 AAAACCAACTTC
65 AAAACCAACTTC
* *
12513 GTCTCGCTTGAGATAGTTTTCC-CTTGAAATAAGAAATTTTATCTCACTTGAGA
1 GTCTCGCTTGAGACAGTTTTCCTC-TGAAACAAGAAATTTTATCTCACTTGAGA
12566 GAGCTTATCT
Statistics
Matches: 176, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
74 9 0.05
75 137 0.78
76 29 0.16
77 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (76 bp):
GTCTCGCTTGAGACAGTTTTCCTCTGAAACAAGAAATTTTATCTCACTTGAGATGGTTTTTCTTA
AAACCAACTTC
Found at i:12532 original size:36 final size:36
Alignment explanation
Indices: 12411--12532 Score: 100
Period size: 36 Copynumber: 3.3 Consensus size: 36
12401 TATCTCACTC
*
12411 GAGATGGTTTTTCTTAAAACCAACTTCGTCTCGCTT
1 GAGATAGTTTTTCTTAAAACCAACTTCGTCTCGCTT
* * * * ** * ** **
12447 AAGACAGTTTCTGTTGAAACAATAAATTTTATCTTACTT
1 GAGATAGTTTTTCTT--AA-AACCAACTTCGTCTCGCTT
*
12486 GAGATGGTTTTTCTTAAAACCAACTTCGTCTCGCTT
1 GAGATAGTTTTTCTTAAAACCAACTTCGTCTCGCTT
12522 GAGATAGTTTT
1 GAGATAGTTTT
12533 CCCTTGAAAT
Statistics
Matches: 58, Mismatches: 25, Indels: 6
0.65 0.28 0.07
Matches are distributed among these distances:
36 32 0.55
37 2 0.03
38 2 0.03
39 22 0.38
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (36 bp):
GAGATAGTTTTTCTTAAAACCAACTTCGTCTCGCTT
Found at i:13096 original size:135 final size:128
Alignment explanation
Indices: 12852--13183 Score: 377
Period size: 135 Copynumber: 2.6 Consensus size: 128
12842 TCAACATTTC
* * *
12852 TAATGGAGAGTTCATAATGAGAAAAACTCATTCGACAGA--GAG-AGAAGTTCATAATGAAAAGA
1 TAATGGAGAGTTCATAATGAGAAAAACTCA-TCCAAAGAGGGAGAAGAAGTTCATAATGAGAAGA
* * * * *
12914 ACTTGTTGGACCTATCGCTCGATTCACGACATTTCAAATCAGCGATGCCTTGTTTGAGGGATTAA
65 ACTTGTTCGACCTATCACTCGATTCACGACATGTCAAATCAGCGATGCCTCGCTTGAGGGATT--
12979 CA
128 -A
*
12981 CTTTAAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGGAGAAGAAGTTCATAATGAGA
1 ---T-AATGGAGAGTTCATAATGAGAAAAACTCATCCAAAGAGGGAGAAGAAGTTCATAATGAGA
* * * *
13046 AGAGCTTGTTCGACCTATTACTCGATTCACGACATGTCGAATCAGTGATGCCTCGCTTGAGGGAT
62 AGAACTTGTTCGACCTATCACTCGATTCACGACATGTCAAATCAGCGATGCCTCGCTTGAGGGAT
13111 TA
127 TA
* * * * *
13113 TCATGGAGAGTTCATATTGAGAATAAA-TCAT-CAAACAAGGAAGAAGAAGTTCATAATGAGAAT
1 TAATGGAGAGTTCATAATGAGAA-AAACTCATCCAAA-GAGGGAGAAGAAGTTCATAATGAGAAG
13176 AACTTGTT
64 AACTTGTT
13184 TAACCTTGCA
Statistics
Matches: 174, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
127 4 0.02
128 55 0.32
129 3 0.02
132 8 0.05
133 28 0.16
134 3 0.02
135 73 0.42
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.26
Consensus pattern (128 bp):
TAATGGAGAGTTCATAATGAGAAAAACTCATCCAAAGAGGGAGAAGAAGTTCATAATGAGAAGAA
CTTGTTCGACCTATCACTCGATTCACGACATGTCAAATCAGCGATGCCTCGCTTGAGGGATTA
Found at i:13271 original size:91 final size:91
Alignment explanation
Indices: 13116--13365 Score: 365
Period size: 91 Copynumber: 2.7 Consensus size: 91
13106 GGGATTATCA
* * * * *
13116 TGGAGAGTTCATATTGAGAATAAATCATCAAACAAGGAAGAAGAAGTTCATAATGAGAATAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* **
13181 GTTTAACCTTGCATCAACATTTTCAG
66 GTTTAACCCTGCATCAACATTACCAG
* *
13207 TGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAAAAGTTCATAATGAGAAGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* * ** *
13272 GTTTGACCCTGCCTTGACGTTACCAG
66 GTTTAACCCTGCATCAACATTACCAG
13298 TGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
1 TGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
13363 GTT
66 GTT
13366 CGACTTCTAT
Statistics
Matches: 142, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 142 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (91 bp):
TGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
GTTTAACCCTGCATCAACATTACCAG
Found at i:14746 original size:24 final size:24
Alignment explanation
Indices: 14706--14752 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
14696 TTTCTTTATG
*
14706 TTTTAGTTATTTTTATTTTTATTA
1 TTTTAGTTATTTATATTTTTATTA
14730 TTTTA-TTATATTATATTTTTATT
1 TTTTAGTTAT-TTATATTTTTATT
14753 TAGTTTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (24 bp):
TTTTAGTTATTTATATTTTTATTA
Found at i:15965 original size:3 final size:3
Alignment explanation
Indices: 15957--16034 Score: 56
Period size: 3 Copynumber: 26.7 Consensus size: 3
15947 AGTTTGCATA
* * *
15957 TAT TAT TAT TAT TAC TA- TAT TAT TA- TAG TAT TAC TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* * *
16001 TAT TAC AAT TAT CAT TA- TAT ATAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TA
16035 CAAATAATAC
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
2 8 0.14
3 45 0.76
4 6 0.10
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:15977 original size:17 final size:17
Alignment explanation
Indices: 15955--16035 Score: 77
Period size: 17 Copynumber: 5.0 Consensus size: 17
15945 CTAGTTTGCA
15955 TATATTATTATTATTAC
1 TATATTATTATTATTAC
15972 TATATTATTATAGTATTAC
1 TATATTATTAT--TATTAC
15991 --TATTATTTATTATTAC
1 TATATTA-TTATTATTAC
*
16007 -A-ATTATCATTA-TA-
1 TATATTATTATTATTAC
16020 TATATT-TTATTATTAC
1 TATATTATTATTATTAC
16036 AAATAATACA
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
14 8 0.15
15 10 0.19
16 10 0.19
17 16 0.30
18 4 0.07
19 6 0.11
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (17 bp):
TATATTATTATTATTAC
Found at i:22311 original size:20 final size:20
Alignment explanation
Indices: 22282--22354 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
22272 GCAGCCTTCG
*
22282 TGCATGGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
22302 TGCATCGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
*
22322 TGCATCGATGCACATCAGGA
1 TGCATCGATGCACAACAGGA
22342 TGCATCGATGCAC
1 TGCATCGATGCAC
22355 TAAGTGCATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAACAGGA
Found at i:23460 original size:1 final size:1
Alignment explanation
Indices: 23454--23507 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
23444 TCCATCAGAG
* * * * * *
23454 AAAAAAAGAAAAAGAAAAAAAAAAGAGAAAAAAAGAAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23508 TAGAAAAGAA
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:23465 original size:8 final size:8
Alignment explanation
Indices: 23452--23507 Score: 62
Period size: 8 Copynumber: 7.1 Consensus size: 8
23442 CATCCATCAG
23452 AGAAAAAA
1 AGAAAAAA
23460 AGAAAAAGA
1 AGAAAAA-A
*
23469 AAAAAAAA
1 AGAAAAAA
*
23477 AGAGAAAA
1 AGAAAAAA
*
23485 A-AAGAAA
1 AGAAAAAA
23492 A-AAAAAA
1 AGAAAAAA
23499 AGAAAAAA
1 AGAAAAAA
23507 A
1 A
23508 TAGAAAAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
7 11 0.28
8 22 0.55
9 7 0.17
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:23482 original size:27 final size:28
Alignment explanation
Indices: 23450--23505 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
23440 TTCATCCATC
*
23450 AGAGAAAAAAAGAAAAAGAAAAA-AAAA
1 AGAGAAAAAAAGAAAAAAAAAAAGAAAA
23477 AGAGAAAAAAAGAAAAAAAAAAAGAAAA
1 AGAGAAAAAAAGAAAAAAAAAAAGAAAA
23505 A
1 A
23506 AATAGAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (28 bp):
AGAGAAAAAAAGAAAAAAAAAAAGAAAA
Found at i:23484 original size:10 final size:10
Alignment explanation
Indices: 23450--23523 Score: 75
Period size: 10 Copynumber: 7.7 Consensus size: 10
23440 TTCATCCATC
23450 AGAGAAAAAA
1 AGAGAAAAAA
*
23460 AGA-AAAAGA
1 AGAGAAAAAA
23469 A-A-AAAAAA
1 AGAGAAAAAA
23477 AGAGAAAAAA
1 AGAGAAAAAA
*
23487 AGAAAAAAAA
1 AGAGAAAAAA
*
23497 AAAGAAAAAA
1 AGAGAAAAAA
*
23507 ATAGAAAAGAA
1 AGAGAAAA-AA
23518 A-AGAAA
1 AGAGAAA
23524 TTGAATCAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
8 7 0.13
9 7 0.13
10 38 0.69
11 3 0.05
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (10 bp):
AGAGAAAAAA
Found at i:23493 original size:22 final size:21
Alignment explanation
Indices: 23454--23519 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 21
23444 TCCATCAGAG
*
23454 AAAAA-AAGAAAAAG-AAAAA
1 AAAAAGAAAAAAAAGAAAAAA
23473 AAAAAGAGAAAAAAAGAAAAAA
1 AAAAAGA-AAAAAAAGAAAAAA
*
23495 AAAAAGAAAAAAATAGAAAAGA
1 AAAAAGAAAAAAA-AGAAAAAA
23517 AAA
1 AAA
23520 GAAATTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
19 5 0.12
20 1 0.02
21 13 0.32
22 22 0.54
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (21 bp):
AAAAAGAAAAAAAAGAAAAAA
Found at i:23507 original size:20 final size:20
Alignment explanation
Indices: 23454--23523 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
23444 TCCATCAGAG
23454 AAAAAAAG--AAAAAGAAAA
1 AAAAAAAGAAAAAAAGAAAA
23472 AAAAAAGAGAAAAAAAGAAAA
1 AAAAAA-AGAAAAAAAGAAAA
* *
23493 AAAAAAAGAAAAAAATAGAA
1 AAAAAAAGAAAAAAAGAAAA
*
23513 AAGAAAAGAAA
1 AAAAAAAGAAA
23524 TTGAATCAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
18 6 0.13
19 2 0.04
20 22 0.48
21 16 0.35
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAAAGAAAAAAAGAAAA
Found at i:24952 original size:50 final size:50
Alignment explanation
Indices: 24897--25141 Score: 274
Period size: 50 Copynumber: 4.8 Consensus size: 50
24887 GGTCCATATT
* * * *
24897 ATCCATGTGGGTATCTTGAAGACTCACATCAGCATGAAAAGATAGAAGTT
1 ATCCATGTGGGTATCTTGAAGGCTCACATCAACATGAAAAGACAGAAGTA
* * * *
24947 ATCCATGTGGATATCTTGAAGGCTCACATCAGCATGAAAAGATATAAGTA
1 ATCCATGTGGGTATCTTGAAGGCTCACATCAACATGAAAAGACAGAAGTA
* * *
24997 ATCTATGTAGTTATCTTGAAGGCTCACATCAACATGAAAAAGACAGAAGTA
1 ATCCATGTGGGTATCTTGAAGGCTCACATCAACATG-AAAAGACAGAAGTA
* * * * *
25048 ATCCACGTAGGTCATTTTGAAGACTCACATCATCATGAAAAAGACAGAAGTA
1 ATCCATGTGGGT-ATCTTGAAGGCTCACATCAACATG-AAAAGACAGAAGTA
* * * *
25100 ATCTATGTGGGGCATTTTGAAGGCTCACACCAACATGAAAAG
1 ATCCATGT-GGGTATCTTGAAGGCTCACATCAACATGAAAAG
25142 GTTGGGATAT
Statistics
Matches: 169, Mismatches: 23, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
50 78 0.46
51 26 0.15
52 63 0.37
53 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (50 bp):
ATCCATGTGGGTATCTTGAAGGCTCACATCAACATGAAAAGACAGAAGTA
Found at i:26787 original size:42 final size:42
Alignment explanation
Indices: 26728--26809 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
26718 CACAAATTTG
* *
26728 TAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGCT
*
26770 TAAATCCTTCGGGTCATCTGTCAGTCTTTTGAGCAAGATG
1 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
26810 ATAAGTCCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGCT
Found at i:27048 original size:42 final size:43
Alignment explanation
Indices: 26978--27058 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 43
26968 ACAAATTTGT
* * *
26978 AAATCATTCGGGTCATCTATTAGTCTTTCGAGCATGATGTTTA
1 AAATCATTCGGGTCATCTATCAGCCTTTCGAGCAAGATGTTTA
*
27021 AAATC-TTCGGGTCATCTGTCAGCCTTTCGAGCAAGATG
1 AAATCATTCGGGTCATCTATCAGCCTTTCGAGCAAGATG
27059 ATAAGTCCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 29 0.85
43 5 0.15
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (43 bp):
AAATCATTCGGGTCATCTATCAGCCTTTCGAGCAAGATGTTTA
Found at i:27268 original size:249 final size:249
Alignment explanation
Indices: 26643--27246 Score: 971
Period size: 249 Copynumber: 2.4 Consensus size: 249
26633 CCCAACCAAC
* * * *
26643 AAGTTTCTCATTTAATTTTTTTAGAAAAT-GAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGT
1 AAGTTTCTCATTTAA-TGTTCTAGAAAATCAAAATT-TTGAAAAGTAAGAAGTTTCTTACCTAGT
*
26707 AAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTA
64 AAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGTTTA
* * *
26772 AATCCTTCGGGTCATCTGTCAGTCTTTTGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGA
129 AATCCTTCGGGTCATCTGTCAGCCTTTCGAGCAAGATGATAAGTCCTTAAGGCCATCCGTAAAGA
* *
26837 CTTTGGGTAGGATGTTCACATATGATTTTCGCAAGAAAATGAGATAGCGATTTTCA
194 CTTTGGGTAGGATGATCACATATGATTTTCGCAAGAAAATGAGATAACGATTTTCA
* *
26893 AAATTTCTCATTAAATGTTCTAGAAAATCAAAATTTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAAATTTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
* * *
26958 AGTATTTCTCACAAATTTGTAAATCATTCGGGTCATCTATTAGTCTTTCGAGCATGATGTTTAAA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGTTT-AA
*
27023 AT-CTTCGGGTCATCTGTCAGCCTTTCGAGCAAGATGATAAGTCCTTAAGGCCATCCGTAAAGCC
130 ATCCTTCGGGTCATCTGTCAGCCTTTCGAGCAAGATGATAAGTCCTTAAGGCCATCCGTAAAGAC
* *
27087 TTTGGGTAGGATGATCACATATGATTTTCGCATGAAAATGAGATAATGATTTTCA
195 TTTGGGTAGGATGATCACATATGATTTTCGCAAGAAAATGAGATAACGATTTTCA
27142 AAGTTTCTCATTTAATGTTCTAGAAAATCAAAATTTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAAATTTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
* *
27207 AGTATTTCCCACAAATTTGTGAAA-CCTCCGGTTCATCTGT
66 AGTATTTCCCACAAATTTGT-AAATCCTTCGGGTCATCTGT
27247 AAAACCTCAA
Statistics
Matches: 326, Mismatches: 25, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
249 301 0.92
250 25 0.08
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (249 bp):
AAGTTTCTCATTTAATGTTCTAGAAAATCAAAATTTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGTTTAAA
TCCTTCGGGTCATCTGTCAGCCTTTCGAGCAAGATGATAAGTCCTTAAGGCCATCCGTAAAGACT
TTGGGTAGGATGATCACATATGATTTTCGCAAGAAAATGAGATAACGATTTTCA
Found at i:27506 original size:3 final size:3
Alignment explanation
Indices: 27498--27559 Score: 60
Period size: 3 Copynumber: 21.7 Consensus size: 3
27488 AGTTTGCATA
* * *
27498 TAT TAT TAT TAT TAC TA- TAT TAT TA- TAG TAT TAC TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27543 TAT ATAT T-T TAT TAT TA
1 TAT -TAT TAT TAT TAT TA
27560 CAAATAATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
2 8 0.16
3 39 0.78
4 3 0.06
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:27518 original size:17 final size:17
Alignment explanation
Indices: 27496--27560 Score: 77
Period size: 17 Copynumber: 4.0 Consensus size: 17
27486 CTAGTTTGCA
27496 TATATTATTATTATTAC
1 TATATTATTATTATTAC
27513 TATATTATTATAGTATTAC
1 TATATTATTAT--TATTAC
27532 --TATTATTATTA-TA-
1 TATATTATTATTATTAC
27545 TATATT-TTATTATTAC
1 TATATTATTATTATTAC
27561 AAATAATACA
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
14 8 0.19
15 8 0.19
17 20 0.48
19 6 0.14
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (17 bp):
TATATTATTATTATTAC
Found at i:29817 original size:20 final size:20
Alignment explanation
Indices: 29792--29838 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
29782 CCTTAGCTTA
*
29792 ATAAAAAAATAGTGTAAATT
1 ATAAAAAAATAGTGAAAATT
* *
29812 ATAAAAGAATATTGAAAATT
1 ATAAAAAAATAGTGAAAATT
29832 ATAAAAA
1 ATAAAAA
29839 TATTTAGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (20 bp):
ATAAAAAAATAGTGAAAATT
Found at i:38608 original size:9 final size:9
Alignment explanation
Indices: 38594--38626 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
38584 TTGAATTTTA
38594 AAAAATCAG
1 AAAAATCAG
38603 AAAAATACA-
1 AAAAAT-CAG
38612 AAAAATCAG
1 AAAAATCAG
38621 AAAAAT
1 AAAAAT
38627 TACAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 18 0.82
10 2 0.09
ACGTcount: A:0.73, C:0.09, G:0.06, T:0.12
Consensus pattern (9 bp):
AAAAATCAG
Found at i:38616 original size:18 final size:19
Alignment explanation
Indices: 38593--38635 Score: 79
Period size: 18 Copynumber: 2.3 Consensus size: 19
38583 TTTGAATTTT
38593 AAAAAATCAGAAAAA-TAC
1 AAAAAATCAGAAAAATTAC
38611 AAAAAATCAGAAAAATTAC
1 AAAAAATCAGAAAAATTAC
38630 AAAAAA
1 AAAAAA
38636 AATTAGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.74, C:0.09, G:0.05, T:0.12
Consensus pattern (19 bp):
AAAAAATCAGAAAAATTAC
Found at i:38721 original size:10 final size:10
Alignment explanation
Indices: 38706--38741 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
38696 CTTGACTTTA
38706 AAAAAATCAG
1 AAAAAATCAG
*
38716 AAAAAAT-AC
1 AAAAAATCAG
38725 AAAAAATCAG
1 AAAAAATCAG
38735 AAAAAAT
1 AAAAAAT
38742 AAAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.75, C:0.08, G:0.06, T:0.11
Consensus pattern (10 bp):
AAAAAATCAG
Found at i:38730 original size:19 final size:19
Alignment explanation
Indices: 38706--38766 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
38696 CTTGACTTTA
38706 AAAAAATCAGAAAAAATAC
1 AAAAAATCAGAAAAAATAC
38725 AAAAAATCAGAAAAAATA-
1 AAAAAATCAGAAAAAATAC
* *
38743 AAAAAGA-AAGAAAAATTAC
1 AAAAA-ATCAGAAAAAATAC
38762 AAAAA
1 AAAAA
38767 TAATTAGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (19 bp):
AAAAAATCAGAAAAAATAC
Found at i:38841 original size:132 final size:132
Alignment explanation
Indices: 38593--38843 Score: 355
Period size: 132 Copynumber: 1.9 Consensus size: 132
38583 TTTGAATTTT
*
38593 AAAAAATCAGAAAAATACAAAAAATCAGAAAAATTACAAAAAAAATTAGTATGTTTATTTATCTA
1 AAAAAATCAGAAAAATACAAAAAATAAGAAAAATTACAAAAAAAATTAGTATGTTTATTTATCTA
* * * *
38658 ATTTCAATGTATTTTTATCTATCTTGCAAATTAATCTACTTGACTTTAAAAAAATCAGAAAAAAT
66 ATTTCAATGTATTTTTATCTACCTTGCAAATTAATCTACTTAAATTAAAAAAAATCAGAAAAAAT
38723 AC
131 AC
*
38725 AAAAAATCAGAAAAAATA-AAAAAGA-AAGAAAAATTACAAAAATAATTAGTATGTTT-TTATAT
1 AAAAAATCAG-AAAAATACAAAAA-ATAAGAAAAATTACAAAAAAAATTAGTATGTTTATT-TAT
** * * *
38787 CTAATTTCAATGTATTTTTATCTACCTTTTAATTTAATTTATTTAAATTAAAAAAAA
63 CTAATTTCAATGTATTTTTATCTACCTTGCAAATTAATCTACTTAAATTAAAAAAAA
38844 ACGAAAATTG
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
131 2 0.02
132 95 0.90
133 8 0.08
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (132 bp):
AAAAAATCAGAAAAATACAAAAAATAAGAAAAATTACAAAAAAAATTAGTATGTTTATTTATCTA
ATTTCAATGTATTTTTATCTACCTTGCAAATTAATCTACTTAAATTAAAAAAAATCAGAAAAAAT
AC
Found at i:50372 original size:27 final size:22
Alignment explanation
Indices: 50312--50367 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
50302 TTTCTTCAAG
*
50312 GAAGTGGGATTGATTTGATTTT
1 GAAGAGGGATTGATTTGATTTT
50334 GAAGAGGGATTGATTTGATTTT
1 GAAGAGGGATTGATTTGATTTT
50356 GAAGAGGGATTG
1 GAAGAGGGATTG
50368 GATTGTTGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.27, C:0.00, G:0.36, T:0.38
Consensus pattern (22 bp):
GAAGAGGGATTGATTTGATTTT
Found at i:51852 original size:21 final size:21
Alignment explanation
Indices: 51828--51891 Score: 58
Period size: 24 Copynumber: 2.9 Consensus size: 21
51818 TCGGTGCATC
51828 TTCATGATGTATCGATGCACA
1 TTCATGATGTATCGATGCACA
* * *
51849 TTCAAAGGGATGCATCGATGCACT
1 TTC--A-TGATGTATCGATGCACA
51873 TTCAT-AGTGTATCGATGCA
1 TTCATGA-TGTATCGATGCA
51892 TTATGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
22 1 0.03
23 1 0.03
24 17 0.50
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (21 bp):
TTCATGATGTATCGATGCACA
Found at i:51884 original size:45 final size:44
Alignment explanation
Indices: 51789--51891 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 44
51779 AAACCCGACG
* *
51789 GATGCATCGATGCACATTCAAGGCGTGCATCGGTGCATCTTCAT
1 GATGTATCGATGCACATTCAAGGCGTGCATCGATGCATCTTCAT
51833 GATGTATCGATGCACATTCAAAGG-GATGCATCGATGCA-CTTTCAT
1 GATGTATCGATGCACATTC-AAGGCG-TGCATCGATGCATC-TTCAT
51878 -AGTGTATCGATGCA
1 GA-TGTATCGATGCA
51892 TTATGCACAA
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
44 21 0.40
45 32 0.60
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (44 bp):
GATGTATCGATGCACATTCAAGGCGTGCATCGATGCATCTTCAT
Found at i:57770 original size:46 final size:46
Alignment explanation
Indices: 57694--57846 Score: 220
Period size: 46 Copynumber: 3.3 Consensus size: 46
57684 GGTGCACTAA
* * *
57694 GAGTGAATTGATGCATAAAATGAATTCGATGTTTTTAAACAAGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTAAACAAGCCT
* *
57740 GAGTACATCGATGCATAAAATGCATTCGATGTTTTTAAACAGGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTAAACAAGCCT
* *
57786 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CAT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTA-AACAAGCCT
57831 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
57847 GGTAGTGCAT
Statistics
Matches: 97, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
45 18 0.19
46 77 0.79
47 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (46 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTAAACAAGCCT
Found at i:57960 original size:64 final size:63
Alignment explanation
Indices: 57787--58006 Score: 309
Period size: 63 Copynumber: 3.5 Consensus size: 63
57777 AACAGGCCTG
* *
57787 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACATGAGTGCATCGATGCATGGT
1 AGTGTATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
* * * *
57850 AGTGCATCGATGCAAAAAATGTATTCGATGTTTT--TAAACAGGCCTGAGTGCATCGATGAATGG
1 AGTGTATCGATGCATAAAATGCATTCGATGTTTTCATAAA-A--CCTGAGTGCATCGATGCATGG
57913 T
63 T
* * *
57914 CTGTGTATAGATGCATAAAATGCATTCTATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
1 -AGTGTATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
57978 AGTGTATCGATGCATAAAATGCATTCGAT
1 AGTGTATCGATGCATAAAATGCATTCGAT
58007 ATGGTGAGTG
Statistics
Matches: 137, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
61 4 0.03
62 1 0.01
63 58 0.42
64 41 0.30
65 28 0.20
66 1 0.01
67 4 0.03
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (63 bp):
AGTGTATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
Found at i:58046 original size:20 final size:20
Alignment explanation
Indices: 58011--58048 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
58001 TTCGATATGG
*
58011 TGAGTGCATCTATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
58031 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
58049 CCTTCTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:63111 original size:22 final size:22
Alignment explanation
Indices: 63081--63122 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
63071 AACCATGATC
* *
63081 GAGTCGTGCTCGAGTTGTGAAT
1 GAGTCGTGCCCGAGTCGTGAAT
*
63103 GAGTTGTGCCCGAGTCGTGA
1 GAGTCGTGCCCGAGTCGTGA
63123 GTCGAGTAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.29
Consensus pattern (22 bp):
GAGTCGTGCCCGAGTCGTGAAT
Found at i:64725 original size:17 final size:16
Alignment explanation
Indices: 64695--64759 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 16
64685 AATTAATGAA
64695 AATAAATGAATAAAATG
1 AATAAAT-AATAAAATG
*
64712 AATAAATAATTAAATTTTG
1 AATAAATAA-TAAA--ATG
64731 AATAAA-AATAATAATG
1 AATAAATAATAA-AATG
64747 AA-AAATAAATAAA
1 AATAAAT-AATAAA
64760 TTATAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
15 3 0.08
16 7 0.17
17 19 0.47
18 3 0.08
19 8 0.20
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
AATAAATAATAAAATG
Found at i:66241 original size:23 final size:23
Alignment explanation
Indices: 66215--66262 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
66205 CAAGCGCTTA
66215 TTTTTTT-CTCTCATTTTTTT-TTG
1 TTTTTTTACT-TC-TTTTTTTGTTG
66238 TTTTTTTACTTCTTTTTTTGTTG
1 TTTTTTTACTTCTTTTTTTGTTG
66261 TT
1 TT
66263 GTTGAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.30
23 14 0.61
24 2 0.09
ACGTcount: A:0.04, C:0.10, G:0.06, T:0.79
Consensus pattern (23 bp):
TTTTTTTACTTCTTTTTTTGTTG
Found at i:72786 original size:13 final size:13
Alignment explanation
Indices: 72768--72800 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
72758 AGCATTGTGA
72768 AAAGAAAAT-AAT
1 AAAGAAAATAAAT
72780 GAAAGAAAATAAAT
1 -AAAGAAAATAAAT
72794 AAAGAAA
1 AAAGAAA
72801 TATGGAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 16 0.84
14 3 0.16
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (13 bp):
AAAGAAAATAAAT
Found at i:75047 original size:16 final size:15
Alignment explanation
Indices: 75021--75070 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
75011 ATACTTGTTT
*
75021 AATTTTTAAAATTAA
1 AATTATTAAAATTAA
75036 AATATATTAAAATATATA
1 AAT-TATTAAAAT-TA-A
75054 AATTATTAAATATTAA
1 AATTATTAAA-ATTAA
75070 A
1 A
75071 TTGATAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 3 0.10
16 10 0.33
17 11 0.37
18 6 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTATTAAAATTAA
Found at i:75523 original size:43 final size:43
Alignment explanation
Indices: 75462--75548 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
75452 TACATCAAGA
*
75462 ACTTCACTGATATCTGATTGTAGATTTCGGAATTGGGCGATTC
1 ACTTCACTGATATCTGATTGCAGATTTCGGAATTGGGCGATTC
* *
75505 ACTTCACTGATATCTGATTGCAGATTTTGGACTTGGGCGATTC
1 ACTTCACTGATATCTGATTGCAGATTTCGGAATTGGGCGATTC
75548 A
1 A
75549 GAGGACTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
ACTTCACTGATATCTGATTGCAGATTTCGGAATTGGGCGATTC
Done.