Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000907.1 Hibiscus syriacus cultivar Beakdansim tig00001799_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: 656280
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:559368 original size:19 final size:20
Alignment explanation
Indices: 559340--559381 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
559330 AACAACACAG
559340 TCTTTCGTTTT-CATAATAA
1 TCTTTCGTTTTCCATAATAA
*
559359 TCTTTTGTTTTCCATAATAA
1 TCTTTCGTTTTCCATAATAA
559379 TCT
1 TCT
559382 AACTCAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.24, C:0.17, G:0.05, T:0.55
Consensus pattern (20 bp):
TCTTTCGTTTTCCATAATAA
Found at i:565550 original size:79 final size:79
Alignment explanation
Indices: 565419--565714 Score: 250
Period size: 81 Copynumber: 3.7 Consensus size: 79
565409 AAGTAACGAC
* *
565419 GTTTGTTGAAAAAACGCCACTA-TAGATGAACCCTATTACGGC-ATTTTATACAAACACTGCT-A
1 GTTTGTTGAAAAAA-GCCACTATTAG-TGAA-CCTATTGCGGCGTTTTTATACAAACACTGCTAA
*
565481 AGTATTACTCTTTGTGG
63 AGTAATACTCTTTGTGG
* *
565498 GTTTGTTGAAAAAAGCCACT-TTAGTCGAAACCTATTGCGGCGTTTTTATACAAACACCGTTAAA
1 GTTTGTTGAAAAAAGCCACTATTAGT-G-AACCTATTGCGGCGTTTTTATACAAACACTGCTAAA
**
565562 GTAATA--CTTTGTCACATC
64 GTAATACTCTTTGT----GG
* * * * * * * *
565580 GTTTGTTGAGAAACGCCACTATGAATGAACCTATTGTGGCGTTTGTATAAAAACGCTGCTAAAGT
1 GTTTGTTGAAAAAAGCCACTATTAGTGAACCTATTGCGGCGTTTTTATACAAACACTGCTAAAGT
*
565645 ACA-ACTCTGTTGCGG
66 A-ATACTCT-TTGTGG
*
565660 TGTTTGTTGAAAAAAACCACTATATA-TG-ACCATATTGCGGCGTTTTTATACAAAC
1 -GTTTGTTGAAAAAAGCCACTAT-TAGTGAACC-TATTGCGGCGTTTTTATACAAAC
565715 GCCACTAAAC
Statistics
Matches: 173, Mismatches: 27, Indels: 32
0.75 0.12 0.14
Matches are distributed among these distances:
77 1 0.01
78 26 0.15
79 32 0.18
80 10 0.06
81 75 0.43
82 21 0.12
83 5 0.03
84 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (79 bp):
GTTTGTTGAAAAAAGCCACTATTAGTGAACCTATTGCGGCGTTTTTATACAAACACTGCTAAAGT
AATACTCTTTGTGG
Found at i:565665 original size:81 final size:81
Alignment explanation
Indices: 565580--565735 Score: 190
Period size: 81 Copynumber: 1.9 Consensus size: 81
565570 TTGTCACATC
* ** * **
565580 GTTTGTTGAGAAACGCCACTATGA-ATGAACC-TATTGTGGCGTTTGTATAAAAACGCTGCTAAA
1 GTTTGTTGAAAAAAACCACTAT-ATATG-ACCATATTGCGGCGTTTGTATAAAAACGCCACTAAA
*
565643 GTACAACTCTGTTGCGGT
64 CTACAACTCTGTTGCGGT
* *
565661 GTTTGTTGAAAAAAACCACTATATATGACCATATTGCGGCGTTTTTATACAAACGCCACTAAACT
1 GTTTGTTGAAAAAAACCACTATATATGACCATATTGCGGCGTTTGTATAAAAACGCCACTAAACT
*
565726 ACTACTCTGT
66 ACAACTCTGT
565736 CACGGCGTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
80 4 0.06
81 59 0.94
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (81 bp):
GTTTGTTGAAAAAAACCACTATATATGACCATATTGCGGCGTTTGTATAAAAACGCCACTAAACT
ACAACTCTGTTGCGGT
Found at i:572388 original size:3 final size:3
Alignment explanation
Indices: 572382--572435 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
572372 TGTTATTATA
* *
572382 AAT AAT AAT AAT AAT AAT AGT GAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
572430 AAT AAT
1 AAT AAT
572436 CCGGACAAAA
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:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:573556 original size:58 final size:59
Alignment explanation
Indices: 573443--573559 Score: 164
Period size: 58 Copynumber: 2.0 Consensus size: 59
573433 ATCATGTGAT
* * *
573443 ATGATACATTTTGTAACTTTTAATAGCCGAGAGACTTAATAAAACAGCATTCTATAGTC
1 ATGATACATTTTGTAACTTTTAATAGCCAAGAGACTTAATAAAACAACATCCTATAGTC
* * * *
573502 ATGAT-CATTTTGTAACTTTTAATAGTCAAGGGACTTAATAAAGCAATATCCTATAGTC
1 ATGATACATTTTGTAACTTTTAATAGCCAAGAGACTTAATAAAACAACATCCTATAGTC
573560 GGGGAACCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 46 0.90
59 5 0.10
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Consensus pattern (59 bp):
ATGATACATTTTGTAACTTTTAATAGCCAAGAGACTTAATAAAACAACATCCTATAGTC
Found at i:574654 original size:38 final size:38
Alignment explanation
Indices: 574552--574654 Score: 120
Period size: 38 Copynumber: 2.7 Consensus size: 38
574542 TATCGGGTCA
*
574552 ATTATATATATTTAAATTAAATATATAAATATTATATAT
1 ATTATATATATTTAAATTAAAT-TATTAATATTATATAT
* *
574591 ATTTTTTA-ATTTAAATTAAATTTATTAATATTATATAT
1 ATTATATATATTTAAATTAAA-TTATTAATATTATATAT
* *
574629 ATATATATATATATAAAAT-AATTATT
1 AT-TATATATATTTAAATTAAATTATT
574655 TTTAATATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
38 34 0.63
39 13 0.24
40 7 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
ATTATATATATTTAAATTAAATTATTAATATTATATAT
Found at i:574737 original size:36 final size:35
Alignment explanation
Indices: 574697--574778 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 35
574687 ACTAAACTCA
* *
574697 TCCCCGTCCCGGTCCCCGTTTAACATAAACGATTTT
1 TCCCCGTCCC-GTCCCCATATAACATAAACGATTTT
* * *
574733 TCCCCATCTCCGTCCCCATATAGCATAAACGGTTTT
1 TCCCCGTC-CCGTCCCCATATAACATAAACGATTTT
574769 TCCCCGTCCC
1 TCCCCGTCCC
574779 CGTTTAATTC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
35 2 0.05
36 35 0.90
37 2 0.05
ACGTcount: A:0.18, C:0.40, G:0.12, T:0.29
Consensus pattern (35 bp):
TCCCCGTCCCGTCCCCATATAACATAAACGATTTT
Found at i:583320 original size:15 final size:16
Alignment explanation
Indices: 583276--583322 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
583266 AAAATTAAAT
*
583276 TTGAAAGTTAGAGTGA
1 TTGAAAGTTAGAGTAA
583292 TT-AAA-TTAGGAGTAA
1 TTGAAAGTTA-GAGTAA
583307 TTGAAAGTTA-AGTAA
1 TTGAAAGTTAGAGTAA
583322 T
1 T
583323 CAAGTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 3 0.11
15 16 0.59
16 5 0.19
17 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (16 bp):
TTGAAAGTTAGAGTAA
Found at i:584007 original size:2 final size:2
Alignment explanation
Indices: 584000--584029 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
583990 AGATTCATAC
*
584000 AT AT AT AT AC 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
584030 CGATTGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:584011 original size:10 final size:10
Alignment explanation
Indices: 583996--584028 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
583986 TAAAAGATTC
583996 ATACATATAT
1 ATACATATAT
584006 ATACATATAT
1 ATACATATAT
*
584016 ATATATATAT
1 ATACATATAT
584026 ATA
1 ATA
584029 TCGATTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (10 bp):
ATACATATAT
Found at i:585251 original size:182 final size:180
Alignment explanation
Indices: 584938--585514 Score: 842
Period size: 182 Copynumber: 3.2 Consensus size: 180
584928 ATTTGTATAA
* * *
584938 TTTACTTGTTATATTGA-TATGGACCGATACATTTGTATAAAGTATCGACACGTTTTAGGCGCTA
1 TTTACCTGTTATATT-ACTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTA
585002 TAACTTCTTCTCTTTTAAA-TATCAAAAGTATCGATACTTATATTAATTTATCGACACTTTCAAT
65 TAAC-T-TTCTCTTTTAAATTA-CAAAAGTATCGATACTTATATTAATTTATCGACACTTTCAAT
** ** * * *
585066 ATATCCAATAGCTTTTTACCGGTTTTATCAT-TTCGAGACCTGTTTTGTCATATT
127 ATATCCGGTAGCGGTTTACCGGTTTTATCATAAT-GACACCTGTTTTATCATATT
* *
585120 ATTACCTGTTATATTACTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGTTAT
1 TTTACCTGTTATATTACTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTAT
585185 AACTTATACTCTTTTAAATTACAAAAGTATCGATACTTATATTAATTTATCGACACTTTCAATAT
66 AACTT-T-CTCTTTTAAATTACAAAAGTATCGATACTTATATTAATTTATCGACACTTTCAATAT
585250 ATCCGGTAGCGGTTTACCGGTTTTATCATAATGACA-CTGGTTTTATCATATT
129 ATCCGGTAGCGGTTTACCGGTTTTATCATAATGACACCT-GTTTTATCATATT
* ** * *
585302 TTTACCTGTTATATTTCTATTTATCGATATATTTGTATAAAGTATCGACACTTTATAGGCGCTAT
1 TTTACCTGTTATATTACTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTAT
* *
585367 AAC-TTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATTGACACTTTCAATATAT
66 AACTTTCTCTTTTAAATTACAAAAGTATCGATACTTATATTAATTTATCGACACTTTCAATATAT
*
585431 CCGGTAGCGGTTTACCGGTTTTATCATAATGACACCGGTTTTATCATATT
131 CCGGTAGCGGTTTACCGGTTTTATCATAATGACACCTGTTTTATCATATT
*
585481 TTTACCTGTTATA-TAGTTATGGATCGATACATTT
1 TTTACCTGTTATATTA-CTATGGATCGATACATTT
585515 TTCATTTGTA
Statistics
Matches: 360, Mismatches: 27, Indels: 19
0.89 0.07 0.05
Matches are distributed among these distances:
178 1 0.00
179 131 0.36
180 3 0.01
181 6 0.02
182 216 0.60
183 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (180 bp):
TTTACCTGTTATATTACTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTAT
AACTTTCTCTTTTAAATTACAAAAGTATCGATACTTATATTAATTTATCGACACTTTCAATATAT
CCGGTAGCGGTTTACCGGTTTTATCATAATGACACCTGTTTTATCATATT
Found at i:586562 original size:16 final size:17
Alignment explanation
Indices: 586520--586562 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
586510 AATTTTTTCA
*
586520 AAAATATATGAAATTTAT
1 AAAATAT-TTAAATTTAT
586538 AAAAT-TTTAAA-TTAT
1 AAAATATTTAAATTTAT
586553 AAAATATTTA
1 AAAATATTTA
586563 TTATTATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
16 8 0.35
17 1 0.04
18 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAAATATTTAAATTTAT
Found at i:586964 original size:324 final size:325
Alignment explanation
Indices: 586364--587352 Score: 1376
Period size: 324 Copynumber: 3.0 Consensus size: 325
586354 TATTAAATTC
*
586364 TAATTTTATTAAAAATA-AATAAACATTATTAACTTTTGTTAAAAATTAATAATTAATGAATAAT
1 TAATTTTATTAAAAA-AGAATAAACATTATTAAATTTTGTTAAAAA-TAATAATTAATGAATAAT
586428 AATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATA---TTTTTTATATTTTTAAAC
64 AATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTTTATATTTTTAAAC
* *
586490 AATTAATTTTAAAAGTCAATAATTTTTTCAAAAATATATGAAATTTATAAAATTTTAAATTATAA
129 ----AA---T--AAGTCAATAAATTTTTCAAAAATATATGAAATTTAT-AATTTTTAAATTAT-A
586555 AATATTTATTATTATCATCATCATCATTTTGTAAAAGAAATACTGGTTATAAAACTTTTATAAAA
183 AA-A--TATTATTATCATCATCATCATTTTGT-AAA-AAATACTGGTTATAAAACTTTTATAAAA
* **
586620 TTATTCATATTTTAAAATACTCACCCTCAAAGTTTTTTTATACTAAATTATACATATTGTGTAAT
243 TTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCATATACTAAATTATACATATTGTGTAAT
586685 TTCATGCAAAAATCAAAA
308 TTCATGCAAAAATCAAAA
*
586703 TAATTTTATTAAAAAAGAATAAACATTATTAAATTTTGTTAAAAATAATGATTAATGAATAATAA
1 TAATTTTATTAAAAAAGAATAAACATTATTAAATTTTGTTAAAAATAATAATTAATGAATAATAA
*
586768 TTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTTTATATTTTTAAACAA
66 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTTTATATTTTTAAACAA
*
586833 TAAGTCAATAAATTTTTCAAAAATATAT-AACATTTATAATTTTTAAATTGTAAAATA-T-TTAT
131 TAAGTCAATAAATTTTTCAAAAATATATGAA-ATTTATAATTTTTAAATTATAAAATATTATTAT
586895 CATCATCATCATTTTGTAAACAAATACTGGTTATAAAACTTTTATAAAATTATTCATATTTTAAA
195 CATCATCATCATTTTGTAAA-AAATACTGGTTATAAAACTTTTATAAAATTATTCATATTTTAAA
* * * * *
586960 ATACTTACCCTCAAAGTTTTCCTATACTATATTATACGTATTGTATAATTTCAAGCAAAAATCAA
259 ATACTTACCCTCAAAGTTTTCATATACTAAATTATACATATTGTGTAATTTCATGCAAAAATCAA
587025 AA
324 AA
*
587027 TAATTTTATTAAAAATGAATAAACATTATT-AATTGTTGTTAAAAATAATAATTAATGAATAATA
1 TAATTTTATTAAAAAAGAATAAACATTATTAAATT-TTGTTAAAAATAATAATTAATGAATAATA
****
587091 ATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTAAACA-ATTAATTT---
65 ATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTTTATATT--TTTAAA
* *
587152 TAA-AAGTCAATAAA-TTTTAAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTA
128 CAATAAGTCAATAAATTTTTCAAAAATATATGAAATTTATAA-TTTTTAAATTATAAAATA-TTA
* * * *
587215 TTATCATCATCATCATTTTGTAAAAGAAGTAATAGTTATAAAATTTTTAAAAAATTATTCATATT
191 TTATCATCATCATCATTTTGTAAAA-AA-TACTGGTTATAAAACTTTTATAAAATTATTCATATT
* * *
587280 TTAAAATATTTAACCTCAAAGTTTTCATATACTAGATTATACATATTGTGTAATTTCATGCAAAA
254 TTAAAATACTTACCCTCAAAGTTTTCATATACTAAATTATACATATTGTGTAATTTCATGCAAAA
*
587345 ATTAAAA
319 ATCAAAA
587352 T
1 T
587353 TTATCGAGTT
Statistics
Matches: 599, Mismatches: 36, Indels: 44
0.88 0.05 0.06
Matches are distributed among these distances:
320 22 0.04
321 30 0.05
322 2 0.00
323 9 0.02
324 238 0.40
325 121 0.20
326 1 0.00
327 2 0.00
329 1 0.00
330 3 0.01
331 14 0.02
332 32 0.05
334 1 0.00
337 2 0.00
338 61 0.10
339 42 0.07
341 18 0.03
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (325 bp):
TAATTTTATTAAAAAAGAATAAACATTATTAAATTTTGTTAAAAATAATAATTAATGAATAATAA
TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTTTATATTTTTAAACAA
TAAGTCAATAAATTTTTCAAAAATATATGAAATTTATAATTTTTAAATTATAAAATATTATTATC
ATCATCATCATTTTGTAAAAAATACTGGTTATAAAACTTTTATAAAATTATTCATATTTTAAAAT
ACTTACCCTCAAAGTTTTCATATACTAAATTATACATATTGTGTAATTTCATGCAAAAATCAAAA
Found at i:587407 original size:16 final size:16
Alignment explanation
Indices: 587382--587413 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
587372 TTTGTAAAAG
*
587382 AATATTTAAATATTTT
1 AATATATAAATATTTT
587398 AATATATAAATATTTT
1 AATATATAAATATTTT
587414 TTTCACACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATATATAAATATTTT
Found at i:589557 original size:25 final size:24
Alignment explanation
Indices: 589529--589601 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 24
589519 AAAAGAAAAG
589529 AAAATAAATAAATAAAAACAGAATA
1 AAAATAAATAAATAAAAACAGAA-A
* *
589554 AAAATAAAACAAACATAAAACA-AAA
1 AAAAT-AAATAAATA-AAAACAGAAA
*
589579 AAATTAAATTAAATAAAAA-AGAA
1 AAAATAAA-TAAATAAAAACAGAA
589602 CCTAAATAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
23 1 0.03
24 9 0.23
25 14 0.36
26 9 0.23
27 6 0.15
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (24 bp):
AAAATAAATAAATAAAAACAGAAA
Found at i:589612 original size:50 final size:51
Alignment explanation
Indices: 589519--589616 Score: 128
Period size: 50 Copynumber: 1.9 Consensus size: 51
589509 AAAATATCAA
* *
589519 AAAAGAAAAGAAAATAAATAAATAAAAACAGAATAAAAATAAAACAAACAT
1 AAAACAAAAGAAAATAAATAAATAAAAACAGAACAAAAATAAAACAAACAT
* **
589570 AAAACAAAA-AAATTAAATTAAATAAAAA-AGAACCTAAATAAAACAAA
1 AAAACAAAAGAAAATAAA-TAAATAAAAACAGAACAAAAATAAAACAAA
589617 GAAATAACGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 23 0.56
51 18 0.44
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.13
Consensus pattern (51 bp):
AAAACAAAAGAAAATAAATAAATAAAAACAGAACAAAAATAAAACAAACAT
Found at i:589666 original size:3 final size:3
Alignment explanation
Indices: 589658--589863 Score: 105
Period size: 3 Copynumber: 69.7 Consensus size: 3
589648 TATTTGGTAA
* *
589658 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC GAT AAT AAT AAT AA- AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
589704 AAGG AGT GA- AAT GCAT -AT ATAT AAT -AT AAT ATAC AAT AAT AAA AAT
1 AA-T AAT AAT AAT -AAT AAT A-AT AAT AAT AAT A-AT AAT AAT AAT AAT
** * * *
589750 AA- AAT ATAT AAT GGT AA- AAC AA- AAT AAT AAT AAT AAC GAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
589793 AAT AAT AAT AA- AAT GA- AAT -AT ATAT ATAT ATAT ATAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT A-AT A-AT AAT AAT AAT
589838 AAT AAT AA- AAT ATAT AAT AAT AAT AA
1 AAT AAT AAT AAT A-AT AAT AAT AAT AA
589864 AACTTAATAT
Statistics
Matches: 160, Mismatches: 24, Indels: 38
0.72 0.11 0.17
Matches are distributed among these distances:
2 24 0.15
3 107 0.67
4 29 0.18
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:589782 original size:99 final size:94
Alignment explanation
Indices: 589673--589855 Score: 278
Period size: 94 Copynumber: 1.9 Consensus size: 94
589663 TAATAATAAT
589673 AATAATAATAATAACGATAATAATAATAAAAAAGGAGTGAAATGCATATATATA-ATATAATATA
1 AATAATAATAATAACGATAATAATAATAAAAAA--A-TGAAAT--ATATATATATATAT-ATATA
*
589737 CAATAATAAAAATAAAATATATAATGGTAAAACAA
60 AAATAATAAAAATAAAATATATAATGGTAAAACAA
*
589772 AATAATAATAATAACGATAATAATAATAATAAAATGAAATATATATATATATATATATAAAATAA
1 AATAATAATAATAACGATAATAATAATAAAAAAATGAAATATATATATATATATATATAAAATAA
*
589837 TAATAATAAAATATATAAT
66 TAAAAATAAAATATATAAT
589856 AATAATAAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
94 37 0.46
95 4 0.05
96 6 0.08
97 1 0.01
99 32 0.40
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (94 bp):
AATAATAATAATAACGATAATAATAATAAAAAAATGAAATATATATATATATATATATAAAATAA
TAAAAATAAAATATATAATGGTAAAACAA
Found at i:589899 original size:60 final size:60
Alignment explanation
Indices: 589770--589899 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 60
589760 ATGGTAAAAC
* * * *
589770 AAAATAATAATAATAACGATAATAATAATAATAAAATGAAATATATATATATATATATAT
1 AAAAAAATAATAATAACAATAATAATAATAATAAAATGAAATATATATATATAAATAAAT
* *
589830 AAAATAATAATAATAA-AATATATAATAATAATAAAACT-TAATATACTA-ATA-AAATAAAT
1 AAAAAAATAATAATAACAATA-ATAATAATAATAAAA-TGAAATATA-TATATATAAATAAAT
589889 AAAAGAAATAA
1 AAAA-AAATAA
589900 ATAAAGAAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
59 13 0.21
60 45 0.74
61 3 0.05
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (60 bp):
AAAAAAATAATAATAACAATAATAATAATAATAAAATGAAATATATATATATAAATAAAT
Found at i:591541 original size:6 final size:6
Alignment explanation
Indices: 591527--591575 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
591517 TTAAACCCCA
*
591527 TTTTAT TTTTC- TTTTCTT TTTTCT TTTTCT TTTTCT TTTGT-T TTTTCT
1 TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT TTTTCT TTT-TCT TTTTCT
591575 T
1 T
591576 CTTCAAACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 6 0.16
6 26 0.68
7 6 0.16
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:591554 original size:24 final size:24
Alignment explanation
Indices: 591527--591575 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
591517 TTAAACCCCA
591527 TTTTATTTTTCTTTTCTTTTTTCT
1 TTTTATTTTTCTTTTCTTTTTTCT
* *
591551 TTTTCTTTTTCTTTTGTTTTTTCT
1 TTTTATTTTTCTTTTCTTTTTTCT
591575 T
1 T
591576 CTTCAAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (24 bp):
TTTTATTTTTCTTTTCTTTTTTCT
Found at i:594146 original size:3 final size:3
Alignment explanation
Indices: 594138--594250 Score: 74
Period size: 3 Copynumber: 37.7 Consensus size: 3
594128 TATAATATGC
** * *
594138 AAT AAT AAT AAT AA- AAT ATAT AAT GGT AA- AA- AAA AACA AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AA-T AAT AAT
* * * *
594182 AAC GAT AAT AAT AAT AA- AAA AAT GA- AAT ATAT ATAT AAT ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT A-AT AAT
594228 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
594251 AACTTAATAT
Statistics
Matches: 90, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
2 9 0.10
3 65 0.72
4 16 0.18
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:594277 original size:97 final size:95
Alignment explanation
Indices: 594068--594244 Score: 238
Period size: 97 Copynumber: 1.9 Consensus size: 95
594058 TGGTAAAATA
594068 AAAATAAAAAT-AATAATAACGATAATAATAATAAAAAAGGAGTGAAATACATATATATAATATA
1 AAAA-AAAAATAAATAATAACGATAATAATAATAAAAAA-GAGTGAAATACATATATATAATATA
* *
594132 ATATGCAATAATAATAATAAAATATATAATGGT
64 ATAT-CAATAATAATAATAAAAAATATAATGAT
* *
594165 AAAAAAAAACAAATAATAACGATAATAATAATAAAAAA-A-TGAAATATATATATA-ATATATAA
1 AAAAAAAAATAAATAATAACGATAATAATAATAAAAAAGAGTGAAATACATATATATA-ATATAA
594227 TAAT-AATAATAATAATAA
65 T-ATCAATAATAATAATAA
594245 TAATAAAACT
Statistics
Matches: 75, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
93 15 0.20
94 21 0.28
95 3 0.04
96 5 0.07
97 31 0.41
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (95 bp):
AAAAAAAAATAAATAATAACGATAATAATAATAAAAAAGAGTGAAATACATATATATAATATAAT
ATCAATAATAATAATAAAAAATATAATGAT
Found at i:595464 original size:2 final size:2
Alignment explanation
Indices: 595457--595502 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
595447 ATAATAAATA
* * *
595457 AT AT AT AT AT GT TT AT -T AT A- AT AT GT 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
595497 AT AT AT
1 AT AT AT
595503 GATTATTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (2 bp):
AT
Found at i:595527 original size:36 final size:36
Alignment explanation
Indices: 595457--595527 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
595447 ATAATAAATA
* * *
595457 ATATATATATGTTTATTATAATATGTATATATATAT
1 ATATATATATGATTATTATAATATGTACACATATAT
*
595493 ATATATATATGATTATTATTA-ATGTAACACATATA
1 ATATATATATGATTATTATAATATGT-ACACATATA
595528 ATGGGATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 4 0.13
36 26 0.87
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.48
Consensus pattern (36 bp):
ATATATATATGATTATTATAATATGTACACATATAT
Found at i:598870 original size:21 final size:21
Alignment explanation
Indices: 598776--598870 Score: 52
Period size: 21 Copynumber: 4.6 Consensus size: 21
598766 GCGAAATAAA
*
598776 AATCGCAACGCGA-TATCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
598796 AATCGCAAATC-AGTTCCCAG
1 AATCGCAACGCGATTTTCCAG
* * ** *
598816 AATCGCAATGTGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
598836 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
598858 AATCGCAACGCGA
1 AATCGCAACGCGA
598871 ATATGAAAAT
Statistics
Matches: 52, Mismatches: 19, Indels: 7
0.67 0.24 0.09
Matches are distributed among these distances:
19 1 0.02
20 24 0.46
21 25 0.48
22 2 0.04
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:598910 original size:20 final size:20
Alignment explanation
Indices: 598858--598910 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
598848 GATTTTCCAG
*
598858 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAACATGAA
* *
598878 AATCACAATGCGAACAT-ATA
1 AATCGCAACGCGAACATGA-A
598898 AATCGCAACGCGA
1 AATCGCAACGCGA
598911 TTCTGACTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACATGAA
Found at i:598963 original size:20 final size:20
Alignment explanation
Indices: 598919--599132 Score: 252
Period size: 20 Copynumber: 10.6 Consensus size: 20
598909 GATTCTGACT
*
598919 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
598940 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
598960 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
598981 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
599001 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
599021 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
599041 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
599061 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
599081 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
599102 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
599122 ATCGCAACGCG
1 ATCGCAACGCG
599133 ATTTTTAAAG
Statistics
Matches: 162, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
20 111 0.69
21 51 0.31
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:599034 original size:40 final size:41
Alignment explanation
Indices: 598919--599130 Score: 356
Period size: 41 Copynumber: 5.2 Consensus size: 41
598909 GATTCTGACT
* *
598919 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
598960 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
599001 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
599041 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
599081 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
599122 ATCGCAACG
1 ATCGCAACG
599131 CGATTTTTAA
Statistics
Matches: 161, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 76 0.47
41 85 0.53
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.18
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:599715 original size:20 final size:19
Alignment explanation
Indices: 599690--599761 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 19
599680 TTCTAAACTT
599690 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
599710 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
599730 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
599751 AAAATCGCAAC
1 AAAATCGCAAC
599762 GATAGAATCG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:599810 original size:19 final size:19
Alignment explanation
Indices: 599788--599900 Score: 101
Period size: 20 Copynumber: 6.1 Consensus size: 19
599778 GAAACCAAAA
*
599788 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
599807 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
599821 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
**
599840 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
599859 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
599879 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
599899 TC
1 TC
599901 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 3 0.04
19 28 0.36
20 33 0.43
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:603358 original size:14 final size:14
Alignment explanation
Indices: 603339--603374 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
603329 ATTGTTTAAT
603339 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
603353 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
603367 TGATTTGT
1 TGATTTGT
603375 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:603503 original size:19 final size:19
Alignment explanation
Indices: 603481--603579 Score: 67
Period size: 19 Copynumber: 5.7 Consensus size: 19
603471 AAAAATGACT
603481 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
603500 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
603514 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
603533 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
* *
603547 ATCACAACGCGAAACT-AAA
1 ATCGCAATGCGAAA-TGAAA
603566 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
603580 CTAAATTCGT
Statistics
Matches: 61, Mismatches: 8, Indels: 22
0.67 0.09 0.24
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:603523 original size:33 final size:33
Alignment explanation
Indices: 603481--603572 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
603471 AAAAATGACT
* *
603481 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
603514 ATCGCAATGCAAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
603547 ATCACAACGCGAAACT-AAAATCGCAA
1 ATCGCAATGCGAAA-TGAAAATCGCAA
603573 TGCGAAACTA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 51 0.98
34 1 0.02
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:603633 original size:33 final size:33
Alignment explanation
Indices: 603591--603682 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
603581 TAAATTCGTG
* * *
603591 TTGCGATTTTAATTTCGCTTTGTGATTCCCTCA
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCA
* *
603624 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCA
603657 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
603683 AGTCATTTCC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCCTCA
Found at i:603646 original size:19 final size:19
Alignment explanation
Indices: 603622--603736 Score: 106
Period size: 19 Copynumber: 6.5 Consensus size: 19
603612 GTGATTCCCT
603622 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
603641 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
603657 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
**
603674 CATTGCGATAGTCATTTCCG
1 CATTGCGATTTTCATTT-CG
*
603694 CGTTGCGATTTTCA---CG
1 CATTGCGATTTTCATTTCG
*
603710 --TTACGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
603727 CATTGCGATT
1 CATTGCGATT
603737 CTCTCGTTGC
Statistics
Matches: 76, Mismatches: 9, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
14 17 0.22
16 9 0.12
17 9 0.12
19 28 0.37
20 13 0.17
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:603720 original size:53 final size:52
Alignment explanation
Indices: 603622--603735 Score: 165
Period size: 53 Copynumber: 2.2 Consensus size: 52
603612 GTGATTCCCT
** * *
603622 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCG
1 CATTGCGATAGTCATTTCGCATTGCGATTCTCACGTTACGATTTTCATTTCG
* *
603674 CATTGCGATAGTCATTTCCGCGTTGCGATTTTCACGTTACGATTTTCATTTCG
1 CATTGCGATAGTCATTT-CGCATTGCGATTCTCACGTTACGATTTTCATTTCG
603727 CATTGCGAT
1 CATTGCGAT
603736 TCTCTCGTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
52 15 0.27
53 40 0.73
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (52 bp):
CATTGCGATAGTCATTTCGCATTGCGATTCTCACGTTACGATTTTCATTTCG
Found at i:603768 original size:34 final size:34
Alignment explanation
Indices: 603676--603769 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
603666 TCATTTCGCA
* *
603676 TTGCGATAGTCATTTCCGCGTTGCGATTTTCACG
1 TTGCGATAGTCATTTCCGCATTGCGATTCTCACG
* ** *
603710 TTACGATTTTCATTT-CGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTCCGCATTGCGATTCTCACG
*
603743 TTGCGATAGTAATTTCCGCATTGCGAT
1 TTGCGATAGTCATTTCCGCATTGCGAT
603770 AGACATTAAG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
33 26 0.53
34 23 0.47
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.40
Consensus pattern (34 bp):
TTGCGATAGTCATTTCCGCATTGCGATTCTCACG
Found at i:603815 original size:20 final size:20
Alignment explanation
Indices: 603742--603815 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
603732 CGATTCTCTC
* *
603742 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* * **
603762 ATTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
603782 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
603803 GTTGCGATAGTCA
1 GTTGCGATAGTCA
603816 AATGAATGCC
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
19 3 0.08
20 21 0.54
21 12 0.31
22 3 0.08
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:606339 original size:24 final size:24
Alignment explanation
Indices: 606272--606331 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
606262 CTGAAAAATC
*
606272 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAATTTCGAGTATTGACCAAG
* *
606296 ATCAAATTCCGGGTATTGACCAAG
1 ATCAAATTTCGAGTATTGACCAAG
606320 ATCAAATTTCGA
1 ATCAAATTTCGA
606332 ATACTGACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (24 bp):
ATCAAATTTCGAGTATTGACCAAG
Found at i:607203 original size:20 final size:20
Alignment explanation
Indices: 607188--607239 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
607178 AGAATCTCGT
607188 TGCGATTACGTAAATCGAAA
1 TGCGATTACGTAAATCGAAA
*
607208 TGCGATTACGTAAATCGTAA
1 TGCGATTACGTAAATCGAAA
*
607228 TGCGAATACGTA
1 TGCGATTACGTA
607240 TTCGCGTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (20 bp):
TGCGATTACGTAAATCGAAA
Found at i:607271 original size:20 final size:20
Alignment explanation
Indices: 607188--607274 Score: 81
Period size: 20 Copynumber: 4.4 Consensus size: 20
607178 AGAATCTCGT
*
607188 TGCG-ATTACGTAAATCGAAA
1 TGCGAATTACGT-AATCGCAA
*
607208 TGCG-ATTACGTAAATCGTAA
1 TGCGAATTACGT-AATCGCAA
* **
607228 TGCGAA-TACGTATTCGCGT
1 TGCGAATTACGTAATCGCAA
607247 TGCGAATTACGTAATCGCAA
1 TGCGAATTACGTAATCGCAA
*
607267 CGCGAATT
1 TGCGAATT
607275 TGGAAAATCG
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 10 0.18
20 45 0.80
21 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCGAATTACGTAATCGCAA
Found at i:607285 original size:21 final size:21
Alignment explanation
Indices: 607259--607313 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
607249 CGAATTACGT
607259 AATCGCAACGCGAATTTGGAA
1 AATCGCAACGCGAATTTGGAA
*
607280 AATCGCAACGCGAATTTGGGA
1 AATCGCAACGCGAATTTGGAA
*
607301 AATCGCAATGCGA
1 AATCGCAACGCGA
607314 TAGTCAGAAT
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:0.36, C:0.20, G:0.25, T:0.18
Consensus pattern (21 bp):
AATCGCAACGCGAATTTGGAA
Found at i:608895 original size:2 final size:2
Alignment explanation
Indices: 608888--608915 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
608878 ATGTGATAGA
608888 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
608916 CGTTAATTTA
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:609243 original size:20 final size:20
Alignment explanation
Indices: 609206--609245 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
609196 AATGTTAACT
*
609206 TGTGATTGTATTCATGAGAG
1 TGTGATTGTATGCATGAGAG
*
609226 TGTGATTGTATGCGTGAGAG
1 TGTGATTGTATGCATGAGAG
609246 AGTAAGAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.35, T:0.38
Consensus pattern (20 bp):
TGTGATTGTATGCATGAGAG
Found at i:618345 original size:14 final size:14
Alignment explanation
Indices: 618314--618351 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
618304 AAAGTTGTTC
*
618314 GAAAGAAAAAGAGA
1 GAAAGAAAAAGACA
618328 GAAA-AAAAAGACA
1 GAAAGAAAAAGACA
618341 TGAAAGAAAAA
1 -GAAAGAAAAA
618352 AAATGGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 8 0.38
14 8 0.38
15 5 0.24
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.03
Consensus pattern (14 bp):
GAAAGAAAAAGACA
Found at i:622439 original size:18 final size:19
Alignment explanation
Indices: 622408--622450 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
622398 ATCAACATCA
*
622408 TCATCTTCACCAC-ATGAT
1 TCATCTTCACCACAATAAT
* *
622426 TCATCTTGATCACAATAAT
1 TCATCTTCACCACAATAAT
622445 TCATCT
1 TCATCT
622451 CATCTCCATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.37
Consensus pattern (19 bp):
TCATCTTCACCACAATAAT
Found at i:625804 original size:2 final size:2
Alignment explanation
Indices: 625797--625830 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
625787 ATCCTTGATA
625797 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
625831 GATGTGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:627576 original size:23 final size:23
Alignment explanation
Indices: 627506--627582 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
627496 AAACATGATC
*
627506 ATGAACACGTTCATGAACATATAA
1 ATGAACATGTTCATGAACA-ATAA
* * * *
627530 ACGAACATGTTCACGAATATTAA
1 ATGAACATGTTCATGAACAATAA
* *
627553 ATGAAGATGTTCGTGAACAATAA
1 ATGAACATGTTCATGAACAATAA
*
627576 ATAAACA
1 ATGAACA
627583 AATAAAAACA
Statistics
Matches: 40, Mismatches: 13, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
23 25 0.62
24 15 0.38
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (23 bp):
ATGAACATGTTCATGAACAATAA
Found at i:636267 original size:13 final size:13
Alignment explanation
Indices: 636249--636305 Score: 71
Period size: 13 Copynumber: 4.4 Consensus size: 13
636239 TCAATTCACA
*
636249 TCATAAATGAGCG
1 TCATAAATGAGTG
*
636262 TCATAAATGTGTG
1 TCATAAATGAGTG
*
636275 TCATAAATGCGTG
1 TCATAAATGAGTG
636288 TCATAAATGCA-TG
1 TCATAAATG-AGTG
636301 TCATA
1 TCATA
636306 GATTTGTGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (13 bp):
TCATAAATGAGTG
Found at i:636745 original size:20 final size:19
Alignment explanation
Indices: 636701--636774 Score: 53
Period size: 20 Copynumber: 3.7 Consensus size: 19
636691 ACTTATAAAA
636701 AAAT-ATATTAAAAATATT
1 AAATAATATTAAAAATATT
**
636719 AAGATAATATTAATGATATT
1 AA-ATAATATTAAAAATATT
*
636739 GAAATAAATGATCAAAAA-ATAT
1 -AAAT-AAT-ATTAAAAATAT-T
*
636761 AAAAAATATTAAAA
1 AAATAATATTAAAA
636775 TGTGTTAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
18 2 0.05
19 8 0.19
20 17 0.40
21 10 0.23
22 6 0.14
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.31
Consensus pattern (19 bp):
AAATAATATTAAAAATATT
Found at i:639854 original size:17 final size:20
Alignment explanation
Indices: 639816--639858 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
639806 ACCTATTCTG
639816 AAATAATAACATAGATAGAA
1 AAATAATAACATAGATAGAA
639836 AAATAATAA-ATAGA-A-AA
1 AAATAATAACATAGATAGAA
639853 AAATAA
1 AAATAA
639859 ACATTCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.35
18 1 0.04
19 5 0.22
20 9 0.39
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (20 bp):
AAATAATAACATAGATAGAA
Found at i:639857 original size:14 final size:15
Alignment explanation
Indices: 639830--639859 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
639820 AATAACATAG
639830 ATAGAAAAATAATAA
1 ATAGAAAAATAATAA
639845 ATAGAAAAA-AATAA
1 ATAGAAAAATAATAA
639859 A
1 A
639860 CATTCATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
ATAGAAAAATAATAA
Found at i:639925 original size:32 final size:30
Alignment explanation
Indices: 639834--639926 Score: 73
Period size: 32 Copynumber: 2.8 Consensus size: 30
639824 ACATAGATAG
639834 AAAAATAATAAATAGAAAAAAATAAACATTCATTA
1 AAAAATAAT-AATAG-AAAAAAT---CATTCATTA
639869 AAAAAT-A-AATAGAAAATCCCAATCATTCATTCA
1 AAAAATAATAATAGAAAA----AATCATTCATT-A
639902 AAAAATAATATATAGAAAAAATCAT
1 AAAAATAATA-ATAGAAAAAATCAT
639927 CACACTCATT
Statistics
Matches: 50, Mismatches: 0, Indels: 19
0.72 0.00 0.28
Matches are distributed among these distances:
31 4 0.08
32 19 0.38
33 7 0.14
34 2 0.04
35 10 0.20
36 8 0.16
ACGTcount: A:0.63, C:0.10, G:0.03, T:0.24
Consensus pattern (30 bp):
AAAAATAATAATAGAAAAAATCATTCATTA
Found at i:643230 original size:23 final size:24
Alignment explanation
Indices: 643200--643253 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
643190 TTATATGTTA
**
643200 GGTATGGATTA-ACAGGGTATCAG
1 GGTATGGATTACACAGGACATCAG
*
643223 GGTATGGATTACACAGGACATCAT
1 GGTATGGATTACACAGGACATCAG
643247 GGTATGG
1 GGTATGG
643254 TCCAGGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.30, C:0.11, G:0.33, T:0.26
Consensus pattern (24 bp):
GGTATGGATTACACAGGACATCAG
Found at i:645273 original size:14 final size:15
Alignment explanation
Indices: 645254--645282 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
645244 TTTATACAAA
645254 AAAATAAAA-TAAAT
1 AAAATAAAACTAAAT
645268 AAAATAAAACTAAAT
1 AAAATAAAACTAAAT
645283 TCAATTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAAAACTAAAT
Found at i:645997 original size:25 final size:28
Alignment explanation
Indices: 645955--646014 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
645945 ATGTTATCTA
645955 TATTATATAAACATTTAT-TATTATTAT
1 TATTATATAAACATTTATATATTATTAT
* *
645982 TATTATAT-TACATTATACATATTATTAT
1 TATTATATAAACATT-TATATATTATTAT
646010 TATTA
1 TATTA
646015 CAATAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 5 0.17
27 10 0.34
28 14 0.48
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (28 bp):
TATTATATAAACATTTATATATTATTAT
Found at i:646736 original size:23 final size:23
Alignment explanation
Indices: 646710--646757 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
646700 GGCCACCATC
*
646710 CATGGAGGTCGGCAGTGGCAGCT
1 CATGGAGGCCGGCAGTGGCAGCT
* * *
646733 CATGGTGGCCGGCGGTGGCGGCT
1 CATGGAGGCCGGCAGTGGCAGCT
646756 CA
1 CA
646758 CGGTGGCTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.12, C:0.25, G:0.46, T:0.17
Consensus pattern (23 bp):
CATGGAGGCCGGCAGTGGCAGCT
Found at i:646762 original size:23 final size:23
Alignment explanation
Indices: 646719--646764 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
646709 CCATGGAGGT
*
646719 CGGCAGTGGCAGCTCATGGTGGC
1 CGGCAGTGGCAGCTCACGGTGGC
* *
646742 CGGCGGTGGCGGCTCACGGTGGC
1 CGGCAGTGGCAGCTCACGGTGGC
646765 TGGCCGTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.28, G:0.48, T:0.15
Consensus pattern (23 bp):
CGGCAGTGGCAGCTCACGGTGGC
Found at i:651448 original size:96 final size:99
Alignment explanation
Indices: 651328--651521 Score: 286
Period size: 99 Copynumber: 2.0 Consensus size: 99
651318 TAATATTATA
* * * * *
651328 TATACAATAAATCTTGAGTTGTCCCTCTAGAGCAATTGATT-AA-ACCCC-TCTTTATGGATAAG
1 TATACAATAAAGCTAGAGCTGTCCCTCTAGAGCAATTGATTAAATACCCCGGCTCTATGGATAAG
* *
651390 ATTCAGCTAGCCTGATTAAGGTGATTATAATATC
66 ATTCAGCTAACCTGATAAAGGTGATTATAATATC
*
651424 TATACAATAAAGCTAGAGCTGTCCCTCTAGAGCAATTGGTTAAATACCCCGGCTCTATGGATAAG
1 TATACAATAAAGCTAGAGCTGTCCCTCTAGAGCAATTGATTAAATACCCCGGCTCTATGGATAAG
*
651489 ATTCAGTTAACCTGATAAAGGTGATTATAATAT
66 ATTCAGCTAACCTGATAAAGGTGATTATAATAT
651522 TGAGTTATCC
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
96 37 0.43
97 2 0.02
98 5 0.06
99 42 0.49
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (99 bp):
TATACAATAAAGCTAGAGCTGTCCCTCTAGAGCAATTGATTAAATACCCCGGCTCTATGGATAAG
ATTCAGCTAACCTGATAAAGGTGATTATAATATC
Found at i:652853 original size:85 final size:83
Alignment explanation
Indices: 652706--653642 Score: 1091
Period size: 83 Copynumber: 11.3 Consensus size: 83
652696 CTATTTGCAT
* * * *
652706 CATAGCTCAAGGCAAGAAAGGTTATCTGCCAGTAAAAACCTTCGAGTTCGATTACACTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCA--AAAAACCTTCGAGTTCGATTACATTCAGCTCA
*
652771 AGGACATATCAAATTTACAG
64 AGGGCATATCAAATTTACAG
* * *
652791 CATCGCTCAAGGCCAGAAGGGCTATCTGTCAATAAAGACCTTCGAGTTCGATTACATTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAA-AAA-ACCTTCGAGTTCGATTACATTCAGCTCA
*
652856 AGGGCATATCAAATTTACAA
64 AGGGCATATCAAATTTACAG
* * * *
652876 TATAGCTC-AGGCGAGAAGGGTTATTTGTCAACAAACCTTCAAGTTCGATTACATTCAGCTCAAG
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAG
652940 GGCATATCAAATTTACAG
66 GGCATATCAAATTTACAG
* * ** * * * * *
652958 TATAGCTCAAGGTGAGAAGGACTATCTATCAATAAATCTTTGAGTTCGATTACATTCAACTCAAG
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAG
*
653023 GGCATATCAAATTTACCG
66 GGCATATCAAATTTACAG
* * ** *
653041 CATAGCTCAAGACGAGAAGGGCTATCTGT-AAAAATATGTTCGAGTTCGATTACACTCAGCTCAA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAAAAA-ACCTTCGAGTTCGATTACATTCAGCTCAA
* *
653105 GGACATATCAAATTTATAG
65 GGGCATATCAAATTTACAG
* * *
653124 CATAGCTCAAGGCGAGAAGGGTTATATGTCAACAAAGGCCTTCGAGTTCGATTACATTCAGCTTA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAA-AAA-ACCTTCGAGTTCGATTACATTCAGCTCA
653189 AGGGCATATCAAATTTACAG
64 AGGGCATATCAAATTTACAG
* * * * * * * * * *
653209 CATAGCTCGAGACCAGAAGGGCTATCTGTTAACAAACCTTTGAGTTCGATTAAACTCAACTCAAG
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAG
* *
653274 GACATATCAAATTTACAA
66 GGCATATCAAATTTACAG
* * * *
653292 CATAGCTCAAGACGAGAAGGGTTATCTGTAAAAAAACCTTCAAGTTCGATTACACTCAGCTCAAG
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAG
*
653357 GACATATCAAATTTACAG
66 GGCATATCAAATTTACAG
* ** * *
653375 CATAGCTCAAGGCGAGAAAGACTATCTGTCAACAAAGACCTTTGAGTTTGATTACATTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAA-AAA-ACCTTCGAGTTCGATTACATTCAGCTCA
*
653440 AGGGCATATCAAATTTACAA
64 AGGGCATATCAAATTTACAG
* * * * * *
653460 CATAGTTCATGACGAGAAGGGTTATCTGT--ACAAA-TTTCGAGTTCGATTACATTAAGCTCAAG
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAG
*
653522 GACATATCAAATTTACAG
66 GGCATATCAAATTTACAG
* * *
653540 CATAACTCAAGGCGAGAAGGGTTA-CATGTCCAAAAATACCTTTGAGTTCGATTCCATTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGTTATC-TGT-CAAAAA-ACCTTCGAGTTCGATTACATTCAGCTC
*
653604 AAGGGCATGTCAAATTT--A-
63 AAGGGCATATCAAATTTACAG
*
653622 CATAGCTCAAGGCGAAAAGGG
1 CATAGCTCAAGGCGAGAAGGG
653643 CTATTGACAA
Statistics
Matches: 725, Mismatches: 113, Indels: 31
0.83 0.13 0.04
Matches are distributed among these distances:
79 1 0.00
80 63 0.09
81 1 0.00
82 79 0.11
83 302 0.42
84 31 0.04
85 248 0.34
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (83 bp):
CATAGCTCAAGGCGAGAAGGGTTATCTGTCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAG
GGCATATCAAATTTACAG
Found at i:653254 original size:251 final size:249
Alignment explanation
Indices: 652741--653656 Score: 1156
Period size: 251 Copynumber: 3.7 Consensus size: 249
652731 CTGCCAGTAA
* * * * *
652741 AAACCTTCGAGTTCGATTACACTCAGCTCAAGGACATATCAAATTTACAGCATCGCTCAAGGCCA
1 AAACCTTTGAGTTCGATTACACTCAACTCAAGGACATATCAAATTTACAGCATAGCTCAAGACGA
* * *
652806 GAAGGGCTATCTGTCAATAAAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATT
66 GAAGGGCTATCTGTCAA-AAATACCTTCGAGTTCGATTACACTCAGCTCAAGGACATATCAAATT
** * *
652871 TACAATATAGCTC-AGGCGAGAAGGGTTATTTGTCAACAAA-CCTTCAAGTTCGATTACATTCAG
130 TACAGCATAGCTCAAGGCGAGAAGGGCTA-TTGTCAACAAAGCCTTCGAGTTCGATTACATTCAG
* ** * * * *
652934 CTCAAGGGCATATCAAATTTACAGTATAGCTCAAGGTGAGAAGGACTATCTATCAAT
194 CTCAAGGGCATATCAAATTTACAGCATAGCTC-AGACGAGAAGGGCTATCTGTTAAC
* * * *
652991 AAATCTTTGAGTTCGATTACATTCAACTCAAGGGCATATCAAATTTACCGCATAGCTCAAGACGA
1 AAACCTTTGAGTTCGATTACACTCAACTCAAGGACATATCAAATTTACAGCATAGCTCAAGACGA
**
653056 GAAGGGCTATCTGT-AAAAATATGTTCGAGTTCGATTACACTCAGCTCAAGGACATATCAAATTT
66 GAAGGGCTATCTGTCAAAAATACCTTCGAGTTCGATTACACTCAGCTCAAGGACATATCAAATTT
* *
653120 ATAGCATAGCTCAAGGCGAGAAGGGTTATATGTCAACAAAGGCCTTCGAGTTCGATTACATTCAG
131 ACAGCATAGCTCAAGGCGAGAAGGGCTAT-TGTCAACAAA-GCCTTCGAGTTCGATTACATTCAG
* *
653185 CTTAAGGGCATATCAAATTTACAGCATAGCTCGAGACCAGAAGGGCTATCTGTTAAC
194 CTCAAGGGCATATCAAATTTACAGCATAGCTC-AGACGAGAAGGGCTATCTGTTAAC
* *
653242 AAACCTTTGAGTTCGATTAAACTCAACTCAAGGACATATCAAATTTACAACATAGCTCAAGACGA
1 AAACCTTTGAGTTCGATTACACTCAACTCAAGGACATATCAAATTTACAGCATAGCTCAAGACGA
* * *
653307 GAAGGGTTATCTGT-AAAAAAACCTTCAAGTTCGATTACACTCAGCTCAAGGACATATCAAATTT
66 GAAGGGCTATCTGTCAAAAATACCTTCGAGTTCGATTACACTCAGCTCAAGGACATATCAAATTT
* * * *
653371 ACAGCATAGCTCAAGGCGAGAAAGACTATCTGTCAACAAAGACCTTTGAGTTTGATTACATTCAG
131 ACAGCATAGCTCAAGGCGAGAAGGGCTAT-TGTCAACAAAG-CCTTCGAGTTCGATTACATTCAG
* * *
653436 CTCAAGGGCATATCAAATTTACAACATAGTTCATGACGAGAAGGGTTATCTG-T-AC
194 CTCAAGGGCATATCAAATTTACAGCATAGCTCA-GACGAGAAGGGCTATCTGTTAAC
* * *
653491 AAA--TTTCGAGTTCGATTACA-TTAAGCTCAAGGACATATCAAATTTACAGCATAACTCAAGGC
1 AAACCTTT-GAGTTCGATTACACTCAA-CTCAAGGACATATCAAATTTACAGCATAGCTCAAGAC
* * * * * *
653553 GAGAAGGGTTA-CATGTCCAAAAATACCTTTGAGTTCGATTCCATTCAGCTCAAGGGCATGTCAA
64 GAGAAGGGCTATC-TGT-CAAAAATACCTTCGAGTTCGATTACACTCAGCTCAAGGACATATCAA
* *
653617 ATTT--A-CATAGCTCAAGGCGAAAAGGGCTATTGACAACAAA
127 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATTGTCAACAAA
653657 AAATTTTCGA
Statistics
Matches: 588, Mismatches: 67, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
246 9 0.02
247 29 0.05
248 114 0.19
249 32 0.05
250 116 0.20
251 288 0.49
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (249 bp):
AAACCTTTGAGTTCGATTACACTCAACTCAAGGACATATCAAATTTACAGCATAGCTCAAGACGA
GAAGGGCTATCTGTCAAAAATACCTTCGAGTTCGATTACACTCAGCTCAAGGACATATCAAATTT
ACAGCATAGCTCAAGGCGAGAAGGGCTATTGTCAACAAAGCCTTCGAGTTCGATTACATTCAGCT
CAAGGGCATATCAAATTTACAGCATAGCTCAGACGAGAAGGGCTATCTGTTAAC
Found at i:654462 original size:3 final size:3
Alignment explanation
Indices: 654454--654504 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
654444 TATATAAACG
654454 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
654500 TAT TA
1 TAT TA
654505 CAATAAATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:655322 original size:27 final size:29
Alignment explanation
Indices: 655262--655327 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
655252 AGGAAATCCT
655262 AGAGAGAATGGAGAGCTTCTCTCTCTAAG
1 AGAGAGAATGGAGAGCTTCTCTCTCTAAG
*
655291 AGAGAGAATGGAGAGCTTCTCTCTCTACG
1 AGAGAGAATGGAGAGCTTCTCTCTCTAAG
655320 AGAGAGAA
1 AGAGAGAA
655328 GCAAAGTGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (29 bp):
AGAGAGAATGGAGAGCTTCTCTCTCTAAG
Found at i:656058 original size:15 final size:16
Alignment explanation
Indices: 656024--656064 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
656014 AACGCAATCC
656024 AATT-TTTTGTCTTAAA
1 AATTATTTT-TCTTAAA
656040 AATTATTTTTCTT-AA
1 AATTATTTTTCTTAAA
656055 AATTATTTTT
1 AATTATTTTT
656065 AAAAGACGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.50
16 8 0.33
17 4 0.17
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (16 bp):
AATTATTTTTCTTAAA
Done.