Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000138.1 Hibiscus syriacus cultivar Beakdansim tig00000251_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: 59562
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:257 original size:125 final size:125
Alignment explanation
Indices: 20--332 Score: 384
Period size: 125 Copynumber: 2.5 Consensus size: 125
10 GCCGCATCGC
*
20 GTAGGAACTG-GTCAA-CCAGATAACTAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 GTAGGAACTGTGTCAACCCAGATACCT--CCATCCTCATCACGTAGGAACCGTGTTATCACCTTT
* * * *
83 AGATGGCCAGAACTCTTCATCACGTATGAGACGTGTCATCAACTGCCAGATCTCCTCATTAT
64 AGATGGCCACAACTCCTCATCACGTAGGAGACGTGTCATCAACCGCCAGATCTCCTCATTAT
* *
145 GTAGGAGCTGTGTCAACCCAGATACCTCCGTCCTCATCACGTAGGAACCGTGTTATCACC-TTAG
1 GTAGGAACTGTGTCAACCCAGATACCTCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAG
* * * * *
209 ATGGTCTACCA-TCCTCATCGCGTAGGA-ACCGTGTCATCACCCGACCAGATTTCCTCATTAT
66 ATGG-CCACAACTCCTCATCACGTAGGAGA-CGTGTCATCAACCG-CCAGATCTCCTCATTAT
* * *
270 GTAGGAACTGTGTCAACCCAGATAACCAGTTCATCCTCATCACGTAGGAATCGAGTTATCACC
1 GTAGGAACTGTGTCAACCCAGAT-ACC--TCCATCCTCATCACGTAGGAACCGTGTTATCACC
333 CTTCCTAAAG
Statistics
Matches: 163, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
123 1 0.01
124 33 0.20
125 82 0.50
126 8 0.05
127 9 0.06
128 30 0.18
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.26
Consensus pattern (125 bp):
GTAGGAACTGTGTCAACCCAGATACCTCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAG
ATGGCCACAACTCCTCATCACGTAGGAGACGTGTCATCAACCGCCAGATCTCCTCATTAT
Found at i:1255 original size:19 final size:21
Alignment explanation
Indices: 1233--1276 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1223 GCAAAATTCC
1233 ACTTGGTAC-T-TTAAATTTT
1 ACTTGGTACTTCTTAAATTTT
1252 ACTTGGTACTTCTTAAATTTT
1 ACTTGGTACTTCTTAAATTTT
1273 ACTT
1 ACTT
1277 TTCTGTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 9 0.39
20 1 0.04
21 13 0.57
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (21 bp):
ACTTGGTACTTCTTAAATTTT
Found at i:5958 original size:2 final size:2
Alignment explanation
Indices: 5953--5977 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5943 ATATATATAT
5953 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
5978 ATAAGCTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:7372 original size:34 final size:33
Alignment explanation
Indices: 7328--7398 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
7318 TGATGGTGTT
**
7328 TTTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
1 TTTCTAAAAACAAATTTCATCTCGCTTGA-ACAA
* *
7362 TTTCTCAAAACAAATTTCATCTCGCTTGAACAT
1 TTTCTAAAAACAAATTTCATCTCGCTTGAACAA
7395 TTTC
1 TTTC
7399 CTTTGAGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.38
Consensus pattern (33 bp):
TTTCTAAAAACAAATTTCATCTCGCTTGAACAA
Found at i:7748 original size:33 final size:34
Alignment explanation
Indices: 7711--7794 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 34
7701 ATTCTGAAAT
* **
7711 TGTTTCACTTGAAATAAAAATTATCTTTGAG-TC
1 TGTTTCACTTGAAACAAAAACCATCTTTGAGATC
* *
7744 TGTTTCACTGGAAACAACAACCATCTTTGAGATC
1 TGTTTCACTTGAAACAAAAACCATCTTTGAGATC
*
7778 -GTTTCTCTTGAAACAAA
1 TGTTTCACTTGAAACAAA
7795 TCTTATTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 40 0.95
34 2 0.05
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (34 bp):
TGTTTCACTTGAAACAAAAACCATCTTTGAGATC
Found at i:7986 original size:33 final size:35
Alignment explanation
Indices: 7901--7986 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
7891 GTGAAACACC
* *
7901 CATCTTTGAGTATGTTTCCCTTGAAACAAAACAAA
1 CATCTTTGAGTCTGTTTCCCATGAAACAAAACAAA
**
7936 CATCTTTGAGATC-GTTTCCCATGAAAC-AAATTAA
1 CATCTTTGAG-TCTGTTTCCCATGAAACAAAACAAA
7970 -ATCTTTGAGTCTGTTTC
1 CATCTTTGAGTCTGTTTC
7987 TTGAAACATA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 2 0.04
33 14 0.31
34 5 0.11
35 23 0.51
36 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (35 bp):
CATCTTTGAGTCTGTTTCCCATGAAACAAAACAAA
Found at i:8016 original size:61 final size:65
Alignment explanation
Indices: 7902--8028 Score: 154
Period size: 61 Copynumber: 2.0 Consensus size: 65
7892 TGAAACACCC
*
7902 ATCTTTGAGTATGTTTCCCTTGAAACAAAACAAACATCTTTGAGATCGTTTCCCATGAAACAAAT
1 ATCTTTGAGTATGTTT-CCTTGAAACAAAAC--ACATCTTTGAGATCGATTCCCATGAAACAAAT
7967 TAA
63 TAA
* * * *
7970 ATCTTTGAGTCTGTTT-CTTGAAACATAAC-CATCTTTGAG-TC-ATTCCCTTGAAACGAATT
1 ATCTTTGAGTATGTTTCCTTGAAACAAAACACATCTTTGAGATCGATTCCCATGAAACAAATT
8029 TTGTCTCTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
61 15 0.28
62 2 0.04
63 10 0.19
66 12 0.22
68 15 0.28
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (65 bp):
ATCTTTGAGTATGTTTCCTTGAAACAAAACACATCTTTGAGATCGATTCCCATGAAACAAATTAA
Found at i:8346 original size:128 final size:123
Alignment explanation
Indices: 8173--8561 Score: 365
Period size: 123 Copynumber: 3.0 Consensus size: 123
8163 GCGTAGGAAT
* * *
8173 TGTCAA-CCAGATAACTAGTCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGGTGGTCAG
1 TGTCAACCCAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGG-CA-
*
8237 AACTCTTCATCACGTATGAGTCGTGTTATCAACTGACCAGATCTCCTCATTATGTAGGAGTTG
64 AACTCTTCATCACGTATGAG-CGTG-TATC-ACCGACCAGATCTCCTCATTATGTAGGAGTTG
* * *
8300 TGTCAACCCAGATAACCAATCGTCCTTATCACGTAGGAACCATGTTATCACCCTTAGATGG-AAT
1 TGTCAACCCAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCAA-
* * * * * * * **
8364 GCGTCCTCATCGCGTAGGAACCGTG--TCACCCACCAGATTTCCTCATTATGTAGGAACTG
65 AC-TCTTCATCACGTATG-AGCGTGTATCACCGACCAGATCTCCTCATTATGTAGGAGTTG
* *
8423 TGTCAACCCAAATAACCAGCCGTCCTCATCACGTAGGAACCGA-GTTATCATCCTTCCTAAAGAT
1 TGTCAACCCAGATAACCAGTCGTCCTCATCACGTAGGAACC-ATGTTATCA-CCTT--T--AGAT
* * *
8487 GGCCAATAACTTTTCATCACGTATGAGCAGTGTCATCCCCCGACTAGATCTCCTCATTATGTAGG
60 GG-C-A-AACTCTTCATCACGTATGAGC-GTGT-AT-CACCGACCAGATCTCCTCATTATGTAGG
*
8552 AGTCG
119 AGTTG
8557 TGTCA
1 TGTCA
8562 CCCTTAGACG
Statistics
Matches: 209, Mismatches: 34, Indels: 31
0.76 0.12 0.11
Matches are distributed among these distances:
123 71 0.34
124 6 0.03
125 1 0.00
126 3 0.01
127 22 0.11
128 55 0.26
129 2 0.01
130 14 0.07
131 2 0.01
132 1 0.00
133 1 0.00
134 31 0.15
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (123 bp):
TGTCAACCCAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCAAA
CTCTTCATCACGTATGAGCGTGTATCACCGACCAGATCTCCTCATTATGTAGGAGTTG
Found at i:14783 original size:94 final size:94
Alignment explanation
Indices: 14618--14790 Score: 228
Period size: 94 Copynumber: 1.8 Consensus size: 94
14608 ATTCAATCAT
** *
14618 TATCGGTATCCAAGCGATGTGGTATTGATACCATGGTAAGGGTATCGATACCAAGAAACATCGAA
1 TATCGGTATCCAAGCGATGTGGTATCAATAACATGGTAAGGGTATCGATACCAAGAAACATCGAA
14683 TCTAATTTTGGTATCAATACCTAAGGGGG
66 TCTAATTTTGGTATCAATACCTAAGGGGG
* **
14712 TATCGGTA-CCATAGC-ATAGTGGTATCAATAACATGGTGAGGGTATCGATACCATA-TTACATC
1 TATCGGTATCCA-AGCGAT-GTGGTATCAATAACATGGTAAGGGTATCGATACCA-AGAAACATC
14774 GAAGT-TAATTTTGGTAT
63 GAA-TCTAATTTTGGTAT
14791 TGATACTGGA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
93 5 0.07
94 62 0.90
95 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (94 bp):
TATCGGTATCCAAGCGATGTGGTATCAATAACATGGTAAGGGTATCGATACCAAGAAACATCGAA
TCTAATTTTGGTATCAATACCTAAGGGGG
Found at i:14834 original size:22 final size:22
Alignment explanation
Indices: 14806--14847 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
14796 CTGGAAGGGG
14806 GTATCAATACCATAATAGGGTA
1 GTATCAATACCATAATAGGGTA
*
14828 GTATCAATACCATAGTAGGG
1 GTATCAATACCATAATAGGG
14848 GTATCGATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.26
Consensus pattern (22 bp):
GTATCAATACCATAATAGGGTA
Found at i:14853 original size:95 final size:93
Alignment explanation
Indices: 14645--14857 Score: 229
Period size: 95 Copynumber: 2.3 Consensus size: 93
14635 TGTGGTATTG
*
14645 ATACCATGGTAAGGGTATCGATACCAAGAAACATCGAATCTAATTTTGGTATCAATACCTAAGGG
1 ATACCATGGTAGGGGTATCGATACCAAGAAACATCGAATCTAATTTTGGTATCAATACCTAAGGG
** *
14710 GGTATCGGTACCATAGCATAGTGGTATCA
66 GGTATCAATACCATA-CATAGTAGTATCA
* ** **
14739 ATAACATGGT-GAGGGTATCGATACCATA-TTACATCGAAGT-TAATTTTGGTATTGATA-CTGG
1 ATACCATGGTAG-GGGTATCGATACCA-AGAAACATCGAA-TCTAATTTTGGTATCAATACCT--
14800 AAGGGGGTATCAATACCATA-ATAGGGTAGTATCA
61 AAGGGGGTATCAATACCATACATA--GTAGTATCA
*
14834 ATACCATAGTAGGGGTATCGATAC
1 ATACCATGGTAGGGGTATCGATAC
14858 TGAAGGGCCA
Statistics
Matches: 100, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
93 5 0.05
94 46 0.46
95 48 0.48
96 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (93 bp):
ATACCATGGTAGGGGTATCGATACCAAGAAACATCGAATCTAATTTTGGTATCAATACCTAAGGG
GGTATCAATACCATACATAGTAGTATCA
Found at i:14857 original size:20 final size:20
Alignment explanation
Indices: 14803--14857 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
14793 ATACTGGAAG
14803 GGGGTATCAATACCATAATA
1 GGGGTATCAATACCATAATA
*
14823 GGGTAGTATCAATACCATAGTA
1 GGG--GTATCAATACCATAATA
*
14845 GGGGTATCGATAC
1 GGGGTATCAATAC
14858 TGAAGGGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.39
22 19 0.61
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (20 bp):
GGGGTATCAATACCATAATA
Found at i:15318 original size:45 final size:43
Alignment explanation
Indices: 15262--15607 Score: 302
Period size: 45 Copynumber: 7.7 Consensus size: 43
15252 AATGAAAACT
* * * *
15262 AATGCATATGGGTGCATTATTAGCATG-AAAGGATGCTATGGTTGA
1 AATGTATATGGGTACATTATCA-CA-GAAAAGTATGCTA-GGTTGA
* ** *
15307 AATGTATATGGGTACATTAACAACAGAAAAACATACTTTA-GTTGA
1 AATGTATATGGGTACATTATC-ACAGAAAAGTATGC--TAGGTTGA
*
15352 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTGG
1 AATGTATATGGGTACATTATC-ACAGAAAAGTATGCTAG-GTTGA
* * *
15397 AATGCATATGGGTGCATTATCAACAGATAAGTATGCTAGAGTTGA
1 AATGTATATGGGTACATTATC-ACAGAAAAGTATGCTAG-GTTGA
* * * *
15442 AATGCATATGGGTGCATTATCAATAGAAGAA-CATGCTAGAGTTGA
1 AATGTATATGGGTACATTATC-ACAGAA-AAGTATGCTAG-GTTGA
* *
15487 AATGTATATGGGTACATTATCAATAGAAAAGTATGCTATGGTTAA
1 AATGTATATGGGTACATTATC-ACAGAAAAGTATGCTA-GGTTGA
* * *
15532 AATGTATATGGGTACATTATCAAAGGAAAAGTATACTACAGTTGA
1 AATGTATATGGGTACATTATCACA-GAAAAGTATGCTA-GGTTGA
* *
15577 AATGTATATGGGTGCATTATCAAAGGAAAAG
1 AATGTATATGGGTACATTATCACA-GAAAAG
15608 ATGTTACAAA
Statistics
Matches: 262, Mismatches: 29, Indels: 20
0.84 0.09 0.06
Matches are distributed among these distances:
43 2 0.01
44 5 0.02
45 249 0.95
46 4 0.02
47 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (43 bp):
AATGTATATGGGTACATTATCACAGAAAAGTATGCTAGGTTGA
Found at i:15388 original size:90 final size:91
Alignment explanation
Indices: 15262--15607 Score: 382
Period size: 90 Copynumber: 3.8 Consensus size: 91
15252 AATGAAAACT
* * * * *
15262 AATGCATATGGGTGCATTATTAGCATG-AAAGGATGCTATG-GTTGAAATGTATATGGGTACATT
1 AATGCATATGGGTACATTATCAACAGGAAAAGTATGCTA-GAGTTGAAATGTATATGGGTACATT
* ** * *
15325 AACAACAGAAAAACATACTTTAGTTGA
65 ATCAACAGAAAAGTATGCTATAGTTGA
* * * *
15352 AATGTATATGGGTACATTATCAACA-GAAAAGTATGCTAGAGTTGGAATGCATATGGGTGCATTA
1 AATGCATATGGGTACATTATCAACAGGAAAAGTATGCTAGAGTTGAAATGTATATGGGTACATTA
* *
15416 TCAACAGATAAGTATGCTAGAGTTGA
66 TCAACAGAAAAGTATGCTATAGTTGA
* * *
15442 AATGCATATGGGTGCATTATCAATA-GAAGAA-CATGCTAGAGTTGAAATGTATATGGGTACATT
1 AATGCATATGGGTACATTATCAACAGGAA-AAGTATGCTAGAGTTGAAATGTATATGGGTACATT
* * *
15505 ATCAATAGAAAAGTATGCTATGGTTAA
65 ATCAACAGAAAAGTATGCTATAGTTGA
* * * *
15532 AATGTATATGGGTACATTATCAA-AGGAAAAGTATACTACAGTTGAAATGTATATGGGTGCATTA
1 AATGCATATGGGTACATTATCAACAGGAAAAGTATGCTAGAGTTGAAATGTATATGGGTACATTA
15596 TCAA-AGGAAAAG
66 TCAACA-GAAAAG
15608 ATGTTACAAA
Statistics
Matches: 217, Mismatches: 33, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
89 6 0.03
90 209 0.96
91 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (91 bp):
AATGCATATGGGTACATTATCAACAGGAAAAGTATGCTAGAGTTGAAATGTATATGGGTACATTA
TCAACAGAAAAGTATGCTATAGTTGA
Found at i:15504 original size:135 final size:135
Alignment explanation
Indices: 15262--15599 Score: 441
Period size: 135 Copynumber: 2.5 Consensus size: 135
15252 AATGAAAACT
* * * * *
15262 AATGCATATGGGTGCATTATTAGCATGAAAGGATGCTATG-GTTGAAATGTATATGGGTACATTA
1 AATGCATATGGGTGCATTATCAACAGGAAAGTATGCTA-GAGTTGAAATGTATATGGGTGCATTA
* **
15326 ACAACAGAAAAACATACTTTAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTA-
65 TCAACAGAAAAACATACTAGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTAT
**
15390 GAGTTGG
130 G-GTTAA
*
15397 AATGCATATGGGTGCATTATCAACA-GATAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTA
1 AATGCATATGGGTGCATTATCAACAGGA-AAGTATGCTAGAGTTGAAATGTATATGGGTGCATTA
* * * *
15461 TCAATAGAAGAACATGCTAGAGTTGAAATGTATATGGGTACATTATCAATAGAAAAGTATGCTAT
65 TCAACAGAAAAACATACTAGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTAT
15526 GGTTAA
130 GGTTAA
* * * *
15532 AATGTATATGGGTACATTATCAA-AGGAAAAGTATACTACAGTTGAAATGTATATGGGTGCATTA
1 AATGCATATGGGTGCATTATCAACAGG-AAAGTATGCTAGAGTTGAAATGTATATGGGTGCATTA
15596 TCAA
65 TCAA
15600 AGGAAAAGAT
Statistics
Matches: 179, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
134 4 0.02
135 173 0.97
136 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.30
Consensus pattern (135 bp):
AATGCATATGGGTGCATTATCAACAGGAAAGTATGCTAGAGTTGAAATGTATATGGGTGCATTAT
CAACAGAAAAACATACTAGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTATG
GTTAA
Found at i:17664 original size:59 final size:59
Alignment explanation
Indices: 17599--17713 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 59
17589 ATATCCTCAG
** * ** *
17599 ACTATGACCCTCATTTTAGATTAGTCCTTAAACTTTT-AAACATTCTAATTTCATCCCAA
1 ACTATGACCCTCATTCCAAATTAGTCCCCAAACTTTTGAAAC-TTCCAATTTCATCCCAA
* *
17658 ACTATGACTCTCATTCCAAATTAGTCCCCAAACTTTTGAATCTTCCAATTTCATCC
1 ACTATGACCCTCATTCCAAATTAGTCCCCAAACTTTTGAAACTTCCAATTTCATCC
17714 TAAATTTATC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 44 0.94
60 3 0.06
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.37
Consensus pattern (59 bp):
ACTATGACCCTCATTCCAAATTAGTCCCCAAACTTTTGAAACTTCCAATTTCATCCCAA
Found at i:21289 original size:8 final size:8
Alignment explanation
Indices: 21278--21312 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
21268 AAAGAAAAAT
21278 AATAAGAA
1 AATAAGAA
21286 AATAATGAA
1 AATAA-GAA
*
21295 AATAAAAA
1 AATAAGAA
21303 AATAAGAA
1 AATAAGAA
21311 AA
1 AA
21313 CGAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (8 bp):
AATAAGAA
Found at i:21290 original size:25 final size:25
Alignment explanation
Indices: 21261--21339 Score: 72
Period size: 25 Copynumber: 3.1 Consensus size: 25
21251 AAAATGAAGT
*
21261 AATAAAAAAAGAAAAATAATAAGAA
1 AATAAAAAAAAAAAAATAATAAGAA
* *
21286 AATAATGAAAATAAAAA-AATAAGAA
1 AATAA-AAAAAAAAAAATAATAAGAA
*
21311 AACGAAATAAAATAAAAAATAATAA-AA
1 AA-TAAA-AAAA-AAAAAATAATAAGAA
21338 AA
1 AA
21340 GGTTAAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
25 15 0.34
26 15 0.34
27 9 0.20
28 5 0.11
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (25 bp):
AATAAAAAAAAAAAAATAATAAGAA
Found at i:21290 original size:42 final size:42
Alignment explanation
Indices: 21236--21338 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 42
21226 TAAAAGGGAT
* * **
21236 AAATAAATAATAATGAAAATGAAGTAATAA-AAAAAGAAA-A
1 AAATAAAAAATAATGAAAATAAAAAAATAAGAAAAAGAAATA
*
21276 ATAATAAGAAAATAATGAAAATAAAAAAATAAGAAAACGAAATA
1 A-AATAA-AAAATAATGAAAATAAAAAAATAAGAAAAAGAAATA
*
21320 AAATAAAAAATAATAAAAA
1 AAATAAAAAATAATGAAAA
21339 AGGTTAAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
40 1 0.02
41 5 0.09
42 32 0.60
43 13 0.25
44 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.17
Consensus pattern (42 bp):
AAATAAAAAATAATGAAAATAAAAAAATAAGAAAAAGAAATA
Found at i:21295 original size:21 final size:23
Alignment explanation
Indices: 21244--21296 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
21234 ATAAATAAAT
*
21244 AATAATG-AAAATGAAGTAATAA
1 AATAATGAAAAATGAAGTAAGAA
*
21266 AA-AAAGAAAAAT-AA-TAAGAA
1 AATAATGAAAAATGAAGTAAGAA
21286 AATAATGAAAA
1 AATAATGAAAA
21297 TAAAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 7 0.27
21 12 0.46
22 7 0.27
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (23 bp):
AATAATGAAAAATGAAGTAAGAA
Found at i:21296 original size:20 final size:21
Alignment explanation
Indices: 21244--21299 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
21234 ATAAATAAAT
*
21244 AATAATGAAAATGAAGTAATAA
1 AATAATGAAAAT-AAGTAAGAA
*
21266 AA-AAAGAAAAATAA-TAAGAA
1 AATAATG-AAAATAAGTAAGAA
21286 AATAATGAAAATAA
1 AATAATGAAAATAA
21300 AAAAATAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 14 0.48
21 8 0.28
22 7 0.24
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (21 bp):
AATAATGAAAATAAGTAAGAA
Found at i:21299 original size:34 final size:34
Alignment explanation
Indices: 21240--21304 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
21230 AGGGATAAAT
*
21240 AAATAATAATGAAAATGAAGTAATAAAAAAAGAA
1 AAATAATAATGAAAATGAAGAAATAAAAAAAGAA
21274 AAATAATAA-GAAAAT-AATGAAAATAAAAAAA
1 AAATAATAATGAAAATGAA-G-AAATAAAAAAA
21305 TAAGAAAACG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 2 0.07
33 7 0.25
34 19 0.68
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (34 bp):
AAATAATAATGAAAATGAAGAAATAAAAAAAGAA
Found at i:21302 original size:26 final size:26
Alignment explanation
Indices: 21267--21339 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
21257 AAGTAATAAA
* *
21267 AAAAGAAAAATAATAAGAAAA-TAAT
1 AAAATAAAAATAATAAGAAAACAAAT
21292 GAAAATAAAAA-AATAAGAAAACGAAAT
1 -AAAATAAAAATAATAAGAAAAC-AAAT
21319 AAAATAAAAAATAATAA-AAAA
1 AAAAT-AAAAATAATAAGAAAA
21340 GGTTAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 10 0.24
26 14 0.34
27 12 0.29
28 5 0.12
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.14
Consensus pattern (26 bp):
AAAATAAAAATAATAAGAAAACAAAT
Found at i:22074 original size:2 final size:2
Alignment explanation
Indices: 22067--22101 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
22057 CTTCGATGTT
22067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22102 TCTATAGTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22575 original size:4 final size:4
Alignment explanation
Indices: 22566--22609 Score: 56
Period size: 4 Copynumber: 11.2 Consensus size: 4
22556 AAAAAAAGGG
*
22566 AATA AATA AATA AATA AAT- AACA AATAA AATA AAT- AATA AATA A
1 AATA AATA AATA AATA AATA AATA AAT-A AATA AATA AATA AATA A
22610 TAATAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 5 0.14
4 26 0.74
5 4 0.11
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:22596 original size:16 final size:16
Alignment explanation
Indices: 22573--22621 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
22563 GGGAATAAAT
22573 AAAT-AAATAAATAAC
1 AAATAAAATAAATAAC
*
22588 AAATAAAATAAATAAT
1 AAATAAAATAAATAAC
*
22604 AAATAATAATAAAAAAC
1 AAATAA-AATAAATAAC
22621 A
1 A
22622 TTTTAAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 4 0.14
16 16 0.55
17 9 0.31
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (16 bp):
AAATAAAATAAATAAC
Found at i:22604 original size:7 final size:7
Alignment explanation
Indices: 22570--22612 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
22560 AAAGGGAATA
22570 AATAAAT
1 AATAAAT
22577 AAATAAAT
1 -AATAAAT
*
22585 AACAAAT
1 AATAAAT
22592 AAAATAAAT
1 --AATAAAT
22601 AATAAAT
1 AATAAAT
22608 AATAA
1 AATAA
22613 TAAAAAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
7 18 0.58
8 7 0.23
9 6 0.19
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (7 bp):
AATAAAT
Found at i:22668 original size:37 final size:37
Alignment explanation
Indices: 22622--23318 Score: 175
Period size: 37 Copynumber: 18.9 Consensus size: 37
22612 ATAAAAAACA
* * *
22622 TTTTAAAACTGTATATTATATATGCTTTT-AAAAATTG
1 TTTTAAAACTATATAATATATAT-ATTTTCAAAAATTG
* *
22659 TTTTCAAACTATATAATATATATATTTTCAAAATTTG
1 TTTTAAAACTATATAATATATATATTTTCAAAAATTG
* * * * *
22696 TTTTAAAACTAATATATTTTCAAAAATATTTC-AAAATTA
1 TTTTAAAACT-ATATAATAT-ATATAT-TTTCAAAAATTG
* * * * **
22735 TATTATATACATTTTCAAAAATTATATATTATTGTTTTAAAA-TG
1 T-TT-TA-AAACTAT--ATAA-TATATA-TATT-TTCAAAAATTG
22779 TTTTCAAAACTATAT-AT-TATATATTTTCAAAAA-TG
1 TTTT-AAAACTATATAATATATATATTTTCAAAAATTG
22814 TTTTTAAAAACTATAT-AT-TATATATTTTC-AAAA-TG
1 -TTTT-AAAACTATATAATATATATATTTTCAAAAATTG
22849 TTTTAAAAACTATATATTATATATATATTTTCAAAAA---
1 TTTT-AAAACTATATA--ATATATATATTTTCAAAAATTG
* * * *
22886 ----AAAAAT-TA-AAAACTATATA-TAT-ATAAATT-
1 TTTTAAAACTATATAATA-TATATATTTTCAAAAATTG
** * *
22915 TTCAAAAACTATATATTATATA-AGTTTTC-TAAATGT-
1 TTTTAAAACTATATAATATATATA-TTTTCAAAAAT-TG
* * *
22951 TTTAAAGACTATATATTATATATATTTTTTCAAAAATTG
1 TTTTAAAACTATATA--ATATATATATTTTCAAAAATTG
* *
22990 TTTT-AAACTAATAAATTTTAAAAAACTATATATTTTCCAAAATTG
1 TTTTAAAACT-AT--A---T--AATA-TATATATTTTCAAAAATTG
23035 TTTT-AAACTAATAAATTTTAAAAATATATATATTTT--AAAA---
1 TTTTAAAACT-AT--A---T---AATATATATATTTTCAAAAATTG
* * * *
23075 TTTTAAAGACTATAT-AT-TATA-AGTTT--GAATTTT
1 TTTTAAA-ACTATATAATATATATATTTTCAAAAATTG
* **
23108 TTTTAAAAACTATATATTATATATATTTTTCAAAAA-AA
1 TTTT-AAAACTATATAATATATATA-TTTTCAAAAATTG
* * * *
23146 ATTAAAAACTATATATTATATAAAATTTTCAAAATATT-
1 TTTTAAAACTATATAATATAT-ATATTTTCAAAA-ATTG
* * *
23184 TTTAAAAACTATATATTATATATGTTTTC-AAAA-TG
1 TTTTAAAACTATATAATATATATATTTTCAAAAATTG
*
23219 TTTTAAAGACTATATATTATATATATTTTC-AAAATTG
1 TTTTAAA-ACTATATAATATATATATTTTCAAAAATTG
23256 TTTT-AAAC----TAATA-A-ATATTTTCAAAAATAT-
1 TTTTAAAACTATATAATATATATATTTTCAAAAAT-TG
* * *
23286 TTTCAAAA-T-TATATTATATACATTTTCAAAAAT
1 TTTTAAAACTATATAATATATATATTTTCAAAAAT
23319 ATTTTCAAAA
Statistics
Matches: 516, Mismatches: 70, Indels: 150
0.70 0.10 0.20
Matches are distributed among these distances:
27 4 0.01
28 4 0.01
29 14 0.03
30 16 0.03
31 14 0.03
32 7 0.01
33 21 0.04
34 27 0.05
35 49 0.09
36 81 0.16
37 83 0.16
38 60 0.12
39 27 0.05
40 11 0.02
41 8 0.02
42 11 0.02
43 12 0.02
44 11 0.02
45 50 0.10
46 6 0.01
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (37 bp):
TTTTAAAACTATATAATATATATATTTTCAAAAATTG
Found at i:22742 original size:30 final size:31
Alignment explanation
Indices: 22674--22742 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 31
22664 AAACTATATA
* * *
22674 ATATATATATTTTCAAAATTTGTTTTAAAACT
1 ATAT-TATATTTTCAAAATATATTTCAAAACT
*
22706 A-A-TATATTTTCAAAA-ATATTTCAAAATT
1 ATATTATATTTTCAAAATATATTTCAAAACT
22734 ATATTATAT
1 ATATTATAT
22743 ACATTTTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
28 10 0.32
29 14 0.45
30 5 0.16
31 1 0.03
32 1 0.03
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (31 bp):
ATATTATATTTTCAAAATATATTTCAAAACT
Found at i:22836 original size:34 final size:34
Alignment explanation
Indices: 22746--23359 Score: 256
Period size: 36 Copynumber: 17.2 Consensus size: 34
22736 ATTATATACA
* *
22746 TTTTCAAAAATTATATATTAT-TGTTTT-AAAATG
1 TTTT-AAAAACTATATATTATATATTTTCAAAATG
*
22779 TTTTCAAAACTATATATTATATATTTTCAAAAATG
1 TTTTAAAAACTATATATTATATATTTTC-AAAATG
22814 TTTTTAAAAACTATATATTATATATTTTCAAAATG
1 -TTTTAAAAACTATATATTATATATTTTCAAAATG
**
22849 TTTTAAAAACTATATATTATATATATATTTTCAAAAAAAA
1 TTTTAAAAAC--TATA-TAT-TATATATTTTC--AAAATG
**
22889 AATTAAAAAC--TATA-TATATA---T--AAAT-
1 TTTTAAAAACTATATATTATATATTTTCAAAATG
* *
22914 TTTCAAAAACTATATATTATATAAGTTTTCTAAATG
1 TTTTAAAAACTATATATTATAT-A-TTTTCAAAATG
*
22950 TTTTAAAGACTATATATTATATATATTTTTTCAAAAATTG
1 TTTTAAAAACTATATA-T-TATATA--TTTTC-AAAA-TG
* *
22990 TTTTAAACTAA-TAAATTTTAAAAAACTATATATTTTCCAAAATTG
1 TTTTAAA--AACT--A---T---ATATTATATATTTT-CAAAA-TG
*
23035 TTTTAAACTAA-TAAATTTTAAAAATATATATATTTT-AAAA--
1 TTTTAAA--AACT--A---T--ATAT-TATATATTTTCAAAATG
* * * ** *
23075 TTTTAAAGACTATATATTATA-AGTTTGAATTTT
1 TTTTAAAAACTATATATTATATATTTTCAAAATG
**
23108 TTTTAAAAACTATATATTATATATATTTTTCAAAAAA
1 TTTTAAAAACTATATA-T-TATATA-TTTTCAAAATG
** *
23145 AATTAAAAACTATATATTATATAAAATTTTCAAAATAT
1 TTTTAAAAACTATATATTATAT---ATTTTCAAAAT-G
23183 TTTTAAAAACTATATATTATATATGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATA--TTTTCAAAATG
*
23219 TTTTAAAGACTATATATTATATATATTTTCAAAATTG
1 TTTTAAAAACTATATA-T-TATATATTTTCAAAA-TG
*
23256 TTTT--AAACTA-ATA--A-ATATTTTCAAAAATA
1 TTTTAAAAACTATATATTATATATTTTC-AAAATG
* *
23285 TTTTCAAAA-T-TATATTATATACATTTTCAAAAATA
1 TTTTAAAAACTATATATTATAT--ATTTTC-AAAATG
* * *
23320 TTTTCAAAAATTATATATTAT-TGTTTT-AAAATA
1 TTTT-AAAAACTATATATTATATATTTTCAAAATG
23353 TTTTAAA
1 TTTTAAA
23360 TAAAAAAACA
Statistics
Matches: 470, Mismatches: 44, Indels: 135
0.72 0.07 0.21
Matches are distributed among these distances:
25 7 0.01
26 3 0.01
27 4 0.01
28 5 0.01
29 14 0.03
30 14 0.03
31 9 0.02
32 21 0.04
33 43 0.09
34 15 0.03
35 54 0.11
36 77 0.16
37 53 0.11
38 57 0.12
39 4 0.01
40 28 0.06
41 1 0.00
42 1 0.00
43 5 0.01
44 5 0.01
45 40 0.09
46 2 0.00
47 6 0.01
49 2 0.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (34 bp):
TTTTAAAAACTATATATTATATATTTTCAAAATG
Found at i:22922 original size:25 final size:26
Alignment explanation
Indices: 22893--22943 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
22883 AAAAAAAATT
22893 AAAAACTATATA-TATATAAATTTTC
1 AAAAACTATATATTATATAAATTTTC
*
22918 AAAAACTATATATTATATAAGTTTTC
1 AAAAACTATATATTATATAAATTTTC
22944 TAAATGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (26 bp):
AAAAACTATATATTATATAAATTTTC
Found at i:23020 original size:45 final size:45
Alignment explanation
Indices: 22968--23074 Score: 173
Period size: 45 Copynumber: 2.4 Consensus size: 45
22958 ACTATATATT
*
22968 ATATATATTTTTTCAAAAATTGTTTTAAACTAATAAATTTTAAAA
1 ATATATATATTTTCAAAAATTGTTTTAAACTAATAAATTTTAAAA
*
23013 A-ACTATATATTTTCCAAAATTGTTTTAAACTAATAAATTTTAAAA
1 ATA-TATATATTTTCAAAAATTGTTTTAAACTAATAAATTTTAAAA
23058 ATATATATATTTT-AAAA
1 ATATATATATTTTCAAAA
23075 TTTTAAAGAC
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
44 4 0.07
45 52 0.91
46 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.45
Consensus pattern (45 bp):
ATATATATATTTTCAAAAATTGTTTTAAACTAATAAATTTTAAAA
Found at i:23285 original size:12 final size:12
Alignment explanation
Indices: 23268--23330 Score: 74
Period size: 12 Copynumber: 5.3 Consensus size: 12
23258 TTAAACTAAT
23268 AAATATTTTCAA
1 AAATATTTTCAA
23280 AAATATTTTCAA
1 AAATATTTTCAA
* * *
23292 AATTATATT-AT
1 AAATATTTTCAA
* *
23303 ATACATTTTCAA
1 AAATATTTTCAA
23315 AAATATTTTCAA
1 AAATATTTTCAA
23327 AAAT
1 AAAT
23331 TATATATTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
11 6 0.15
12 34 0.85
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (12 bp):
AAATATTTTCAA
Found at i:32228 original size:129 final size:129
Alignment explanation
Indices: 31998--32260 Score: 526
Period size: 129 Copynumber: 2.0 Consensus size: 129
31988 CCCGATGTTA
31998 CTGCTCCAGGGCTAAACATACTAGGTGCCTACACAGAATTGACCTCGATAACCGGCGATCCAACT
1 CTGCTCCAGGGCTAAACATACTAGGTGCCTACACAGAATTGACCTCGATAACCGGCGATCCAACT
32063 GACCGACGCTATTCGGCATTTAACATTATGTCCGGCATATCTATGTCTTGTCCCCATGCTGCAG
66 GACCGACGCTATTCGGCATTTAACATTATGTCCGGCATATCTATGTCTTGTCCCCATGCTGCAG
32127 CTGCTCCAGGGCTAAACATACTAGGTGCCTACACAGAATTGACCTCGATAACCGGCGATCCAACT
1 CTGCTCCAGGGCTAAACATACTAGGTGCCTACACAGAATTGACCTCGATAACCGGCGATCCAACT
32192 GACCGACGCTATTCGGCATTTAACATTATGTCCGGCATATCTATGTCTTGTCCCCATGCTGCAG
66 GACCGACGCTATTCGGCATTTAACATTATGTCCGGCATATCTATGTCTTGTCCCCATGCTGCAG
32256 CTGCT
1 CTGCT
32261 GCAGCATATG
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 134 1.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (129 bp):
CTGCTCCAGGGCTAAACATACTAGGTGCCTACACAGAATTGACCTCGATAACCGGCGATCCAACT
GACCGACGCTATTCGGCATTTAACATTATGTCCGGCATATCTATGTCTTGTCCCCATGCTGCAG
Found at i:35470 original size:17 final size:17
Alignment explanation
Indices: 35445--35478 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35435 TGAAAAGTAA
*
35445 TATCCGTACTAAAATAG
1 TATCCGTACCAAAATAG
*
35462 TATCGGTACCAAAATAG
1 TATCCGTACCAAAATAG
35479 CATTCTGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (17 bp):
TATCCGTACCAAAATAG
Found at i:36286 original size:20 final size:21
Alignment explanation
Indices: 36263--36322 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
36253 GAGGTTGCGT
*
36263 GAACAATATCAGTACT-TGAA
1 GAACAATATCAGTACTATAAA
36283 GAACAATATC-GATACTGACTAAA
1 GAACAATATCAG-TACT-A-TAAA
36306 GAACAATATCAGTACTA
1 GAACAATATCAGTACTA
36323 AATGAATAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 1 0.03
20 14 0.41
22 1 0.03
23 17 0.50
24 1 0.03
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (21 bp):
GAACAATATCAGTACTATAAA
Found at i:37576 original size:31 final size:31
Alignment explanation
Indices: 37538--37612 Score: 150
Period size: 31 Copynumber: 2.4 Consensus size: 31
37528 CCTTGATGTA
37538 CTTTGCTTGATTTATGAGGATGTCATATTTT
1 CTTTGCTTGATTTATGAGGATGTCATATTTT
37569 CTTTGCTTGATTTATGAGGATGTCATATTTT
1 CTTTGCTTGATTTATGAGGATGTCATATTTT
37600 CTTTGCTTGATTT
1 CTTTGCTTGATTT
37613 GGAGCCCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.17, C:0.11, G:0.19, T:0.53
Consensus pattern (31 bp):
CTTTGCTTGATTTATGAGGATGTCATATTTT
Found at i:41409 original size:63 final size:63
Alignment explanation
Indices: 41339--41473 Score: 180
Period size: 63 Copynumber: 2.1 Consensus size: 63
41329 CACATTCAAT
* * * * *
41339 GTGCATCGATGCATCCTCAAGTAATTGAACATCAAATATCGTCAGTGCATCGATGCATAAGGA
1 GTGCATCGATGCATCCTCAAGTAAATGAACATCAAATACCCTCAGTCCATCGATGCATAAAGA
** * * *
41402 GTGCATCGATGCATTTTCAATTAAATGAACATCGAATGCCCTCAGTCCATCGATGCATAAAGA
1 GTGCATCGATGCATCCTCAAGTAAATGAACATCAAATACCCTCAGTCCATCGATGCATAAAGA
41465 GTGCATCGA
1 GTGCATCGA
41474 AACACCTCCT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCATCCTCAAGTAAATGAACATCAAATACCCTCAGTCCATCGATGCATAAAGA
Found at i:42252 original size:23 final size:23
Alignment explanation
Indices: 42184--42244 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
42174 CAATCTTATA
* *
42184 TGGCACTACGGTACAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
42207 TGGCACTTCGATGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
42230 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
42245 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:42705 original size:2 final size:2
Alignment explanation
Indices: 42698--42725 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42688 TGTATAAACC
42698 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42726 AAATCTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48513 original size:20 final size:23
Alignment explanation
Indices: 48467--48521 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 23
48457 ATGCACATGT
48467 AGTGCATCGATGAACACACTAAGG
1 AGTGCATCGAT-AACACACTAAGG
*
48491 AGTGCATCGAT-ACACAGT-A-G
1 AGTGCATCGATAACACACTAAGG
48511 AGTGCATCGAT
1 AGTGCATCGAT
48522 GCAAACCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 12 0.40
21 1 0.03
22 6 0.20
24 11 0.37
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (23 bp):
AGTGCATCGATAACACACTAAGG
Found at i:49192 original size:23 final size:23
Alignment explanation
Indices: 49124--49182 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
49114 CAATCTTATA
*
49124 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
49147 CGGTACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
49170 TGGCACTTCGGTG
1 TGGCACTTCGGTG
49183 TATTTATACG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:56334 original size:16 final size:16
Alignment explanation
Indices: 56315--56352 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
56305 TATTTTGGAA
56315 TATGCTGATTTATAAG
1 TATGCTGATTTATAAG
56331 TATGCTGATTTATAAG
1 TATGCTGATTTATAAG
56347 TATGCT
1 TATGCT
56353 AGGTATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (16 bp):
TATGCTGATTTATAAG
Found at i:59107 original size:18 final size:19
Alignment explanation
Indices: 59084--59120 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
59074 AGATCATTTT
59084 TATTTTTCA-ATTTTGAAA
1 TATTTTTCATATTTTGAAA
*
59102 TATTTTTCATGTTTTGAAA
1 TATTTTTCATATTTTGAAA
59121 ACATAGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (19 bp):
TATTTTTCATATTTTGAAA
Done.