Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008302.1 Hibiscus syriacus cultivar Beakdansim tig00110988_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: 3402722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 17
Found at i:1454309 original size:112 final size:112
Alignment explanation
Indices: 1453948--1454484 Score: 813
Period size: 113 Copynumber: 4.8 Consensus size: 112
1453938 GATGTAATCT
* * *
1453948 AGCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-CTTCTTCAGATAAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* **
1454012 CATTATGAACTTTCTCTGGAAATATTGATCCATC-AAGTGATGAATT--
66 CATTATGAACTCTC-CTGGAAATGCTGATCCATCGAA-TGATGAATTCA
*
1454058 TGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
1454119 CATTATGAACTCCTTCTGGAAATGCTGATCCATCGAATGATGAATTCA
66 CATTATGAACT-CTCCTGGAAATGCTGATCCATCGAATGATGAATTCA
*
1454167 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
1454232 CATTATGAACTCTACCTGGAAATGTTGATCCATC-AATGATGAATTCA
66 CATTATGAACTCT-CCTGGAAATGCTGATCCATCGAATGATGAATTCA
* * *
1454279 AGCGAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
1454344 CATTATGAACTCTACCTGGTAATGCTGATCCATCGAATGATGAATTCA
66 CATTATGAACTCT-CCTGGAAATGCTGATCCATCGAATGATGAATTCA
* *
1454392 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
1454457 CATTATGAACTCTTCTGGAAATGCTGAT
66 CATTATGAACTCTCCTGGAAATGCTGAT
1454485 GACCCGAAGG
Statistics
Matches: 395, Mismatches: 22, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
107 63 0.16
108 3 0.01
109 33 0.08
110 32 0.08
112 127 0.32
113 137 0.35
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (112 bp):
AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTCTCCTGGAAATGCTGATCCATCGAATGATGAATTCA
Found at i:1454381 original size:225 final size:219
Alignment explanation
Indices: 1453948--1454484 Score: 828
Period size: 225 Copynumber: 2.4 Consensus size: 219
1453938 GATGTAATCT
* * *
1453948 AGCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-CTTCTTCAGATAAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
1454012 CATTATGAACTTTCTCTGGAAATATTGATCCATCAAGTGATGAATTTGCAAAAAGTTGAACAAGT
66 CATTATGAACTCTC-CTGGAAATGTTGATCCATCAAGTGATGAATTAGCAAAAAGTTGAACAAGT
*
1454077 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAAT
130 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTCCTGGAAAT
1454142 GCTGATCCATCGAATGATGAATTCA
195 GCTGATCCATCGAATGATGAATTCA
*
1454167 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
1454232 CATTATGAACTCTACCTGGAAATGTTGATCCATCAA-TGATGAATTCAAGCGAAAGGTTGAATAA
66 CATTATGAACTCT-CCTGGAAATGTTGATCCATCAAGTGATGAATT--AGCAAAAAGTTGAACAA
1454296 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-CTACC
128 GTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCCT-CC
*
1454360 TGGTAATGCTGATCCATCGAATGATGAATTCA
188 TGGAAATGCTGATCCATCGAATGATGAATTCA
* *
1454392 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
1454457 CATTATGAACTCTTCTGGAAATGCTGAT
66 CATTATGAACTCTCCTGGAAATGTTGAT
1454485 GACCCGAAGG
Statistics
Matches: 292, Mismatches: 17, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
219 50 0.17
220 51 0.17
221 31 0.11
224 21 0.07
225 139 0.48
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (219 bp):
AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTCTCCTGGAAATGTTGATCCATCAAGTGATGAATTAGCAAAAAGTTGAACAAGTT
CTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTCCTGGAAATG
CTGATCCATCGAATGATGAATTCA
Found at i:1454610 original size:76 final size:76
Alignment explanation
Indices: 1454482--1454711 Score: 390
Period size: 76 Copynumber: 3.0 Consensus size: 76
1454472 TGGAAATGCT
* * *
1454482 GATGACCCGAAGGTTTTG-AAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1454546 TAGGACTTACA
66 TAGGACTTACA
* *
1454557 GATGACCCTAAGGCTTTGAAAACATTAAAAAGCTCCCGAAGGCTTTTTTGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1454622 TAGGACTTACA
66 TAGGACTTACA
*
1454633 TATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
*
1454698 TAGGACCTACA
66 TAGGACTTACA
1454709 GAT
1 GAT
1454712 TTGAGAAATA
Statistics
Matches: 144, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
75 16 0.11
76 128 0.89
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (76 bp):
GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
TAGGACTTACA
Found at i:1455411 original size:22 final size:22
Alignment explanation
Indices: 1455386--1455462 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
1455376 AATAAAGCTT
1455386 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
1455408 TCATTTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1455430 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1455452 TCATCTTTGAA
1 TCATCTTTGAA
1455463 GAGTGTAGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1458286 original size:3 final size:3
Alignment explanation
Indices: 1458280--1458309 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1458270 TTTACTCATT
1458280 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1458310 AAAAATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1463766 original size:15 final size:15
Alignment explanation
Indices: 1463746--1463777 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1463736 ATCAATACCT
1463746 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1463761 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1463776 TT
1 TT
1463778 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1470806 original size:113 final size:112
Alignment explanation
Indices: 1470672--1471062 Score: 608
Period size: 113 Copynumber: 3.5 Consensus size: 112
1470662 CTTTAGTCTA
1470672 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
1 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
* *
1470737 TCATTCGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAAC
66 TCATTCGATGGATCAGCTTTTCCAGA-AAAGTTCATAATGAGAAGAAT
1470785 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
1 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
1470850 TCATTCGATGGATCAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAAT
66 TCATTCGATGGATCAGCTTTTCCAGAAA-AGTTCATAATGAGAAGAAT
* *
1470898 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATTCA
1 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
***
1470963 TCACTT-GATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAAT
66 TCA-TTCGATGGATCAGCTTTTCCAG-AAAAGTTCATAATGAGAAGAAT
* * * * *
1471011 TTATCTGAAG-AGGAAGAAGAAGTTCACAATGAGAA-AAGCTTATTCAACCTTT
1 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA-TTTGTTCAACCTTT
1471063 GGAATGACTC
Statistics
Matches: 261, Mismatches: 13, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
111 2 0.01
112 36 0.14
113 221 0.85
114 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (112 bp):
TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
TCATTCGATGGATCAGCTTTTCCAGAAAAGTTCATAATGAGAAGAAT
Found at i:1470933 original size:24 final size:23
Alignment explanation
Indices: 1470890--1470934 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1470880 GTTCATAATG
*
1470890 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
1470913 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
1470935 AATTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:1471295 original size:3 final size:3
Alignment explanation
Indices: 1471289--1471342 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
1471279 TTTACTCATT
* *
1471289 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1471337 TTA TTA
1 TTA TTA
1471343 AAAAATAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1471786 original size:22 final size:21
Alignment explanation
Indices: 1471761--1471806 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1471751 AAAAAAAGAG
*
1471761 AACACAGAGCCAGAGAGACAAA
1 AACACAGAG-CAAAGAGACAAA
* *
1471783 AACAGAGAGCAAAGATACAAA
1 AACACAGAGCAAAGAGACAAA
1471804 AAC
1 AAC
1471807 GAAGAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.59, C:0.20, G:0.20, T:0.02
Consensus pattern (21 bp):
AACACAGAGCAAAGAGACAAA
Found at i:1475439 original size:6 final size:5
Alignment explanation
Indices: 1475437--1475520 Score: 67
Period size: 4 Copynumber: 17.8 Consensus size: 5
1475427 TTTTTTTCAT
* *
1475437 TTTTC TTTTC TTTTTC TTTTC TTTT- TTCT- TTTTC -TTTC TTTTT TCTTTC
1 TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC
1475486 TTTT- TTTTC -TTTC -TTT- TTTTC -TTTC TTTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTT
1475521 TCCTTCTTCT
Statistics
Matches: 66, Mismatches: 4, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
4 28 0.42
5 25 0.38
6 13 0.20
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:1475451 original size:12 final size:12
Alignment explanation
Indices: 1475430--1475532 Score: 90
Period size: 11 Copynumber: 8.7 Consensus size: 12
1475420 ATTTTCCTTT
*
1475430 TTTTCATTTTTC
1 TTTTCTTTTTTC
1475442 TTTTC-TTTTTC
1 TTTTCTTTTTTC
1475453 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
1475465 TTTTTCTTTCTT-
1 -TTTTCTTTTTTC
*
1475477 TTTTCTTTCTT-
1 TTTTCTTTTTTC
*
1475488 TTTT-TTCTTTC
1 TTTTCTTTTTTC
1475499 TTTT-TTTCTTTC
1 TTTTCTTT-TTTC
*
1475511 TTTTTCTTTTTCC
1 -TTTTCTTTTTTC
1475524 TTCTTCTTT
1 TT-TTCTTT
1475533 CTTTGCTGGA
Statistics
Matches: 79, Mismatches: 5, Indels: 13
0.81 0.05 0.13
Matches are distributed among these distances:
10 4 0.05
11 32 0.41
12 17 0.22
13 23 0.29
14 3 0.04
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:1475456 original size:17 final size:17
Alignment explanation
Indices: 1475429--1475536 Score: 98
Period size: 18 Copynumber: 6.2 Consensus size: 17
1475419 AATTTTCCTT
1475429 TTTTTCATTTTTCTTTTC
1 TTTTTC-TTTTTCTTTTC
*
1475447 TTTTTCTTTTCTTTTTTC
1 TTTTTCTTTT-TCTTTTC
1475465 TTTTTCTTTCTT-TTTTC
1 TTTTTCTTT-TTCTTTTC
*
1475482 TTTCTTTTTTTTC-TTTC
1 TTT-TTCTTTTTCTTTTC
1475499 TTTTT-TTCTTTCTTTTTC
1 TTTTTCTT-TTTC-TTTTC
*
1475517 TTTTTCCTTCTTC-TTTC
1 TTTTT-CTTTTTCTTTTC
1475534 TTT
1 TTT
1475537 GCTGGATGAG
Statistics
Matches: 78, Mismatches: 3, Indels: 19
0.78 0.03 0.19
Matches are distributed among these distances:
15 2 0.03
16 6 0.08
17 28 0.36
18 36 0.46
19 4 0.05
20 2 0.03
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTTC
Found at i:1475476 original size:4 final size:4
Alignment explanation
Indices: 1475449--1475536 Score: 71
Period size: 4 Copynumber: 22.8 Consensus size: 4
1475439 TTCTTTTCTT
*
1475449 TTTC TTTTC TTT- TTTC -TT- TTTC TTTC TTT- TTTC TTTC TTTTT TTTC
1 TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC
* * *
1475495 TTTC TTTT TTTC TTTC TTT- TTCTT TTTC CTTC -TTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TT-TC TTTC TTTC TTTC TTTC TTT
1475537 GCTGGATGAG
Statistics
Matches: 69, Mismatches: 6, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
3 15 0.22
4 45 0.65
5 9 0.13
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (4 bp):
TTTC
Found at i:1475530 original size:13 final size:13
Alignment explanation
Indices: 1475429--1475536 Score: 99
Period size: 12 Copynumber: 8.7 Consensus size: 13
1475419 AATTTTCCTT
1475429 TTTTTCATTT-TTC
1 TTTTTC-TTTCTTC
1475442 -TTTTCTTT-TTC
1 TTTTTCTTTCTTC
*
1475453 -TTTTCTTTTTTC
1 TTTTTCTTTCTTC
1475465 TTTTTCTTTC-T-
1 TTTTTCTTTCTTC
*
1475476 TTTTTCTTTCTTT
1 TTTTTCTTTCTTC
1475489 TTTTTCTTTCTT-
1 TTTTTCTTTCTTC
1475501 TTTTTCTTTCTT-
1 TTTTTCTTTCTTC
1475513 TTTCTT-TTTCCTTC
1 TTT-TTCTTT-CTTC
1475527 TTCTTTCTTT
1 TT-TTTCTTT
1475537 GCTGGATGAG
Statistics
Matches: 85, Mismatches: 1, Indels: 16
0.83 0.01 0.16
Matches are distributed among these distances:
11 24 0.28
12 28 0.33
13 25 0.29
14 4 0.05
15 4 0.05
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTCTTTCTTC
Found at i:1475534 original size:52 final size:53
Alignment explanation
Indices: 1475436--1475536 Score: 152
Period size: 52 Copynumber: 1.9 Consensus size: 53
1475426 CTTTTTTTCA
* *
1475436 TTTTTCTTTTCTTTTTCTTTTCTTTTTTCTTTTTCTTTCTTTTTTCTTTCTTT
1 TTTTTCTTTTCTTTTTCTTTTCTTTTTTCTTTTTCCTTCTTCTTTCTTTCTTT
*
1475489 TTTTTC-TTTCTTTTTTTCTTTC-TTTTTCTTTTTCCTTCTTCTTTCTTT
1 TTTTTCTTTTCTTTTTCT-TTTCTTTTTTCTTTTTCCTTCTTCTTTCTTT
1475537 GCTGGATGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 34 0.77
53 10 0.23
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (53 bp):
TTTTTCTTTTCTTTTTCTTTTCTTTTTTCTTTTTCCTTCTTCTTTCTTTCTTT
Found at i:1480773 original size:20 final size:22
Alignment explanation
Indices: 1480750--1480789 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1480740 TTAATACTTG
1480750 AATAAAATAA-A-AAAAATATT
1 AATAAAATAATATAAAAATATT
1480770 AATAAAATAATATAAAAATA
1 AATAAAATAATATAAAAATA
1480790 ATAAGTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (22 bp):
AATAAAATAATATAAAAATATT
Found at i:1481435 original size:119 final size:118
Alignment explanation
Indices: 1481325--1481542 Score: 287
Period size: 120 Copynumber: 1.8 Consensus size: 118
1481315 TATATTTTAT
* *
1481325 AAATAAAATATTTATTTATTTAGAAATATCAGAAAAT-GACTTCTAAG-TGCCTTAAGACAGCTA
1 AAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGACATC-AAGTTGCCTTAAGACAGC-A
*
1481388 TTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAATATATAATTAAAA
64 CTTTCTT-AATATTAAAAAATAAATAAAT-ATTAAAACAATTAATATATAATTAAAA
** * ** * *
1481445 AAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGTTTTAAGACTGCCCT
1 AAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGACATCAAGTTGCCTTAAGACAGCACT
*
1481510 TTCTTAATATTGAAAAATAAATAAATATTAAAA
66 TTCTTAATATTAAAAAATAAATAAATATTAAAA
1481543 TATGATTATT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
118 7 0.08
119 20 0.24
120 42 0.49
121 16 0.19
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.35
Consensus pattern (118 bp):
AAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGACATCAAGTTGCCTTAAGACAGCACT
TTCTTAATATTAAAAAATAAATAAATATTAAAACAATTAATATATAATTAAAA
Found at i:1481438 original size:20 final size:19
Alignment explanation
Indices: 1481399--1481446 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
1481389 TTTCTTCAAT
1481399 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1481418 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
1481438 ATTAAAAAA
1 ATTAAAAAA
1481447 ATAGGATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1481645 original size:3 final size:3
Alignment explanation
Indices: 1481625--1481673 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
1481615 ATTTATTTAT
*
1481625 ATA ACTA ATA AAA ATA ATA ATA A-A A-A ATA ATA ATA ATA ATA A-A
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1481668 ATA ATA
1 ATA ATA
1481674 TTACAAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 6 0.15
3 32 0.78
4 3 0.07
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:1481650 original size:13 final size:13
Alignment explanation
Indices: 1481625--1481673 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
1481615 ATTTATTTAT
1481625 ATAACTAAT-AAAA
1 ATAA-TAATAAAAA
1481638 ATAATAATAAAAA
1 ATAATAATAAAAA
1481651 ATAATAATAATAATA
1 ATAATAATAA-AA-A
1481666 A-AATAATA
1 ATAATAATA
1481674 TTACAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.12
13 18 0.55
14 9 0.27
15 2 0.06
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (13 bp):
ATAATAATAAAAA
Found at i:1481653 original size:19 final size:20
Alignment explanation
Indices: 1481630--1481673 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
1481620 TTTATATAAC
1481630 TAATAAAAATAATAATAAAA
1 TAATAAAAATAATAATAAAA
*
1481650 -AATAATAATAATAATAAAA
1 TAATAAAAATAATAATAAAA
1481669 TAATA
1 TAATA
1481674 TTACAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
TAATAAAAATAATAATAAAA
Found at i:1481683 original size:17 final size:17
Alignment explanation
Indices: 1481625--1481673 Score: 68
Period size: 16 Copynumber: 3.0 Consensus size: 17
1481615 ATTTATTTAT
1481625 ATAACTAAT-AAA-AATA
1 ATAA-TAATAAAATAATA
1481641 ATAATAA-AAAATAATA
1 ATAATAATAAAATAATA
1481657 ATAATAATAAAATAATA
1 ATAATAATAAAATAATA
1481674 TTACAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.20
16 15 0.50
17 9 0.30
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAATAATAAAATAATA
Found at i:1483843 original size:19 final size:19
Alignment explanation
Indices: 1483821--1483860 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1483811 TGGTAAACGT
1483821 TAAATGAACCGAACAAGAA
1 TAAATGAACCGAACAAGAA
1483840 TAAATGAACCGAACAAGAA
1 TAAATGAACCGAACAAGAA
1483859 TA
1 TA
1483861 CATTAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.15, G:0.15, T:0.12
Consensus pattern (19 bp):
TAAATGAACCGAACAAGAA
Found at i:1488806 original size:30 final size:30
Alignment explanation
Indices: 1488772--1488840 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
1488762 TATGTATCAA
1488772 GAATTGATACAGGATGCCCCGTTATGTTAT
1 GAATTGATACAGGATGCCCCGTTATGTTAT
* * * *
1488802 GAATTGATACGGGATGCTCTGTTATTTTAT
1 GAATTGATACAGGATGCCCCGTTATGTTAT
*
1488832 TAATTGATA
1 GAATTGATA
1488841 GCAGTGTGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.39
Consensus pattern (30 bp):
GAATTGATACAGGATGCCCCGTTATGTTAT
Found at i:1500206 original size:73 final size:72
Alignment explanation
Indices: 1500109--1500247 Score: 233
Period size: 72 Copynumber: 1.9 Consensus size: 72
1500099 GGTACAATAA
*
1500109 CGTTCATGTCCGCCATAGTACTTATTAAATAAATGGGGGGCCTATTTTATAATTGAATTGTAAGA
1 CGTTCATGTCCGCCATAGTACTTATTAAATAAAT-GGGGCCCTATTTTATAATTGAATTGTAAGA
1500174 AATTGTAC
65 AATTGTAC
* * *
1500182 CGTTCATGTCTGTCATAGTGCTTATTAAATAAATGGGGCCCTATTTTATAATTGAATTGTAAGAA
1 CGTTCATGTCCGCCATAGTACTTATTAAATAAATGGGGCCCTATTTTATAATTGAATTGTAAGAA
1500247 A
66 A
1500248 AATTGTACAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
72 31 0.50
73 31 0.50
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (72 bp):
CGTTCATGTCCGCCATAGTACTTATTAAATAAATGGGGCCCTATTTTATAATTGAATTGTAAGAA
ATTGTAC
Found at i:1511400 original size:2 final size:2
Alignment explanation
Indices: 1511393--1511424 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1511383 TAACAAAATA
1511393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1511425 CTAACATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1513234 original size:9 final size:9
Alignment explanation
Indices: 1513220--1513300 Score: 58
Period size: 9 Copynumber: 9.0 Consensus size: 9
1513210 ATTTAATTCC
1513220 TTATTTTTT
1 TTATTTTTT
1513229 TTATTTTTT
1 TTATTTTTT
**
1513238 CCA-TTTTT
1 TTATTTTTT
*
1513246 TTA-TATTT
1 TTATTTTTT
* *
1513254 TCATATTCTT
1 TTAT-TTTTT
*
1513264 TTCTTTTTT
1 TTATTTTTT
* *
1513273 TTCTCATTTT
1 TTAT-TTTTT
1513283 TTATTTTTT
1 TTATTTTTT
1513292 TTATTTTTT
1 TTATTTTTT
1513301 CAATTTCATT
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
8 12 0.22
9 31 0.56
10 12 0.22
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (9 bp):
TTATTTTTT
Found at i:1513244 original size:17 final size:18
Alignment explanation
Indices: 1513224--1513291 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 18
1513214 AATTCCTTAT
1513224 TTTTTTTATTTTTTC-CA
1 TTTTTTTATTTTTTCACA
* *
1513241 TTTTTTTATATTTTCATA
1 TTTTTTTATTTTTTCACA
* *
1513259 TTCTTTTCTTTTTTTTCTCA
1 TT-TTTT-TATTTTTTCACA
1513279 -TTTTTTATTTTTT
1 TTTTTTTATTTTTT
1513292 TTATTTTTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
17 21 0.51
18 7 0.17
19 5 0.12
20 8 0.20
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTTATTTTTTCACA
Found at i:1513260 original size:27 final size:26
Alignment explanation
Indices: 1513225--1513300 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 26
1513215 ATTCCTTATT
*
1513225 TTTTTTATTTTTTCCATTTTTTTAT-A
1 TTTTATATTTTTT-CATTTTTTTATCA
* *
1513251 TTTTCATATTCTTTTCTTTTTTTTCTCA
1 TTTT-ATATT-TTTTCATTTTTTTATCA
* *
1513279 TTTTTTATTTTTTTTATTTTTT
1 TTTTATA-TTTTTTCATTTTTT
1513301 CAATTTCATT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
26 4 0.10
27 25 0.62
28 11 0.28
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTATATTTTTTCATTTTTTTATCA
Found at i:1513274 original size:20 final size:19
Alignment explanation
Indices: 1513222--1513293 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
1513212 TTAATTCCTT
1513222 ATTTTTT-TTATTTTTTC-C
1 ATTTTTTATT-TTTTTTCTC
* *
1513240 ATTTTTT-TATATTTTCAT-
1 ATTTTTTATTTTTTTTC-TC
*
1513258 ATTCTTTTCTTTTTTTTCTC
1 ATT-TTTTATTTTTTTTCTC
1513278 ATTTTTTATTTTTTTT
1 ATTTTTTATTTTTTTT
1513294 ATTTTTTCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
17 6 0.14
18 11 0.25
19 17 0.39
20 10 0.23
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (19 bp):
ATTTTTTATTTTTTTTCTC
Found at i:1521928 original size:20 final size:20
Alignment explanation
Indices: 1521903--1521940 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1521893 ATTCCTTGAA
*
1521903 TGTGTATCGATACACTCAAG
1 TGTGTACCGATACACTCAAG
1521923 TGTGTACCGATACACTCA
1 TGTGTACCGATACACTCA
1521941 TCGGGTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (20 bp):
TGTGTACCGATACACTCAAG
Found at i:1524206 original size:12 final size:13
Alignment explanation
Indices: 1524187--1524220 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1524177 GGGAGTAGTA
*
1524187 ATTTTCAAAATTG
1 ATTTTCAAAAATG
1524200 A-TTTCAAAAATG
1 ATTTTCAAAAATG
1524212 ATTTTCAAA
1 ATTTTCAAA
1524221 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:1530929 original size:14 final size:14
Alignment explanation
Indices: 1530910--1530942 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1530900 TGGGGAGTAA
*
1530910 TCCCTGTAAATAAT
1 TCCCTGCAAATAAT
1530924 TCCCTGCAAATAAT
1 TCCCTGCAAATAAT
1530938 TCCCT
1 TCCCT
1530943 ACATAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (14 bp):
TCCCTGCAAATAAT
Found at i:1537228 original size:15 final size:16
Alignment explanation
Indices: 1537208--1537237 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1537198 CTACGATTGA
1537208 ATCCTA-TATTTTTTC
1 ATCCTATTATTTTTTC
1537223 ATCCTATTATTTTTT
1 ATCCTATTATTTTTT
1537238 TTAGGGTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (16 bp):
ATCCTATTATTTTTTC
Found at i:1537863 original size:13 final size:13
Alignment explanation
Indices: 1537845--1537872 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1537835 ATTTATCAGG
1537845 TTTACATACTATA
1 TTTACATACTATA
1537858 TTTACATACTATA
1 TTTACATACTATA
1537871 TT
1 TT
1537873 GGTCCCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTACATACTATA
Found at i:1539186 original size:15 final size:17
Alignment explanation
Indices: 1539168--1539200 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1539158 TTTTTTTAAA
1539168 ATTTTA-AT-TTATAAT
1 ATTTTAGATATTATAAT
1539183 ATTTTAGATATTATAAT
1 ATTTTAGATATTATAAT
1539200 A
1 A
1539201 ATAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTTAGATATTATAAT
Found at i:1540152 original size:2 final size:2
Alignment explanation
Indices: 1540145--1540186 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1540135 TTAACACAAA
1540145 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1540187 TGTAACATCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1541092 original size:20 final size:21
Alignment explanation
Indices: 1541047--1541104 Score: 82
Period size: 20 Copynumber: 2.7 Consensus size: 21
1541037 GCATGGGTAG
1541047 TGCATCGATGCACATGTCAAAGAA
1 TGCATCGATGCAC-TGT--AAGAA
1541071 TGCATCGATGCACTGT-AGAA
1 TGCATCGATGCACTGTAAGAA
1541091 TGCATCGATGCACT
1 TGCATCGATGCACT
1541105 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
23 3 0.09
24 13 0.38
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCATCGATGCACTGTAAGAA
Found at i:1541576 original size:16 final size:17
Alignment explanation
Indices: 1541550--1541587 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1541540 TCTATGTTTT
1541550 TATATGTCTATGAGAAG
1 TATATGTCTATGAGAAG
* *
1541567 TATATG-CTATGTGATG
1 TATATGTCTATGAGAAG
1541583 TATAT
1 TATAT
1541588 ATGAGCTACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (17 bp):
TATATGTCTATGAGAAG
Found at i:1541851 original size:18 final size:18
Alignment explanation
Indices: 1541828--1541863 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1541818 GTGGGTCTAC
*
1541828 GTGGTCCTTCAGGACATA
1 GTGGTCATTCAGGACATA
*
1541846 GTGGTCATTCGGGACATA
1 GTGGTCATTCAGGACATA
1541864 TGTGTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (18 bp):
GTGGTCATTCAGGACATA
Found at i:1542740 original size:2 final size:2
Alignment explanation
Indices: 1542733--1542760 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1542723 GGGGTGTTAC
1542733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1542761 TATCTAACAT
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):
AT
Found at i:1545589 original size:28 final size:28
Alignment explanation
Indices: 1545553--1545607 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1545543 ATTTTTTTCT
*
1545553 TTTCTTTTGCACAATCTCTTTTTCTTTA
1 TTTCCTTTGCACAATCTCTTTTTCTTTA
* * *
1545581 TTTCCTTTGCACGATTTTTTTTTCTTT
1 TTTCCTTTGCACAATCTCTTTTTCTTT
1545608 TTTTTTCTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.11, C:0.20, G:0.05, T:0.64
Consensus pattern (28 bp):
TTTCCTTTGCACAATCTCTTTTTCTTTA
Found at i:1551899 original size:5 final size:5
Alignment explanation
Indices: 1551879--1551933 Score: 62
Period size: 5 Copynumber: 11.2 Consensus size: 5
1551869 CCATTTTTCA
*
1551879 TCTTT TCATAT TCTTT TC-TT T-TTT TCTTTT TCTTT TCTTT TCTTT T-TTT
1 TCTTT TC-TTT TCTTT TCTTT TCTTT TC-TTT TCTTT TCTTT TCTTT TCTTT
1551928 TCTTT T
1 TCTTT T
1551934 TTCAATTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
4 10 0.23
5 24 0.56
6 9 0.21
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (5 bp):
TCTTT
Found at i:1551900 original size:24 final size:24
Alignment explanation
Indices: 1551873--1551924 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1551863 CTTTTTCCAT
1551873 TTTTCATC-TTTTCATATTCTTTTC
1 TTTTCATCTTTTTC-TATTCTTTTC
** *
1551897 TTTTTTTCTTTTTCTTTTCTTTTC
1 TTTTCATCTTTTTCTATTCTTTTC
1551921 TTTT
1 TTTT
1551925 TTTTCTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTCATCTTTTTCTATTCTTTTC
Found at i:1551903 original size:19 final size:19
Alignment explanation
Indices: 1551881--1551919 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1551871 ATTTTTCATC
1551881 TTTTCATATTCTTTTCTTT
1 TTTTCATATTCTTTTCTTT
* *
1551900 TTTTCTTTTTCTTTTCTTT
1 TTTTCATATTCTTTTCTTT
1551919 T
1 T
1551920 CTTTTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTCATATTCTTTTCTTT
Found at i:1551927 original size:19 final size:19
Alignment explanation
Indices: 1551889--1551933 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1551879 TCTTTTCATA
1551889 TTCTTTTCTTTTTTTCTTT
1 TTCTTTTCTTTTTTTCTTT
1551908 TTCTTTTCTTTTCTTT-TTT
1 TTCTTTTCTTTT-TTTCTTT
1551927 TTCTTTT
1 TTCTTTT
1551934 TTCAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 22 0.88
20 3 0.12
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTCTTTTCTTTTTTTCTTT
Found at i:1551936 original size:51 final size:52
Alignment explanation
Indices: 1551872--1551973 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 52
1551862 ACTTTTTCCA
* **
1551872 TTTTTCATCTTTTCATATTCT-TTTC-TTTTTTTCTTTTTCTTTTCTTTTCTTT
1 TTTTTCATCTTTTCA-ATTCTATTTCATTGTTTTC-ACTTCTTTTCTTTTCTTT
* *
1551924 TTTTTC-TTTTTTCAATTTTATTTCATTGTTTTCACTTCTTTTCTTTTCTT
1 TTTTTCATCTTTTCAATTCTATTTCATTGTTTTCACTTCTTTTCTTTTCTT
1551974 CATGTGTAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 4 0.09
51 26 0.60
52 13 0.30
ACGTcount: A:0.08, C:0.17, G:0.01, T:0.75
Consensus pattern (52 bp):
TTTTTCATCTTTTCAATTCTATTTCATTGTTTTCACTTCTTTTCTTTTCTTT
Found at i:1556576 original size:117 final size:117
Alignment explanation
Indices: 1556365--1556581 Score: 312
Period size: 117 Copynumber: 1.9 Consensus size: 117
1556355 TAAAAATGAT
* *
1556365 CTTCTTTTGAAAGCTAAAATAGACTTAGAAAATCAAAATGAAATGTTGAAAAAGGAATTAGAGCT
1 CTTCTTTAGAAAGCTAAAATAGACTTAGAAAATCAAAATGAAATATTGAAAAAGGAATTAGAGCT
* *
1556430 TTCAAAAATGACATATGAAAACTTTGAAAAAGAAATTTTTGAATTAAACAAA
66 TTCAAAAATGAAATATGAAAACTTGGAAAAAGAAATTTTTGAATTAAACAAA
* * * *
1556482 CTTCTTCTAGAAA-CTAAAATAGATTTTGAAAATCAAAATGAAATATTGAAGAAGGATTTAGAGC
1 CTTCTT-TAGAAAGCTAAAATAGACTTAGAAAATCAAAATGAAATATTGAAAAAGGAATTAGAGC
* *
1556546 TTTCAAAAATGAAATTTG-AAAGTATGGAAAAAGAAA
65 TTTCAAAAATGAAATATGAAAACT-TGGAAAAAGAAA
1556582 ATTTCGATTT
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
116 4 0.05
117 79 0.90
118 5 0.06
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (117 bp):
CTTCTTTAGAAAGCTAAAATAGACTTAGAAAATCAAAATGAAATATTGAAAAAGGAATTAGAGCT
TTCAAAAATGAAATATGAAAACTTGGAAAAAGAAATTTTTGAATTAAACAAA
Found at i:1564746 original size:17 final size:17
Alignment explanation
Indices: 1564724--1564763 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
1564714 TTAACAAAAA
1564724 GGGGAGAATAAAGTAAG
1 GGGGAGAATAAAGTAAG
1564741 GGGGAGAATAAAGTAAG
1 GGGGAGAATAAAGTAAG
1564758 GGGGAG
1 GGGGAG
1564764 TAGTGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.47, T:0.10
Consensus pattern (17 bp):
GGGGAGAATAAAGTAAG
Found at i:1574934 original size:23 final size:22
Alignment explanation
Indices: 1574889--1574934 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1574879 ATGATTTAAT
* *
1574889 TATTAATTTGATTTTTAATAGA
1 TATTAATTTGATTGTTAAGAGA
*
1574911 TATTAATTTTATTGGTTAAGAGA
1 TATTAATTTGATT-GTTAAGAGA
1574934 T
1 T
1574935 TTATAGTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (22 bp):
TATTAATTTGATTGTTAAGAGA
Found at i:1576022 original size:15 final size:17
Alignment explanation
Indices: 1576004--1576036 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1575994 TTTTTAAAAA
1576004 ATTTTA-AT-TTATAAT
1 ATTTTAGATATTATAAT
1576019 ATTTTAGATATTATAAT
1 ATTTTAGATATTATAAT
1576036 A
1 A
1576037 ATAGCAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTTAGATATTATAAT
Found at i:1578812 original size:33 final size:33
Alignment explanation
Indices: 1578770--1578908 Score: 215
Period size: 33 Copynumber: 4.2 Consensus size: 33
1578760 TTTAACAGGA
* * *
1578770 TTCTCTTGGACCTACTGACTCGACTGATGGTGT
1 TTCTCTTGGACCTACTGACTCGAATGATGATGC
1578803 TTCTCTTGGACCTACTGACTCGAATGATGATGC
1 TTCTCTTGGACCTACTGACTCGAATGATGATGC
* * *
1578836 TTCTCCTGGACCTACCGACTCGAATAATGATGC
1 TTCTCTTGGACCTACTGACTCGAATGATGATGC
*
1578869 TTCTCCTGGACCTACTGACTCGAATGATGATGC
1 TTCTCTTGGACCTACTGACTCGAATGATGATGC
1578902 TTCTCTT
1 TTCTCTT
1578909 CACATTGATC
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 97 1.00
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (33 bp):
TTCTCTTGGACCTACTGACTCGAATGATGATGC
Found at i:1596916 original size:150 final size:150
Alignment explanation
Indices: 1596645--1596943 Score: 510
Period size: 150 Copynumber: 2.0 Consensus size: 150
1596635 TGTTGACGAA
* * *
1596645 ATCTAGTCATAATTGAAAGATGATGGATCTACTACTGAGATGGATTTCTTGAATCCTGTTAAAAC
1 ATCTAGTCATAATTAAAAGATGATGGATCTACTACTGAGATGAATTTCTTCAATCCTGTTAAAAC
*
1596710 AAGTAATATGCTATGATTCTATACATGTCATATGCATCATGTCCTAAAAATGATCTAATGTGGTT
66 AAGTAATATGCTATGATTCCATACATGTCATATGCATCATGTCCTAAAAATGATCTAATGTGGTT
*
1596775 TGATATGATGAATGTTGGAG
131 TGATATGATGAATGGTGGAG
1596795 ATCTAGTCATAATTAAAAGATGATGGATCTACTACTGAGATGAATTT-TTCAGATCCTGTTAAAA
1 ATCTAGTCATAATTAAAAGATGATGGATCTACTACTGAGATGAATTTCTTCA-ATCCTGTTAAAA
* * *
1596859 TAAGTAATATGTTATGATTCCATACATGTCATATGCATCATGTCCTAAATATGATCTAATGTGGT
65 CAAGTAATATGCTATGATTCCATACATGTCATATGCATCATGTCCTAAAAATGATCTAATGTGGT
1596924 TTGATATGATGAATGGTGGA
130 TTGATATGATGAATGGTGGA
1596944 TGCAATTTTG
Statistics
Matches: 140, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
149 3 0.02
150 137 0.98
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.36
Consensus pattern (150 bp):
ATCTAGTCATAATTAAAAGATGATGGATCTACTACTGAGATGAATTTCTTCAATCCTGTTAAAAC
AAGTAATATGCTATGATTCCATACATGTCATATGCATCATGTCCTAAAAATGATCTAATGTGGTT
TGATATGATGAATGGTGGAG
Found at i:1597880 original size:15 final size:16
Alignment explanation
Indices: 1597862--1597898 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
1597852 CATTCTCTCT
1597862 TTTTTC-ATTTTTTTC
1 TTTTTCAATTTTTTTC
1597877 TTTTTCATATTTTTTTC
1 TTTTTCA-ATTTTTTTC
1597894 TTTTT
1 TTTTT
1597899 TTTCTCCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
17 14 0.70
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCAATTTTTTTC
Found at i:1602445 original size:11 final size:10
Alignment explanation
Indices: 1602431--1602468 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
1602421 TAAAAAAAAT
1602431 ATTTTTTATTA
1 ATTTTTT-TTA
1602442 A-TTTTTTTA
1 ATTTTTTTTA
1602451 ATATTTTTTTA
1 AT-TTTTTTTA
1602462 ATTTTTT
1 ATTTTTT
1602469 AAATAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.16
10 10 0.40
11 11 0.44
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:1602462 original size:20 final size:22
Alignment explanation
Indices: 1602427--1602473 Score: 71
Period size: 20 Copynumber: 2.2 Consensus size: 22
1602417 GATATAAAAA
1602427 AAATATTTTTTATTAATTTTTT
1 AAATATTTTTTATTAATTTTTT
*
1602449 TAATA-TTTTT-TTAATTTTTT
1 AAATATTTTTTATTAATTTTTT
1602469 AAATA
1 AAATA
1602474 ATTAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.61
21 5 0.22
22 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
AAATATTTTTTATTAATTTTTT
Found at i:1602482 original size:20 final size:20
Alignment explanation
Indices: 1602438--1602484 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1602428 AATATTTTTT
* * *
1602438 ATTAATTTTTTTAATATTTT
1 ATTAATTTTTTAAATAATTA
*
1602458 TTTAATTTTTTAAATAATTA
1 ATTAATTTTTTAAATAATTA
1602478 ATTAATT
1 ATTAATT
1602485 ATGACGTTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTAATTTTTTAAATAATTA
Found at i:1604636 original size:6 final size:6
Alignment explanation
Indices: 1604625--1604671 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
1604615 AATCCGTTGC
*
1604625 TTTGTG TTTGTG TTTGTG TTTGCTA TTCT-TG CTTTGTG TTTGTG TTT
1 TTTGTG TTTGTG TTTGTG TTTG-TG TT-TGTG -TTTGTG TTTGTG TTT
1604672 CCGAATAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
6 27 0.77
7 7 0.20
8 1 0.03
ACGTcount: A:0.02, C:0.06, G:0.26, T:0.66
Consensus pattern (6 bp):
TTTGTG
Found at i:1608568 original size:12 final size:13
Alignment explanation
Indices: 1608549--1608582 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1608539 GGGAGTAGTA
*
1608549 ATTTTCAAAATTG
1 ATTTTCAAAAATG
1608562 A-TTTCAAAAATG
1 ATTTTCAAAAATG
1608574 ATTTTCAAA
1 ATTTTCAAA
1608583 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:1627503 original size:429 final size:429
Alignment explanation
Indices: 1626704--1627567 Score: 1674
Period size: 429 Copynumber: 2.0 Consensus size: 429
1626694 TTCACTAAGC
*
1626704 TTTATTTGAGAAGGTTGTCCTCTTACTACGTGAATTAACAAAAATTGGAATCCAGTTATGTTGGA
1 TTTATTTGAGAAGGTTGTCATCTTACTACGTGAATTAACAAAAATTGGAATCCAGTTATGTTGGA
1626769 TGTAATTTTGTTAATACACGACGCAAAACAACATTGTATTTGATAATTTTTTTAATGCAACAGGA
66 TGTAATTTTGTTAATACACGACGCAAAACAACATTGTATTTGATAATTTTTTTAATGCAACAGGA
1626834 ATAAATGACATATATAAAAAATGGATGAGATATTTATATGATGTAACAAGTAACTAAATAAACCA
131 ATAAATGACATATATAAAAAATGGATGAGATATTTATATGATGTAACAAGTAACTAAATAAACCA
1626899 AAAAATAACAAGAACTAAATAAATAAAATAGATAATAAATATTTATTTATTAAAATAATTTCATG
196 AAAAATAACAAGAACTAAATAAATAAAATAGATAATAAATATTTATTTATTAAAATAATTTCATG
1626964 ACAAAAAAAATGAAAATTTTACATTCATTTAAAGTGAATAAAATATATCTAATTAAATTAATATA
261 ACAAAAAAAATGAAAATTTTACATTCATTTAAAGTGAATAAAATATATCTAATTAAATTAATATA
1627029 ACATAAATATAGATAAATTAAAAATATTAATATTAATATTATTTTTATTTGAATAATCCTCGGAA
326 ACATAAATATAGATAAATTAAAAATATTAATATTAATATTATTTTTATTTGAATAATCCTCGGAA
1627094 GGATACCTTAGGTGTTTGGAGGTCTTCCATAGATTAGAA
391 GGATACCTTAGGTGTTTGGAGGTCTTCCATAGATTAGAA
*
1627133 TTTATTTGAGAAGGTTGTCATCTTACTTCGTGAATTAACAAAAATTGGAATCCAGTTATGTTGGA
1 TTTATTTGAGAAGGTTGTCATCTTACTACGTGAATTAACAAAAATTGGAATCCAGTTATGTTGGA
* *
1627198 TGTAATTTTGTTAATACACGACGCAAAACAACATTGTCTTTGATAATTTTTTTAATGCAACATGA
66 TGTAATTTTGTTAATACACGACGCAAAACAACATTGTATTTGATAATTTTTTTAATGCAACAGGA
1627263 ATAAATGACATATATAAAAAATGGATGAGATATTTATATGATGTAACAAGTAACTAAATAAACCA
131 ATAAATGACATATATAAAAAATGGATGAGATATTTATATGATGTAACAAGTAACTAAATAAACCA
1627328 AAAAATAACAAGAACTAAATAAATAAAATAGATAATAAATATTTATTTATTAAAATAATTTCATG
196 AAAAATAACAAGAACTAAATAAATAAAATAGATAATAAATATTTATTTATTAAAATAATTTCATG
*
1627393 ATAAAAAAAATGAAAATTTTACATTCATTTAAAGTGAATAAAATATATCTAATTAAATTAATATA
261 ACAAAAAAAATGAAAATTTTACATTCATTTAAAGTGAATAAAATATATCTAATTAAATTAATATA
1627458 ACATAAATATAGATAAATTAAAAATATTAATATTAATATTATTTTTATTTGAATAATCCTCGGAA
326 ACATAAATATAGATAAATTAAAAATATTAATATTAATATTATTTTTATTTGAATAATCCTCGGAA
*
1627523 TGATACCTTAGGTGTTTGGAGGTCTTCCATAGATTAGAA
391 GGATACCTTAGGTGTTTGGAGGTCTTCCATAGATTAGAA
1627562 TTTATT
1 TTTATT
1627568 AAAAATAATT
Statistics
Matches: 429, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
429 429 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (429 bp):
TTTATTTGAGAAGGTTGTCATCTTACTACGTGAATTAACAAAAATTGGAATCCAGTTATGTTGGA
TGTAATTTTGTTAATACACGACGCAAAACAACATTGTATTTGATAATTTTTTTAATGCAACAGGA
ATAAATGACATATATAAAAAATGGATGAGATATTTATATGATGTAACAAGTAACTAAATAAACCA
AAAAATAACAAGAACTAAATAAATAAAATAGATAATAAATATTTATTTATTAAAATAATTTCATG
ACAAAAAAAATGAAAATTTTACATTCATTTAAAGTGAATAAAATATATCTAATTAAATTAATATA
ACATAAATATAGATAAATTAAAAATATTAATATTAATATTATTTTTATTTGAATAATCCTCGGAA
GGATACCTTAGGTGTTTGGAGGTCTTCCATAGATTAGAA
Found at i:1628107 original size:473 final size:473
Alignment explanation
Indices: 1627133--1628505 Score: 2656
Period size: 473 Copynumber: 2.9 Consensus size: 473
1627123 TAGATTAGAA
* *
1627133 TTTATTTGAGAAGGTTGTCATCTTACTTCGTGAATTAACAAAAATTGGAATCCAGTTATGTTGGA
1 TTTATTTGAGAAGGTTGTCATCTCACTACGTGAATTAACAAAAATTGGAATCCAGTTATGTTGGA
* *
1627198 TGTAATTTTGTTAATACACGACGCAAAACAACATTGTCTTTGATAATTTTTTTAATGCAACATGA
66 TGTAATTTCGTTAATACACGACGCAAAACAACATTGTCTTTGATAATTTTTTTAATGCAACAGGA
1627263 ATAAATGACATATATAAAAAATGGATGAGATATTTATATGATGTAACAAGTAACTAAATAAACCA
131 ATAAATGACATATATAAAAAATGGATGAGATATTTATATGATGTAACAAGTAACTAAATAAACCA
1627328 AAAAATAACAAGAACTAAATAAATAAAATAGATAATAAATATTTATTTATTAAAATAATTTCATG
196 AAAAATAACAAGAACTAAATAAATAAAATAGATAATAAATATTTATTTATTAAAATAATTTCATG
1627393 ATAAAAAAAATGAAAATTTTACATTCATTTAAAGTGAATAAAATATATCTAATTAAATTAATATA
261 AT-AAAAAAATGAAAATTTTACATTCATTTAAAGTGAATAAAATATATCTAATTAAATTAATATA
1627458 ACATAAATATAGATAAATTAAAAATATTAATATTAATATTATTTTTATTTGAATAATCCTCGGAA
325 ACATAAATATAGATAAATTAAAAATATTAATATTAATATTATTTTTATTTGAATAATCCTCGGAA
1627523 TGATACCTTAGGTGTTTGGAGGTCTTCCATAGATTAGAATTTATTAAAAATAATTGACTCGATAA
390 TGATACCTTAGGTGTTTGGAGGTCTTCCATAGATTAGAATTTATTAAAAATAATTGACTCGATAA
1627588 ATGATATATTTCACTAAGC
455 ATGATATATTTCACTAAGC
*
1627607 TTTATTTGAGAAGGTTGTCATCTCACTACGTGAATTAACAAAAATTGGAATCCAATTATGTTGGA
1 TTTATTTGAGAAGGTTGTCATCTCACTACGTGAATTAACAAAAATTGGAATCCAGTTATGTTGGA
1627672 TGTAATTTCGTTAATACACGACGCAAAACAACATTGTCTTTGATAATTTTTTTAATGCAACAGGA
66 TGTAATTTCGTTAATACACGACGCAAAACAACATTGTCTTTGATAATTTTTTTAATGCAACAGGA
1627737 ATAAATGACATATATAAAAAATGGATGAGATATTTATATGATGTAACAAGTAACTAAATAAACCA
131 ATAAATGACATATATAAAAAATGGATGAGATATTTATATGATGTAACAAGTAACTAAATAAACCA
1627802 AAAAATAACAAGAACTAAATAAATAAAATAGATAATAAATATTTATTTATTAAAATAATTTCATG
196 AAAAATAACAAGAACTAAATAAATAAAATAGATAATAAATATTTATTTATTAAAATAATTTCATG
1627867 ATAAAAAAATGAAAATTTTACATTCATTTAAAGTGAATAAAATATATCTAATTAAATTAATATAA
261 ATAAAAAAATGAAAATTTTACATTCATTTAAAGTGAATAAAATATATCTAATTAAATTAATATAA
*
1627932 CATAAATATAGATAAATTAAAAATATTAATATTAATATTATTTTTATTTGAGTAATCCTCGGAAT
326 CATAAATATAGATAAATTAAAAATATTAATATTAATATTATTTTTATTTGAATAATCCTCGGAAT
1627997 GATACCTTAGGTGTTTGGAGGTCTTCCATAGATTAGAATTTATTAAAAATAATTGACTCGATAAA
391 GATACCTTAGGTGTTTGGAGGTCTTCCATAGATTAGAATTTATTAAAAATAATTGACTCGATAAA
1628062 TGATATATTTCACTAAGC
456 TGATATATTTCACTAAGC
1628080 TTTATTTGAGAAGGTTGTCATCTCACTACGTGAATTAACAAAAATTGGAATCCAGTTATGTTGGA
1 TTTATTTGAGAAGGTTGTCATCTCACTACGTGAATTAACAAAAATTGGAATCCAGTTATGTTGGA
*
1628145 TGTAATTTCGTTAATACATGACGCAAAACAACATTGTCTTTGATAATTTTTTTAATGCAACAGGA
66 TGTAATTTCGTTAATACACGACGCAAAACAACATTGTCTTTGATAATTTTTTTAATGCAACAGGA
1628210 ATAAATGACATATATAAAAAATGGATGAGATATTTATATGATGTAACAAGTAACTAAATAAACCA
131 ATAAATGACATATATAAAAAATGGATGAGATATTTATATGATGTAACAAGTAACTAAATAAACCA
1628275 AAAAATAACAAGAACTAAATAAATAAAATAGATAATAAATATTTATTTATTAAAATAATTTCATG
196 AAAAATAACAAGAACTAAATAAATAAAATAGATAATAAATATTTATTTATTAAAATAATTTCATG
1628340 ATAAAAAAATGAAAATTTTACATTCATTTAAAGTGAATAAAATATATCTAATTAAATTAATATAA
261 ATAAAAAAATGAAAATTTTACATTCATTTAAAGTGAATAAAATATATCTAATTAAATTAATATAA
*
1628405 CATAAATATAGATAAATTAAAAATATTAATATTAATATTATTTTTATTTGAATAATCCTCAGAAT
326 CATAAATATAGATAAATTAAAAATATTAATATTAATATTATTTTTATTTGAATAATCCTCGGAAT
*
1628470 GACACCTTAGGTGTTTGGAGGTCTTCCATAGATTAG
391 GATACCTTAGGTGTTTGGAGGTCTTCCATAGATTAG
1628506 TCGAATAATT
Statistics
Matches: 888, Mismatches: 11, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
473 631 0.71
474 257 0.29
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (473 bp):
TTTATTTGAGAAGGTTGTCATCTCACTACGTGAATTAACAAAAATTGGAATCCAGTTATGTTGGA
TGTAATTTCGTTAATACACGACGCAAAACAACATTGTCTTTGATAATTTTTTTAATGCAACAGGA
ATAAATGACATATATAAAAAATGGATGAGATATTTATATGATGTAACAAGTAACTAAATAAACCA
AAAAATAACAAGAACTAAATAAATAAAATAGATAATAAATATTTATTTATTAAAATAATTTCATG
ATAAAAAAATGAAAATTTTACATTCATTTAAAGTGAATAAAATATATCTAATTAAATTAATATAA
CATAAATATAGATAAATTAAAAATATTAATATTAATATTATTTTTATTTGAATAATCCTCGGAAT
GATACCTTAGGTGTTTGGAGGTCTTCCATAGATTAGAATTTATTAAAAATAATTGACTCGATAAA
TGATATATTTCACTAAGC
Found at i:1630070 original size:18 final size:18
Alignment explanation
Indices: 1630047--1630083 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1630037 CTTGGATTAC
1630047 ATTTGGGTCTAAT-TTGTA
1 ATTTGGGTC-AATCTTGTA
1630065 ATTTGGGTCAATCTTGTA
1 ATTTGGGTCAATCTTGTA
1630083 A
1 A
1630084 CCTATTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (18 bp):
ATTTGGGTCAATCTTGTA
Found at i:1631966 original size:15 final size:17
Alignment explanation
Indices: 1631929--1631969 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1631919 TTTCATATAC
*
1631929 TATTATTTTTTCTCTAT
1 TATTATTTTTTATCTAT
*
1631946 TTTTATTTTTTAT-T-T
1 TATTATTTTTTATCTAT
1631961 TATTATTTT
1 TATTATTTT
1631970 ATTTCATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 9 0.43
16 1 0.05
17 11 0.52
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (17 bp):
TATTATTTTTTATCTAT
Found at i:1640104 original size:34 final size:34
Alignment explanation
Indices: 1640056--1640138 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 34
1640046 ACCGATACTC
1640056 CCTTCAGTATCGATATCATTTTGGCATTATGGAAT
1 CCTT-AGTATCGATATCATTTTGGCATTATGGAAT
*
1640091 CCTTAGTATCGATATCATTTTTGCATTATGGAAT
1 CCTTAGTATCGATATCATTTTGGCATTATGGAAT
1640125 CCTTAGTATCGATA
1 CCTTAGTATCGATA
1640139 CCTTCCTCTT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 43 0.91
35 4 0.09
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.41
Consensus pattern (34 bp):
CCTTAGTATCGATATCATTTTGGCATTATGGAAT
Found at i:1644974 original size:39 final size:37
Alignment explanation
Indices: 1644918--1645149 Score: 170
Period size: 40 Copynumber: 5.9 Consensus size: 37
1644908 ACATAAATTT
*
1644918 TAAATAAATC-AAGGAAAAAACATAAAATAATAATA-A
1 TAAATAAATCAAAGGAAAAAAAATAAAATAA-AATAGA
*
1644954 T-AATAAATCAAAAGGAGAAAAAATAAAATAAAATAAGA
1 TAAATAAATC-AAAGGAAAAAAAATAAAATAAAAT-AGA
*
1644992 TAAATAAATCAAAGGAAAATAAAATAAAATAAAAATATA
1 TAAATAAATCAAAGGAAAA-AAAATAAAAT-AAAATAGA
**
1645031 TCAAATAAATCAAAGGAAAAAATGTAAAAATAAAAATA-A
1 T-AAATAAATCAAAGGAAAAAAAAT-AAAAT-AAAATAGA
* * *
1645070 AATAATAAAT-ATAA-GATAAAAAAATTAAAAATATATATAAA
1 TA-AATAAATCA-AAGGA-AAAAAAA-T-AAAATA-AAATAGA
1645111 TAAAAATAAATCAAAGAGAAAACATGAAATAAAATAAAA
1 T--AAATAAATCAAAG-GAAAA-A--AAATAAAATAAAA
1645150 AATAAAATAA
Statistics
Matches: 161, Mismatches: 12, Indels: 39
0.76 0.06 0.18
Matches are distributed among these distances:
35 8 0.05
36 4 0.02
37 19 0.12
38 14 0.09
39 40 0.25
40 46 0.29
41 1 0.01
42 9 0.06
43 7 0.04
44 9 0.06
45 1 0.01
46 3 0.02
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (37 bp):
TAAATAAATCAAAGGAAAAAAAATAAAATAAAATAGA
Found at i:1644980 original size:20 final size:20
Alignment explanation
Indices: 1644955--1645019 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
1644945 TAATAATAAT
1644955 AATAAATCAAAAGGAGAAAA
1 AATAAATCAAAAGGAGAAAA
** *
1644975 AATAAAAT-AAAATAAG-ATA
1 AAT-AAATCAAAAGGAGAAAA
*
1644994 AATAAATC-AAAGGAAAATAA
1 AATAAATCAAAAGGAGAA-AA
1645014 AATAAA
1 AATAAA
1645020 ATAAAAATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 16 0.47
21 4 0.12
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.15
Consensus pattern (20 bp):
AATAAATCAAAAGGAGAAAA
Found at i:1645028 original size:6 final size:5
Alignment explanation
Indices: 1644973--1645170 Score: 58
Period size: 5 Copynumber: 39.4 Consensus size: 5
1644963 AAAAGGAGAA
* **
1644973 AAAAT AAAAT AAAAT AAGAT -AAAT -AAAT CAAAGG AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT
* * ** **
1645022 AAAA- ATATAT CAAAT -AAAT CAAAGG AAAA- AATGT AAAAAT AAAAAT
1 AAAAT A-AAAT AAAAT AAAAT -AAAAT AAAAT AAAAT -AAAAT -AAAAT
* * *
1645068 AAAAT --AAT AAATAT AAGAT AAAA- AAATT AAAA- ATATAT ATAAAT
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT A-AAAT A-AAAT
* * * * *
1645112 AAAA- ATAAAT CAAAG AGAA- AACAT GAAAT AAAAT AAAAAAT AAAAT
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT
1645158 AATAAT AAAAT AA
1 AA-AAT AAAAT AA
1645171 TAAATGAATC
Statistics
Matches: 142, Mismatches: 31, Indels: 40
0.67 0.15 0.19
Matches are distributed among these distances:
3 3 0.02
4 21 0.15
5 85 0.60
6 28 0.20
7 5 0.04
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1645038 original size:40 final size:37
Alignment explanation
Indices: 1644918--1645150 Score: 190
Period size: 39 Copynumber: 5.9 Consensus size: 37
1644908 ACATAAATTT
* *
1644918 TAAATAAATC-AAGGAAAAAACATAAAATAATAATAA
1 TAAATAAATCAAAGGAAAAAAAATAAAATAAAAATAA
*
1644954 T-AATAAATCAAAAGGAGAAAAAATAAAAT-AAAATAAGA
1 TAAATAAATC-AAAGGAAAAAAAATAAAATAAAAAT-A-A
1644992 TAAATAAATCAAAGGAAAATAAAATAAAATAAAAATATA
1 TAAATAAATCAAAGGAAAA-AAAATAAAATAAAAATA-A
**
1645031 TCAAATAAATCAAAGGAAAAAATGTAAAAATAAAAATAA
1 T-AAATAAATCAAAGGAAAAAAAAT-AAAATAAAAATAA
*
1645070 AATAATAAAT-ATAA-GATAAAAAAATTAAAAATATATATAAATAA
1 TA-AATAAATCA-AAGGA-AAAAAAA-T--AAA-ATA-A-AAATAA
1645114 -AAATAAATCAAAGAGAAAACATGAAATAAAATAAAAA
1 TAAATAAATCAAAG-GAAAA-A--AAATAAAATAAAAA
1645151 ATAAAATAAT
Statistics
Matches: 164, Mismatches: 10, Indels: 42
0.76 0.05 0.19
Matches are distributed among these distances:
35 8 0.05
36 5 0.03
37 17 0.10
38 14 0.09
39 39 0.24
40 39 0.24
41 5 0.03
42 15 0.09
43 9 0.05
44 9 0.05
45 1 0.01
46 3 0.02
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (37 bp):
TAAATAAATCAAAGGAAAAAAAATAAAATAAAAATAA
Found at i:1645091 original size:26 final size:24
Alignment explanation
Indices: 1645058--1645120 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 24
1645048 AAAAATGTAA
1645058 AAAT-AAAAATAAAATAATAAATAT
1 AAATAAAAAATAAAA-AATAAATAT
* *
1645082 AAGATAAAAAAATTAAAAATATATAT
1 AA-AT-AAAAAATAAAAAATAAATAT
1645108 AAAT-AAAAATAAA
1 AAATAAAAAATAAA
1645121 TCAAAGAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 8 0.24
24 2 0.06
25 4 0.12
26 10 0.30
27 9 0.27
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (24 bp):
AAATAAAAAATAAAAAATAAATAT
Found at i:1645115 original size:22 final size:22
Alignment explanation
Indices: 1645064--1645120 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
1645054 GTAAAAATAA
1645064 AAATAAAATAATAAATATAAGAT
1 AAATAAAATAA-AAATATAAGAT
*
1645087 AAA-AAAATTAAAAATAT-ATAT
1 AAATAAAA-TAAAAATATAAGAT
1645108 AAATAAAAATAAA
1 AAAT-AAAATAAA
1645121 TCAAAGAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 6 0.20
22 14 0.47
23 10 0.33
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (22 bp):
AAATAAAATAAAAATATAAGAT
Found at i:1645169 original size:8 final size:8
Alignment explanation
Indices: 1645138--1645174 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1645128 GAAAACATGA
1645138 AATAAAAT
1 AATAAAAT
1645146 AA-AAAAT
1 AATAAAAT
1645153 AA-AATAAT
1 AATAA-AAT
1645161 AATAAAAT
1 AATAAAAT
1645169 AATAAA
1 AATAAA
1645175 TGAATCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 9 0.33
8 16 0.59
9 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AATAAAAT
Found at i:1646845 original size:106 final size:106
Alignment explanation
Indices: 1646664--1647621 Score: 1585
Period size: 106 Copynumber: 9.0 Consensus size: 106
1646654 GTATTGCTCC
* * *
1646664 GAGTCCAATATCCTTCG-TCGTGAAGTTAAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * ** *
1646728 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTATTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1646770 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
1646835 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1646876 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1646941 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1646982 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1647047 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1647088 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
1647153 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1647194 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
1647259 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1647300 GAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1647365 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1647406 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1647471 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1647512 GAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
1647577 CCAACCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1647618 GAGT
1 GAGT
1647622 GGCACGATAT
Statistics
Matches: 804, Mismatches: 47, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
106 803 1.00
107 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1649313 original size:36 final size:36
Alignment explanation
Indices: 1649273--1649351 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
1649263 TTTGCATGTG
1649273 CTTTTTGTCCCTTT-TTCTT-TTTGATCTTTGTTCTTT
1 CTTTTT-TCCCTTTGTTCTTGTTT-ATCTTTGTTCTTT
* * *
1649309 CTTTTTTCCTTTTGTTCTTGTTTCTCTTTTTTCTTT
1 CTTTTTTCCCTTTGTTCTTGTTTATCTTTGTTCTTT
*
1649345 GTTTTTT
1 CTTTTTT
1649352 TGCTTTTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
35 6 0.16
36 28 0.76
37 3 0.08
ACGTcount: A:0.01, C:0.18, G:0.08, T:0.73
Consensus pattern (36 bp):
CTTTTTTCCCTTTGTTCTTGTTTATCTTTGTTCTTT
Found at i:1649314 original size:27 final size:25
Alignment explanation
Indices: 1649284--1649344 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 25
1649274 TTTTTGTCCC
*
1649284 TTTTTCTTTTTGATCTTTGTTCTTTCT
1 TTTTTCTTTTTGATC-TTGTT-TCTCT
* *
1649311 TTTTTCCTTTTGTTCTTGTTTCTCT
1 TTTTTCTTTTTGATCTTGTTTCTCT
1649336 TTTTTCTTT
1 TTTTTCTTT
1649345 GTTTTTTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 12 0.40
26 5 0.17
27 13 0.43
ACGTcount: A:0.02, C:0.16, G:0.07, T:0.75
Consensus pattern (25 bp):
TTTTTCTTTTTGATCTTGTTTCTCT
Found at i:1649326 original size:16 final size:15
Alignment explanation
Indices: 1649306--1649376 Score: 65
Period size: 16 Copynumber: 4.7 Consensus size: 15
1649296 ATCTTTGTTC
1649306 TTTCTTTTTTCCTTT
1 TTTCTTTTTTCCTTT
*
1649321 TGTTCTTGTTTCTCTTT
1 T-TTCTTTTTTC-CTTT
*
1649338 TTTCTTTGTT--TTT
1 TTTCTTTTTTCCTTT
* *
1649351 TTGCTTTTTTGCTTCT
1 TTTCTTTTTTCCTT-T
1649367 TTTCTTTTTT
1 TTTCTTTTTT
1649377 GTTCTTGATT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
13 11 0.24
15 3 0.07
16 26 0.58
17 5 0.11
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTCTTTTTTCCTTT
Found at i:1652402 original size:20 final size:20
Alignment explanation
Indices: 1652377--1652441 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
1652367 AAATAATAAT
1652377 AATAAATCAAAAGGAGAAAA
1 AATAAATCAAAAGGAGAAAA
** *
1652397 AATAAAAT-AAAATAAG-ATA
1 AAT-AAATCAAAAGGAGAAAA
*
1652416 AATAAATC-AAAGGAAAATAA
1 AATAAATCAAAAGGAGAA-AA
1652436 AATAAA
1 AATAAA
1652442 ATAAAAATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 16 0.47
21 4 0.12
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.15
Consensus pattern (20 bp):
AATAAATCAAAAGGAGAAAA
Found at i:1652420 original size:39 final size:38
Alignment explanation
Indices: 1652343--1652581 Score: 176
Period size: 39 Copynumber: 6.1 Consensus size: 38
1652333 ACATAAATTT
*
1652343 TAAATAAATC-AAGGAAAAAACATAAAAT--AAT--AA
1 TAAATAAATCAAAGGAAAAAAAATAAAATAAAATAAAA
* *
1652376 T-AATAAATCAAAAGGAGAAAAAATAAAATAAAATAAGA
1 TAAATAAATC-AAAGGAAAAAAAATAAAATAAAATAAAA
*
1652414 TAAATAAATCAAAGGAAAATAAAATAAAATAAAA-ATATA
1 TAAATAAATCAAAGGAAAA-AAAATAAAATAAAATA-AAA
**
1652453 TCAAATAAATCAAAGGAAAAAATGTAAAAATAAAAATAAAA
1 T-AAATAAATCAAAGGAAAAAAAAT-AAAAT-AAAATAAAA
1652494 T-AATAAAT-ATAA-GATAAAAAAATAAAA-AATATATATAAA
1 TAAATAAATCA-AAGGA-AAAAAAATAAAATAA-A-ATA-AAA
1652533 TAAAAATAAATCAAAGAGAAAACATGAAATAAAATAAAAAATAAAA
1 T--AAATAAATCAAAG-GAAAA-A--AAATAAAAT--AAAATAAAA
1652579 TAA
1 TAA
1652582 TAATAAAATA
Statistics
Matches: 166, Mismatches: 10, Indels: 49
0.74 0.04 0.22
Matches are distributed among these distances:
32 8 0.05
33 1 0.01
34 16 0.10
36 5 0.03
37 1 0.01
38 21 0.13
39 47 0.28
40 23 0.14
41 7 0.04
42 10 0.06
43 4 0.02
44 5 0.03
46 12 0.07
47 3 0.02
48 1 0.01
49 2 0.01
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.19
Consensus pattern (38 bp):
TAAATAAATCAAAGGAAAAAAAATAAAATAAAATAAAA
Found at i:1652450 original size:6 final size:5
Alignment explanation
Indices: 1652395--1652592 Score: 60
Period size: 5 Copynumber: 39.4 Consensus size: 5
1652385 AAAAGGAGAA
* **
1652395 AAAAT AAAAT AAAAT AAGAT -AAAT -AAAT CAAAGG AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT
* * ** **
1652444 AAAA- ATATAT CAAAT -AAAT CAAAGG AAAA- AATGT AAAAAT AAAAAT
1 AAAAT A-AAAT AAAAT AAAAT -AAAAT AAAAT AAAAT -AAAAT -AAAAT
*
1652490 AAAAT --AAT AAATAT AAGAT -AAA- AAAAT AAAA- AATATAT ATAAAT
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AA-A-AT A-AAAT
* * * * *
1652534 AAAA- ATAAAT CAAAG AGAA- AACAT GAAAT AAAAT AAAAAAT AAAAT
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT
1652580 AATAAT AAAAT AA
1 AA-AAT AAAAT AA
1652593 TAAATGAATC
Statistics
Matches: 143, Mismatches: 27, Indels: 46
0.66 0.12 0.21
Matches are distributed among these distances:
3 3 0.02
4 24 0.17
5 82 0.57
6 26 0.18
7 7 0.05
8 1 0.01
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1652513 original size:26 final size:24
Alignment explanation
Indices: 1652480--1652542 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
1652470 AAAAATGTAA
1652480 AAAT-AAAAATAAAATAATAAATAT
1 AAATAAAAAATAAAA-AATAAATAT
*
1652504 AAGATAAAAAAATAAAAAATATATAT
1 AA-AT-AAAAAATAAAAAATAAATAT
1652530 AAAT-AAAAATAAA
1 AAATAAAAAATAAA
1652543 TCAAAGAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
23 9 0.26
24 2 0.06
25 4 0.11
26 10 0.29
27 10 0.29
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (24 bp):
AAATAAAAAATAAAAAATAAATAT
Found at i:1652518 original size:22 final size:21
Alignment explanation
Indices: 1652490--1652543 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
1652480 AAATAAAAAT
1652490 AAAATAATAAATATAAGATAAA
1 AAAATAATAAATAT-AGATAAA
* *
1652512 AAAATAAAAAATATATATAAA
1 AAAATAATAAATATAGATAAA
*
1652533 TAAA-AATAAAT
1 AAAATAATAAAT
1652544 CAAAGAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 6 0.21
21 9 0.32
22 13 0.46
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAATAATAAATATAGATAAA
Found at i:1652534 original size:50 final size:49
Alignment explanation
Indices: 1652429--1652542 Score: 126
Period size: 50 Copynumber: 2.3 Consensus size: 49
1652419 AAATCAAAGG
* *
1652429 AAAAT-AAAATAAAATAAAAATATATCAAATAAATCAAAGGAAAAAATGTA
1 AAAATAAAAATAAAATAAAAATATA-CAAATAAA-CAAAAGAAAAAATATA
* *
1652479 AAAATAAAAATAAAATAATAAATATA-AGATAAA-AAAATAAAAAATATA
1 AAAATAAAAATAAAATAA-AAATATACAAATAAACAAAAGAAAAAATATA
1652527 TATAAATAAAAATAAA
1 -A-AAATAAAAATAAA
1652543 TCAAAGAGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
48 12 0.21
49 1 0.02
50 24 0.43
51 12 0.21
52 7 0.12
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (49 bp):
AAAATAAAAATAAAATAAAAATATACAAATAAACAAAAGAAAAAATATA
Found at i:1660762 original size:64 final size:64
Alignment explanation
Indices: 1660649--1660858 Score: 219
Period size: 64 Copynumber: 3.2 Consensus size: 64
1660639 TGCACTAAGA
* * * *
1660649 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAATAGTCTG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAA-A-TCAGAGTGCATCGATGCATGGAT
1660712 T
64 T
* * **
1660713 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
* * * * *
1660777 GTGCATCGGTGCATGGAATGCATTCAATGTTTCAATTTATTCATTGA-TGCATCGATGCATGGTA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCA--GAGTGCATCGATGCATGG-A
1660841 TT
63 TT
*
1660843 GATGCATCGGTGCATG
1 G-TGCATCGATGCATG
1660859 CCTTTGAAAA
Statistics
Matches: 124, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
63 3 0.02
64 86 0.69
65 17 0.14
66 4 0.03
67 14 0.11
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
Found at i:1660779 original size:19 final size:19
Alignment explanation
Indices: 1660755--1660793 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1660745 TAATTAAATC
1660755 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1660774 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1660793 A
1 A
1660794 ATGCATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1660845 original size:21 final size:21
Alignment explanation
Indices: 1660819--1660858 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1660809 CAATTTATTC
1660819 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
1660840 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
1660859 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:1663424 original size:24 final size:23
Alignment explanation
Indices: 1663353--1663430 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 23
1663343 CATGGTCTTG
*
1663353 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
1663376 TGCATCGGTGCATCATGC-A--GA
1 TGCATCGATGCA-CATTCAAGGGA
1663397 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
1663421 TGCATCGATG
1 TGCATCGATG
1663431 AATTGTTAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
20 4 0.09
21 12 0.27
22 1 0.02
23 12 0.27
24 16 0.36
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:1663445 original size:44 final size:42
Alignment explanation
Indices: 1663330--1663452 Score: 120
Period size: 44 Copynumber: 2.8 Consensus size: 42
1663320 AAAACTCGAC
* *
1663330 GGATGCATCGATGCATGGTCTTGTGCATCGATGCACATTCAAG
1 GGATGCATCGATGCATCGT-TAGTGCATCGATGCACATTCAAG
* * * *
1663373 GCATGCATCGGTGCATCATGCAGATGCATCGATGCACATTCAAAG
1 GGATGCATCGATGCATCGT-TAG-TGCATCGATGCACATTC-AAG
* * *
1663418 GGATGCATCGATGAATTGTTAAGTGCATCGGTGCA
1 GGATGCATCGATGCATCGTT-AGTGCATCGATGCA
1663453 TTAAGCACAA
Statistics
Matches: 63, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
43 16 0.25
44 28 0.44
45 19 0.30
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (42 bp):
GGATGCATCGATGCATCGTTAGTGCATCGATGCACATTCAAG
Found at i:1669264 original size:18 final size:17
Alignment explanation
Indices: 1669210--1669258 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1669200 TTGGACTCCT
* *
1669210 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
1669228 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
1669246 AGTGCATTCGATG
1 AGTGCA-TCGATG
1669259 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:1669343 original size:64 final size:64
Alignment explanation
Indices: 1669230--1669439 Score: 203
Period size: 64 Copynumber: 3.2 Consensus size: 64
1669220 TGCACTAAGA
* * *
1669230 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAAT-AGCCTGGTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG---AGTGCATCGATGCATGGA
1669292 TT
63 TT
* * * **
1669294 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCACCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
* * * *
1669358 GTGCATCGGTGCATGGAATGCATTCGATGTTTCAATTTATTCATTGA-TGCATCGATGCATGGTA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCA--GAGTGCATCGATGCATGG-A
1669422 TT
63 TT
* *
1669424 GACGCATCGGTGCATG
1 G-TGCATCGATGCATG
1669440 CCTTTGAAAA
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
64 85 0.70
65 14 0.11
66 8 0.07
67 15 0.12
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
Found at i:1669360 original size:19 final size:19
Alignment explanation
Indices: 1669336--1669374 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1669326 TAATTAAATC
1669336 AGAGTGCACCGATGCATGG
1 AGAGTGCACCGATGCATGG
* *
1669355 AGAGTGCATCGGTGCATGG
1 AGAGTGCACCGATGCATGG
1669374 A
1 A
1669375 ATGCATTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.38, T:0.18
Consensus pattern (19 bp):
AGAGTGCACCGATGCATGG
Found at i:1669424 original size:21 final size:21
Alignment explanation
Indices: 1669400--1669439 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1669390 CAATTTATTC
*
1669400 ATTGATGCATCGATGCATGGT
1 ATTGACGCATCGATGCATGGT
*
1669421 ATTGACGCATCGGTGCATG
1 ATTGACGCATCGATGCATG
1669440 CCTTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
ATTGACGCATCGATGCATGGT
Found at i:1670609 original size:19 final size:20
Alignment explanation
Indices: 1670576--1670617 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1670566 GGCTAAAAAT
1670576 ACTGTAGCAGTGTATCGATAC
1 ACTGTAGCAG-GTATCGATAC
1670597 ACTGTAGCA-GTATCGATAC
1 ACTGTAGCAGGTATCGATAC
1670616 AC
1 AC
1670618 ATTTTACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.57
21 9 0.43
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
ACTGTAGCAGGTATCGATAC
Found at i:1670684 original size:20 final size:20
Alignment explanation
Indices: 1670669--1670719 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1670659 CTCAGTATTG
*
1670669 GTACTATTTATACAGTATCT
1 GTACTATTCATACAGTATCT
*
1670689 GTACTATTCATACA-TCA-CA
1 GTACTATTCATACAGT-ATCT
1670708 GTACTATTCATA
1 GTACTATTCATA
1670720 AAAACATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (20 bp):
GTACTATTCATACAGTATCT
Found at i:1670955 original size:21 final size:19
Alignment explanation
Indices: 1670931--1670988 Score: 73
Period size: 18 Copynumber: 3.0 Consensus size: 19
1670921 ATGTTTAATG
1670931 AAAAATATATCAATTGTTA
1 AAAAATATATCAATTGTTA
*
1670950 ACAAAATGATATCAATTCTT-
1 A-AAAAT-ATATCAATTGTTA
*
1670970 AAAAAGATATCAATTGTTA
1 AAAAATATATCAATTGTTA
1670989 CCAATTGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 11 0.33
19 5 0.15
20 6 0.18
21 11 0.33
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (19 bp):
AAAAATATATCAATTGTTA
Found at i:1670978 original size:18 final size:19
Alignment explanation
Indices: 1670931--1670984 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
1670921 ATGTTTAATG
* *
1670931 AAAAATATATCAATTGTTA
1 AAAAAGATATCAATTCTTA
1670950 ACAAAATGATATCAATTCTT-
1 A-AAAA-GATATCAATTCTTA
1670970 AAAAAGATATCAATT
1 AAAAAGATATCAATT
1670985 GTTACCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 10 0.32
19 5 0.16
20 5 0.16
21 11 0.35
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (19 bp):
AAAAAGATATCAATTCTTA
Found at i:1673704 original size:34 final size:32
Alignment explanation
Indices: 1673642--1673711 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1673632 CCTTTACAAC
*
1673642 TCCCTAGTTTTCAATGGCTAAACTAGAACATT
1 TCCCTAGTTTTCAAGGGCTAAACTAGAACATT
* * *
1673674 TCCCTAGCTTTTACAAGGGCTTAGCTAGAACCTT
1 TCCCTAG-TTTT-CAAGGGCTAAACTAGAACATT
1673708 TCCC
1 TCCC
1673712 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 21 0.66
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTCAAGGGCTAAACTAGAACATT
Found at i:1674042 original size:21 final size:21
Alignment explanation
Indices: 1673991--1674045 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
1673981 CCCATAACAT
* *
1673991 GGTGTATTGATACACTATCAA
1 GGTGTATCGGTACACTATCAA
1674012 GGTGTATCGGTACACTATCAA
1 GGTGTATCGGTACACTATCAA
1674033 GGTGTATCGGTAC
1 GGTGTATCGGTAC
1674046 CCCTTCATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (21 bp):
GGTGTATCGGTACACTATCAA
Found at i:1681238 original size:56 final size:56
Alignment explanation
Indices: 1681157--1681269 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 56
1681147 TTCTGAAACG
* *
1681157 ATAACTCTTCTACGATACAATTATATGTTAACTTTTCTATGATACAACTATAATTT
1 ATAACTCTTCTACGATACAACTATATGTTAACTCTTCTATGATACAACTATAATTT
* * * *
1681213 ATAATTCTTTTACGATATAACTATATGTTAACTCTTCTATGATATAACTATAATTT
1 ATAACTCTTCTACGATACAACTATATGTTAACTCTTCTATGATACAACTATAATTT
1681269 A
1 A
1681270 ATCTATTGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.44
Consensus pattern (56 bp):
ATAACTCTTCTACGATACAACTATATGTTAACTCTTCTATGATACAACTATAATTT
Found at i:1681270 original size:27 final size:27
Alignment explanation
Indices: 1681158--1681264 Score: 115
Period size: 27 Copynumber: 3.9 Consensus size: 27
1681148 TCTGAAACGA
*
1681158 TAACTCTTCTACGATACAATTATATGT
1 TAACTCTTCTACGATACAACTATATGT
* * *
1681185 TAACTTTTCTATGATACAACTATAATTT
1 TAACTCTTCTACGATACAACTAT-ATGT
* * *
1681213 ATAATTCTTTTACGATATAACTATATGT
1 -TAACTCTTCTACGATACAACTATATGT
* *
1681241 TAACTCTTCTATGATATAACTATA
1 TAACTCTTCTACGATACAACTATA
1681265 ATTTAATCTA
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
27 41 0.63
28 6 0.09
29 18 0.28
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.44
Consensus pattern (27 bp):
TAACTCTTCTACGATACAACTATATGT
Found at i:1682418 original size:31 final size:31
Alignment explanation
Indices: 1682382--1682459 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
1682372 AAATAATATT
*
1682382 GAGGTTAAATTAGTATTTTATCTAAAATTTA
1 GAGGTTAAATTAATATTTTATCTAAAATTTA
*
1682413 GAGGTTAAATTAATATTTTATCTAAAGTTTA
1 GAGGTTAAATTAATATTTTATCTAAAATTTA
* *
1682444 -AGGTCAAATTGATATT
1 GAGGTTAAATTAATATT
1682460 ATGCTTGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 14 0.33
31 29 0.67
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.44
Consensus pattern (31 bp):
GAGGTTAAATTAATATTTTATCTAAAATTTA
Found at i:1683546 original size:14 final size:15
Alignment explanation
Indices: 1683527--1683572 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1683517 GCTACTCGAA
1683527 AAAATTAT-ATTATT
1 AAAATTATAATTATT
*
1683541 AAAATTATAATTTTT
1 AAAATTATAATTATT
*
1683556 AAAA-AATAAATTATT
1 AAAATTAT-AATTATT
1683571 AA
1 AA
1683573 TAATATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTATAATTATT
Found at i:1686224 original size:20 final size:20
Alignment explanation
Indices: 1686199--1686305 Score: 84
Period size: 20 Copynumber: 5.6 Consensus size: 20
1686189 TAGTTGAAAA
1686199 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTTCATT
1686219 TCGCGTT--G----TTCATT
1 TCGCGTTGCGATTTTTCATT
* ** **
1686233 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTTCATT
* *
1686254 TCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATTTTTCATT
1686274 TCGCGTTGCGA-TTTTCAATT
1 TCGCGTTGCGATTTTTC-ATT
1686294 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1686306 AGTCTACAGT
Statistics
Matches: 66, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
14 13 0.20
16 1 0.02
18 1 0.02
19 4 0.06
20 34 0.52
21 13 0.20
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTTCATT
Found at i:1686232 original size:14 final size:14
Alignment explanation
Indices: 1686213--1686240 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1686203 GTTGCGATTT
1686213 TTCATTTCGCGTTG
1 TTCATTTCGCGTTG
1686227 TTCATTTCGCGTTG
1 TTCATTTCGCGTTG
1686241 CGATAGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.21, T:0.50
Consensus pattern (14 bp):
TTCATTTCGCGTTG
Found at i:1686247 original size:55 final size:55
Alignment explanation
Indices: 1686165--1686308 Score: 202
Period size: 55 Copynumber: 2.5 Consensus size: 55
1686155 CTATCGCAAA
*
1686165 TTCGCGTTG--CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCAT
1 TTCGCGTTGTTCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
*
1686218 TTCGCGTTGTTCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCAT
1 TTCGCGTTGTTCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1686273 TTCGCGTTGCGATTTTCAATTTCGCGTTGCGATAGT
1 TTCGCGTT--G---TTC-ATTTCGCGTTGCGATAGT
1686309 CTACAGTTGT
Statistics
Matches: 81, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
53 9 0.11
55 50 0.62
57 1 0.01
60 3 0.04
61 18 0.22
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.40
Consensus pattern (55 bp):
TTCGCGTTGTTCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
Found at i:1686325 original size:22 final size:22
Alignment explanation
Indices: 1686297--1686390 Score: 131
Period size: 22 Copynumber: 4.4 Consensus size: 22
1686287 TTCAATTTCG
1686297 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
1686319 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
1686338 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1686360 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1686382 CGTTGCGAT
1 CGTTGCGAT
1686391 TTTCCAAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 10 0.16
20 5 0.08
21 5 0.08
22 41 0.67
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1686350 original size:41 final size:41
Alignment explanation
Indices: 1686277--1686368 Score: 150
Period size: 41 Copynumber: 2.2 Consensus size: 41
1686267 TTCCATTTCG
*
1686277 CGTTGCGATTTTCAATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCAAATTC-CGTTGCGATAGTCTACAGTTGT
1686319 CGTTGCGATTTTCCAAATT-CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTT-CAAATTCCGTTGCGATAGTCTACAGTTGT
1686360 CGTTGCGAT
1 CGTTGCGAT
1686369 AGTCTACAGT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
41 31 0.65
42 12 0.25
43 5 0.10
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTCAAATTCCGTTGCGATAGTCTACAGTTGT
Found at i:1689951 original size:24 final size:27
Alignment explanation
Indices: 1689910--1689963 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
1689900 ATATAAATTT
* *
1689910 TATAAATTTAAATTTAATA-AA-AATA
1 TATAAATTGAAATATAATACAATAATA
1689935 TATAAATTGAAA-ATAATACAATAATA
1 TATAAATTGAAATATAATACAATAATA
1689961 TAT
1 TAT
1689964 TTTCTATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 13 0.52
26 7 0.28
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
TATAAATTGAAATATAATACAATAATA
Found at i:1690886 original size:2 final size:2
Alignment explanation
Indices: 1690879--1690918 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1690869 AGAAATACAT
1690879 TA TA TA TA TA TA 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 TA TA TA TA TA TA
1690919 AATTGTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1690981 original size:28 final size:27
Alignment explanation
Indices: 1690945--1690998 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
1690935 AGATTTACAA
1690945 TAAAATAAATTTAATAT-TTTTATATAT
1 TAAAATAAATTTAATATATTTT-TATAT
1690972 TAAAATTAAATTTAATATATTTTTATA
1 TAAAA-TAAATTTAATATATTTTTATA
1690999 GTTTTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 5 0.20
28 16 0.64
29 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAAAATAAATTTAATATATTTTTATAT
Found at i:1691179 original size:20 final size:19
Alignment explanation
Indices: 1691133--1691181 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1691123 ATGACCAACA
* * *
1691133 AATTCGCAATGCGATCTCG
1 AATTCGCAACGCGAACTCC
1691152 AATTCGCAACGCGAACTCC
1 AATTCGCAACGCGAACTCC
1691171 AATTTCGCAAC
1 AA-TTCGCAAC
1691182 TCAGTTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (19 bp):
AATTCGCAACGCGAACTCC
Found at i:1691238 original size:20 final size:20
Alignment explanation
Indices: 1691215--1691260 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1691205 AATATGTAAA
*
1691215 TCGCAACACATAAGTCAAAC
1 TCGCAACACAGAAGTCAAAC
*
1691235 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAC
1691255 TCGCAA
1 TCGCAA
1691261 AGCGCATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.28, G:0.13, T:0.15
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAC
Found at i:1691441 original size:22 final size:22
Alignment explanation
Indices: 1691402--1691452 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1691392 CCACTCTCTA
* *
1691402 CGGCGATATCCGTCCCCATCTC
1 CGGCGACATCCGTCCCCATATC
* *
1691424 CGGCGACATTCGTTCCCATATC
1 CGGCGACATCCGTCCCCATATC
*
1691446 CGACGAC
1 CGGCGAC
1691453 CCCCTCTATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.18, C:0.41, G:0.20, T:0.22
Consensus pattern (22 bp):
CGGCGACATCCGTCCCCATATC
Found at i:1691813 original size:20 final size:20
Alignment explanation
Indices: 1691790--1691828 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1691780 TTTGAAACTT
*
1691790 AAATTCGCAACATGAAAATG
1 AAATTCGCAACACGAAAATG
1691810 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
1691829 CGCAACGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:1693450 original size:42 final size:42
Alignment explanation
Indices: 1693360--1693458 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 42
1693350 ACCCCCACTT
* * * *
1693360 CGAGAGCCATCACCTGATCGAGCCGATTCTACAACTAGATAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACAACTACACAA
* * * *
1693402 CCAGAGCCATCACCTGATCGAGTCGATTATACACCTCCACAA
1 CGAGAGCCATCACCTGATCGAGCCGATTATACAACTACACAA
1693444 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
1693459 ATTCCATCAC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.18
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACAACTACACAA
Found at i:1693630 original size:21 final size:21
Alignment explanation
Indices: 1693578--1693637 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
1693568 GGGAGTTACG
* *
1693578 TGATGAGGTCAGTGCTTTGCG
1 TGATGAGGTCGGTGCTTTGCA
*
1693599 TAATGAGGTCGGTGCTTTGCA
1 TGATGAGGTCGGTGCTTTGCA
*
1693620 TGATGAGGTCGGTACTTT
1 TGATGAGGTCGGTGCTTT
1693638 ACGTGACGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.17, C:0.13, G:0.35, T:0.35
Consensus pattern (21 bp):
TGATGAGGTCGGTGCTTTGCA
Found at i:1693702 original size:63 final size:63
Alignment explanation
Indices: 1693635--1693756 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 63
1693625 AGGTCGGTAC
* * *
1693635 TTTACGTGACGACAATGGTGCATGGCGTGATGAGGTA-CAATCTTTACGTGGTGAGGTAGATGT
1 TTTACGCGACGACAATGGTGCATGACGTGATGAGGTATCAA-CTTTACGTGATGAGGTAGATGT
* * * * * *
1693698 TTTACGCGATGATAATGGTGCTTTACGTGGTGAGGTATCTACTTTACGTGATGAGGTAG
1 TTTACGCGACGACAATGGTGCATGACGTGATGAGGTATCAACTTTACGTGATGAGGTAG
1693757 CCGCTCTACG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
63 47 0.96
64 2 0.04
ACGTcount: A:0.23, C:0.12, G:0.32, T:0.33
Consensus pattern (63 bp):
TTTACGCGACGACAATGGTGCATGACGTGATGAGGTATCAACTTTACGTGATGAGGTAGATGT
Found at i:1694071 original size:21 final size:21
Alignment explanation
Indices: 1694043--1694140 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
1694033 GATTCACCTG
1694043 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
1694064 -CTATCGTTCAAGAGGCCTCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* * *
1694085 TCATCGTTCAAGAGGTCCATT
1 TCATCGTTCAAGAGGCCCCTC
*
1694106 TCATCGTTCAAAAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
1694127 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
1694141 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
20 1 0.02
21 61 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1695544 original size:16 final size:16
Alignment explanation
Indices: 1695520--1695550 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1695510 AAGAATTGTT
*
1695520 TTTTTTTGTTTAATTG
1 TTTTGTTGTTTAATTG
1695536 TTTTGTTGTTTAATT
1 TTTTGTTGTTTAATT
1695551 TGAATCTGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (16 bp):
TTTTGTTGTTTAATTG
Found at i:1695921 original size:18 final size:18
Alignment explanation
Indices: 1695898--1695933 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1695888 AAGCCGGTTG
*
1695898 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1695916 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1695934 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1698243 original size:24 final size:24
Alignment explanation
Indices: 1698216--1698262 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1698206 CAAAATCCGA
1698216 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
1698240 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
1698263 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Done.