Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009458.1 Hibiscus syriacus cultivar Beakdansim tig00113719_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: 1407308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1303662 original size:25 final size:25
Alignment explanation
Indices: 1303591--1303662 Score: 63
Period size: 31 Copynumber: 2.6 Consensus size: 25
1303581 GTGAATGATG
* *
1303591 TTGATAATGATGATGAGAACAAATG
1 TTGATAATGATAATGAGAACAAATA
*
1303616 TTGATAATGATATCGATGATGAGAACATATA
1 TTGATAATG--AT--A--ATGAGAACAAATA
1303647 TTGATAATGATAATGA
1 TTGATAATGATAATGA
1303663 TGTTGATACT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
25 13 0.34
27 3 0.08
29 2 0.05
31 20 0.53
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (25 bp):
TTGATAATGATAATGAGAACAAATA
Found at i:1303670 original size:18 final size:18
Alignment explanation
Indices: 1303647--1303687 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1303637 AGAACATATA
1303647 TTGATAATGATAATGATG
1 TTGATAATGATAATGATG
*
1303665 TTGATACTGATAATGATG
1 TTGATAATGATAATGATG
*
1303683 ATGAT
1 TTGAT
1303688 GACGTGTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.39
Consensus pattern (18 bp):
TTGATAATGATAATGATG
Found at i:1304607 original size:2 final size:2
Alignment explanation
Indices: 1304600--1304629 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1304590 CAAGAATAAC
1304600 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
1304630 TCAAATACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1305705 original size:21 final size:21
Alignment explanation
Indices: 1305679--1305724 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1305669 GTTAATTCTG
1305679 TCGGCCACCGAATTAGTTCGA
1 TCGGCCACCGAATTAGTTCGA
*
1305700 TCGGCCACCGAATTAGTTCGG
1 TCGGCCACCGAATTAGTTCGA
1305721 TCGG
1 TCGG
1305725 GGAACGGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.24
Consensus pattern (21 bp):
TCGGCCACCGAATTAGTTCGA
Found at i:1306124 original size:186 final size:184
Alignment explanation
Indices: 1305810--1306177 Score: 637
Period size: 186 Copynumber: 2.0 Consensus size: 184
1305800 ATTTTAAATT
*
1305810 TTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAATCCAATTAATAATTTAA
1 TTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAATTTAA
1305875 GATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTACATAAAATTTTTATT
66 GATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTACATAAAATTTTTA-T
*
1305940 TTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTGAATTAAAAAAAA
130 TTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTT-AATTAAAAAAAA
* * *
1305996 TTAAATATATTATATATAACTTATGGGCTCATCCCAAATCATTTAAAACCCAATTAATAATTTAA
1 TTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAATTTAA
* * *
1306061 GATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAGTTTATATAAAATTTTTATT
66 GATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTACATAAAATTTTTATT
*
1306126 TATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATTATAAAA
131 TATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATTAAAAAA
1306178 TATTTATTTT
Statistics
Matches: 173, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
184 9 0.05
185 43 0.25
186 121 0.70
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (184 bp):
TTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAATTTAA
GATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTACATAAAATTTTTATT
TATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATTAAAAAAAA
Found at i:1308069 original size:132 final size:133
Alignment explanation
Indices: 1307900--1308219 Score: 389
Period size: 139 Copynumber: 2.4 Consensus size: 133
1307890 TGGCCATAAG
* *
1307900 ATCAAGAATCTTATGCAATATCTTCTGATACTAGTTAGTAAATGGGTGTTTAGTTAGTT-A-ATT
1 ATCAAGAATCTTATGCAATATCTTCTGATACTAGTTAGT-AATTGGTGTTTAGTTAATTCATATT
* **
1307963 TTTC-TTC-AGATTATTGCTATT-TGCAGAAGCACTGAGCATTTTGTATATGTTTAGTCATATAA
65 TTTCTTTCTAGATTATTGCTATTGT-CAGAAGCACCGAGCA-TTTG-ATATGTTTAACCATATAA
*
1308025 CCAAAAC
127 CCAAAAA
* *
1308032 ATCAAGAATCTTATGCAATATCTTCTGATAGTAGTTAGTAATTGGTGTTTAGTTAATTCATTTTT
1 ATCAAGAATCTTATGCAATATCTTCTGATACTAGTTAGTAATTGGTGTTTAGTTAATTCATATTT
* * *
1308097 TTCTTTTTTTCTTTTGATTATTGCTATTGTCCGAAGCACCGAGCATTTGGTATGTTTAACCATAT
66 TTC----TTTC--TAGATTATTGCTATTGTCAGAAGCACCGAGCATTTGATATGTTTAACCATAT
* *
1308162 AGCGAAAAA
125 AACCAAAAA
*
1308171 ATCAAGAATCTTATGCAATATCTTCTGATACTAGTTGGTAATTGGTGTT
1 ATCAAGAATCTTATGCAATATCTTCTGATACTAGTTAGTAATTGGTGTT
1308220 CAGTCAAATT
Statistics
Matches: 162, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
131 17 0.10
132 39 0.24
133 6 0.04
138 3 0.02
139 66 0.41
140 4 0.02
141 26 0.16
142 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (133 bp):
ATCAAGAATCTTATGCAATATCTTCTGATACTAGTTAGTAATTGGTGTTTAGTTAATTCATATTT
TTCTTTCTAGATTATTGCTATTGTCAGAAGCACCGAGCATTTGATATGTTTAACCATATAACCAA
AAA
Found at i:1309873 original size:14 final size:14
Alignment explanation
Indices: 1309854--1309894 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
1309844 GATAAACAAA
1309854 TTAAAATTTAATTT
1 TTAAAATTTAATTT
*
1309868 TTAAAATTAAAATTT
1 TTAAAATT-TAATTT
*
1309883 TTAAAGTTTAAT
1 TTAAAATTTAAT
1309895 AACAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TTAAAATTTAATTT
Found at i:1324617 original size:3 final size:3
Alignment explanation
Indices: 1324609--1324636 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1324599 GAATTGGGTT
1324609 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1324637 GTATACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1335034 original size:2 final size:2
Alignment explanation
Indices: 1335027--1335052 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1335017 TAATCACAAG
1335027 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
1335053 CACACACAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1337702 original size:31 final size:31
Alignment explanation
Indices: 1337583--1337703 Score: 131
Period size: 31 Copynumber: 3.9 Consensus size: 31
1337573 AAACTTTAAA
* * * *
1337583 ATTATAAACTAATCATTAAAGTTCTCAAA-C
1 ATTATAAAATAATCATTAAATTTATCAAATT
1337613 AGTTATAAAATAATCATTAAATCTTATCAAATT
1 A-TTATAAAATAATCATTAAAT-TTATCAAATT
* * *
1337646 ATTAT-AAA-AGTCATTAAAATGATCAAATT
1 ATTATAAAATAATCATTAAATTTATCAAATT
*
1337675 ATTATAAAATAATCTTTAAATTTATCAAA
1 ATTATAAAATAATCATTAAATTTATCAAA
1337704 AAAAATCATT
Statistics
Matches: 75, Mismatches: 11, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
29 14 0.19
30 13 0.17
31 36 0.48
32 11 0.15
33 1 0.01
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (31 bp):
ATTATAAAATAATCATTAAATTTATCAAATT
Found at i:1337963 original size:25 final size:22
Alignment explanation
Indices: 1337935--1337979 Score: 54
Period size: 25 Copynumber: 1.9 Consensus size: 22
1337925 AAATTAAAGT
1337935 TTTTTAATGATAAATACTAAAATGA
1 TTTTTAAT-ATAAA-A-TAAAATGA
*
1337960 TTTTTGATATAAAATAAAAT
1 TTTTTAATATAAAATAAAAT
1337980 AAAATTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 1 0.05
24 5 0.26
25 7 0.37
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (22 bp):
TTTTTAATATAAAATAAAATGA
Found at i:1339559 original size:17 final size:18
Alignment explanation
Indices: 1339526--1339559 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1339516 CCGTTATTAG
1339526 TGAACCGGTCGAAACCGC
1 TGAACCGGTCGAAACCGC
*
1339544 TGAACCGTTC-AAACCG
1 TGAACCGGTCGAAACCG
1339560 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCGAAACCGC
Found at i:1348427 original size:2 final size:2
Alignment explanation
Indices: 1348420--1348447 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1348410 ACAACGTTAC
1348420 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
1348448 GTACAATGTC
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:1348922 original size:14 final size:14
Alignment explanation
Indices: 1348903--1348942 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1348893 AAATTCGACT
*
1348903 ATTTATTTTTATTA
1 ATTTATTTTTAATA
*
1348917 ATTTATTATTAATA
1 ATTTATTTTTAATA
1348931 ATTT-TTTTTAAT
1 ATTTATTTTTAAT
1348943 CTTTAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTATTTTTAATA
Found at i:1349598 original size:48 final size:49
Alignment explanation
Indices: 1349542--1349635 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
1349532 CTTATCTCTC
1349542 AGTTTTATTCA-TTTTTTGTCACTGATTTCAAAATACATAAGATATTTT
1 AGTTTTATTCATTTTTTTGTCACTGATTTCAAAATACATAAGATATTTT
1349590 AGTTTTATTCATTTTTTTGTCACTGATTTCAAAATACATAAGATAT
1 AGTTTTATTCATTTTTTTGTCACTGATTTCAAAATACATAAGATAT
1349636 GGTTACTTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 11 0.24
49 34 0.76
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (49 bp):
AGTTTTATTCATTTTTTTGTCACTGATTTCAAAATACATAAGATATTTT
Found at i:1350159 original size:23 final size:22
Alignment explanation
Indices: 1350107--1350163 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
1350097 ATTATTTCAC
*
1350107 TCTAACATTCTGAAATCATAATT
1 TCTAA-ATTCTGAAATCATAAGT
* *
1350130 TCTTAAATTTTGACATCATAACGT
1 TC-TAAATTCTGAAATCATAA-GT
1350154 TCTAAATTCT
1 TCTAAATTCT
1350164 TAATTTCTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (22 bp):
TCTAAATTCTGAAATCATAAGT
Found at i:1350278 original size:24 final size:24
Alignment explanation
Indices: 1350234--1350279 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1350224 TTTTAAAAAC
* *
1350234 ATTTTAATTTTATTTATATTTTTT
1 ATTTTAATTTTATATAAATTTTTT
1350258 ATTTTAAATTTTA-ATAAATTTT
1 ATTTT-AATTTTATATAAATTTT
1350280 ATTTCAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTTTAATTTTATATAAATTTTTT
Found at i:1351036 original size:14 final size:13
Alignment explanation
Indices: 1351005--1351034 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1350995 TTTTATAAGT
1351005 AAAATATTATTTA
1 AAAATATTATTTA
*
1351018 AAAATATTTTTTA
1 AAAATATTATTTA
1351031 AAAA
1 AAAA
1351035 ATCTGAACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAATATTATTTA
Found at i:1351393 original size:17 final size:17
Alignment explanation
Indices: 1351371--1351405 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1351361 TATAGACGAT
1351371 AATAACATTTAAATTAA
1 AATAACATTTAAATTAA
1351388 AATAACATTTAAATTAA
1 AATAACATTTAAATTAA
1351405 A
1 A
1351406 CTCAATCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAACATTTAAATTAA
Found at i:1351767 original size:3 final size:3
Alignment explanation
Indices: 1351761--1351798 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
1351751 AATAAATAGC
1351761 ATT ATT AATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1351799 ATTACGATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1353820 original size:21 final size:21
Alignment explanation
Indices: 1353791--1353830 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1353781 TAAAAGAAAT
* *
1353791 TAATTTTTTTTATAAATATTA
1 TAATATTTTTAATAAATATTA
*
1353812 TAATATTTTTAATATATAT
1 TAATATTTTTAATAAATAT
1353831 ATTTTAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATATTTTTAATAAATATTA
Found at i:1360724 original size:30 final size:28
Alignment explanation
Indices: 1360685--1360766 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 28
1360675 TTTAAGTGCC
*
1360685 TAAAATATTTGTTGGTCAAAATAAATACT
1 TAAAGTATTT-TTGGTCAAAATAAATACT
*
1360714 TAAAGTTATTTTTTTGGTCAAAATAGATACT
1 TAAAG-TA--TTTTTGGTCAAAATAAATACT
1360745 TAAAGTATTTTAT-GTCAAAATA
1 TAAAGTATTTT-TGGTCAAAATA
1360767 GGTACATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
28 13 0.28
29 5 0.11
30 4 0.09
31 22 0.47
32 3 0.06
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.41
Consensus pattern (28 bp):
TAAAGTATTTTTGGTCAAAATAAATACT
Found at i:1360731 original size:31 final size:30
Alignment explanation
Indices: 1360696--1360755 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 30
1360686 AAAATATTTG
1360696 TTGGTCAAAATAAATACTTAAAGTTATTTTT
1 TTGGTCAAAATAAATACTTAAAG-TATTTTT
*
1360727 TTGGTCAAAATAGATACTTAAAGTATTTT
1 TTGGTCAAAATAAATACTTAAAGTATTTT
1360756 ATGTCAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 6 0.21
31 22 0.79
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (30 bp):
TTGGTCAAAATAAATACTTAAAGTATTTTT
Found at i:1360764 original size:28 final size:29
Alignment explanation
Indices: 1360697--1360782 Score: 102
Period size: 28 Copynumber: 2.9 Consensus size: 29
1360687 AAATATTTGT
* *
1360697 TGGTCAAAATAAATACTTAAAGTTATTTTTT
1 TGGTCAAAATAGATACTTAAAG-TA-TTTTA
1360728 TGGTCAAAATAGATACTTAAAGTATTTTA
1 TGGTCAAAATAGATACTTAAAGTATTTTA
* * *
1360757 T-GTCAAAATAGGTACATAAACTATTT
1 TGGTCAAAATAGATACTTAAAGTATTT
1360783 AAACCTTTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 22 0.44
29 5 0.10
30 2 0.04
31 21 0.42
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.40
Consensus pattern (29 bp):
TGGTCAAAATAGATACTTAAAGTATTTTA
Found at i:1363462 original size:36 final size:36
Alignment explanation
Indices: 1363422--1363490 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
1363412 CACTCCTGAA
*
1363422 ACCACCTCCTGCGAG-ACCAACTCCTCCTCCTCCAGC
1 ACCACCGCCTGC-AGCACCAACTCCTCCTCCTCCAGC
*
1363458 ACCACCGCCTGCAGCACCAGCTCCTCCTCCTCC
1 ACCACCGCCTGCAGCACCAACTCCTCCTCCTCC
1363491 TCGTGCTGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 2 0.07
36 28 0.93
ACGTcount: A:0.17, C:0.55, G:0.12, T:0.16
Consensus pattern (36 bp):
ACCACCGCCTGCAGCACCAACTCCTCCTCCTCCAGC
Found at i:1365275 original size:18 final size:18
Alignment explanation
Indices: 1365252--1365305 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
1365242 GTGTTCGCTC
*
1365252 ATCATCATCAAACCAGGG
1 ATCATCATCAAGCCAGGG
*
1365270 ATCATCATCTAGCCAGGG
1 ATCATCATCAAGCCAGGG
1365288 ATCATCATCAAGCCAGGG
1 ATCATCATCAAGCCAGGG
1365306 CTCTAGCCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (18 bp):
ATCATCATCAAGCCAGGG
Found at i:1365930 original size:81 final size:81
Alignment explanation
Indices: 1365821--1366408 Score: 590
Period size: 81 Copynumber: 7.5 Consensus size: 81
1365811 GGTTCAACAG
* * ** *
1365821 CAGCTTCTAAAGTGAACCAACAAAAATCGTCTTTGGAGCGTCAGCAAGACAAGGATTCCAAGAAA
1 CAGCTTCTCAAGAGAACCAACAGCAATCGTCTTTGGAGCGTCAGCAAGACGAGGATTCCAAGAAA
1365886 GAAGGTTCATCAGAGC
66 GAAGGTTCATCAGAGC
* * * * * *
1365902 CAGCTTCTGAAGACAGCCAACAGCAATCGTCTTCGGAGCCTCAGCAAGACGAGGATTCTAAGAAA
1 CAGCTTCTCAAGAGAACCAACAGCAATCGTCTTTGGAGCGTCAGCAAGACGAGGATTCCAAGAAA
1365967 GAAGGTTCATCAGAGC
66 GAAGGTTCATCAGAGC
* * * ** * * *
1365983 CAGCTTCTGAAGAGAACCAACAGCAGTTGTCTTCAGAACCTCAGCAACACGAGGATTCC-AGAAA
1 CAGCTTCTCAAGAGAACCAACAGCAATCGTCTTTGGAGCGTCAGCAAGACGAGGATTCCAAG-AA
*
1366047 AGAAGGTTCATCAGCGC
65 AGAAGGTTCATCAGAGC
* * * * *
1366064 CAGCTTCTCAAGAGAACCAACGGCAGTTGTCTTTGGAGCCTCAGCAAGACGAGGATTCCAATAAA
1 CAGCTTCTCAAGAGAACCAACAGCAATCGTCTTTGGAGCGTCAGCAAGACGAGGATTCCAAGAAA
*
1366129 GAAGATTCATCAGAGC
66 GAAGGTTCATCAGAGC
* * * *
1366145 CAGCTTGTCAAGAGAACCAACAACAA-CTGTC-TT-CA--G--AGCAAGACGAGGATTCCGAGAA
1 CAGCTTCTCAAGAGAACCAACAGCAATC-GTCTTTGGAGCGTCAGCAAGACGAGGATTCCAAGAA
* * *
1366203 GGAAGGATCATTAGAGC
65 AGAAGGTTCATCAGAGC
* * *
1366220 CAGCTTCTCAAGAGAACCAACAGCAATCGTC-TT----CG-GAGCAAGATGAGGATTCTGAA-AA
1 CAGCTTCTCAAGAGAACCAACAGCAATCGTCTTTGGAGCGTCAGCAAGACGAGGATTC-CAAGAA
* * *
1366278 GGAAGGATCATTAGAGC
65 AGAAGGTTCATCAGAGC
*
1366295 CAGCTTCTCAAGAGAACCAACAGCAATCGTC-TT----CG-GAGCAAGACGAGGATTCCGAA-AA
1 CAGCTTCTCAAGAGAACCAACAGCAATCGTCTTTGGAGCGTCAGCAAGACGAGGATTCC-AAGAA
* * *
1366353 GGAAGGATCATTAGAGC
65 AGAAGGTTCATCAGAGC
*
1366370 CAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGC
1 CAGCTTCTCAAGAGAACCAACAGCAATCGTCTTTGGAGC
1366409 AAGACGAGGA
Statistics
Matches: 445, Mismatches: 49, Indels: 27
0.85 0.09 0.05
Matches are distributed among these distances:
74 1 0.00
75 199 0.45
76 3 0.01
79 1 0.00
80 5 0.01
81 235 0.53
82 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (81 bp):
CAGCTTCTCAAGAGAACCAACAGCAATCGTCTTTGGAGCGTCAGCAAGACGAGGATTCCAAGAAA
GAAGGTTCATCAGAGC
Found at i:1366225 original size:75 final size:75
Alignment explanation
Indices: 1365863--1366446 Score: 613
Period size: 75 Copynumber: 7.5 Consensus size: 75
1365853 TTGGAGCGTC
* * * * * *
1365863 AGCAAGACAAGGATTCCAAGAAAGAAGGTTCATCAGAGCCAGCTTCTGAAGACAGCCAACAGCAA
1 AGCAAGACGAGGATTCCGAGAAAGAAGGATCATCAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
1365928 TCGTCTTCGGAG
66 TCGTCTTC--AG
** * *
1365940 CCTCAGCAAGACGAGGATTCTAAGAAAGAAGGTTCATCAGAGCCAGCTTCTGAAGAGAACCAACA
1 ----AGCAAGACGAGGATTCCGAGAAAGAAGGATCATCAGAGCCAGCTTCTCAAGAGAACCAACA
* *
1366005 GCAGTTGTCTTCAG
62 GCAATCGTCTTCAG
* * *
1366019 AACCTCAGCAACACGAGGATTCC-AGAAAAGAAGGTTCATCAGCGCCAGCTTCTCAAGAGAACCA
1 ------AGCAAGACGAGGATTCCGAG-AAAGAAGGATCATCAGAGCCAGCTTCTCAAGAGAACCA
* * * *
1366083 ACGGCAGTTGTCTTTGGAG
59 ACAGCAATCGTC-TT-CAG
* * *
1366102 CCTCAGCAAGACGAGGATTCCAATAAAGAA-GATTCATCAGAGCCAGCTTGTCAAGAGAACCAAC
1 ----AGCAAGACGAGGATTCCGAGAAAGAAGGA-TCATCAGAGCCAGCTTCTCAAGAGAACCAAC
*
1366166 AACAA-CTGTCTTCAG
61 AGCAATC-GTCTTCAG
* *
1366181 AGCAAGACGAGGATTCCGAGAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
1 AGCAAGACGAGGATTCCGAGAAAGAAGGATCATCAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
*
1366246 TCGTCTTCGG
66 TCGTCTTCAG
* * *
1366256 AGCAAGATGAGGATTCTGA-AAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCA
1 AGCAAGACGAGGATTCCGAGAAA-GAAGGATCATCAGAGCCAGCTTCTCAAGAGAACCAACAGCA
*
1366320 ATCGTCTTCGG
65 ATCGTCTTCAG
*
1366331 AGCAAGACGAGGATTCCGA-AAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCA
1 AGCAAGACGAGGATTCCGAGAAA-GAAGGATCATCAGAGCCAGCTTCTCAAGAGAACCAACAGCA
*
1366395 ATCGTCTTCGG
65 ATCGTCTTCAG
*
1366406 AGCAAGACGAGGATTCCGA-AAAGGAAGGATCATTAGAGCCA
1 AGCAAGACGAGGATTCCGAGAAA-GAAGGATCATCAGAGCCA
1366447 TCTTTAAGGA
Statistics
Matches: 458, Mismatches: 34, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
74 2 0.00
75 246 0.54
76 3 0.01
79 4 0.01
80 5 0.01
81 193 0.42
82 3 0.01
83 2 0.00
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (75 bp):
AGCAAGACGAGGATTCCGAGAAAGAAGGATCATCAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
TCGTCTTCAG
Found at i:1366336 original size:150 final size:152
Alignment explanation
Indices: 1365863--1367035 Score: 931
Period size: 150 Copynumber: 7.4 Consensus size: 152
1365853 TTGGAGCGTC
* * * * * * * *
1365863 AGCAAGACAAGGATTCCAAGAAAGAAGGTTCATCAGAGCCAGCTTCTGAAGACAGCCAACAGCAA
1 AGCAAGACGAGGATTCCGAGAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
* * * * *
1365928 TCGTCTTCGGAGCCTCAGCAAGACGAGGATT-CTAAGAAAGAAGGTTCATCAGAGCCAGCTTCTG
66 TCGTCTTC-G-G----AGCAAGACGAGGATTCCGAA-AAGGAAGGATCATTAGAGCCAGCTTCTC
* * *
1365992 AAGAGAACCAACAGCAGTTGTCTTCAGAACCTC
124 AAGAGAACCAACAGCAATCGTCTTCAG-A---G
* * * * * *
1366025 AGCAACACGAGGATTCC-AGAAAAGAAGGTTCATCAGCGCCAGCTTCTCAAGAGAACCAACGGCA
1 AGCAAGACGAGGATTCCGAG-AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCA
* * * * * *
1366089 GTTGTCTTTGGAGCCTCAGCAAGACGAGGATTCC-AATAAAGAA-GATTCATCAGAGCCAGCTTG
65 ATCGTC-TTCG-G----AGCAAGACGAGGATTCCGAA-AAGGAAGGA-TCATTAGAGCCAGCTTC
*
1366152 TCAAGAGAACCAACAACAA-CTGTCTTC--AG
122 TCAAGAGAACCAACAGCAATC-GTCTTCAGAG
1366181 AGCAAGACGAGGATTCCGAGAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
1 AGCAAGACGAGGATTCCGAGAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
* *
1366246 TCGTCTTCGGAGCAAGATGAGGATTCTGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAA
66 TCGTCTTCGGAGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAA
1366311 CCAACAGCAATCGTCTTC-G-G
131 CCAACAGCAATCGTCTTCAGAG
*
1366331 AGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
1 AGCAAGACGAGGATTCCGAGAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
*
1366396 TCGTCTTCGGAGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCATCTT-T-AAGGAAG
66 TCGTCTTCGGAGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAA-G-AG
* * * * * *
1366459 GATCATTAGAGCCAGCTTC-TCAAGAG
129 AACCA--ACAGCAATCGTCTTC-AGAG
* * * ** *
1366485 AACCAACAGCAATCGTCTTCGGAGCAAGACGAGGATTCCGAAAAGGAAGGATTATTAGAGCCAGC
1 -AGCAAGA-CGA--GGATTC----C--GA-GA--A---------GGAAGGATCATTAGAGCCAGC
*
1366550 TTCTCAAGAGAACCAACAGCAATCGTATTCGGAGCAAGACGAGGATTCCGAAAAGGAAGGATCAT
44 TTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGAGGATTCCGAAAAGGAAGGATCAT
*
1366615 TAGAGCCAGCTTTTCAAGAGAACCAACAGCAATCGTCTTC-G-G
109 TAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCAGAG
* * *
1366657 AGCAAGACGAGGATTCCGA-AAAGAATGGACCATTAGAGCCAGCTTCTCGAGAGAACCAACAGCA
1 AGCAAGACGAGGATTCCGAGAAGGAA-GGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCA
* * * **
1366721 ATCGTCTTCGGAGCAAGACAAGGATTCCGGAAAGGAAGGATCATTAGAGTCAGCTTCTTTAGAGA
65 ATCGTCTTCGGAGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGA
* *
1366786 ACCAACAGCAATTGTCTTCGGAGCATC
130 ACCAACAGCAATCGTCTTC--AG-A-G
* * *
1366813 AGCAAGATGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCCAGAGAACCAA-ATGCA
1 AGCAAGACGAGGATTCCGAGAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACA-GCA
* * * * * * * *
1366877 ATTGTCTTTGGAGCATCACCAAGATGAAGACTCCGAAAAGGAAGGTTCATCA-ACACCAGCTTCT
65 ATCGTCTTCGGAG------CAAGACGAGGATTCCGAAAAGGAAGGATCATTAGA-GCCAGCTTCT
* * * *
1366941 CAGGAGAACCAACAGCAATCATGTTCGGAG
123 CAAGAGAACCAACAGCAATCGTCTTCAGAG
* * * * * * *
1366971 CCTCAGCAAGACAATGATTCTGAAAAGGATGGATCCTTAGCGCCAGCTTCTCAAGAGAACCAACA
1 ----AGCAAGACGAGGATTCCGAGAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACA
1367036 ACAACCGACT
Statistics
Matches: 841, Mismatches: 107, Indels: 125
0.78 0.10 0.12
Matches are distributed among these distances:
148 2 0.00
149 5 0.01
150 292 0.35
151 7 0.01
152 8 0.01
153 2 0.00
154 2 0.00
155 9 0.01
156 124 0.15
157 7 0.01
158 5 0.01
159 2 0.00
160 2 0.00
161 4 0.00
162 234 0.28
163 4 0.00
164 3 0.00
165 1 0.00
167 1 0.00
168 4 0.00
170 2 0.00
171 5 0.01
172 1 0.00
173 1 0.00
174 8 0.01
175 2 0.00
176 100 0.12
177 2 0.00
178 2 0.00
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.18
Consensus pattern (152 bp):
AGCAAGACGAGGATTCCGAGAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
TCGTCTTCGGAGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAA
CCAACAGCAATCGTCTTCAGAG
Found at i:1366482 original size:101 final size:101
Alignment explanation
Indices: 1366351--1366547 Score: 385
Period size: 101 Copynumber: 2.0 Consensus size: 101
1366341 GGATTCCGAA
1366351 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
1366416 GGATTCCGAAAAGGAAGGATCATTAGAGCCATCTTT
66 GGATTCCGAAAAGGAAGGATCATTAGAGCCATCTTT
1366452 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
*
1366517 GGATTCCGAAAAGGAAGGATTATTAGAGCCA
66 GGATTCCGAAAAGGAAGGATCATTAGAGCCA
1366548 GCTTCTCAAG
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 95 1.00
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (101 bp):
AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
GGATTCCGAAAAGGAAGGATCATTAGAGCCATCTTT
Found at i:1366543 original size:75 final size:75
Alignment explanation
Indices: 1366452--1367035 Score: 688
Period size: 75 Copynumber: 7.5 Consensus size: 75
1366442 AGCCATCTTT
1366452 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
1366517 GGATTCCGAA
66 GGATTCCGAA
* *
1366527 AAGGAAGGATTATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTCGGAGCAAGACGA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
1366592 GGATTCCGAA
66 GGATTCCGAA
*
1366602 AAGGAAGGATCATTAGAGCCAGCTTTTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
1366667 GGATTCCGAA
66 GGATTCCGAA
* * *
1366677 AA-GAATGGACCATTAGAGCCAGCTTCTCGAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACA
1 AAGGAA-GGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACG
*
1366741 AGGATTCCGGA
65 AGGATTCCGAA
* ** *
1366752 AAGGAAGGATCATTAGAGTCAGCTTCTTTAGAGAACCAACAGCAATTGTCTTCGGAGCATCAGCA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTC-G-G----AGCA
*
1366817 AGATGAGGATTCCGAA
60 AGACGAGGATTCCGAA
* * *
1366833 AAGGAAGGATCATTAGAGCCAGCTTCTCCAGAGAACCAA-ATGCAATTGTCTTTGGAGCATCACC
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACA-GCAATCGTCTTCGGAG------C
* * *
1366897 AAGATGAAGACTCCGAA
59 AAGACGAGGATTCCGAA
* * * * * *
1366914 AAGGAAGGTTCATCA-ACACCAGCTTCTCAGGAGAACCAACAGCAATCATGTTCGGAGCCTCAGC
1 AAGGAAGGATCATTAGA-GCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTC-G-G----AGC
* * *
1366978 AAGACAATGATTCTGAA
59 AAGACGAGGATTCCGAA
* * *
1366995 AAGGATGGATCCTTAGCGCCAGCTTCTCAAGAGAACCAACA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACA
1367036 ACAACCGACT
Statistics
Matches: 440, Mismatches: 45, Indels: 42
0.83 0.09 0.08
Matches are distributed among these distances:
74 3 0.01
75 257 0.58
76 4 0.01
77 1 0.00
79 1 0.00
80 3 0.01
81 166 0.38
82 2 0.00
83 1 0.00
87 2 0.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (75 bp):
AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
GGATTCCGAA
Found at i:1366570 original size:176 final size:176
Alignment explanation
Indices: 1366276--1366627 Score: 677
Period size: 176 Copynumber: 2.0 Consensus size: 176
1366266 GGATTCTGAA
1366276 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
*
1366341 GGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGG
66 GGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTCGG
*
1366406 AGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCATCTTT
131 AGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTT
1366452 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
*
1366517 GGATTCCGAAAAGGAAGGATTATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTCGG
66 GGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTCGG
1366582 AGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTT
131 AGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTT
1366628 TCAAGAGAAC
Statistics
Matches: 173, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
176 173 1.00
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (176 bp):
AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
GGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTCGG
AGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTT
Found at i:1366644 original size:251 final size:251
Alignment explanation
Indices: 1366201--1366697 Score: 924
Period size: 251 Copynumber: 2.0 Consensus size: 251
1366191 GGATTCCGAG
*
1366201 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGATGA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
* *
1366266 GGATTCTGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGG
66 GGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTCGG
1366331 AGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
131 AGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
*
1366396 TCGTCTTCGGAGCAAGACGAGGATTCCGAAAAGGAA-GGATCATTAGAGCCATCTTT
196 TCGTCTTCGGAGCAAGACGAGGATTCCGAAAA-GAATGGACCATTAGAGCCATCTTT
1366452 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
*
1366517 GGATTCCGAAAAGGAAGGATTATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTCGG
66 GGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTCGG
*
1366582 AGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTTTCAAGAGAACCAACAGCAA
131 AGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
1366647 TCGTCTTCGGAGCAAGACGAGGATTCCGAAAAGAATGGACCATTAGAGCCA
196 TCGTCTTCGGAGCAAGACGAGGATTCCGAAAAGAATGGACCATTAGAGCCA
1366698 GCTTCTCGAG
Statistics
Matches: 239, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
250 3 0.01
251 236 0.99
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.17
Consensus pattern (251 bp):
AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGACGA
GGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTCGG
AGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAA
TCGTCTTCGGAGCAAGACGAGGATTCCGAAAAGAATGGACCATTAGAGCCATCTTT
Found at i:1366733 original size:326 final size:326
Alignment explanation
Indices: 1366135--1366769 Score: 1112
Period size: 326 Copynumber: 1.9 Consensus size: 326
1366125 TAAAGAAGAT
*
1366135 TCATCAGAGCCAGCTTGTCAAGAGAACCAACAACAACTGTCTTCAGAGCAAGACGAGGATTCCGA
1 TCATCAGAGCCAGCTTCTCAAGAGAACCAACAACAACTGTCTTCAGAGCAAGACGAGGATTCCGA
* * *
1366200 GAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAAGATG
66 AAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTCGGAGCAAGACG
*
1366265 AGGATTCTGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCG
131 AGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCG
*
1366330 GAGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCA
196 GAGCAAGACGAGGATTCCGAAAAGGAAGGACCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCA
*
1366395 ATCGTCTTCGGAGCAAGACGAGGATTCCGAAAAGGAAGGATCATTAGAGCCATCTTTAAGGAAGG
261 ATCGTCTTCGGAGCAAGACAAGGATTCCGAAAAGGAAGGATCATTAGAGCCATCTTTAAGGAAGG
1366460 A
326 A
* * *
1366461 TCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAA-TCGTCTTCGGAGCAAGACGAGGATTCCG
1 TCATCAGAGCCAGCTTCTCAAGAGAACCAACAACAACT-GTCTTCAGAGCAAGACGAGGATTCCG
*
1366525 AAAAGGAAGGATTATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTCGGAGCAAGAC
65 AAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTCGGAGCAAGAC
*
1366590 GAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTTTCAAGAGAACCAACAGCAATCGTCTTC
130 GAGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTC
*
1366655 GGAGCAAGACGAGGATTCCGAAAA-GAATGGACCATTAGAGCCAGCTTCTCGAGAGAACCAACAG
195 GGAGCAAGACGAGGATTCCGAAAAGGAA-GGACCATTAGAGCCAGCTTCTCAAGAGAACCAACAG
*
1366719 CAATCGTCTTCGGAGCAAGACAAGGATTCCGGAAAGGAAGGATCATTAGAG
259 CAATCGTCTTCGGAGCAAGACAAGGATTCCGAAAAGGAAGGATCATTAGAG
1366770 TCAGCTTCTT
Statistics
Matches: 293, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
325 4 0.01
326 289 0.99
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (326 bp):
TCATCAGAGCCAGCTTCTCAAGAGAACCAACAACAACTGTCTTCAGAGCAAGACGAGGATTCCGA
AAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTCGGAGCAAGACG
AGGATTCCGAAAAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCG
GAGCAAGACGAGGATTCCGAAAAGGAAGGACCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCA
ATCGTCTTCGGAGCAAGACAAGGATTCCGAAAAGGAAGGATCATTAGAGCCATCTTTAAGGAAGG
A
Found at i:1366856 original size:81 final size:78
Alignment explanation
Indices: 1366452--1367275 Score: 747
Period size: 81 Copynumber: 10.5 Consensus size: 78
1366442 AGCCATCTTT
1366452 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTC-G-G-AGCAAGA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAGCAAGA
1366514 CGAGGATTCCGAA
66 CGAGGATTCCGAA
* *
1366527 AAGGAAGGATTATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTATTC-G-G-AGCAAGA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAGCAAGA
1366589 CGAGGATTCCGAA
66 CGAGGATTCCGAA
*
1366602 AAGGAAGGATCATTAGAGCCAGCTTTTCAAGAGAACCAACAGCAATCGTCTTC-G-G-AGCAAGA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAGCAAGA
1366664 CGAGGATTCCGAA
66 CGAGGATTCCGAA
* *
1366677 AA-GAATGGACCATTAGAGCCAGCTTCTCGAGAGAACCAACAGCAATCGTCTTC-G-G-AGCAAG
1 AAGGAA-GGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAGCAAG
* *
1366738 ACAAGGATTCCGGA
65 ACGAGGATTCCGAA
* ** *
1366752 AAGGAAGGATCATTAGAGTCAGCTTCTTTAGAGAACCAACAGCAATTGTCTTCGGAGCATCAGCA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAG---CAGCA
*
1366817 AGATGAGGATTCCGAA
63 AGACGAGGATTCCGAA
* * * *
1366833 AAGGAAGGATCATTAGAGCCAGCTTCTCCAGAGAACCAA-ATGCAATTGTCTTTGGAGCATCACC
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACA-GCAATCGTCTTCGGAG---CAGC
* * *
1366897 AAGATGAAGACTCCGAA
62 AAGACGAGGATTCCGAA
* * * * * *
1366914 AAGGAAGGTTCATCA-ACACCAGCTTCTCAGGAGAACCAACAGCAATCATGTTCGGAGCCTCAGC
1 AAGGAAGGATCATTAGA-GCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAG---CAGC
* * *
1366978 AAGACAATGATTCTGAA
62 AAGACGAGGATTCCGAA
* * * * * * *
1366995 AAGGATGGATCCTTAGCGCCAGCTTCTCAAGAGAACCAACAACAACCGACTTTGGAGCCTCAGCA
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAG---CAGCA
*
1367060 AGATGAGGATTCCGAGA
63 AGACGAGGATTCCGA-A
* * * * * ** * *
1367077 AA-GAAGGTTCATCA-ATTCCAGCTTCTCAACAGAGCCAACAGCAGCCGTCTTTGGAGCACCACC
1 AAGGAAGGATCATTAGA-GCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAGCA--
* *
1367140 ACGACAATGATTCCGAA
63 A-GACGAGGATTCCGAA
* * * * * *
1367157 AAGGAAGG-T--TCAGCGCCATCTTCTCAAGTGAACCAACAGCGAA-CATATTCGGAGCCTCAGC
1 AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGC-AATCGTCTTCGGAG---CAGC
*
1367218 AAGACGAGGATTCCAAA
62 AAGACGAGGATTCCGAA
* * * *
1367235 AAAGAA-GATTCAATAGTGCCAGCTTCTCAAGAGAAACAACA
1 AAGGAAGGA-TCATTAGAGCCAGCTTCTCAAGAGAACCAACA
1367276 ACAACAACCG
Statistics
Matches: 628, Mismatches: 94, Indels: 48
0.82 0.12 0.06
Matches are distributed among these distances:
74 3 0.00
75 255 0.41
76 4 0.01
77 2 0.00
78 53 0.08
79 3 0.00
80 7 0.01
81 297 0.47
82 4 0.01
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (78 bp):
AAGGAAGGATCATTAGAGCCAGCTTCTCAAGAGAACCAACAGCAATCGTCTTCGGAGCAGCAAGA
CGAGGATTCCGAA
Found at i:1372307 original size:20 final size:20
Alignment explanation
Indices: 1372213--1372561 Score: 418
Period size: 20 Copynumber: 17.4 Consensus size: 20
1372203 GATTTTCCAT
* ** *
1372213 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1372233 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1372253 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1372273 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1372293 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1372313 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1372333 TATCGCAACGCATATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1372353 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1372373 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1372393 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1372413 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1372433 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1372453 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1372473 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1372493 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1372513 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1372533 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1372553 AATCACAAC
1 AATCGCAAC
1372562 ACTTAAATTT
Statistics
Matches: 285, Mismatches: 36, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
19 3 0.01
20 279 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1373477 original size:12 final size:12
Alignment explanation
Indices: 1373460--1373484 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1373450 ATATAATCCT
1373460 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1373472 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1373484 G
1 G
1373485 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1375786 original size:19 final size:19
Alignment explanation
Indices: 1375764--1376017 Score: 298
Period size: 19 Copynumber: 14.4 Consensus size: 19
1375754 CGGAAAATAC
*
1375764 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1375783 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1375797 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1375817 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1375831 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1375850 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
1375864 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
1375883 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1375902 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
1375920 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
1375939 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1375958 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1375972 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1375991 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1376010 AATCGCAA
1 AATCGCAA
1376018 CGAGATAATC
Statistics
Matches: 203, Mismatches: 10, Indels: 44
0.79 0.04 0.17
Matches are distributed among these distances:
14 38 0.19
15 1 0.00
16 14 0.07
17 12 0.06
18 19 0.09
19 106 0.52
20 13 0.06
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1375851 original size:33 final size:34
Alignment explanation
Indices: 1375764--1376017 Score: 286
Period size: 33 Copynumber: 7.2 Consensus size: 34
1375754 CGGAAAATAC
* *
1375764 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
1375797 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
* *
1375831 AATCGCAATGCGAAATGAAAATCGCAACGA-CAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
1375864 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
1375902 AATCGCAATGCGAAATG-AAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-A-ACG--ATGAA
1375939 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
1375971 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
1376010 AATCGCAA
1 AATCGCAA
1376018 CGAGATAATC
Statistics
Matches: 196, Mismatches: 8, Indels: 29
0.84 0.03 0.12
Matches are distributed among these distances:
32 2 0.01
33 84 0.43
34 30 0.15
35 5 0.03
36 3 0.02
37 36 0.18
38 33 0.17
39 3 0.02
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:1375955 original size:108 final size:105
Alignment explanation
Indices: 1375764--1376017 Score: 369
Period size: 108 Copynumber: 2.4 Consensus size: 105
1375754 CGGAAAATAC
* *
1375764 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCA
* *
1375824 ACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGACAG
66 ACGAGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
1375864 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATG-AAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGC-
1375927 ATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
65 A-ACG--A-GAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
1375972 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1376018 CGAGATAATC
Statistics
Matches: 138, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
100 24 0.17
102 1 0.01
103 7 0.05
104 7 0.05
105 19 0.14
107 1 0.01
108 79 0.57
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (105 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCA
ACGAGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:1376055 original size:52 final size:52
Alignment explanation
Indices: 1375831--1376039 Score: 337
Period size: 52 Copynumber: 3.9 Consensus size: 52
1375821 GCAACGAGAG
* *
1375831 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
*
1375883 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G-AATCGCAATGCGAAATGAA
1375939 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
* *
1375991 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
1376040 TATAAACGCA
Statistics
Matches: 147, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
52 92 0.63
53 1 0.01
54 9 0.06
55 1 0.01
56 44 0.30
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:1376155 original size:19 final size:19
Alignment explanation
Indices: 1376046--1376147 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1376036 AAATTATAAA
1376046 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1376065 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1376085 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1376101 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1376118 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1376137 CGCATTGCGAT
1 CGCATTGCGAT
1376148 AGTCATTTTG
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1376272 original size:14 final size:14
Alignment explanation
Indices: 1376253--1376289 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1376243 CATCAATTAC
1376253 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1376267 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1376281 ACAAATCAA
1 ACAAATCAA
1376290 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1378254 original size:14 final size:14
Alignment explanation
Indices: 1378235--1378291 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1378225 GCGAAATGAA
*
1378235 AATCGCAACGACAG
1 AATCGCAACGAAAG
1378249 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1378266 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1378282 AATCGCAACG
1 AATCGCAACG
1378292 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1378262 original size:33 final size:33
Alignment explanation
Indices: 1378216--1378308 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1378206 GCGAAACCAA
*
1378216 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1378249 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1378282 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1378309 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1378273 original size:19 final size:19
Alignment explanation
Indices: 1378179--1378313 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1378169 TAGTTTACTT
* *
1378179 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1378199 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1378218 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1378237 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1378251 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1378270 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1378284 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1378303 TCGCAATGCGA
1 TCGCAACGCGA
1378314 TTTTGTTTCG
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1378363 original size:33 final size:32
Alignment explanation
Indices: 1378309--1378399 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 32
1378299 AAAATCGCAA
*
1378309 TGCGATTTTGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTATTTCGCGTTGCGATTC-TGTCGT
*
1378341 TGCGATTTTAATTTCGCATTGCGATTCTGTCGT
1 TGCGATTTT-ATTTCGCGTTGCGATTCTGTCGT
1378374 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTT-ATTTCGCGTTGCGATT
1378400 TTGGTTTCGT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
32 9 0.17
33 42 0.79
34 2 0.04
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (32 bp):
TGCGATTTTATTTCGCGTTGCGATTCTGTCGT
Found at i:1378364 original size:19 final size:19
Alignment explanation
Indices: 1378338--1378436 Score: 82
Period size: 19 Copynumber: 5.4 Consensus size: 19
1378328 GCGATCTTGT
1378338 CGTTGCGATTTTAATTTCG
1 CGTTGCGATTTTAATTTCG
* * *
1378357 CATTGCGA--TT-CTGT--
1 CGTTGCGATTTTAATTTCG
*
1378371 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTAATTTCG
**
1378390 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAATTTCG
*
1378409 TGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTAA-TTTCG
*
1378429 TGTTGCGA
1 CGTTGCGA
1378437 AAGTAAACTA
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
14 7 0.11
16 4 0.06
17 4 0.06
19 35 0.56
20 13 0.21
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTAATTTCG
Found at i:1378428 original size:20 final size:19
Alignment explanation
Indices: 1378372--1378436 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
1378362 CGATTCTGTC
*
1378372 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTT-AGTTTCGT
*
1378391 GTTGCGATTTTGGTTTCGT
1 GTTGCGATTTTAGTTTCGT
1378410 GTTGCGATTTTAAGTTTCGT
1 GTTGCGATTTT-AGTTTCGT
1378430 GTTGCGA
1 GTTGCGA
1378437 AAGTAAACTA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 27 0.66
20 14 0.34
ACGTcount: A:0.11, C:0.14, G:0.28, T:0.48
Consensus pattern (19 bp):
GTTGCGATTTTAGTTTCGT
Found at i:1378689 original size:92 final size:93
Alignment explanation
Indices: 1378480--1378943 Score: 840
Period size: 92 Copynumber: 5.1 Consensus size: 93
1378470 TTGAATGGAT
1378480 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA-ACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1378544 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1378572 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC--A-A-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1378633 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1378661 -AATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1378724 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1378752 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1378816 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1378844 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1378908 AGTTTAGCAGAATTGGCAGCAA-CGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1378935 AAATTTACT
1 AAATTTACT
1378944 AAGCAATCTA
Statistics
Matches: 361, Mismatches: 3, Indels: 17
0.95 0.01 0.04
Matches are distributed among these distances:
87 17 0.05
88 35 0.10
89 34 0.09
90 2 0.01
91 70 0.19
92 181 0.50
93 22 0.06
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1378783 original size:180 final size:184
Alignment explanation
Indices: 1378480--1378943 Score: 852
Period size: 180 Copynumber: 2.6 Consensus size: 184
1378470 TTGAATGGAT
1378480 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA-ACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1378544 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC-A-
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAT
1378607 ATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 ATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1378661 -AATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1378724 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA
*
1378789 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
130 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1378844 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1378908 AGTTTAGCAGAATTGGCAGCAA-CGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1378944 AAGCAATCTA
Statistics
Matches: 275, Mismatches: 2, Indels: 10
0.96 0.01 0.03
Matches are distributed among these distances:
179 43 0.16
180 81 0.29
182 1 0.00
183 66 0.24
184 67 0.24
185 17 0.06
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (184 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAT
ATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1380639 original size:14 final size:14
Alignment explanation
Indices: 1380620--1380709 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1380610 TTGAAATGAA
1380620 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1380634 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1380651 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1380667 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1380686 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1380700 AATCGCAACG
1 AATCGCAACG
1380710 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1380657 original size:33 final size:33
Alignment explanation
Indices: 1380612--1380726 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1380602 TCTTTTGGTT
1380612 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1380645 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1380678 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1380711 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1380727 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1380658 original size:19 final size:18
Alignment explanation
Indices: 1380619--1380731 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1380609 GTTGAAATGA
1380619 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1380634 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1380651 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1380667 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1380684 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1380700 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1380717 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1380732 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1380762 original size:14 final size:14
Alignment explanation
Indices: 1380743--1380797 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1380733 TTTGGTTTCG
1380743 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1380757 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1380776 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1380790 CGTTGCGA
1 CGTTGCGA
1380798 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1380775 original size:33 final size:33
Alignment explanation
Indices: 1380727--1380797 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1380717 AAAATCGCAA
**
1380727 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1380760 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1380793 TGCGA
1 TGCGA
1380798 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1380805 original size:33 final size:33
Alignment explanation
Indices: 1380738--1380819 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1380728 GCGATTTTGG
***
1380738 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1380771 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1380804 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1380820 TTCATTATCT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1380808 original size:20 final size:20
Alignment explanation
Indices: 1380783--1380838 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1380773 TCGCGTTGCG
1380783 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGACAGTC
***
1380803 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
*
1380823 ATTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGAC
1380839 TCTTCTGCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.14, C:0.27, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:1380958 original size:33 final size:33
Alignment explanation
Indices: 1380916--1380986 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1380906 AATACTAACT
*
1380916 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1380949 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1380982 TGAAA
1 TGAAA
1380987 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1381218 original size:22 final size:22
Alignment explanation
Indices: 1381166--1381220 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1381156 TGGTTGTGAG
**
1381166 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1381188 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1381210 GGATTTCTTCG
1 GGATTTCTTCG
1381221 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1381391 original size:20 final size:20
Alignment explanation
Indices: 1381366--1381557 Score: 226
Period size: 20 Copynumber: 9.6 Consensus size: 20
1381356 CTTTAAATAT
1381366 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1381386 CGCGTTGCGATTTATGTATTA
1 CGCGTTGCGATTTACGGA-TA
*
1381407 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1381426 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1381446 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1381466 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1381486 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1381506 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1381526 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1381546 CGCGTTGCGATT
1 CGCGTTGCGATT
1381558 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 141 0.97
21 3 0.02
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1381442 original size:60 final size:60
Alignment explanation
Indices: 1381366--1381557 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1381356 CTTTAAATAT
*
1381366 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
* * ***
1381426 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCA-TACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTA-GCGTTGCGATTTACGGATA
* * * * ** *
1381486 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
1381546 CGCGTTGCGATT
1 CGCGTTGCGATT
1381558 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
59 2 0.02
60 108 0.97
61 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
Found at i:1381646 original size:20 final size:20
Alignment explanation
Indices: 1381613--1381663 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1381603 AAGAATCGCG
1381613 TTGCGATT-TGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1381632 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1381652 TTGCGATTCTGG
1 TTGCGATTCTGG
1381664 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1384965 original size:2 final size:2
Alignment explanation
Indices: 1384958--1384982 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1384948 GCATGTTAAT
1384958 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 T
1384983 GCTAGAAGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1386937 original size:61 final size:61
Alignment explanation
Indices: 1386842--1386968 Score: 236
Period size: 61 Copynumber: 2.1 Consensus size: 61
1386832 ACTGAACATT
1386842 AACATGCTATCTGGGATATAATAAAATCTGATGTCATAATCTCAAATGATTATACCATTCA
1 AACATGCTATCTGGGATATAATAAAATCTGATGTCATAATCTCAAATGATTATACCATTCA
* *
1386903 AACATGTTATCTGGGATATAATAAAATCTGATGTCATAATCTCAAATGATTATACTATTCA
1 AACATGCTATCTGGGATATAATAAAATCTGATGTCATAATCTCAAATGATTATACCATTCA
1386964 AACAT
1 AACAT
1386969 TTCTGAGATC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (61 bp):
AACATGCTATCTGGGATATAATAAAATCTGATGTCATAATCTCAAATGATTATACCATTCA
Found at i:1388861 original size:14 final size:14
Alignment explanation
Indices: 1388842--1388868 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1388832 GGACGGAGGG
1388842 TTGTTTTCATGGCA
1 TTGTTTTCATGGCA
1388856 TTGTTTTCATGGC
1 TTGTTTTCATGGC
1388869 TTGGCAGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.15, G:0.22, T:0.52
Consensus pattern (14 bp):
TTGTTTTCATGGCA
Found at i:1390561 original size:21 final size:21
Alignment explanation
Indices: 1390517--1390561 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1390507 AAATTACGTA
*
1390517 TTTAGTACCTAAACTATCAGT
1 TTTAGTACCTAAACTATCAAT
* * *
1390538 TTTAGTACTTAAACTTTTAAT
1 TTTAGTACCTAAACTATCAAT
1390559 TTT
1 TTT
1390562 TTTAAAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTAGTACCTAAACTATCAAT
Found at i:1392164 original size:6 final size:5
Alignment explanation
Indices: 1392083--1392163 Score: 74
Period size: 5 Copynumber: 15.2 Consensus size: 5
1392073 ACTGGAATAA
* *
1392083 TTATT TTATT TTATT TTATT TTATT TTATT TTATGT TGCGATT GCTT-TG
1 TTATT TTATT TTATT TTATT TTATT TTATT TTAT-T T--TATT --TTATT
*
1392132 TTGTT TTATT TTATT TTATT TTATT TATATT T
1 TTATT TTATT TTATT TTATT TTATT T-TATT T
1392164 AGATAATTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
4 2 0.03
5 50 0.78
6 8 0.12
7 1 0.02
8 2 0.03
9 1 0.02
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.73
Consensus pattern (5 bp):
TTATT
Found at i:1399159 original size:8 final size:8
Alignment explanation
Indices: 1399146--1399171 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1399136 TCGGGGCCCA
1399146 ATATTTTT
1 ATATTTTT
1399154 ATATTTTT
1 ATATTTTT
1399162 ATATTTTT
1 ATATTTTT
1399170 AT
1 AT
1399172 TACGTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
ATATTTTT
Found at i:1400615 original size:36 final size:36
Alignment explanation
Indices: 1400523--1400695 Score: 221
Period size: 36 Copynumber: 4.9 Consensus size: 36
1400513 AAACAAGAAT
* * *
1400523 AACGGAAGGAAACGTCG-CACTTCCGATTCAAAGTG
1 AACGGAAGGAAGCATCGACACTTCCGATTCAAACTG
1400558 AACGGAA-GAA-CATCGACACTTCCGATTCAAACTG
1 AACGGAAGGAAGCATCGACACTTCCGATTCAAACTG
1400592 AACGGAAGGAAGCATCGACACTTCCGATTCAAACTG
1 AACGGAAGGAAGCATCGACACTTCCGATTCAAACTG
* *
1400628 AACGGAAGGAAGCATCGACACTTTCGATTC-AAGTCG
1 AACGGAAGGAAGCATCGACACTTCCGATTCAAACT-G
* * *
1400664 ACCGGAAGGAGGCGTCTG-CACTTCCGATTCAA
1 AACGGAAGGAAGCATC-GACACTTCCGATTCAA
1400696 CTAGAACAGA
Statistics
Matches: 124, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
33 4 0.03
34 27 0.22
35 13 0.10
36 78 0.63
37 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.18
Consensus pattern (36 bp):
AACGGAAGGAAGCATCGACACTTCCGATTCAAACTG
Found at i:1401726 original size:32 final size:31
Alignment explanation
Indices: 1401663--1401761 Score: 135
Period size: 31 Copynumber: 3.2 Consensus size: 31
1401653 GTTATAATAA
* *
1401663 TTGTAAAAATTCGATAAATTTAATGACCATT
1 TTGTAACAATTCGATAAATTTAATAACCATT
* *
1401694 TTGTAACATTTCGATAAAATTTAATAATCATT
1 TTGTAACAATTCGAT-AAATTTAATAACCATT
* *
1401726 TTGTAACAGTTCGATAAATTTAATTACCATT
1 TTGTAACAATTCGATAAATTTAATAACCATT
1401757 TTGTA
1 TTGTA
1401762 TTGTTTGAAG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.42
Consensus pattern (31 bp):
TTGTAACAATTCGATAAATTTAATAACCATT
Done.