Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008717.1 Hibiscus syriacus cultivar Beakdansim tig00111772_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: 3453450
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 16
Found at i:1464082 original size:12 final size:12
Alignment explanation
Indices: 1464065--1464102 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1464055 AATCCCCCTA
1464065 CTACATTCTCTT
1 CTACATTCTCTT
*
1464077 CTACATTTTCTT
1 CTACATTCTCTT
*
1464089 CTTCATTCTCTT
1 CTACATTCTCTT
1464101 CT
1 CT
1464103 TCCTCCTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.13, C:0.32, G:0.00, T:0.55
Consensus pattern (12 bp):
CTACATTCTCTT
Found at i:1464127 original size:21 final size:21
Alignment explanation
Indices: 1464088--1464127 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1464078 TACATTTTCT
* *
1464088 TCTTCATTCTCTTCTTCCTCC
1 TCTTCATTCTCTACATCCTCC
*
1464109 TCTTCCTTCTCTACATCCT
1 TCTTCATTCTCTACATCCT
1464128 TGCCAATAAC
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:0.07, C:0.42, G:0.00, T:0.50
Consensus pattern (21 bp):
TCTTCATTCTCTACATCCTCC
Found at i:1466877 original size:204 final size:194
Alignment explanation
Indices: 1466368--1466936 Score: 562
Period size: 204 Copynumber: 2.9 Consensus size: 194
1466358 TCAATACTTT
* * *
1466368 TGTGTAAGGTATCGATACTTTTGATACGTTTTCATTTTTTCCATTTCTTTTCAATTCCTAAAGTA
1 TGTGTAAGGTATCGATAC-TTTAAGAC-TTTTCATTTTTT-CATTT-TTTTTAATTCCTAAAGTA
* * * * * * *
1466433 CTGATACTATGATACATA-ACCTTATAAAAGTATTGATACCG--TT-AACATATCCCGTAGT-GC
62 C-GATACTTTGGTACATATA-CTTATAAAAGTATCGATACAGATTTCAACAT-TTCGGTA-TCTC
* * *
1466493 TTTACCGATTTTGTCATATTGAAATTGGTTTTGTCAAATTTTAACCTGTTATATTGTCATTTATC
123 TTTATCGATTTTGTCAAATTGAAA-TGGTTTTGTCAAATTTCAACCTGTTATATTGTCATTTATC
1466558 GATACATG
187 GATACATG
* * ** * * * *
1466566 TGTCTAAGGTATCGATACTTTATAGGC-GCT-ATTGTTGCA-ATTTTTTAATTCATAAAGTACCG
1 TGTGTAAGGTATCGATACTTTA-AGACTTTTCATTTTTTCATTTTTTTTAATTCCTAAAGTA-CG
* *
1466628 ATACTTTGGTGCATATACTTATAAAAGTATCGATACAAATTTCAACCATTTCGGTATCTCTTTAT
64 ATACTTTGGTACATATACTTATAAAAGTATCGATACAGATTTCAA-CATTTCGGTATCTCTTTAT
* * * *
1466693 CGGTTTTGTCAAACTGAAACTGATTTTGTCAAACTTCAACCTGTTATATTGTCATGTATCGATCG
128 CGATTTTGTCAAATTGAAA-TGGTTTTGTCAAATTTCAACCTGTTATATTGTCAT-T-T--ATCG
1466758 ATACATG
188 ATACATG
* *
1466765 TGTGTAAGGTATCGATACTTTCAAGACATTTTCCTTTTTTCATTTTTTTTAAATTCCTACAGTAT
1 TGTGTAAGGTATCGATACTTT-AAGAC-TTTTCATTTTTTCATTTTTTTT-AATTCCTAAAGTA-
* * * *
1466830 CGATACTTTGGTACATATACTTATACATGTATCGATACAGATTTCAACAATTCTGGTAGCTCTTT
62 CGATACTTTGGTACATATACTTATAAAAGTATCGATACAGATTTCAACATTTC-GGTATCTCTTT
*
1466895 AT-GATTTTCTCAAATTGAAATCGGTTTTGTCAAATTTCAACC
126 ATCGATTTTGTCAAATTGAAAT-GGTTTTGTCAAATTTCAACC
1466937 AGTTTTGTCA
Statistics
Matches: 301, Mismatches: 50, Indels: 35
0.78 0.13 0.09
Matches are distributed among these distances:
192 47 0.16
193 3 0.01
194 5 0.02
195 65 0.22
196 5 0.02
197 4 0.01
198 19 0.06
199 34 0.11
200 1 0.00
201 1 0.00
202 7 0.02
203 44 0.15
204 66 0.22
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (194 bp):
TGTGTAAGGTATCGATACTTTAAGACTTTTCATTTTTTCATTTTTTTTAATTCCTAAAGTACGAT
ACTTTGGTACATATACTTATAAAAGTATCGATACAGATTTCAACATTTCGGTATCTCTTTATCGA
TTTTGTCAAATTGAAATGGTTTTGTCAAATTTCAACCTGTTATATTGTCATTTATCGATACATG
Found at i:1466927 original size:20 final size:20
Alignment explanation
Indices: 1466899--1466990 Score: 76
Period size: 20 Copynumber: 4.6 Consensus size: 20
1466889 CTCTTTATGA
* *
1466899 TTTTCTCAAATTGAAATCGG
1 TTTTGTCAAATTGAAACCGG
** *
1466919 TTTTGTCAAATTTCAACCAG
1 TTTTGTCAAATTGAAACCGG
* ** **
1466939 TTTTGTCAATTTCCAATTGG
1 TTTTGTCAAATTGAAACCGG
1466959 TTTTGTCAAATTGAAACCGG
1 TTTTGTCAAATTGAAACCGG
* *
1466979 ATTTCTCAAATT
1 TTTTGTCAAATT
1466991 TCAACCTGTT
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.42
Consensus pattern (20 bp):
TTTTGTCAAATTGAAACCGG
Found at i:1466996 original size:20 final size:20
Alignment explanation
Indices: 1466916--1466996 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
1466906 AAATTGAAAT
1466916 CGGTTTTGTCAAATTTCAAC
1 CGGTTTTGTCAAATTTCAAC
* *
1466936 CAGTTTTGTC-AATTTCCAAT
1 CGGTTTTGTCAAATTT-CAAC
* **
1466956 TGGTTTTGTCAAATTGAAAC
1 CGGTTTTGTCAAATTTCAAC
* *
1466976 CGGATTTCTCAAATTTCAAC
1 CGGTTTTGTCAAATTTCAAC
1466996 C
1 C
1466997 TGTTATATTA
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
19 5 0.11
20 38 0.81
21 4 0.09
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (20 bp):
CGGTTTTGTCAAATTTCAAC
Found at i:1467419 original size:2 final size:2
Alignment explanation
Indices: 1467412--1467441 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1467402 ATATTCAATA
1467412 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
1467442 GAGATAGGAT
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:1467671 original size:2 final size:2
Alignment explanation
Indices: 1467664--1467730 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1467654 GATCATGTTC
1467664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1467706 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1467731 ACAAAGAATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1468441 original size:20 final size:21
Alignment explanation
Indices: 1468416--1468455 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1468406 CTCTGTATAG
1468416 TAGTATCGATACCA-TAGGCA
1 TAGTATCGATACCATTAGGCA
1468436 TAGTATCGATACCATTAGGC
1 TAGTATCGATACCATTAGGC
1468456 CCCAACGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATTAGGCA
Found at i:1472112 original size:2 final size:2
Alignment explanation
Indices: 1472105--1472180 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
1472095 TGACACATTC
1472105 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1472147 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
1472181 CTCGAAGGCC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1475103 original size:8 final size:7
Alignment explanation
Indices: 1475090--1475135 Score: 56
Period size: 8 Copynumber: 6.1 Consensus size: 7
1475080 CCCATAAATA
1475090 ATTATAT
1 ATTATAT
1475097 GATTATAT
1 -ATTATAT
1475105 ATATATAT
1 AT-TATAT
1475113 ATATATAT
1 AT-TATAT
1475121 ATTATAT
1 ATTATAT
*
1475128 AATATAT
1 ATTATAT
1475135 A
1 A
1475136 ATGTTATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
7 14 0.39
8 22 0.61
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (7 bp):
ATTATAT
Found at i:1475107 original size:2 final size:2
Alignment explanation
Indices: 1475100--1475135 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1475090 ATTATATGAT
1475100 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1475136 ATGTTATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1476022 original size:12 final size:13
Alignment explanation
Indices: 1476005--1476058 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 13
1475995 CGTTTTTTTG
1476005 TTTTTT-TATTAT
1 TTTTTTATATTAT
1476017 TTTTTTAATATTAT
1 TTTTTT-ATATTAT
1476031 ATTTTTTATATTAT
1 -TTTTTTATATTAT
1476045 TTTCTTTAGTATTA
1 TTT-TTTA-TATTA
1476059 ATATTATATG
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.16
13 3 0.08
14 17 0.46
15 11 0.30
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (13 bp):
TTTTTTATATTAT
Found at i:1476044 original size:28 final size:29
Alignment explanation
Indices: 1476005--1476063 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
1475995 CGTTTTTTTG
1476005 TTTTTTTATTATTTT-TTTAATATT-ATA
1 TTTTTTTATTATTTTCTTTAATATTAATA
*
1476032 TTTTTTATATTATTTTCTTTAGTATTAATA
1 TTTTTT-TATTATTTTCTTTAATATTAATA
1476062 TT
1 TT
1476064 ATATGTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 6 0.21
28 9 0.32
29 8 0.29
30 5 0.18
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (29 bp):
TTTTTTTATTATTTTCTTTAATATTAATA
Found at i:1476179 original size:15 final size:16
Alignment explanation
Indices: 1476149--1476196 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
1476139 ATATATTATT
*
1476149 TTTATTATTTTATTTTC
1 TTTATTA-TCTATTTTC
1476166 TTTA-TATCTATTTTC
1 TTTATTATCTATTTTC
1476181 TTTATTTATCTATTTT
1 TTTA-TTATCTATTTT
1476197 TATTTTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 12 0.43
16 2 0.07
17 14 0.50
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATTATCTATTTTC
Found at i:1476192 original size:17 final size:15
Alignment explanation
Indices: 1476159--1476196 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 15
1476149 TTTATTATTT
1476159 TATTTTCTTTATATC
1 TATTTTCTTTATATC
1476174 TATTTTCTTTATTTATC
1 TATTTTCTTTA--TATC
1476191 TATTTT
1 TATTTT
1476197 TATTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.52
17 10 0.48
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTCTTTATATC
Found at i:1476220 original size:4 final size:4
Alignment explanation
Indices: 1476211--1476479 Score: 84
Period size: 4 Copynumber: 62.8 Consensus size: 4
1476201 TTTTCTTGCT
* * *
1476211 TTTA TTTA TTTA TTTA -TTA TGTA TATA TTATT TTTA CTATTA TTT- TCCTTCA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA -T-TTA TTTA T--TT-A
* * * *
1476263 TTTTA TTTA TTTCA TTTT TTTCT TTTC TTTA TTT- TTTA TTT- TTTG TTTA
1 -TTTA TTTA TTT-A TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * *
1476312 TTTTG TTTA TTTT TTTG TTTA TTTA TTTTA TTTT TTTA TTTTA TTTA TGTTTC
1 -TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA -TTTA TTTA --TTTA
* *
1476365 TTTA TTTTCA TTTTG TTTA TTTTA TTTA CTTT- TTATC TTTA TTTCA -TTA
1 TTTA -TTT-A -TTTA TTTA -TTTA TTTA -TTTA TT-TA TTTA TTT-A TTTA
* * * * *
1476414 TTTT TATTA TTT- TTTC TTTA CTCA TTTTA TTTTA TTTC TTTA TTTCA
1 TTTA T-TTA TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA TTT-A
*
1476461 TTTG TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTT
1476480 TTATTACCTT
Statistics
Matches: 203, Mismatches: 32, Indels: 60
0.69 0.11 0.20
Matches are distributed among these distances:
3 16 0.08
4 119 0.59
5 54 0.27
6 13 0.06
8 1 0.00
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:1476281 original size:15 final size:14
Alignment explanation
Indices: 1476263--1476484 Score: 72
Period size: 14 Copynumber: 15.5 Consensus size: 14
1476253 TTTTCCTTCA
1476263 TTTTATTTATTTCA-
1 TTTTATTTATTT-AT
*
1476277 TTTT-TTTCTTT-T
1 TTTTATTTATTTAT
*
1476289 CTTTATTT-TTTATT
1 TTTTATTTATTTA-T
*
1476303 TTTTGTTTATTT-T
1 TTTTATTTATTTAT
*
1476316 GTTTATTT-TTT-T
1 TTTTATTTATTTAT
*
1476328 GTTTATTTATTT-T
1 TTTTATTTATTTAT
1476341 ATTTT-TTTATTTTAT
1 -TTTTATTTA-TTTAT
* * *
1476356 TTATGTTTCTTTAT
1 TTTTATTTATTTAT
* *
1476370 TTTCATTTTGTTTA-
1 TTTTA-TTTATTTAT
1476384 TTTTATTTACTTTTTAT
1 TTTTATTTA---TTTAT
*
1476401 CTTTATTTCA-TTAT
1 TTTTATTT-ATTTAT
*
1476415 TTTTA-TTATTTTT
1 TTTTATTTATTTAT
* *
1476428 TCTTTACTCATTTTATTT
1 T-TTTATTTA-TTTA--T
*
1476446 TATTTCTTTATTTCATT
1 T-TTTATTTATTT-A-T
1476463 TGTTTATTTATTTAT
1 T-TTTATTTATTTAT
1476478 TTTTATT
1 TTTTATT
1476485 ACCTTTTTTA
Statistics
Matches: 159, Mismatches: 26, Indels: 46
0.69 0.11 0.20
Matches are distributed among these distances:
12 19 0.12
13 33 0.21
14 49 0.31
15 18 0.11
16 8 0.05
17 23 0.14
18 9 0.06
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTATTTATTTAT
Found at i:1476297 original size:9 final size:9
Alignment explanation
Indices: 1476276--1476426 Score: 66
Period size: 9 Copynumber: 16.6 Consensus size: 9
1476266 TATTTATTTC
1476276 ATTTT-TTT
1 ATTTTCTTT
*
1476284 CTTTTCTTT
1 ATTTTCTTT
1476293 ATTTT-TTAT
1 ATTTTCTT-T
* *
1476302 TTTTTGTTT
1 ATTTTCTTT
*
1476311 ATTTTGTTT
1 ATTTTCTTT
*
1476320 ATTTTTTTGTTT
1 A---TTTTCTTT
1476332 ATTTAT-TTT
1 ATTT-TCTTT
1476341 ATTTT-TTT
1 ATTTTCTTT
*
1476349 ATTTTATTT
1 ATTTTCTTT
1476358 ATGTTTCTTT
1 AT-TTTCTTT
1476368 ATTTTCATTT
1 ATTTTC-TTT
*
1476378 -TGTTTATTTT
1 AT-TTT-CTTT
*
1476388 ATTTACTTT
1 ATTTTCTTT
*
1476397 -TTATCTTT
1 ATTTTCTTT
*
1476405 A-TTTCATT
1 ATTTTCTTT
1476413 ATTTT-TATT
1 ATTTTCT-TT
1476422 ATTTT
1 ATTTT
1476427 TTCTTTACTC
Statistics
Matches: 114, Mismatches: 13, Indels: 31
0.72 0.08 0.20
Matches are distributed among these distances:
8 27 0.24
9 55 0.48
10 22 0.19
11 1 0.01
12 9 0.08
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (9 bp):
ATTTTCTTT
Found at i:1476304 original size:5 final size:5
Alignment explanation
Indices: 1476262--1476450 Score: 62
Period size: 5 Copynumber: 37.8 Consensus size: 5
1476252 ATTTTCCTTC
* * * * *
1476262 ATTTT A-TTT ATTTC A-TTT -TTTT CTTTT CTTTAT TTTTT ATTTT TTGTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT-T ATTTT ATTTT AT-TTT
* *
1476311 ATTTT -GTTT ATTTT -TTTGT TTATTT ATTTT A-TTT -TTTT ATTTT A-TTT
1 ATTTT ATTTT ATTTT ATTT-T AT-TTT ATTTT ATTTT ATTTT ATTTT ATTTT
* *
1476358 ATGTTT -CTTT ATTTT CATTTT -GTTT ATTTT A-TTT ACTTTTT ATCTTT
1 AT-TTT ATTTT ATTTT -ATTTT ATTTT ATTTT ATTTT A--TTTT AT-TTT
* * *
1476405 ATTTC ATTAT -TTTT ATTATT -TTTT CTTTACT CATTTT ATTTT ATTT
1 ATTTT ATTTT ATTTT ATT-TT ATTTT ATTT--T -ATTTT ATTTT ATTT
1476451 CTTTATTTCA
Statistics
Matches: 140, Mismatches: 18, Indels: 52
0.67 0.09 0.25
Matches are distributed among these distances:
4 40 0.29
5 63 0.45
6 27 0.19
7 7 0.05
8 3 0.02
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:1486505 original size:7 final size:7
Alignment explanation
Indices: 1486493--1486529 Score: 51
Period size: 6 Copynumber: 5.4 Consensus size: 7
1486483 GTCTTAAGTC
1486493 AAAAAAG
1 AAAAAAG
1486500 AAAAAAG
1 AAAAAAG
1486507 -AAAAAG
1 AAAAAAG
1486513 ATAAAAAG
1 A-AAAAAG
1486521 -AAAAAG
1 AAAAAAG
1486527 AAA
1 AAA
1486530 GAACGTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 12 0.44
7 9 0.33
8 6 0.22
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:1486518 original size:14 final size:13
Alignment explanation
Indices: 1486494--1486529 Score: 63
Period size: 14 Copynumber: 2.7 Consensus size: 13
1486484 TCTTAAGTCA
1486494 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
1486507 AAAAAGATAAAAAG
1 AAAAAGA-AAAAAG
1486521 AAAAAGAAA
1 AAAAAGAAA
1486530 GAACGTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:1486587 original size:6 final size:6
Alignment explanation
Indices: 1486572--1486617 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
1486562 CTAAATTGAA
*
1486572 AAAAATG AAAAAG AAAAAGG AAAAAG AAAAA- TAAAAG -AAAAG AAAA
1 AAAAA-G AAAAAG AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1486618 TAAGGAGGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
5 9 0.26
6 15 0.43
7 11 0.31
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:1486594 original size:13 final size:13
Alignment explanation
Indices: 1486572--1486602 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1486562 CTAAATTGAA
*
1486572 AAAAATGAAAAAG
1 AAAAAGGAAAAAG
1486585 AAAAAGGAAAAAG
1 AAAAAGGAAAAAG
1486598 AAAAA
1 AAAAA
1486603 TAAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (13 bp):
AAAAAGGAAAAAG
Found at i:1487644 original size:58 final size:58
Alignment explanation
Indices: 1487574--1487782 Score: 195
Period size: 58 Copynumber: 3.5 Consensus size: 58
1487564 AGCCATCCAT
*
1487574 GATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGCAGCATCCATCTCTAGATTG
1 GATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGCAACATCCATCTCTAGATTG
***** * * **
1487632 GATTTCAACTTCACAACGAAGGATATCCAATTCA-AAGCTCAACTTCACAACGAATGAGTCATCC
1 GATTTCAACTTCACAACGAAGGATATCGTGCCCACAAG--CAACATC-CATC-TCT-AG--AT--
**
1487696 AC
57 TG
* **
1487698 GATTTCAAATTCACGGCGAAGGATATCGTGCCCACAAGCAACATCCATCTCTAGATTG
1 GATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGCAACATCCATCTCTAGATTG
1487756 GATTTCAACTTCACAACGAAGGATATC
1 GATTTCAACTTCACAACGAAGGATATC
1487783 CAATTCAAAG
Statistics
Matches: 112, Mismatches: 29, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
57 3 0.03
58 53 0.47
59 5 0.04
60 5 0.04
61 1 0.01
62 4 0.04
63 1 0.01
64 5 0.04
65 6 0.05
66 26 0.23
67 3 0.03
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (58 bp):
GATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGCAACATCCATCTCTAGATTG
Found at i:1487658 original size:124 final size:124
Alignment explanation
Indices: 1487505--1487804 Score: 521
Period size: 124 Copynumber: 2.4 Consensus size: 124
1487495 GAAACAACCC
*
1487505 TTGGATTTCAACTTCACAACGAAGAATATCCAATTC-AAGACTCAACTTCACAACGAATGAGCCA
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAG-CTCAACTTCACAACGAATGAGCCA
* * *
1487569 TCCATGATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGCAGCATCCATCTCTAGA
65 TCCACGATTTCAAATTCACAACGAAGGATATCGTGCCCACAAGCAACATCCATCTCTAGA
*
1487629 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGTCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
**
1487694 CCACGATTTCAAATTCACGGCGAAGGATATCGTGCCCACAAGCAACATCCATCTCTAGA
66 CCACGATTTCAAATTCACAACGAAGGATATCGTGCCCACAAGCAACATCCATCTCTAGA
1487753 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACA
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACA
1487805 GTGAAGGAGC
Statistics
Matches: 168, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
124 165 0.98
125 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (124 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
CCACGATTTCAAATTCACAACGAAGGATATCGTGCCCACAAGCAACATCCATCTCTAGA
Found at i:1488416 original size:16 final size:17
Alignment explanation
Indices: 1488386--1488427 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
1488376 GTCCCCATAA
1488386 ATAAT-TATATGATTAT
1 ATAATATATATGATTAT
1488402 ATAATATATAT-ATTAT
1 ATAATATATATGATTAT
*
1488418 ATGATATATA
1 ATAATATATA
1488428 ATTTTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (17 bp):
ATAATATATATGATTAT
Found at i:1489735 original size:18 final size:18
Alignment explanation
Indices: 1489714--1489754 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1489704 TTATTATTAA
1489714 ATTTTTTATATCTA-TTTT
1 ATTTTTT-TATCTATTTTT
*
1489732 ATTTATTTATCTATTTTT
1 ATTTTTTTATCTATTTTT
1489750 ATTTT
1 ATTTT
1489755 CTTCTTGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTTTTATCTATTTTT
Found at i:1489819 original size:89 final size:91
Alignment explanation
Indices: 1489674--1489841 Score: 195
Period size: 89 Copynumber: 1.9 Consensus size: 91
1489664 TTAATATTAG
*
1489674 TATTTATATATATATATATATATATTATTTTTATTATTAAATTTTTTATATCTATTTTATTT-AT
1 TATTTATATATATATATATATATATTATTTTTACTATT-AATTTTTTATATCTA-TTTATTTCAT
1489738 TTATCTATTTTTATTTTCTTCTTGCTTT
64 TTATCTATTTTTATTTTCTTCTTGCTTT
* * *
1489766 TATTTAT-T-TAT-TATGTATATATTATTTTTACTATT-ATTTTCCTTCAT-TTTATTTATTTCT
1 TATTTATATATATATATATATATATTATTTTTACTATTAATTTT--TT-ATATCTATTTATTTCA
* *
1489826 TTTATTTCTTTTTATT
63 TTTATCTATTTTTATT
1489842 GTTTTTTGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
87 5 0.08
88 7 0.11
89 41 0.62
90 5 0.08
91 1 0.02
92 7 0.11
ACGTcount: A:0.24, C:0.07, G:0.01, T:0.68
Consensus pattern (91 bp):
TATTTATATATATATATATATATATTATTTTTACTATTAATTTTTTATATCTATTTATTTCATTT
ATCTATTTTTATTTTCTTCTTGCTTT
Found at i:1489839 original size:19 final size:18
Alignment explanation
Indices: 1489817--1489976 Score: 69
Period size: 20 Copynumber: 8.4 Consensus size: 18
1489807 CTTCATTTTA
1489817 TTTATTTCTTTTATTTCTT
1 TTTATTT-TTTTATTTCTT
* *
1489836 TTTATTGTTTTTTGTTTATT
1 TTTA-T-TTTTTTATTTCTT
* * *
1489856 TTAATTTGTTTATTT-TA
1 TTTATTTTTTTATTTCTT
*
1489873 TTTATGTTTCTTTATTTTCAT
1 TTTAT-TTT-TTTA-TTTCTT
*
1489894 TTTGTTTATTTTATTTACTT
1 TTTATTT-TTTTATTT-CTT
1489914 TTTATCTTTATTTCATTAT-TT
1 TTTAT-TTT-TTT-ATT-TCTT
1489935 TTT-TTTATTTT-TTTCTT
1 TTTATTT-TTTTATTTCTT
* * * *
1489952 TATCTTTCTTTA-CTCTT
1 TTTATTTTTTTATTTCTT
1489969 TTTATTTT
1 TTTATTTT
1489977 ATATTCTTTA
Statistics
Matches: 106, Mismatches: 19, Indels: 34
0.67 0.12 0.21
Matches are distributed among these distances:
16 1 0.01
17 23 0.22
18 13 0.12
19 17 0.16
20 31 0.29
21 17 0.16
22 3 0.03
23 1 0.01
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTATTTTTTTATTTCTT
Found at i:1489855 original size:14 final size:14
Alignment explanation
Indices: 1489846--1489872 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1489836 TTTATTGTTT
1489846 TTTGTTTATTTTAA
1 TTTGTTTATTTTAA
1489860 TTTGTTTATTTTA
1 TTTGTTTATTTTA
1489873 TTTATGTTTC
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:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (14 bp):
TTTGTTTATTTTAA
Found at i:1489895 original size:25 final size:25
Alignment explanation
Indices: 1489867--1489926 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1489857 TAATTTGTTT
*
1489867 ATTTTATTTATGTTTCTTTA-TTTTC
1 ATTTTATTTAT-TTTATTTACTTTTC
* *
1489892 ATTTTGTTTATTTTATTTACTTTTT
1 ATTTTATTTATTTTATTTACTTTTC
1489917 ATCTTTATTT
1 AT-TTTATTT
1489927 CATTATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.24
25 16 0.55
26 6 0.21
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (25 bp):
ATTTTATTTATTTTATTTACTTTTC
Found at i:1490012 original size:10 final size:10
Alignment explanation
Indices: 1489825--1490014 Score: 56
Period size: 10 Copynumber: 18.7 Consensus size: 10
1489815 TATTTATTTC
*
1489825 TTTTATTTCT
1 TTTTATTTAT
1489835 TTTTATTGT-T
1 TTTTATT-TAT
*
1489845 TTTTGTTTAT
1 TTTTATTTAT
* *
1489855 TTTAATTTGT
1 TTTTATTTAT
*
1489865 TTAT-TTTAT
1 TTTTATTTAT
* * *
1489874 TTATGTTTCT
1 TTTTATTTAT
*
1489884 TTATT-TTCA-
1 TT-TTATTTAT
*
1489893 TTTTGTTTA-
1 TTTTATTTAT
1489902 TTTTATTTACT
1 TTTTATTTA-T
1489913 TTTTATCTTTAT
1 TTTTA--TTTAT
*
1489925 TTCATTATTTTT
1 TT--TTATTTAT
1489937 TTTTA-TT-T
1 TTTTATTTAT
*
1489945 TTTTCTTTAT
1 TTTTATTTAT
* * *
1489955 CTTTCTTTAC
1 TTTTATTTAT
*
1489965 TCTT-TTTAT
1 TTTTATTTAT
1489974 TTTATATTCT-T
1 TTT-TATT-TAT
*
1489985 TATTTCATTTGCT
1 T-TTT-ATTT-AT
1489998 TTTTATTTAT
1 TTTTATTTAT
1490008 TTTTATT
1 TTTTATT
1490015 ACATTTTTTT
Statistics
Matches: 138, Mismatches: 22, Indels: 40
0.69 0.11 0.20
Matches are distributed among these distances:
8 7 0.05
9 32 0.23
10 55 0.40
11 17 0.12
12 18 0.13
13 6 0.04
14 3 0.02
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:1490757 original size:12 final size:12
Alignment explanation
Indices: 1490709--1490760 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
1490699 ATTTTAGTCA
1490709 TTTAATTATTATTT
1 TTTAA-TATTA-TT
* *
1490723 TTTAAAATTATA
1 TTTAATATTATT
*
1490735 TTTAACATTATT
1 TTTAATATTATT
*
1490747 TTTAATTTTATT
1 TTTAATATTATT
1490759 TT
1 TT
1490761 GATCATCCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 23 0.72
13 4 0.12
14 5 0.16
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTAATATTATT
Found at i:1491672 original size:14 final size:14
Alignment explanation
Indices: 1491653--1491685 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1491643 TATTATATTA
1491653 ATTATGATTCTTAT
1 ATTATGATTCTTAT
1491667 ATTATGATTCTTAT
1 ATTATGATTCTTAT
*
1491681 GTTAT
1 ATTAT
1491686 AAATATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (14 bp):
ATTATGATTCTTAT
Found at i:1492667 original size:25 final size:25
Alignment explanation
Indices: 1492639--1492739 Score: 80
Period size: 25 Copynumber: 4.0 Consensus size: 25
1492629 ATGCATAATT
*
1492639 AATAATATATAATGTATATTGTATG
1 AATAATATATAATGTATAATGTATG
* **
1492664 AATAAT-TAATTAACGCGTAATGTATG
1 AATAATAT-A-TAATGTATAATGTATG
* *
1492690 AATTGATATATAA-GTATAATGTGTG
1 AA-TAATATATAATGTATAATGTATG
* * *
1492715 TATAATTTATTATGTATAATGTATG
1 AATAATATATAATGTATAATGTATG
1492740 TATGTATGTA
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
24 8 0.14
25 28 0.48
26 17 0.29
27 4 0.07
28 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.43
Consensus pattern (25 bp):
AATAATATATAATGTATAATGTATG
Found at i:1492732 original size:14 final size:15
Alignment explanation
Indices: 1492708--1492746 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1492698 TATAAGTATA
* *
1492708 ATGTGTGTATAATTT
1 ATGTATGTATAATGT
1492723 AT-TATGTATAATGT
1 ATGTATGTATAATGT
1492737 ATGTATGTAT
1 ATGTATGTAT
1492747 GTATATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (15 bp):
ATGTATGTATAATGT
Found at i:1492866 original size:18 final size:18
Alignment explanation
Indices: 1492843--1493046 Score: 133
Period size: 18 Copynumber: 11.4 Consensus size: 18
1492833 ATTTTTAGCG
1492843 TATACTATATAGTTTATA
1 TATACTATATAGTTTATA
*
1492861 TATACTA-AT-G--AACTA
1 TATACTATATAGTTTA-TA
*
1492876 TATAATATATAGTTTATA
1 TATACTATATAGTTTATA
*
1492894 TATACCATATAGTTTATA
1 TATACTATATAGTTTATA
1492912 TATACTATATAGTTTATA
1 TATACTATATAGTTTATA
* *
1492930 TATAGTTTATATGTACTAATGAACTA
1 TATACTATATA-GT--T--T--A-TA
* *
1492956 TATAATATATAATTTATA
1 TATACTATATAGTTTATA
**
1492974 TATACTA-ATGAACTT-TA
1 TATACTATAT-AGTTTATA
1492991 TA-A-TATATAGTTTATA
1 TATACTATATAGTTTATA
***
1493007 TATACTA-ATAAACTATA
1 TATACTATATAGTTTATA
1493024 TA-A-TATATAGTTTATA
1 TATACTATATAGTTTATA
1493040 TATACTA
1 TATACTA
1493047 ATGAACTATA
Statistics
Matches: 144, Mismatches: 21, Indels: 42
0.70 0.10 0.20
Matches are distributed among these distances:
14 1 0.01
15 15 0.10
16 20 0.14
17 20 0.14
18 67 0.47
19 4 0.03
21 2 0.01
23 2 0.01
25 2 0.01
26 11 0.08
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.45
Consensus pattern (18 bp):
TATACTATATAGTTTATA
Found at i:1492889 original size:33 final size:33
Alignment explanation
Indices: 1492843--1493058 Score: 243
Period size: 33 Copynumber: 6.1 Consensus size: 33
1492833 ATTTTTAGCG
*
1492843 TATACTATATAGTTTATATATACTAATGAACTA
1 TATAATATATAGTTTATATATACTAATGAACTA
*
1492876 TATAATATATAGTTTATATATACCATATAGTTTATATATACTA
1 TATAATATATAGTTTATATATA-C---TA----AT-GA-ACTA
* *
1492919 TATAGTTTATATATAGTTTATATGTACTAATGAACTA
1 TATAAT----ATATAGTTTATATATACTAATGAACTA
* *
1492956 TATAATATATAATTTATATATACTAATGAACTT
1 TATAATATATAGTTTATATATACTAATGAACTA
*
1492989 TATAATATATAGTTTATATATACTAATAAACTA
1 TATAATATATAGTTTATATATACTAATGAACTA
1493022 TATAATATATAGTTTATATATACTAATGAACTA
1 TATAATATATAGTTTATATATACTAATGAACTA
1493055 TATA
1 TATA
1493059 GTTTATTAAT
Statistics
Matches: 156, Mismatches: 13, Indels: 28
0.79 0.07 0.14
Matches are distributed among these distances:
33 111 0.71
34 1 0.01
37 11 0.07
38 1 0.01
39 2 0.01
41 2 0.01
42 1 0.01
43 11 0.07
46 1 0.01
47 15 0.10
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (33 bp):
TATAATATATAGTTTATATATACTAATGAACTA
Found at i:1492947 original size:80 final size:77
Alignment explanation
Indices: 1492848--1493010 Score: 238
Period size: 80 Copynumber: 2.1 Consensus size: 77
1492838 TAGCGTATAC
* **
1492848 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACCATAT-AGTTTATA
1 TATATAGTTTATATATACTAATGAACTATATAATATATAATTTATATATACCA-ATGAACTT-TA
1492912 TATACTATATAGTTTA
64 TA-A-TATATAGTTTA
* *
1492928 TATATAGTTTATATGTACTAATGAACTATATAATATATAATTTATATATACTAATGAACTTTATA
1 TATATAGTTTATATATACTAATGAACTATATAATATATAATTTATATATACCAATGAACTTTATA
1492993 ATATATAGTTTA
66 ATATATAGTTTA
1493005 TATATA
1 TATATA
1493011 CTAATAAACT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
77 17 0.22
78 1 0.01
79 6 0.08
80 53 0.69
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (77 bp):
TATATAGTTTATATATACTAATGAACTATATAATATATAATTTATATATACCAATGAACTTTATA
ATATATAGTTTA
Found at i:1493084 original size:30 final size:29
Alignment explanation
Indices: 1493012--1493117 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 29
1493002 TTATATATAC
1493012 TAATA-AACTATAT-AA-TATATAGTTTA
1 TAATATAACTATATAAACTATATAGTTTA
*
1493038 T-ATAT-ACTA-ATGAACTATATAGTTTA
1 TAATATAACTATATAAACTATATAGTTTA
*
1493064 TTAATATAATTATATAAACTATATAGTTTA
1 -TAATATAACTATATAAACTATATAGTTTA
* * *
1493094 TAGT-TTATTAATATAAACTATATA
1 TAATATAACT-ATATAAACTATATA
1493118 TATAAAAACT
Statistics
Matches: 68, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
24 2 0.03
25 9 0.13
26 12 0.18
27 1 0.01
28 8 0.12
29 20 0.29
30 16 0.24
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (29 bp):
TAATATAACTATATAAACTATATAGTTTA
Found at i:1493137 original size:37 final size:38
Alignment explanation
Indices: 1493036--1493145 Score: 125
Period size: 37 Copynumber: 2.9 Consensus size: 38
1493026 ATATATAGTT
* *
1493036 TATATATACTAATGAACTATATAGTTTATTAATAT-AAT
1 TATATATACTAA-AAACTATATAGTTTATTAATATAAAC
* * * * *
1493074 TATATAAACTATATAGTTTATAGTTTATTAATATAAAC
1 TATATATACTAAAAACTATATAGTTTATTAATATAAAC
*
1493112 TATATATA-TAAAAACTATATGGTTTATTAATATA
1 TATATATACTAAAAACTATATAGTTTATTAATATA
1493146 TATATAGTTC
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
37 39 0.67
38 19 0.33
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (38 bp):
TATATATACTAAAAACTATATAGTTTATTAATATAAAC
Found at i:1493221 original size:2 final size:2
Alignment explanation
Indices: 1493194--1493276 Score: 54
Period size: 2 Copynumber: 44.0 Consensus size: 2
1493184 TATATAAAAT
* * *
1493194 TA TA AA TA TA AA T- TA TA TA GTT TA TA TA TA T- TA TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
1493233 TA TA TA CTT TA TT TA TA TA TA TA TA TA TA TA T- TA -A TA TA T-
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1493273 TA TA
1 TA TA
1493277 ATTGTTTTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
1 7 0.11
2 53 0.85
3 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1494030 original size:49 final size:49
Alignment explanation
Indices: 1493966--1494074 Score: 209
Period size: 49 Copynumber: 2.2 Consensus size: 49
1493956 ATTGAAAGTA
*
1493966 ACCCGACTTGAACCCAAGCTGAACCTGGTGTCAAATCAACCTGAAAATG
1 ACCCGACTTGAACCCAAGCTGAACCTGGTGTCAAATCAACCTAAAAATG
1494015 ACCCGACTTGAACCCAAGCTGAACCTGGTGTCAAATCAACCTAAAAATG
1 ACCCGACTTGAACCCAAGCTGAACCTGGTGTCAAATCAACCTAAAAATG
1494064 ACCCGACTTGA
1 ACCCGACTTGA
1494075 TTTGACATGG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.18
Consensus pattern (49 bp):
ACCCGACTTGAACCCAAGCTGAACCTGGTGTCAAATCAACCTAAAAATG
Found at i:1502966 original size:17 final size:16
Alignment explanation
Indices: 1502941--1503004 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 16
1502931 ATTTAGTTTA
1502941 ATAAATGAACTACTTT
1 ATAAATGAACTACTTT
* *
1502957 GATGAATGAACTAGTTT
1 -ATAAATGAACTACTTT
*
1502974 AATTAATGAACTAACTTT
1 -ATAAATGAACT-ACTTT
1502992 ATTAAATGAACTA
1 A-TAAATGAACTA
1503005 GATGCATGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
17 26 0.67
18 13 0.33
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (16 bp):
ATAAATGAACTACTTT
Found at i:1502973 original size:34 final size:35
Alignment explanation
Indices: 1502934--1503005 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
1502924 AATTAAGATT
*
1502934 TAGTTTAATAAATGAACT-ACTTTGA-TGAATGAAC
1 TAGTTTAATAAATGAACTAACTTT-ATTAAATGAAC
*
1502968 TAGTTTAATTAATGAACTAACTTTATTAAATGAAC
1 TAGTTTAATAAATGAACTAACTTTATTAAATGAAC
1503003 TAG
1 TAG
1503006 ATGCATGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 18 0.53
35 16 0.47
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (35 bp):
TAGTTTAATAAATGAACTAACTTTATTAAATGAAC
Found at i:1503017 original size:35 final size:34
Alignment explanation
Indices: 1502944--1503018 Score: 80
Period size: 35 Copynumber: 2.2 Consensus size: 34
1502934 TAGTTTAATA
* * * *
1502944 AATGAACTACTTTGATGAATGAACTAGTTTAATT
1 AATGAACTACTTTGATAAATGAACTAGATGAATG
*
1502978 AATGAACTAACTTT-ATTAAATGAACTAGATGCATG
1 AATGAACT-ACTTTGA-TAAATGAACTAGATGAATG
1503013 AATGAA
1 AATGAA
1503019 GTAGCTTACT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 9 0.26
35 25 0.74
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (34 bp):
AATGAACTACTTTGATAAATGAACTAGATGAATG
Found at i:1509105 original size:226 final size:228
Alignment explanation
Indices: 1508711--1509169 Score: 879
Period size: 226 Copynumber: 2.0 Consensus size: 228
1508701 AGGACCTTTG
1508711 TACAACAAAAAGGAAGCTTTCTGGGATCGAGAAGGTAAATTTGGGAGAACATGTCTCAGCTATTT
1 TACAACAAAAAGGAAGCTTTCTGGGATCGAGAAGGTAAATTTGGGAGAACATGTCTCAGCTATTT
*
1508776 TCCAACGAAAGTTTCCACCAAAATTAAAAGACAAAGGTATTTTTGCAATACCCTGTAAATTGGTG
66 TCCAACGAAAGTTTCCACCAAAATTAAAAGACAAAGGTATGTTTGCAATACCCTGTAAATTGGTG
1508841 AAGTTGGGTTAAAAGCGAGCCATGTTTGATCTTGGTGCCTCTATTAATGTGATGTCTCTC-CTGT
131 AAGTTGGGTTAAAAGCGAGCCATGTTTGATCTTGGTGCCTCTATTAATGTGATGTCTCTCTCTGT
1508905 TTATAATATGATCACTAACGAG-CCTTGAAGGA
196 TTATAATATGATCACTAACGAGCCCTTGAAGGA
1508937 TACAACAAAAAGGAAGCTTTCTGGGATCGAGAAGGTAAATTTGGGAGAACATGTCTCAGCTATTT
1 TACAACAAAAAGGAAGCTTTCTGGGATCGAGAAGGTAAATTTGGGAGAACATGTCTCAGCTATTT
1509002 TCCAACGAAAGTTTCCACCAAAATTAAAAGACAAAGGTATGTTTGCAATACCCTGTAAAATTGGT
66 TCCAACGAAAGTTTCCACCAAAATTAAAAGACAAAGGTATGTTTGCAATACCCTGT-AAATTGGT
1509067 GAAGTTGGGTT-AAAGCGAGCCATGTTTGATCTTGGTGCCTCTATTAATGTGATGTCTCTCTCTG
130 GAAGTTGGGTTAAAAGCGAGCCATGTTTGATCTTGGTGCCTCTATTAATGTGATGTCTCTCTCTG
1509131 TTTATAATATGATCACTAACGAGCCCTTGAAGGA
195 TTTATAATATGATCACTAACGAGCCCTTGAAGGA
1509165 TACAA
1 TACAA
1509170 AAATATCAAT
Statistics
Matches: 229, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
226 169 0.74
227 45 0.20
228 15 0.07
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (228 bp):
TACAACAAAAAGGAAGCTTTCTGGGATCGAGAAGGTAAATTTGGGAGAACATGTCTCAGCTATTT
TCCAACGAAAGTTTCCACCAAAATTAAAAGACAAAGGTATGTTTGCAATACCCTGTAAATTGGTG
AAGTTGGGTTAAAAGCGAGCCATGTTTGATCTTGGTGCCTCTATTAATGTGATGTCTCTCTCTGT
TTATAATATGATCACTAACGAGCCCTTGAAGGA
Found at i:1516707 original size:23 final size:24
Alignment explanation
Indices: 1516661--1516707 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1516651 TTTCTTTTCT
1516661 TTTATTTCAAGTTTTCATTTTTAA
1 TTTATTTCAAGTTTTCATTTTTAA
*
1516685 TTTATTTTAAGTTTT-ATTTTTAA
1 TTTATTTCAAGTTTTCATTTTTAA
1516708 ACATGCTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTATTTCAAGTTTTCATTTTTAA
Found at i:1522292 original size:2 final size:2
Alignment explanation
Indices: 1522281--1522334 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1522271 GTATAAACAA
1522281 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1522322 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1522335 AGAATAATGA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1529083 original size:18 final size:16
Alignment explanation
Indices: 1529055--1529109 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 16
1529045 CCCTAAAAAT
*
1529055 AAATCAAATAATATTA
1 AAATAAAATAATATTA
1529071 AACCATAAAATAA-ATTA
1 AA--ATAAAATAATATTA
*
1529088 AAATAAAAAAATATT-
1 AAATAAAATAATATTA
1529103 AAATAAA
1 AAATAAA
1529110 TAAAAGAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
15 15 0.44
16 5 0.15
17 6 0.18
18 8 0.24
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATAAAATAATATTA
Found at i:1529167 original size:16 final size:15
Alignment explanation
Indices: 1529116--1529164 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
1529106 TAAATAAAAG
1529116 AATTAAAAGAGAATTCA
1 AATTAAAA-AGAATT-A
*
1529133 AATTAAAAAGGATTA
1 AATTAAAAAGAATTA
*
1529148 AATTGAAAAGAATTA
1 AATTAAAAAGAATTA
1529163 AA
1 AA
1529165 ATTCAAGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 16 0.55
16 5 0.17
17 8 0.28
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.24
Consensus pattern (15 bp):
AATTAAAAAGAATTA
Found at i:1530312 original size:4 final size:4
Alignment explanation
Indices: 1530293--1530343 Score: 50
Period size: 4 Copynumber: 12.2 Consensus size: 4
1530283 CTTGGATCTG
* *
1530293 AAAT -AAT AATT AAAT AAAT AAAT AAAT AATGT AAAT ATAAT ATAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT A-AAT A-AAT AAAT
1530343 A
1 A
1530344 CATATAAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 3 0.08
4 25 0.62
5 12 0.30
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (4 bp):
AAAT
Found at i:1530361 original size:31 final size:29
Alignment explanation
Indices: 1530296--1530371 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 29
1530286 GGATCTGAAA
*
1530296 TAATAAT-TAA-ATAAATAAATAAATAATG
1 TAATAATATAATAT-AATAAATAAATAAGG
1530324 T-A-AATATAATATAATAAATACATATAAGG
1 TAATAATATAATATAATAAATA-A-ATAAGG
1530353 TAATAATATAACTATAATA
1 TAATAATATAA-TATAATA
1530372 TAAATATATG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
26 3 0.08
27 12 0.30
28 4 0.10
29 6 0.15
30 1 0.03
31 7 0.17
32 7 0.17
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (29 bp):
TAATAATATAATATAATAAATAAATAAGG
Found at i:1530371 original size:11 final size:11
Alignment explanation
Indices: 1530293--1530643 Score: 94
Period size: 11 Copynumber: 31.2 Consensus size: 11
1530283 CTTGGATCTG
1530293 AAATAATAAT-T
1 AAAT-ATAATAT
1530304 AAATA-AATA-
1 AAATATAATAT
* *
1530313 AATAAATAATGT
1 AA-ATATAATAT
1530325 AAATATAATAT
1 AAATATAATAT
*
1530336 AATAAATACATAT
1 AA-ATATA-ATAT
*
1530349 AAGGTAATAATAT
1 AA-AT-ATAATAT
*
1530362 AACTATAATAT
1 AAATATAATAT
*
1530373 AAATAT-AT-G
1 AAATATAATAT
* * *
1530382 CACTTTAATAT
1 AAATATAATAT
*
1530393 ATAATAT-ATAAC
1 A-AATATAAT-AT
1530405 AAATAT-ATAT
1 AAATATAATAT
1530415 AAATATATATTAT
1 AAATATA-A-TAT
*
1530428 AATTATAATAGT
1 AAATATAATA-T
*
1530440 AATATTTAATATT
1 AA-ATATAATA-T
*
1530453 TAATAT-ATAT
1 AAATATAATAT
* *
1530463 AATATATATTGT
1 AA-ATATAATAT
*
1530475 -ACTAT-ATAT
1 AAATATAATAT
1530484 -AATAT-ATAT
1 AAATATAATAT
*
1530493 AATATATAATAAC
1 AA-ATATAAT-AT
*
1530506 ATAATACTACTAT
1 A-AATA-TAATAT
1530519 AATATATAATAT
1 AA-ATATAATAT
1530531 ATAATAT-ATAT
1 A-AATATAATAT
*
1530542 AAATACATATACT
1 AAATATA-ATA-T
1530555 ATAATAT-ATAT
1 A-AATATAATAT
1530566 -AATATAATAT
1 AAATATAATAT
1530576 AAAT-T-ATAT
1 AAATATAATAT
*
1530585 ACTATATAA-AT
1 A-AATATAATAT
*
1530596 ATTATATAATAAT
1 A-AATATAAT-AT
*
1530609 ACATACT-ATAT
1 AAATA-TAATAT
*
1530620 AAATATTATACT
1 AAATATAATA-T
*
1530632 ATATAT-ATAT
1 AAATATAATAT
1530642 AA
1 AA
1530644 TACCATACCA
Statistics
Matches: 255, Mismatches: 45, Indels: 81
0.67 0.12 0.21
Matches are distributed among these distances:
9 28 0.11
10 34 0.13
11 83 0.33
12 53 0.21
13 46 0.18
14 11 0.04
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (11 bp):
AAATATAATAT
Found at i:1530394 original size:2 final size:2
Alignment explanation
Indices: 1530389--1530707 Score: 139
Period size: 2 Copynumber: 170.5 Consensus size: 2
1530379 ATGCACTTTA
* * *
1530389 AT AT AT A- AT AT AT A- AC AA AT AT AT AT AA AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1530428 A- AT -T AT A- AT AGT A- AT AT TT A- AT AT TT A- AT AT AT AT A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1530464 AT AT AT AT -T GT ACT AT AT AT A- AT AT AT AT A- AT AT AT A- AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1530503 A- AC AT A- AT ACT ACT AT A- AT AT AT A- AT AT AT A- AT AT AT AT
1 AT AT AT AT AT A-T A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1530542 AA AT AC AT AT ACT AT A- AT AT AT AT A- AT AT A- AT AT AA AT -T
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1530581 AT AT ACT AT AT AA AT AT -T AT AT A- AT A- AT AC AT ACT AT AT AA
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
1530622 AT AT -T AT ACT AT AT AT AT AT A- AT ACC AT ACC AT A- AA AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT
*
1530662 AT ACT AT AT A- AA AT A- AT AT AT A- AT AT AT A- AT AT AT A- AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1530700 AT GAT AT A
1 AT -AT AT A
1530708 ATAAAAGAAA
Statistics
Matches: 244, Mismatches: 28, Indels: 90
0.67 0.08 0.25
Matches are distributed among these distances:
1 34 0.14
2 187 0.77
3 23 0.09
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1530399 original size:7 final size:7
Alignment explanation
Indices: 1530387--1530701 Score: 192
Period size: 7 Copynumber: 44.9 Consensus size: 7
1530377 ATATGCACTT
1530387 TAATATA
1 TAATATA
1530394 TAATATA
1 TAATATA
* *
1530401 TAACAAA
1 TAATATA
1530408 T-ATATA
1 TAATATA
1530414 TAA-ATA
1 TAATATA
1530420 T-ATATTA
1 TAATA-TA
1530427 TAAT-TA
1 TAATATA
*
1530433 TAATA-G
1 TAATATA
*
1530439 TAATATT
1 TAATATA
*
1530446 TAATATT
1 TAATATA
1530453 TAATATATA
1 T-A-ATATA
1530462 TAATATA
1 TAATATA
* *
1530469 TATTGTA
1 TAATATA
1530476 CT-ATATA
1 -TAATATA
1530483 TAATATA
1 TAATATA
1530490 T-ATA-A
1 TAATATA
1530495 T-ATATAA
1 TAATAT-A
*
1530502 TAACATAA
1 TAATAT-A
*
1530510 TACTACTA
1 TAATA-TA
1530518 TAATATA
1 TAATATA
1530525 TAATATA
1 TAATATA
1530532 TAATATA
1 TAATATA
*
1530539 TATAAATA
1 TA-ATATA
*
1530547 CATATACTA
1 TA-ATA-TA
1530556 TAATATA
1 TAATATA
1530563 T-ATAATA
1 TAAT-ATA
1530570 TAATATA
1 TAATATA
1530577 -AATTATA
1 TAA-TATA
*
1530584 TACTATA
1 TAATATA
1530591 TAA-ATA
1 TAATATA
*
1530597 TTATATAA
1 TAATAT-A
*
1530605 TAATACA
1 TAATATA
*
1530612 TACTATA
1 TAATATA
1530619 TAA-ATA
1 TAATATA
*
1530625 TTATACTA
1 TAATA-TA
1530633 TATATATA
1 TA-ATATA
*
1530641 TAATACCA
1 TAATA-TA
**
1530649 TACCATA
1 TAATATA
*
1530656 AAATATA
1 TAATATA
*
1530663 TACTATA
1 TAATATA
1530670 TAA-A-A
1 TAATATA
1530675 TAATATA
1 TAATATA
1530682 TAATATA
1 TAATATA
1530689 TAATATA
1 TAATATA
1530696 TAATAT
1 TAATAT
1530702 GATATAATAA
Statistics
Matches: 241, Mismatches: 39, Indels: 56
0.72 0.12 0.17
Matches are distributed among these distances:
5 10 0.04
6 40 0.17
7 131 0.54
8 48 0.20
9 12 0.05
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (7 bp):
TAATATA
Found at i:1530429 original size:66 final size:64
Alignment explanation
Indices: 1530332--1530576 Score: 175
Period size: 66 Copynumber: 3.7 Consensus size: 64
1530322 TGTAAATATA
* *
1530332 ATATAATAAATACATATAAGGTA-ATA-ATATAACTATAATATAAATATATGCACTTTAATATAT
1 ATATAATAAATATATATAA-ATATATATA-ATAA-TATAATATAAATATAT-CACTTTAATATAT
1530395 AAT
62 AAT
* * *
1530398 ATATAACAAATATATATAAATATATATTATAATTATAATAGTAATATTTAAT-A-TTTAATATAT
1 ATATAATAAATATATATAAATATATATAATAA-TATAATA-TAA-ATAT-ATCACTTT-A-ATAT
1530461 ATAAT
60 ATAAT
* * * * *
1530466 ATATATTGTACTATATAT-AATATATATAAT-ATATAATA-ACATA-ATACTACTATAATATATA
1 ATATAAT-AAATATATATAAATATATATAATAATATAATATAAATATAT-C-ACTTTAATATATA
1530527 AT
63 AT
* * *
1530529 ATATAATATATATAAATACATATACTATAATATATATAATAT-AATATA
1 ATATAATAAATATATATAAATATA-TATAATA-ATATAATATAAATATA
1530577 AATTATATAC
Statistics
Matches: 140, Mismatches: 21, Indels: 35
0.71 0.11 0.18
Matches are distributed among these distances:
61 2 0.01
62 6 0.04
63 22 0.16
64 9 0.06
65 4 0.03
66 52 0.37
67 7 0.05
68 28 0.20
69 10 0.07
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (64 bp):
ATATAATAAATATATATAAATATATATAATAATATAATATAAATATATCACTTTAATATATAAT
Found at i:1530437 original size:28 final size:26
Alignment explanation
Indices: 1530355--1530712 Score: 122
Period size: 26 Copynumber: 13.7 Consensus size: 26
1530345 ATATAAGGTA
1530355 ATAATATAACTATAATATAAATATATGCACT
1 ATAATATAA-TAT-ATATAAATATAT--A-T
* *
1530386 TTAATAT-ATAATATATAACAAATATAT
1 ATAATATAAT-ATATATAA-ATATATAT
*
1530413 ATAA-AT-ATATATTATAATTATA-AT
1 ATAATATAATATA-TATAAATATATAT
* **
1530437 AGTAATAT-TTA-ATATTTA-ATATAT
1 A-TAATATAATATATATAAATATATAT
* *
1530461 ATAATAT-ATAT-TGTACTATATATAAT
1 ATAATATAATATATATA-AATATAT-AT
1530487 AT-ATATAATATATAATAACATAATACTACT
1 ATAATATAATATAT-ATAA-AT-ATA-TA-T
1530517 ATAATAT-ATA-ATATATAATATATAT
1 ATAATATAATATATATA-AATATATAT
*
1530542 A-AATA-CATATACTATAATATATATAAT
1 ATAATATAATATA-TATAA-ATATAT-AT
1530569 ATAATATAA-AT-TAT--ATACTATAT
1 ATAATATAATATATATAAATA-TATAT
* *
1530592 A-AATATTATATA-AT-AATACATACT
1 ATAATATAATATATATAAATATATA-T
*
1530616 AT-ATA-AATAT-TATACTATATATAT
1 ATAATATAATATATATA-AATATATAT
** *
1530640 ATAATACCATACCATA-AAATATATACT
1 ATAATATAATA-TATATAAATATATA-T
*
1530667 AT-ATAAAATAATATATAATATATAATAT
1 ATAATATAAT-ATATATAA-ATAT-ATAT
*
1530695 ATAATATGATATA-ATAAA
1 ATAATATAATATATATAAA
1530713 AGAAACTCAG
Statistics
Matches: 254, Mismatches: 28, Indels: 95
0.67 0.07 0.25
Matches are distributed among these distances:
22 6 0.02
23 32 0.13
24 32 0.13
25 31 0.12
26 55 0.22
27 22 0.09
28 28 0.11
29 23 0.09
30 15 0.06
31 10 0.04
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (26 bp):
ATAATATAATATATATAAATATATAT
Found at i:1530529 original size:33 final size:33
Alignment explanation
Indices: 1530365--1530701 Score: 161
Period size: 33 Copynumber: 10.0 Consensus size: 33
1530355 ATAATATAAC
* *
1530365 TATAATATAAATATATGC-ACTTTAATATATAATA
1 TATAATAT-AATA-ATACTACTATAATATATAATA
*
1530399 TATAACA-AAT-ATA-TA-TA-AATATAT-AT-
1 TATAATATAATAATACTACTATAATATATAATA
* * * *
1530425 TATAATTATAATAGTAATA-TTTAATATTTAATATA
1 TATAA-TATAATAATACTACTATAATATAT-A-ATA
** *
1530460 TATAATATATATTGTACTATATATAATATATATAATA
1 TATAATATA-ATAATACTA-CTAT-A-ATATATAATA
1530497 TATAATA-ACATAATACTACTATAATATATAATA
1 TATAATATA-ATAATACTACTATAATATATAATA
1530530 TATAATATATATAAATACATATACTATAATATAT-ATAA
1 TATAATATA-AT-AATAC---TACTATAATATATAAT-A
* * *
1530568 TATAATATAAATTATA-TACTAT-ATAAATATTA
1 TATAATAT-AATAATACTACTATAATATATAATA
*
1530600 TAT-A-ATAATACATACTA-TATAAATATTATACTA
1 TATAATATAATA-ATACTACTAT-AATA-TATAATA
* * *
1530633 TATATATATAATACCATACCA-TAAAATATATACTA
1 TATA-ATATAATA--ATACTACTATAATATATAATA
* *
1530668 TATAAAATAATATATAATA-TATAATATATAATA
1 TATAATATAATA-ATACTACTATAATATATAATA
1530701 T
1 T
1530702 GATATAATAA
Statistics
Matches: 241, Mismatches: 30, Indels: 65
0.72 0.09 0.19
Matches are distributed among these distances:
26 5 0.02
27 3 0.01
28 10 0.04
29 6 0.02
30 14 0.06
31 9 0.04
32 15 0.06
33 49 0.20
34 23 0.10
35 32 0.13
36 18 0.07
37 25 0.10
38 26 0.11
39 6 0.02
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (33 bp):
TATAATATAATAATACTACTATAATATATAATA
Found at i:1530620 original size:131 final size:138
Alignment explanation
Indices: 1530387--1530710 Score: 314
Period size: 131 Copynumber: 2.4 Consensus size: 138
1530377 ATATGCACTT
* * *
1530387 TAATATATAATATATAACAA-ATATATATAAATATATATTATA-ATTATAATAGTAATATTTAAT
1 TAATATATAATATATAA-AATATATAAATAAATATATATAATATA-TATAATAGTAATATTAAAT
* ** * * *
1530450 ATTTAATATATATAATATATATTGTACTATATATAATATATATAATATA-TA-ATA-ACATAATA
64 ATATAATATATATAATATATATAATAATACATATAATATAAATAATATACTATATATACATAATA
1530512 -C-TA-C-TA
129 CCATACCATA
* *
1530518 TAATATATAATATATAATATATATAAATACATATACTATAATATATATAATA-TAATA-TAAATT
1 TAATATATAATATATAAAATATATAAATAAATATA-TATAATATATATAATAGTAATATTAAA-T
* * *
1530581 ATATACTATATA-AATATTATATAATAATACATACT-ATATAAATATTATACTATATATATATAA
64 ATATAATATATATAATA-TATATAATAATACATA-TAATATAAATAATATACTATATATACATAA
1530644 TACCATACCATA
127 TACCATACCATA
* * *
1530656 AAATATATACTATATAAAATAATATATAATATATAATATATAATATGATATAATA
1 TAATATATAATATATAAAAT-ATATA-AATAAAT-ATATATAATAT-ATATAATA
1530711 AAAGAAACTC
Statistics
Matches: 158, Mismatches: 18, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
130 8 0.05
131 70 0.44
132 16 0.10
133 4 0.03
134 7 0.04
135 1 0.01
136 2 0.01
137 1 0.01
138 19 0.12
139 5 0.03
140 14 0.09
141 11 0.07
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (138 bp):
TAATATATAATATATAAAATATATAAATAAATATATATAATATATATAATAGTAATATTAAATAT
ATAATATATATAATATATATAATAATACATATAATATAAATAATATACTATATATACATAATACC
ATACCATA
Found at i:1531752 original size:13 final size:13
Alignment explanation
Indices: 1531731--1531760 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1531721 ACTTTGAGAA
*
1531731 TTGTGTCTCAAAG
1 TTGTCTCTCAAAG
1531744 TTGTCTCTCAAAG
1 TTGTCTCTCAAAG
1531757 TTGT
1 TTGT
1531761 GTCTAAGATT
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:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (13 bp):
TTGTCTCTCAAAG
Found at i:1531778 original size:25 final size:26
Alignment explanation
Indices: 1531731--1531779 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
1531721 ACTTTGAGAA
*
1531731 TTGTGTCTCAAAGTTGTCTCTCAAAG
1 TTGTGTCTCAAAGTTGTCCCTCAAAG
1531757 TTGTGTCT--AAGATTGTCCCTCAA
1 TTGTGTCTCAAAG-TTGTCCCTCAA
1531780 CTATCCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 10 0.48
26 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (26 bp):
TTGTGTCTCAAAGTTGTCCCTCAAAG
Found at i:1536601 original size:22 final size:22
Alignment explanation
Indices: 1536574--1536616 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1536564 TTGATTGTTG
1536574 ACTTTGAC-CAGAGTTGACTTTA
1 ACTTTGACTC-GAGTTGACTTTA
*
1536596 ACTTTGACTCGCGTTGACTTT
1 ACTTTGACTCGAGTTGACTTT
1536617 GACCAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (22 bp):
ACTTTGACTCGAGTTGACTTTA
Found at i:1542245 original size:24 final size:23
Alignment explanation
Indices: 1542218--1542267 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
1542208 AATGTTTGCA
*
1542218 AACGAGTTCATTTATATGTTCACG
1 AACGAGTTCATTTA-ACGTTCACG
*
1542242 AACGTGTTCATTTAACGTTCACG
1 AACGAGTTCATTTAACGTTCACG
1542265 AAC
1 AAC
1542268 ATGTTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (23 bp):
AACGAGTTCATTTAACGTTCACG
Found at i:1542265 original size:23 final size:24
Alignment explanation
Indices: 1542218--1542272 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
1542208 AATGTTTGCA
* *
1542218 AACGAGTTCATTTATATGTTCACG
1 AACGTGTTCATTTATACGTTCACG
1542242 AACGTGTTCATTTA-ACGTTCACG
1 AACGTGTTCATTTATACGTTCACG
*
1542265 AACATGTT
1 AACGTGTT
1542273 TGTTTAGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (24 bp):
AACGTGTTCATTTATACGTTCACG
Found at i:1543183 original size:49 final size:50
Alignment explanation
Indices: 1543118--1543223 Score: 151
Period size: 49 Copynumber: 2.1 Consensus size: 50
1543108 TATACTAGCG
* * *
1543118 CTATCAACACATTCTTAAACCGGTTTAAGTTAGTT-TTTCATTTACTAAA
1 CTATCAACACATTCTTAAACCGATATAAGTTAGTTCTTCCATTTACTAAA
* * *
1543167 CTATCAACACCTTCTTATACCGATATAAGTTAGTTCTTCCATTTACTAAC
1 CTATCAACACATTCTTAAACCGATATAAGTTAGTTCTTCCATTTACTAAA
1543217 CTATCAA
1 CTATCAA
1543224 TGCTTCCTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
49 31 0.62
50 19 0.38
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (50 bp):
CTATCAACACATTCTTAAACCGATATAAGTTAGTTCTTCCATTTACTAAA
Found at i:1543497 original size:50 final size:50
Alignment explanation
Indices: 1543418--1543521 Score: 145
Period size: 50 Copynumber: 2.1 Consensus size: 50
1543408 TATACTGGCG
* * * *
1543418 CTATCAACACATTCTTAAACTGGTTTAAGTTAGTTCTTTCATTTACTAAA
1 CTATCAACACATTCTTAAACCGATATAAGTTAGTTCTTCCATTTACTAAA
* * *
1543468 CTATCAACACCTTCTTATACCGATATAAGTTAGTTCTTCCATTTACTAAC
1 CTATCAACACATTCTTAAACCGATATAAGTTAGTTCTTCCATTTACTAAA
1543518 CTAT
1 CTAT
1543522 ATCAATGCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (50 bp):
CTATCAACACATTCTTAAACCGATATAAGTTAGTTCTTCCATTTACTAAA
Found at i:1543637 original size:303 final size:301
Alignment explanation
Indices: 1542840--1543964 Score: 1752
Period size: 303 Copynumber: 3.8 Consensus size: 301
1542830 CTTAAATCGA
* * * **
1542840 TTTAATTTAGTTCTTTCATTCACTAAACTATCAACACCTCCTCTTTATACCGATGTAAGTCGGTT
1 TTTAAGTTAGTTCTTTCATTTACTAAACTATCAACACCT--TC-TTATACCGATATAAGTTAGTT
* ** *
1542905 CTTCCATTTTCTAACCTATCAATAATTCCTTACACCGGTGTAAGCTAGTTCTTTCCTTTACTCAA
63 CTTCCATTTACTAACCTATCAATGCTTCCTTACACCAGTGTAAGCTAGTTCTTTCCTTTACTCAA
1542970 CCATCAACACCTAATTACATCTGCTTACACACGACACTC-C-CATTTCACGTATTGTATTTGATG
128 CCATCAACACCTAATTACATCTGCTTACACACGACACTCTCTCATTTCACGTATTGTATTTGATG
* *
1543033 TTGAGAACACAAG-T-TTTTGTTGATGAGATGTAGACAATTCCAAATTGATGGTGTAGAAGCCTG
193 TTGAGAACAC-AGTTCTTTTGTTGATGAGATGTAGAAAATTCCAAATTGATGGTGCAGAAGCCTG
*
1543096 TCTATCCCTCCTTATACTAGCGCTATCAACACATTCTTAAACCGG
257 TCTATCCCTCCTTATACTAGCGCTATCAACACATTCTTAAACTGG
1543141 TTTAAGTTAGTT-TTTCATTTACTAAACTATCAACACCTTCTTATACCGATATAAGTTAGTTCTT
1 TTTAAGTTAGTTCTTTCATTTACTAAACTATCAACACCTTCTTATACCGATATAAGTTAGTTCTT
*
1543205 CCATTTACTAACCTATCAATGCTTCCTTGCACCAGTGTAAGCTAGTTCTTTCCTTTACTCAACCA
66 CCATTTACTAACCTATCAATGCTTCCTTACACCAGTGTAAGCTAGTTCTTTCCTTTACTCAACCA
*
1543270 TCAACACCTAATTACATCTGCTTACACACGACACTCTCTCATTTCACGTATTGCATTTGATGTTG
131 TCAACACCTAATTACATCTGCTTACACACGACACTCTCTCATTTCACGTATTGTATTTGATGTTG
*
1543335 AGAACACAGTTCTTTTGTTGATGAGATGTAGAAAATTCCAAATTGATGGTGCAGAAGCTTGTCTA
196 AGAACACAGTTCTTTTGTTGATGAGATGTAGAAAATTCCAAATTGATGGTGCAGAAGCCTGTCTA
*
1543400 TCCCTCCTTATACTGGCGCTATCAACACATTCTTAAACTGG
261 TCCCTCCTTATACTAGCGCTATCAACACATTCTTAAACTGG
1543441 TTTAAGTTAGTTCTTTCATTTACTAAACTATCAACACCTTCTTATACCGATATAAGTTAGTTCTT
1 TTTAAGTTAGTTCTTTCATTTACTAAACTATCAACACCTTCTTATACCGATATAAGTTAGTTCTT
* * *
1543506 CCATTTACTAACCTATATCAATGCTTCTTTACACCAGTGTATGCTAGTTATTTCCTTTACTCAAC
66 CCATTTACTAACC--TATCAATGCTTCCTTACACCAGTGTAAGCTAGTTCTTTCCTTTACTCAAC
* * * *
1543571 CATCAACACCTAATTACATCTGCTTGCACACGGCACTCTCTCATTTCATGCATTGTATTTGATGT
129 CATCAACACCTAATTACATCTGCTTACACACGACACTCTCTCATTTCACGTATTGTATTTGATGT
*
1543636 TGAGAACACAGTTCTTTTGTTCATGAGATGTA-AACAATTCCAAATTGATGGTGCAGAAGCCTGT
194 TGAGAACACAGTTCTTTTGTTGATGAGATGTAGAA-AATTCCAAATTGATGGTGCAGAAGCCTGT
* *
1543700 CTATCCCTCATTATACTAGCGCTATCAGCACATTCTTAAACTGG
258 CTATCCCTCCTTATACTAGCGCTATCAACACATTCTTAAACTGG
* * *
1543744 --T---TTAGTTCTTTCATTTACTAAACTATCAACACCTTCTTTTATCGATGTAAGTTAGTTCTT
1 TTTAAGTTAGTTCTTTCATTTACTAAACTATCAACACCTTCTTATACCGATATAAGTTAGTTCTT
** *
1543804 CCATTTACTAAAATATCAATGCTTCCTTACACCAGTGTAAGCTAGTTCTTTCTTTTACTCAACCA
66 CCATTTACTAACCTATCAATGCTTCCTTACACCAGTGTAAGCTAGTTCTTTCCTTTACTCAACCA
* * *
1543869 TCAACACCTAATTACATCTGCTTGCACAC-AGCACTCTCCCATTTCACGTATAGTATTTGATGTT
131 TCAACACCTAATTACATCTGCTTACACACGA-CACTCTCTCATTTCACGTATTGTATTTGATGTT
* **
1543933 GAGAACACAATTCTTTTACTGATGAGATGTAG
195 GAGAACACAGTTCTTTTGTTGATGAGATGTAG
1543965 GCATGGGTTT
Statistics
Matches: 766, Mismatches: 48, Indels: 24
0.91 0.06 0.03
Matches are distributed among these distances:
296 133 0.17
297 117 0.15
298 72 0.09
299 33 0.04
300 126 0.16
301 77 0.10
302 2 0.00
303 206 0.27
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (301 bp):
TTTAAGTTAGTTCTTTCATTTACTAAACTATCAACACCTTCTTATACCGATATAAGTTAGTTCTT
CCATTTACTAACCTATCAATGCTTCCTTACACCAGTGTAAGCTAGTTCTTTCCTTTACTCAACCA
TCAACACCTAATTACATCTGCTTACACACGACACTCTCTCATTTCACGTATTGTATTTGATGTTG
AGAACACAGTTCTTTTGTTGATGAGATGTAGAAAATTCCAAATTGATGGTGCAGAAGCCTGTCTA
TCCCTCCTTATACTAGCGCTATCAACACATTCTTAAACTGG
Found at i:1544672 original size:49 final size:49
Alignment explanation
Indices: 1544580--1544676 Score: 117
Period size: 49 Copynumber: 2.0 Consensus size: 49
1544570 AACCGTAATA
* * * *
1544580 AAAATTAATCCTTACTTATACGGGTGGAAGAATGTGTACCACCATCATG
1 AAAATTAAACCTTACTTACACGGGTGGAAGAATGTGCAACACCATCATG
*
1544629 AAAATTAAACCTTAGTTACACGGGT-GAATGTAA-GTGCAACACCATCAT
1 AAAATTAAACCTTACTTACACGGGTGGAA-G-AATGTGCAACACCATCAT
1544677 AATTACACAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 3 0.07
49 36 0.88
50 2 0.05
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (49 bp):
AAAATTAAACCTTACTTACACGGGTGGAAGAATGTGCAACACCATCATG
Found at i:1546605 original size:39 final size:39
Alignment explanation
Indices: 1546551--1546627 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
1546541 AACAATAAAT
*
1546551 TATTTGATTTAGTAGTTTAGATTAACTAGAACTCTATCA
1 TATTTCATTTAGTAGTTTAGATTAACTAGAACTCTATCA
* * *
1546590 TATTTCATTTAGTAGTTTATATTAACTATAACTTTATC
1 TATTTCATTTAGTAGTTTAGATTAACTAGAACTCTATC
1546628 CTTTTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.48
Consensus pattern (39 bp):
TATTTCATTTAGTAGTTTAGATTAACTAGAACTCTATCA
Found at i:1553182 original size:250 final size:248
Alignment explanation
Indices: 1552744--1553241 Score: 937
Period size: 250 Copynumber: 2.0 Consensus size: 248
1552734 CGTGATCTTC
1552744 CCCTAAAGTTTTTGGTTGTTCTACATTTGTTCATATTTATCCTATTCATAGATCTAAAAGGATCC
1 CCCTAAAGTTTTTGGTTGTTCTACATTTGTTCATATTTATCCTATTCATAGATCTAAAAGGATCC
1552809 AGGTCAGTAAAAATGCATTTTTCTCAGCTATTCATCTACTAAGAAGGACTACAAATCCATTCTCT
66 AGGTCAGTAAAAATGCATTTTTCTCAGCTATTCATCTACTAAGAAGGACTACAAATCCATTCTCT
1552874 GTTACAAGAAAGACAAATCTCTATGGATGTTACTTTCTGGAAATTATTCCTTGAAATCTGAAATT
131 GTTACAAGAAAGACAAATCTCTATGGATGTTACTTTCTGGAAATTATTCCTTGAAATCTGAAATT
1552939 CAGGGGAGATTCAGGATGAATTTCATGTACAG-TTTTGACAGCCTTCAACATT
196 CAGGGGAGATTCAGGATGAATTTCATGTACAGTTTTTGACAGCCTTCAACATT
*
1552991 CCCTAAAGTTTTTGGTTGTTCTACATTTGTTCATATTTATCCTATTCATAGATCTAAACTGGATC
1 CCCTAAAGTTTTTGGTTGTTCTACATTTGTTCATATTTATCCTATTCATAGATCTAAA-AGGATC
1553056 CAAGGTCAGT-AAAATGCATTTTTCTCAGCTATTCATCTACTAAGAAGGACTACAAATCCTATTC
65 C-AGGTCAGTAAAAATGCATTTTTCTCAGCTATTCATCTACTAAGAAGGACTACAAATCC-ATTC
1553120 TCTGGTTACAAGAAAGACAAATCTCTATGGATGTTACTTTCTGGAAATTATTCCTTGAAATCTGA
128 TCT-GTTACAAGAAAGACAAATCTCTATGGATGTTACTTTCTGGAAATTATTCCTTGAAATCTGA
1553185 AATTCAGGGGAGATTCAGGATGAATTTCATGTACAGTTTTTGACAGCCTTCAACATT
192 AATTCAGGGGAGATTCAGGATGAATTTCATGTACAGTTTTTGACAGCCTTCAACATT
1553242 TGACATGTTT
Statistics
Matches: 245, Mismatches: 1, Indels: 6
0.97 0.00 0.02
Matches are distributed among these distances:
247 58 0.24
248 55 0.22
249 15 0.06
250 97 0.40
251 20 0.08
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (248 bp):
CCCTAAAGTTTTTGGTTGTTCTACATTTGTTCATATTTATCCTATTCATAGATCTAAAAGGATCC
AGGTCAGTAAAAATGCATTTTTCTCAGCTATTCATCTACTAAGAAGGACTACAAATCCATTCTCT
GTTACAAGAAAGACAAATCTCTATGGATGTTACTTTCTGGAAATTATTCCTTGAAATCTGAAATT
CAGGGGAGATTCAGGATGAATTTCATGTACAGTTTTTGACAGCCTTCAACATT
Found at i:1553306 original size:42 final size:42
Alignment explanation
Indices: 1553259--1553339 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
1553249 TTTTCTTTTT
1553259 AATCCTACATCTCAACCGATACTAGCTTTTGAACCTCATTCC
1 AATCCTACATCTCAACCGATACTAGCTTTTGAACCTCATTCC
* *
1553301 AATCCTACATCTCAACCGATATTAGCTTTTGAATCTCAT
1 AATCCTACATCTCAACCGATACTAGCTTTTGAACCTCAT
1553340 CCTTCACCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (42 bp):
AATCCTACATCTCAACCGATACTAGCTTTTGAACCTCATTCC
Found at i:1555710 original size:27 final size:27
Alignment explanation
Indices: 1555637--1555710 Score: 114
Period size: 26 Copynumber: 2.8 Consensus size: 27
1555627 GACGTGGCAG
1555637 TTTCTAGAAGGTCCAGTCAGCAACAGT
1 TTTCTAGAAGGTCCAGTCAGCAACAGT
*
1555664 TTT-TAGAAGGTCCAGCCAGCAACAGT
1 TTTCTAGAAGGTCCAGTCAGCAACAGT
* *
1555690 TTTCTAGAAGATCTAGTCAGC
1 TTTCTAGAAGGTCCAGTCAGC
1555711 GCATTTTGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 25 0.60
27 17 0.40
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (27 bp):
TTTCTAGAAGGTCCAGTCAGCAACAGT
Found at i:1555969 original size:24 final size:24
Alignment explanation
Indices: 1555927--1555977 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
1555917 AAATTCTTTC
* *
1555927 TTTTCTTTTCTTTTCAAGTTTTCAT
1 TTTTATTTTATTTTCAAGTTTT-AT
1555952 TTTTATTTTATTTT-AAGTTTTAT
1 TTTTATTTTATTTTCAAGTTTTAT
1555975 TTT
1 TTT
1555978 AAATATGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.21
24 7 0.29
25 12 0.50
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.73
Consensus pattern (24 bp):
TTTTATTTTATTTTCAAGTTTTAT
Found at i:1555972 original size:12 final size:12
Alignment explanation
Indices: 1555932--1555979 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
1555922 CTTTCTTTTC
*
1555932 TTTTCTTTTCAAG
1 TTTTATTTT-AAG
*
1555945 TTTTCATTTTTA-
1 TTTT-ATTTTAAG
1555957 TTTTATTTTAAG
1 TTTTATTTTAAG
1555969 TTTTATTTTAA
1 TTTTATTTTAA
1555980 ATATGCTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 6 0.20
12 15 0.50
13 5 0.17
14 4 0.13
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (12 bp):
TTTTATTTTAAG
Found at i:1561614 original size:202 final size:207
Alignment explanation
Indices: 1561268--1561676 Score: 767
Period size: 202 Copynumber: 2.0 Consensus size: 207
1561258 AACACTTATT
1561268 CTCGCCACACACGAGTAAAACCATGGAGAAATTATCTTAAGCAATCGTACAGAAAGCCAACAGTG
1 CTCGCCACACACGAGTAAAACCATGGAGAAATTATCTTAAGCAATCGTACAGAAAGCCAACAGTG
1561333 GTTGGCGCTAGGTTGAATTTCAACCTAAACATCATATTAAAAGACTTGTATGTAAAAGAGGATTT
66 GTTGGCGCTAGGTTGAATTTCAACCTAAACATCATATTAAAAGACTTGTATGTAAAAGAGGATTT
1561398 CAAGACTACAAGAAATCAGTTCCTAAAAGAGAAAAAA-C-CGAATAAAACACAT-AA-AC-CA-C
131 CAAGACTACAAGAAATCAGTTCCTAAAA-AGAAAAAACCTCGAATAAAACACATAAAGACACATC
1561457 ACATTGATCCTGG
195 ACATTGATCCTGG
1561470 CTCGCCACACACGAGTAAAACCATGGAGAAATTATCTTAAGCAATCGTACAGAAAGCCAACAGTG
1 CTCGCCACACACGAGTAAAACCATGGAGAAATTATCTTAAGCAATCGTACAGAAAGCCAACAGTG
1561535 GTTGGCGCTAGGTTGAATTTCAACCTAAACATCATATTAAAAGACTTGTATGTAAAAGAGGATTT
66 GTTGGCGCTAGGTTGAATTTCAACCTAAACATCATATTAAAAGACTTGTATGTAAAAGAGGATTT
1561600 CAAGACTACAAGAAATCAGTTCCTAAAAAGAAAAAACCTCGAATAAAACACATAAAGACACATCA
131 CAAGACTACAAGAAATCAGTTCCTAAAAAGAAAAAACCTCGAATAAAACACATAAAGACACATCA
1561665 CATTGATCCTGG
196 CATTGATCCTGG
1561677 TAAATGTTTC
Statistics
Matches: 201, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
201 8 0.04
202 159 0.79
203 14 0.07
204 2 0.01
205 2 0.01
206 2 0.01
207 14 0.07
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.22
Consensus pattern (207 bp):
CTCGCCACACACGAGTAAAACCATGGAGAAATTATCTTAAGCAATCGTACAGAAAGCCAACAGTG
GTTGGCGCTAGGTTGAATTTCAACCTAAACATCATATTAAAAGACTTGTATGTAAAAGAGGATTT
CAAGACTACAAGAAATCAGTTCCTAAAAAGAAAAAACCTCGAATAAAACACATAAAGACACATCA
CATTGATCCTGG
Found at i:1565381 original size:16 final size:17
Alignment explanation
Indices: 1565344--1565375 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1565334 GGAGGCAACC
1565344 CATTTTTAATTTTATTG
1 CATTTTTAATTTTATTG
1565361 CATTTTT-ATTTTATT
1 CATTTTTAATTTTATT
1565376 TTATTTCGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (17 bp):
CATTTTTAATTTTATTG
Found at i:1567608 original size:134 final size:134
Alignment explanation
Indices: 1567364--1567630 Score: 525
Period size: 134 Copynumber: 2.0 Consensus size: 134
1567354 CTTAAAGTTA
1567364 TAACATATTAAATATTACAATAACCATAAGACAACTACATTTCAGAGCATTTTCATAAGTCTATT
1 TAACATATTAAATATTACAATAACCATAAGACAACTACATTTCAGAGCATTTTCATAAGTCTATT
1567429 ACATGTCATCTAGTTATCAAAAGTAGACATATTTGTCATACAGTTACTGATGAGGCAACCTTTGA
66 ACATGTCATCTAGTTATCAAAAGTAGACATATTTGTCATACAGTTACTGATGAGGCAACCTTTGA
1567494 TTTT
131 TTTT
1567498 TAACATATTAAATATTACAATAACCATAAGACAACTACATTTCAGAGCATTTTCATAAGTCTATT
1 TAACATATTAAATATTACAATAACCATAAGACAACTACATTTCAGAGCATTTTCATAAGTCTATT
*
1567563 ACATGTCATCTAGTTATCAAAAGTAGACATATTTGTCATATAGTTACTGATGAGGCAACCTTTGA
66 ACATGTCATCTAGTTATCAAAAGTAGACATATTTGTCATACAGTTACTGATGAGGCAACCTTTGA
1567628 TTT
131 TTT
1567631 ATAATGTCTG
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 132 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (134 bp):
TAACATATTAAATATTACAATAACCATAAGACAACTACATTTCAGAGCATTTTCATAAGTCTATT
ACATGTCATCTAGTTATCAAAAGTAGACATATTTGTCATACAGTTACTGATGAGGCAACCTTTGA
TTTT
Found at i:1568298 original size:132 final size:133
Alignment explanation
Indices: 1567989--1568393 Score: 525
Period size: 132 Copynumber: 3.0 Consensus size: 133
1567979 CAAACTCATT
* * * * *
1567989 ATGAATTCCATGGATGCATA-CATAGTGCCGAAAGTACATATAGTACTGATAAGAAAATGCAACA
1 ATGAATACCATGGTTGCACATC-TAGTGCCGAAAGTACACATAGTACTGATACGAAAATGCAACA
* ** * * * * * * * *
1568053 -TATGCATTAAACAAAATC-ATCGATAACTTTTATACATAATTGTAT-GTCAAAATTGTAAT-TC
65 TTATGCATTACACAAAATCGATCGATAACCATTATATACACTT-TTTGGT-GAAA-TGCACTATG
*
1568114 ACAAACTCA
127 AC--TCTCA
1568123 TTATGAATACCATGGTTGCACATCTAGTGCCGAAAGTACACATAGTACTGATACGAAAATGCAAC
1 --ATGAATACCATGGTTGCACATCTAGTGCCGAAAGTACACATAGTACTGATACGAAAATGCAAC
1568188 ATTATGCATTACACAAAATCGATCGATAACCATTATATACACTTTTTGGTGAAATGCACTATGAC
64 ATTATGCATTACACAAAATCGATCGATAACCATTATATACACTTTTTGGTGAAATGCACTATGAC
1568253 TCTCA
129 TCTCA
1568258 ATGAATA-CATGGTTGCACATCTAGTGCCGAAAGTACACATAGTACTGATACGAAAATGCAACAT
1 ATGAATACCATGGTTGCACATCTAGTGCCGAAAGTACACATAGTACTGATACGAAAATGCAACAT
*
1568322 TATGCATTACACAAAATCGATCGATAACCATTATATACACTTTTTGTTGAAATGCAACTATGACT
66 TATGCATTACACAAAATCGATCGATAACCATTATATACACTTTTTGGTGAAATGC-ACTATGACT
1568387 CTCA
130 CTCA
1568391 ATG
1 ATG
1568394 CACATACACT
Statistics
Matches: 245, Mismatches: 18, Indels: 15
0.88 0.06 0.05
Matches are distributed among these distances:
132 111 0.45
133 23 0.09
135 4 0.02
136 61 0.25
137 26 0.11
138 20 0.08
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (133 bp):
ATGAATACCATGGTTGCACATCTAGTGCCGAAAGTACACATAGTACTGATACGAAAATGCAACAT
TATGCATTACACAAAATCGATCGATAACCATTATATACACTTTTTGGTGAAATGCACTATGACTC
TCA
Found at i:1575501 original size:137 final size:137
Alignment explanation
Indices: 1575230--1575508 Score: 411
Period size: 137 Copynumber: 2.0 Consensus size: 137
1575220 CTAAGTGCCA
* * *
1575230 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATGAACACATAGTGCCGAAAGTACATATA
1 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGAACACATAGTGCCAAAAGTACAGATA
* ** *
1575295 GTACTGATATGAAAATGCAACATATGCATTAAGCAAAATCGATCGATAACTTTTATACATAATTA
66 GTACTGATACGAAAATGCAACATATGCATTAAGCAAAATCGATCGATAACCATTATACACAATTA
1575360 TATGTCG
131 TATGTCG
* *
1575367 AAATGGTAATTCACAAACTCATTATGAATACCATGGTTGCACATC-TAGTGCCAAAAGTACAGAT
1 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGAACA-CATAGTGCCAAAAGTACAGAT
* *
1575431 AGTACTGATACGAAAATGCAACATTATGCATTACA-CAAAATCGATCGATGACCATTATATACAA
65 AGTACTGATACGAAAATGCAACA-TATGCATTA-AGCAAAATCGATCGATAACCATTATACACAA
1575495 TT-TATGTCG
128 TTATATGTCG
1575504 AAATG
1 AAATG
1575509 AACCTATGAC
Statistics
Matches: 128, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
137 91 0.71
138 36 0.28
139 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (137 bp):
AAATGGTAATTCACAAACTCATTATGAATACCATGGATGAACACATAGTGCCAAAAGTACAGATA
GTACTGATACGAAAATGCAACATATGCATTAAGCAAAATCGATCGATAACCATTATACACAATTA
TATGTCG
Found at i:1577263 original size:26 final size:26
Alignment explanation
Indices: 1577230--1577292 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
1577220 GTCGGTTCTA
1577230 ACATTGAGTGTTTCTATACCCCAAAC
1 ACATTGAGTGTTTCTATACCCCAAAC
* * *
1577256 ACATTGAGTATTTCTGTACTCCAAAC
1 ACATTGAGTGTTTCTATACCCCAAAC
*
1577282 ATATTGAGTGT
1 ACATTGAGTGT
1577293 GTTAGGTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (26 bp):
ACATTGAGTGTTTCTATACCCCAAAC
Found at i:1578518 original size:244 final size:244
Alignment explanation
Indices: 1578089--1578576 Score: 976
Period size: 244 Copynumber: 2.0 Consensus size: 244
1578079 TGATATCGCG
1578089 CCCATACACGATAGAATCCCTAAGGGTGATCACTGGACCCCATAAACCAACAGAGTGATTTGAGT
1 CCCATACACGATAGAATCCCTAAGGGTGATCACTGGACCCCATAAACCAACAGAGTGATTTGAGT
1578154 GAATCCAGGTAAGGTGTTGAGTTATGAGCATTGATATTGATGAATGAATGGATGTTACAATTGTA
66 GAATCCAGGTAAGGTGTTGAGTTATGAGCATTGATATTGATGAATGAATGGATGTTACAATTGTA
1578219 TTTAGCTTATTCCATTTGGTGATGTTCAATTGATTGGTGTCTTGACTTGGATGATTATTGTGGTC
131 TTTAGCTTATTCCATTTGGTGATGTTCAATTGATTGGTGTCTTGACTTGGATGATTATTGTGGTC
1578284 TCTACCTTTCATCCTCTAATGTGAGACTTGACAAAGAAAGGTAAATGTA
196 TCTACCTTTCATCCTCTAATGTGAGACTTGACAAAGAAAGGTAAATGTA
1578333 CCCATACACGATAGAATCCCTAAGGGTGATCACTGGACCCCATAAACCAACAGAGTGATTTGAGT
1 CCCATACACGATAGAATCCCTAAGGGTGATCACTGGACCCCATAAACCAACAGAGTGATTTGAGT
1578398 GAATCCAGGTAAGGTGTTGAGTTATGAGCATTGATATTGATGAATGAATGGATGTTACAATTGTA
66 GAATCCAGGTAAGGTGTTGAGTTATGAGCATTGATATTGATGAATGAATGGATGTTACAATTGTA
1578463 TTTAGCTTATTCCATTTGGTGATGTTCAATTGATTGGTGTCTTGACTTGGATGATTATTGTGGTC
131 TTTAGCTTATTCCATTTGGTGATGTTCAATTGATTGGTGTCTTGACTTGGATGATTATTGTGGTC
1578528 TCTACCTTTCATCCTCTAATGTGAGACTTGACAAAGAAAGGTAAATGTA
196 TCTACCTTTCATCCTCTAATGTGAGACTTGACAAAGAAAGGTAAATGTA
1578577 ATTTTTGGCT
Statistics
Matches: 244, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
244 244 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (244 bp):
CCCATACACGATAGAATCCCTAAGGGTGATCACTGGACCCCATAAACCAACAGAGTGATTTGAGT
GAATCCAGGTAAGGTGTTGAGTTATGAGCATTGATATTGATGAATGAATGGATGTTACAATTGTA
TTTAGCTTATTCCATTTGGTGATGTTCAATTGATTGGTGTCTTGACTTGGATGATTATTGTGGTC
TCTACCTTTCATCCTCTAATGTGAGACTTGACAAAGAAAGGTAAATGTA
Found at i:1579166 original size:24 final size:24
Alignment explanation
Indices: 1579129--1579176 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1579119 TTCTTTTCTC
*
1579129 TTTTTTTTTGAAGTTTTCATTTTTA
1 TTTTATTTTGAAGTTTT-ATTTTTA
1579154 TTTTATTTT-AAGTTTTATTTTTA
1 TTTTATTTTGAAGTTTTATTTTTA
1579177 AATATGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (24 bp):
TTTTATTTTGAAGTTTTATTTTTA
Found at i:1585901 original size:11 final size:11
Alignment explanation
Indices: 1585885--1585913 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1585875 TTCAGACTAT
1585885 GGAATTTTGAA
1 GGAATTTTGAA
1585896 GGAATTTTGAA
1 GGAATTTTGAA
1585907 GGAATTT
1 GGAATTT
1585914 GTTACTGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (11 bp):
GGAATTTTGAA
Found at i:1586073 original size:17 final size:17
Alignment explanation
Indices: 1586033--1586077 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1586023 GATATTCCGT
* *
1586033 AAGAATTGAAGTTGTTG
1 AAGACTTGAAGTTGTCG
*
1586050 CAGACTTGAAGTTGTCG
1 AAGACTTGAAGTTGTCG
*
1586067 AATACTTGAAG
1 AAGACTTGAAG
1586078 ACCAAATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (17 bp):
AAGACTTGAAGTTGTCG
Found at i:1587071 original size:29 final size:28
Alignment explanation
Indices: 1587025--1587130 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 28
1587015 AAATTAAAGA
* * *
1587025 ATATTTTATATATCTTAAATT-TTAAAATT
1 ATATTTTATTTTTTTTAAATTATT-AAA-T
* *
1587054 ATCTTTTATTTTTTTTAACTTATTAAAT
1 ATATTTTATTTTTTTTAAATTATTAAAT
*
1587082 ATATTTTATTTTTTTCTTAACTTATTAAAT
1 ATATTTTA-TTTTTT-TTAAATTATTAAAT
*
1587112 ATATTTAATTTTATTTTAA
1 ATATTTTATTTT-TTTTAA
1587131 TGTAAAAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
28 8 0.12
29 33 0.50
30 25 0.38
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (28 bp):
ATATTTTATTTTTTTTAAATTATTAAAT
Found at i:1587092 original size:28 final size:28
Alignment explanation
Indices: 1587057--1587130 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 28
1587047 TAAAATTATC
1587057 TTTTATTTTTTTTAACTTATTAAATATA
1 TTTTATTTTTTTTAACTTATTAAATATA
1587085 TTTTATTTTTTTCTTAACTTATTAAATATA
1 TTTTA-TTTTTT-TTAACTTATTAAATATA
*
1587115 TTTAATTTTATTTTAA
1 TTTTATTTT-TTTTAA
1587131 TGTAAAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
28 5 0.12
29 14 0.33
30 23 0.55
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTATTTTTTTTAACTTATTAAATATA
Found at i:1587246 original size:29 final size:29
Alignment explanation
Indices: 1587208--1587302 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 29
1587198 ATATATTTAA
*
1587208 ATATTTTATTCTTATCTTCACTTAAAAAT
1 ATATTTTATTCTTATCTTAACTTAAAAAT
* * *
1587237 ATATTTTATTTTTATTTTAAAATTAAAAAT
1 ATATTTTATTCTTATCTT-AACTTAAAAAT
*
1587267 ATATTTTA-TCGTTATCTAAACTTTCAAAAAT
1 ATATTTTATTC-TTATCTTAAC-TT-AAAAAT
1587298 ATATT
1 ATATT
1587303 AAAATATATT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
29 19 0.35
30 24 0.44
31 11 0.20
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (29 bp):
ATATTTTATTCTTATCTTAACTTAAAAAT
Found at i:1587642 original size:25 final size:23
Alignment explanation
Indices: 1587593--1587645 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 23
1587583 AAATAAAAAT
*
1587593 AAATATATTTAATAAGTTAAGAA
1 AAATATATTTAATAAGTTAACAA
1587616 AAATATATTTAATAAGTTAAAACAA
1 AAATATATTTAATAAGTT--AACAA
1587641 AAATA
1 AAATA
1587646 AAAGATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 18 0.67
25 9 0.33
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (23 bp):
AAATATATTTAATAAGTTAACAA
Found at i:1589742 original size:689 final size:686
Alignment explanation
Indices: 1588336--1590660 Score: 2939
Period size: 689 Copynumber: 3.3 Consensus size: 686
1588326 GCAAGATGGA
* *
1588336 TTTTCAATTGTATGGAAGTAATTCTCGATTGATCTAGTGATACTTCAATGGATATTACGTAAGAA
1 TTTTCAATTGCATGGAAGTAATTCTCAATTGATCTAGTGATACTTCAATGGATATTACGTAAGAA
* ** * * * *
1588401 TTGAAGTTGTTGAAGACTTGACAACGGTGTTTTAACGGATTTGTGACTTACATAAAAATTGAAGT
66 TTGAAGTTATTGAAGACTTGACAATAGTCTTTTAACAGATATGTGACTTACATAAAGATTGAAGT
* * * *
1588466 TGTTGAAAACCTAATA-ACCAAATTTTGATGATATTTGGGTGAAGAGGGAGATTTGTTATATTTT
131 TGTTGAAAACTTAA-AGATCAAATTTTGATGAAATTTGGGTCAAGAGGGAGATTTGTTATATTTT
1588530 CACACAAATTA-AATTTGATAATTAAGTTGGATTTTATTGTAATAAAAATTCTTGGGGTCTTAAC
195 CACACAAATTATAATTTGATAATTAAGTTGGATTTTATTGTAATAAAAATTCTTGGGGTCTTAAC
1588594 CTATTGAGAGAGAATTATATTGGAGAGATGTAATCCTTTTTAGATCTCTACAACTTTTGAGGTTT
260 CTATTGAGAGAGAATTATATTGGAGAGATGTAATCCTTTTTAGATCTCTACAACTTTTGAGGTTT
*
1588659 ATATTGCAGAGATAGTTTTGTTGGGATTGAGAGTGTTTGGGATACAACGGGATGTG----ATATC
325 ATATTACAGAGATAGTTTTGTTGGGATTGAGAGTGTTTGGGATACAACGGGATGTGTTTTATATC
1588720 TATATATGGTTTTGGGATACATGTAATATCATGTACTTGTACTCTTCGTGTTCTCTACATCTATA
390 TATATATGGTTTTGGGATACATGTAATATCATGTACTTGTACTCTTCGTGTTCTCTACATCTATA
1588785 ATGGATTATTGTTCATCTCGTTCATGGAGGTAGGCAAGACCAAACCATGTAAATCTTGTCTTCAA
455 ATGGATTATTGTTCATCTCGTTCATGGAGGTAGGCAAGACCAAACCATGTAAATCTTGTCTTCAA
1588850 TGCATGTCTTATTTTATATTGATATCGCTTTAGTTATTATTCTGCTTCCAAATTTATAATAAGTG
520 TGCATGTCTTATTTTATATTGATATCGCTTTAGTTATTATTCTGCTTCCAAATTTATAATAAGTG
1588915 GTATCAAAGCTATGGTTTGGTCTATGGAATTTTTAAGGAATTTATTGTTTCAGATTTTGTTAGCG
585 GTATCAAAGCTATGGTTTGGTCTATGGAATTTTTAAGGAATTTATTGTTTCAGATTTTGTTAGCG
*
1588980 ATTTTAGAGACACGCAAGATGAATTTGTTGTAATGAG
650 ATTTTAGAGACACGCAAGATGAATTTGTTGCAATGAG
* * * *
1589017 TTTTCAATTGCATGGAAATAATTCTCAATTGATCTAGTGATACTTTAATGGGTATTACGTAATAA
1 TTTTCAATTGCATGGAAGTAATTCTCAATTGATCTAGTGATACTTCAATGGATATTACGTAAGAA
1589082 TTGAAGTTATTGAAGACTTGACAATAGTCTTTTAACAGATATGTGACTTACATAAAGATTGAAGT
66 TTGAAGTTATTGAAGACTTGACAATAGTCTTTTAACAGATATGTGACTTACATAAAGATTGAAGT
* * *
1589147 TATTGAAAACTTAAAGATCAAATTTTGATGATATTTGGGTGAAGAGGGAGATTTGTTATATTTTC
131 TGTTGAAAACTTAAAGATCAAATTTTGATGAAATTTGGGTCAAGAGGGAGATTTGTTATATTTTC
1589212 ACACAAATTA-AATTTGATAATTAAGTTGGATTTTATTGTAATAAAAATTCTTGGGGTCTTAACC
196 ACACAAATTATAATTTGATAATTAAGTTGGATTTTATTGTAATAAAAATTCTTGGGGTCTTAACC
1589276 TATTGAGAGAGAATTATATTGGAGAGATGTAATCCTTTTTAGATCTCTACAACTTTTGAGGTTTA
261 TATTGAGAGAGAATTATATTGGAGAGATGTAATCCTTTTTAGATCTCTACAACTTTTGAGGTTTA
1589341 TATTACAGAGATAGTTTTGTTGGGATTGAGAGTGTTTGGGATACAACGGGATGTGATATATATAT
326 TATTACAGAGATAGTTTTGTTGGGATTGAGAGTGTTTGGGATACAACGGGATGTG-T-T-T-TAT
*
1589406 ATATATATATGGTTTTGGGATACATGTAATATCATGTACTTGTACTCTTCGTGTTCTCTACATCT
387 ATCTATATATGGTTTTGGGATACATGTAATATCATGTACTTGTACTCTTCGTGTTCTCTACATCT
*
1589471 ATAATGGATTCTTGTTCATCTCGTTCATGGAGGTAGGCAAGACCAAACCATGTAAATCTTGTCTT
452 ATAATGGATTATTGTTCATCTCGTTCATGGAGGTAGGCAAGACCAAACCATGTAAATCTTGTCTT
*
1589536 CAATGCATGTCTTATTTTATATTGATATCGCTTTAGTTATTATTCTTCTTCCAAATTTATAATAA
517 CAATGCATGTCTTATTTTATATTGATATCGCTTTAGTTATTATTCTGCTTCCAAATTTATAATAA
1589601 GTGGTATCAAAGCTATGGTTTGGTCTATGGAATTTTTAAGGAATTTATTGTTTCAGATTTTGTTA
582 GTGGTATCAAAGCTATGGTTTGGTCTATGGAATTTTTAAGGAATTTATTGTTTCAGATTTTGTTA
1589666 GCGATTTTAGAGACACGCAAGATGAATTTGTTGCAATGAG
647 GCGATTTTAGAGACACGCAAGATGAATTTGTTGCAATGAG
* *
1589706 TTTTCAATTGCATGGAAGTAATTCTCAATTGATCTAGTGATACTTCAATGGGTATTACGTAATAA
1 TTTTCAATTGCATGGAAGTAATTCTCAATTGATCTAGTGATACTTCAATGGATATTACGTAAGAA
1589771 TTGAAGTTATTGAAGACTTGACAATAGTCTTTTAACAGATATGTGACTTACATAAAGATTGAAGT
66 TTGAAGTTATTGAAGACTTGACAATAGTCTTTTAACAGATATGTGACTTACATAAAGATTGAAGT
* * * * *
1589836 TGTTGAAAACTTAAAGATCAATTTTTGATGAAATTTGGGTCAAGGGGGAGTTTTGTCATATTTTG
131 TGTTGAAAACTTAAAGATCAAATTTTGATGAAATTTGGGTCAAGAGGGAGATTTGTTATATTTTC
* * * ** **
1589901 ACACAAATTATAA-TTGGTAATTAAATTTGATTTTAACGTAATGGAAATTCTTTGTGACCAAGTA
196 ACACAAATTATAATTTGATAATTAAGTTGGATTTTATTGTAATAAAAATTC--T-TG-----G--
* * *
1589965 TTTGGCTCTATAAATAGACATAATGTTTAACCTATTGAGAGAGAAATTTTTTTTTGAGAGATAGT
251 ---GG---------T---C-------TTAACCTATTGAGAGAG-AA-TTATATTGGAGAGAT-GT
** * * * * * * * * * *
1590030 AATTATTTTTGGAATCTTTATAACTTTTGGGGTTTATGTTACAAATATAGTTTTATAGTGATTGA
291 AATCCTTTTTAG-ATCTCTACAACTTTTGAGGTTTATATTACAGAGATAGTTTTGTTGGGATTGA
* * * *
1590095 GAGAGTTTTGGGATAC-AC---AAG-GTTTTGATATCTATATCA-GGTTTGGGGATACATGTGAT
355 GAGTG-TTTGGGATACAACGGGATGTGTTTT-ATATCTATAT-ATGGTTTTGGGATACATGTAAT
* * * * * * *
1590154 ATAATATACTTGTACTCTTTGTGTTCTCTATATCTATAATGGATTATTGTTCATTTTG-TCAATA
417 ATCATGTACTTGTACTCTTCGTGTTCTCTACATCTATAATGGATTATTGTTCATCTCGTTC-ATG
* *** * * * ** * *
1590218 AAGGTAGGCAATG-TTGAACCACGTTAAATCTTTTCTCCTGTGCATGTCGTATTTTATGTTGATA
481 GAGGTAGGCAA-GACCAAACCATG-TAAATCTTGTCTTCAATGCATGTCTTATTTTATATTGATA
* * * * * * * * * *
1590282 TCCCCTTGGTTATTTTTCTGCTTTCAAATTTTTAACAAGTGCTACCAAAGCTATGGTTCTAG-CT
544 TCGCTTTAGTTATTATTCTGCTTCCAAATTTATAATAAGTGGTATCAAAGCTATGGTT-TGGTCT
* * * * * * * * * *
1590346 ATGGAATTTTGAAGGAATGTGTTGCTGCGGATTTTGTAAGCAATTTTAGAGACATGTAAGATGAA
608 ATGGAATTTTTAAGGAATTTATTGTTTCAGATTTTGTTAGCGATTTTAGAGACACGCAAGATGAA
* * *
1590411 TTTGCTACAATTAG
673 TTTGTTGCAATGAG
* * * * * * *
1590425 TTTTTAGTTGCATGGAAGTAATTCTCGATTGATCCAGTGATACTGCAATGTATATTGCGTAAGAA
1 TTTTCAATTGCATGGAAGTAATTCTCAATTGATCTAGTGATACTTCAATGGATATTACGTAAGAA
* * * * * * *
1590490 TTGAAGTTGTTGAAGTCATGACAGTAGTGTTGTAAC-GAATATGT-AGCTTACATAAAGATTAAA
66 TTGAAGTTATTGAAGACTTGACAATAGTCTTTTAACAG-ATATGTGA-CTTACATAAAGATTGAA
* * * * *
1590553 GTTGTTGAATACTTGAAGA-CCAATTTTTATGAAATTTGGGTCAA-AGCGGAGATTTTTTATATT
129 GTTGTTGAAAACTTAAAGATCAAATTTTGATGAAATTTGGGTCAAGAG-GGAGATTTGTTATATT
* * * *
1590616 TTGACCCAAATTATAATTGGA-AATTAAGTTGTATTTTATTGTAAT
193 TTCACACAAATTATAATTTGATAATTAAGTTGGATTTTATTGTAAT
1590661 TATTTTAGGA
Statistics
Matches: 1453, Mismatches: 134, Indels: 77
0.87 0.08 0.05
Matches are distributed among these distances:
680 1 0.00
681 360 0.25
689 523 0.36
690 2 0.00
691 1 0.00
692 2 0.00
697 1 0.00
702 2 0.00
711 1 0.00
714 1 0.00
717 4 0.00
718 168 0.12
719 280 0.19
720 3 0.00
721 18 0.01
722 4 0.00
723 12 0.01
724 11 0.01
725 49 0.03
726 10 0.01
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (686 bp):
TTTTCAATTGCATGGAAGTAATTCTCAATTGATCTAGTGATACTTCAATGGATATTACGTAAGAA
TTGAAGTTATTGAAGACTTGACAATAGTCTTTTAACAGATATGTGACTTACATAAAGATTGAAGT
TGTTGAAAACTTAAAGATCAAATTTTGATGAAATTTGGGTCAAGAGGGAGATTTGTTATATTTTC
ACACAAATTATAATTTGATAATTAAGTTGGATTTTATTGTAATAAAAATTCTTGGGGTCTTAACC
TATTGAGAGAGAATTATATTGGAGAGATGTAATCCTTTTTAGATCTCTACAACTTTTGAGGTTTA
TATTACAGAGATAGTTTTGTTGGGATTGAGAGTGTTTGGGATACAACGGGATGTGTTTTATATCT
ATATATGGTTTTGGGATACATGTAATATCATGTACTTGTACTCTTCGTGTTCTCTACATCTATAA
TGGATTATTGTTCATCTCGTTCATGGAGGTAGGCAAGACCAAACCATGTAAATCTTGTCTTCAAT
GCATGTCTTATTTTATATTGATATCGCTTTAGTTATTATTCTGCTTCCAAATTTATAATAAGTGG
TATCAAAGCTATGGTTTGGTCTATGGAATTTTTAAGGAATTTATTGTTTCAGATTTTGTTAGCGA
TTTTAGAGACACGCAAGATGAATTTGTTGCAATGAG
Found at i:1590898 original size:144 final size:144
Alignment explanation
Indices: 1590638--1590925 Score: 576
Period size: 144 Copynumber: 2.0 Consensus size: 144
1590628 ATAATTGGAA
1590638 ATTAAGTTGTATTTTATTGTAATTATTTTAGGAACAAGAATTCTTTGTGACCAAGTATTTAGCTC
1 ATTAAGTTGTATTTTATTGTAATTATTTTAGGAACAAGAATTCTTTGTGACCAAGTATTTAGCTC
1590703 TATAAATAGAGATAGTCTTAACCTAATTAGAGAAAGAATTATTTTGGAGAGATGTAGTCCTTTTT
66 TATAAATAGAGATAGTCTTAACCTAATTAGAGAAAGAATTATTTTGGAGAGATGTAGTCCTTTTT
1590768 GGGATCTCTGTAAC
131 GGGATCTCTGTAAC
1590782 ATTAAGTTGTATTTTATTGTAATTATTTTAGGAACAAGAATTCTTTGTGACCAAGTATTTAGCTC
1 ATTAAGTTGTATTTTATTGTAATTATTTTAGGAACAAGAATTCTTTGTGACCAAGTATTTAGCTC
1590847 TATAAATAGAGATAGTCTTAACCTAATTAGAGAAAGAATTATTTTGGAGAGATGTAGTCCTTTTT
66 TATAAATAGAGATAGTCTTAACCTAATTAGAGAAAGAATTATTTTGGAGAGATGTAGTCCTTTTT
1590912 GGGATCTCTGTAAC
131 GGGATCTCTGTAAC
1590926 TTTTTGAGTT
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 144 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40
Consensus pattern (144 bp):
ATTAAGTTGTATTTTATTGTAATTATTTTAGGAACAAGAATTCTTTGTGACCAAGTATTTAGCTC
TATAAATAGAGATAGTCTTAACCTAATTAGAGAAAGAATTATTTTGGAGAGATGTAGTCCTTTTT
GGGATCTCTGTAAC
Found at i:1591437 original size:17 final size:17
Alignment explanation
Indices: 1591412--1591445 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1591402 AATGAGATAA
*
1591412 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
1591429 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
1591446 TGGGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:1592106 original size:70 final size:74
Alignment explanation
Indices: 1592021--1592229 Score: 293
Period size: 76 Copynumber: 2.9 Consensus size: 74
1592011 TAAAACATCT
* * *
1592021 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACATAAAA-AAA-AT-AT-TTAA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAATATAAA
*
1592081 AATAATATTC
65 AATAATATCC
*
1592091 TAAATCCTAATTAAAATACTAAAACCTATTTAAAGTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGAT--AATATAA
1592156 AAATAATATCC
64 AAATAATATCC
* *
1592167 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAATATAA
1592230 TGTTTAAAAT
Statistics
Matches: 124, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
69 5 0.04
70 40 0.32
71 3 0.02
72 2 0.02
74 7 0.06
75 2 0.02
76 65 0.52
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.28
Consensus pattern (74 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAATATAAAA
ATAATATCC
Found at i:1592180 original size:76 final size:77
Alignment explanation
Indices: 1592070--1592252 Score: 260
Period size: 76 Copynumber: 2.4 Consensus size: 77
1592060 ATACATAAAA
* * * *
1592070 AAAATATTTAAAATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAAGTAAAATACC
1 AAAATATTAAAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACC
1592135 TAAAACAAAGAT
66 TAAAACAAAGAT
*
1592147 AAAATA-TAAAAATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACC
1 AAAATATTAAAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACC
1592211 TAAAACAAAGAT
66 TAAAACAAAGAT
* * *
1592223 AATATAATGTTTAAAATATTATCCTAAAAC
1 -A-A-AATATTAAAAATAATATCCTAAAAC
1592253 TTTGAGTTTA
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
76 65 0.69
77 7 0.07
78 1 0.01
79 3 0.03
80 18 0.19
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (77 bp):
AAAATATTAAAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACC
TAAAACAAAGAT
Found at i:1594089 original size:22 final size:22
Alignment explanation
Indices: 1594064--1594110 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1594054 AATTTGACTA
* *
1594064 AAAATAAAGCAAAATTAAAATG
1 AAAATAAAACAAAAATAAAATG
1594086 AAAATAAAACAAAAATAAAATG
1 AAAATAAAACAAAAATAAAATG
1594108 AAA
1 AAA
1594111 TGGGTTGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAATAAAACAAAAATAAAATG
Found at i:1596989 original size:14 final size:14
Alignment explanation
Indices: 1596964--1597012 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
1596954 CCCTTTTGAT
1596964 TAATATTATTTTTA
1 TAATATTATTTTTA
*
1596978 TAAT-TTACTTTTGA
1 TAATATTA-TTTTTA
1596992 TTAATATTATTTTTA
1 -TAATATTATTTTTA
1597007 TAATAT
1 TAATAT
1597013 ACATTATTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 15 0.50
15 9 0.30
16 3 0.10
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (14 bp):
TAATATTATTTTTA
Found at i:1597004 original size:15 final size:15
Alignment explanation
Indices: 1596957--1597004 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1596947 ATTTCGTCCC
1596957 TTTTGATTAATATTA
1 TTTTGATTAATATTA
*
1596972 TTTTTA-TAAT-TTA
1 TTTTGATTAATATTA
1596985 CTTTTGATTAATATTA
1 -TTTTGATTAATATTA
1597001 TTTT
1 TTTT
1597005 TATAATATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 9 0.32
15 13 0.46
16 3 0.11
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (15 bp):
TTTTGATTAATATTA
Found at i:1597767 original size:18 final size:18
Alignment explanation
Indices: 1597744--1597780 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1597734 TGGTGTGCCA
1597744 CCGCCGATGAACGGCGGC
1 CCGCCGATGAACGGCGGC
1597762 CCGCCGATGAACGGCGGC
1 CCGCCGATGAACGGCGGC
1597780 C
1 C
1597781 GGCGCCGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.41, G:0.38, T:0.05
Consensus pattern (18 bp):
CCGCCGATGAACGGCGGC
Found at i:1598246 original size:2 final size:2
Alignment explanation
Indices: 1598241--1598276 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1598231 GTCCTTTTTC
*
1598241 TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1598277 AATACTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1598353 original size:9 final size:9
Alignment explanation
Indices: 1598331--1598393 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
1598321 TATATTATAT
1598331 TTTATTTTA
1 TTTATTTTA
*
1598340 ATTATTTCT-
1 TTTATTT-TA
1598349 TTTATATCTTA
1 TTTAT-T-TTA
1598360 TTTATTTGTA
1 TTTATTT-TA
1598370 TTTATTTTA
1 TTTATTTTA
*
1598379 TATA-TTTA
1 TTTATTTTA
1598387 -TTATTTT
1 TTTATTTT
1598394 CGTTTTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
7 2 0.05
8 7 0.16
9 16 0.36
10 13 0.30
11 6 0.14
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1598464 original size:36 final size:33
Alignment explanation
Indices: 1598364--1598465 Score: 89
Period size: 36 Copynumber: 2.9 Consensus size: 33
1598354 ATCTTATTTA
* *
1598364 TTTGTATTTATT-TTATATATTTATTATTTTCGTT
1 TTTGTCTTTATTATTATATA-TTATT-TTTTAGTT
* * *
1598398 TTTATTCATTATTATTATATATTTTATTTTTAGATCT
1 TTT-GTCTTTATTATTATATATTAT-TTTTTAG-T-T
1598435 TTTGTCTTTATTATTATATATATATTTTTTA
1 TTTGTCTTTATTATTATATAT-TATTTTTTA
1598466 TTATTATACT
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
34 3 0.06
35 14 0.26
36 31 0.57
37 6 0.11
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (33 bp):
TTTGTCTTTATTATTATATATTATTTTTTAGTT
Found at i:1598588 original size:2 final size:2
Alignment explanation
Indices: 1598581--1598609 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1598571 GTGTTATTAT
1598581 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1598610 TCTATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1604783 original size:106 final size:106
Alignment explanation
Indices: 1604570--1605941 Score: 1874
Period size: 106 Copynumber: 13.0 Consensus size: 106
1604560 ATATCGTTCC
* * * * * * * *
1604570 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACTGCTGGTTGACAA-CAATAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
1604634 AATTTCGGAGCCAATTACAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1604675 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1604740 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1604781 ACTCCAGATAACACAAGTTCAACTTCACAACGAAGGGACCGTTGGTTGTCAATAAACAACTTT-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCC
*
1604845 CAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1604887 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAATTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1604952 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1604993 ACTCCAGACAACGCAAGTTCAATTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1605058 AATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * *
1605099 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGAATGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1605164 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
1605205 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1605270 AATTTCAGAGCCAATTTCAACTTCACAACGAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1605311 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTC---AAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1605373 AATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * * *
1605414 ACTTAAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
1605479 AATTTCAAAGCCAAATTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1605520 ACTCCAGACAACGCAATTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAA-TTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC-
*
1605584 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1605626 ACTCAAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAA-CTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC-
* * * *
1605690 CAATTTCAGAGCTAATTTTAACTTCTCAGCGAAGGATCTTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
1605732 AC-CCAAGACAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAA-CAA-AATTT--
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
* *
1605792 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
1605832 ACTCGAGAAAACACAAGTTCAACTTCACAACGAAAGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
** * *
1605897 GGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1605938 ACTC
1 ACTC
1605942 AGAAAAATGC
Statistics
Matches: 1140, Mismatches: 110, Indels: 33
0.89 0.09 0.03
Matches are distributed among these distances:
100 75 0.07
101 4 0.00
102 6 0.01
103 93 0.08
104 3 0.00
105 57 0.05
106 899 0.79
107 3 0.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1606360 original size:49 final size:49
Alignment explanation
Indices: 1606297--1606398 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
1606287 TCAACTTCAC
1606297 AAACAGATCGACCCAACTTCACGACGAATGAGTCATCTATAACACAGCA
1 AAACAGATCGACCCAACTTCACGACGAATGAGTCATCTATAACACAGCA
1606346 AAACAGATCGACCCAACTTCACGACGAATGAGTCATCTATAACACAGCA
1 AAACAGATCGACCCAACTTCACGACGAATGAGTCATCTATAACACAGCA
1606395 AAAC
1 AAAC
1606399 CAAAGTCTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.42, C:0.28, G:0.14, T:0.16
Consensus pattern (49 bp):
AAACAGATCGACCCAACTTCACGACGAATGAGTCATCTATAACACAGCA
Found at i:1606754 original size:14 final size:14
Alignment explanation
Indices: 1606729--1606777 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
1606719 CCCTTTTGAT
1606729 TAATATTATTTTTA
1 TAATATTATTTTTA
*
1606743 TAAT-TTACTTTTGA
1 TAATATTA-TTTTTA
1606757 TTAATATTATTTTTA
1 -TAATATTATTTTTA
1606772 TAATAT
1 TAATAT
1606778 ACATTATTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 15 0.50
15 9 0.30
16 3 0.10
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (14 bp):
TAATATTATTTTTA
Found at i:1606769 original size:15 final size:15
Alignment explanation
Indices: 1606722--1606769 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1606712 ATTTCGTCCC
1606722 TTTTGATTAATATTA
1 TTTTGATTAATATTA
*
1606737 TTTTTA-TAAT-TTA
1 TTTTGATTAATATTA
1606750 CTTTTGATTAATATTA
1 -TTTTGATTAATATTA
1606766 TTTT
1 TTTT
1606770 TATAATATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 9 0.32
15 13 0.46
16 3 0.11
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (15 bp):
TTTTGATTAATATTA
Found at i:1607975 original size:2 final size:2
Alignment explanation
Indices: 1607968--1607998 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1607958 TATACTCCTT
1607968 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1607999 TTAAATACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1608058 original size:8 final size:8
Alignment explanation
Indices: 1607966--1608130 Score: 59
Period size: 8 Copynumber: 21.4 Consensus size: 8
1607956 CATATACTCC
1607966 TTTATATA
1 TTTATATA
*
1607974 TATATATA
1 TTTATATA
*
1607982 TATATATA
1 TTTATATA
*
1607990 TATATATA
1 TTTATATA
*
1607998 TTTAAATA
1 TTTATATA
*
1608006 CTATTACA-A
1 -T-TTATATA
1608015 TTT-TGATTA
1 TTTAT-A-TA
1608024 TTT-TAT-
1 TTTATATA
1608030 TTTACTATA
1 TTTA-TATA
* *
1608039 TATATATG
1 TTTATATA
1608047 TTTATATA
1 TTTATATA
*
1608055 TTTATTTA
1 TTTATATA
1608063 TTT-T-TA
1 TTTATATA
1608069 TTT-TA-A
1 TTTATATA
* *
1608075 -TTATTTC
1 TTTATATA
1608082 TTT-TATA
1 TTTATATA
*
1608089 TCTTATGTA
1 T-TTATATA
*
1608098 TATT-TCTA
1 T-TTATATA
*
1608106 TTTAT-TT
1 TTTATATA
1608113 TTTATATA
1 TTTATATA
1608121 TTTA-ATA
1 TTTATATA
1608128 TTT
1 TTT
1608131 TCGTTTTTAT
Statistics
Matches: 122, Mismatches: 19, Indels: 33
0.70 0.11 0.19
Matches are distributed among these distances:
5 2 0.02
6 11 0.09
7 22 0.18
8 67 0.55
9 16 0.13
10 4 0.03
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (8 bp):
TTTATATA
Found at i:1608342 original size:2 final size:2
Alignment explanation
Indices: 1608335--1608379 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1608325 TTGTTATTAT
1608335 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1608377 TA T
1 TA T
1608380 TCTATTTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1609069 original size:7 final size:7
Alignment explanation
Indices: 1609057--1609121 Score: 55
Period size: 7 Copynumber: 9.1 Consensus size: 7
1609047 TATAATTTAA
1609057 AAATAAT
1 AAATAAT
1609064 AAATAAT
1 AAATAAT
1609071 AAAATAA-
1 -AAATAAT
1609078 ATAATAAT
1 A-AATAAT
1609086 AAATAA-
1 AAATAAT
**
1609092 AAAGGGA-
1 AAA-TAAT
1609099 AAATAAT
1 AAATAAT
1609106 AAAATAAT
1 -AAATAAT
1609114 AAATAAT
1 AAATAAT
1609121 A
1 A
1609122 GTAGTAAAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
6 5 0.10
7 29 0.60
8 14 0.29
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (7 bp):
AAATAAT
Found at i:1609074 original size:15 final size:15
Alignment explanation
Indices: 1609057--1609121 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
1609047 TATAATTTAA
1609057 AAATAAT-AAATAAT
1 AAATAATAAAATAAT
*
1609071 AAAATAA-ATAATAAT
1 -AAATAATAAAATAAT
***
1609086 AAATAA-AAAGGGA-
1 AAATAATAAAATAAT
1609099 AAATAATAAAATAAT
1 AAATAATAAAATAAT
1609114 AAATAATA
1 AAATAATA
1609122 GTAGTAAAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
13 6 0.15
14 13 0.33
15 20 0.51
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (15 bp):
AAATAATAAAATAAT
Found at i:1609103 original size:35 final size:36
Alignment explanation
Indices: 1609032--1609121 Score: 105
Period size: 35 Copynumber: 2.5 Consensus size: 36
1609022 GATATAATAA
* * *
1609032 AATAAAATAAATAATTATAATTTAAAAATAATAAAT
1 AATAAAATAAATAATAATAATATAAAAAGAATAAAT
*
1609068 AATAAAATAAATAATAATAA-ATAAAAAGGGA-AAAT
1 AATAAAATAAATAATAATAATATAAAAA-GAATAAAT
1609103 AATAAAAT-AATAAATAATA
1 AATAAAATAAAT-AATAATA
1609122 GTAGTAAAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
34 3 0.06
35 25 0.52
36 20 0.42
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (36 bp):
AATAAAATAAATAATAATAATATAAAAAGAATAAAT
Found at i:1609202 original size:17 final size:17
Alignment explanation
Indices: 1609177--1609210 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1609167 AATGAGATAA
*
1609177 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
1609194 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
1609211 TTGGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:1609846 original size:12 final size:13
Alignment explanation
Indices: 1609830--1609859 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1609820 ACTAAAATAC
1609830 CTAAAATAATATT
1 CTAAAATAATATT
1609843 -TAAAATAATATT
1 CTAAAATAATATT
1609855 CTAAA
1 CTAAA
1609860 TCCTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAAATAATATT
Found at i:1609903 original size:70 final size:68
Alignment explanation
Indices: 1609787--1609994 Score: 247
Period size: 76 Copynumber: 2.9 Consensus size: 68
1609777 TAAAACATCT
*
1609787 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAATAATATTTAAAATAA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAATAA-ATTTAAAATAA
*
1609851 TATTC
64 TATCC
*
1609856 TAAATCCTAATTAAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
1 TAAATCCTAATT-AAAATACTAAAACCTATTTAAACTAAAATACCT-----AAA-AT-AAAT-TT
1609921 AAAATAATATCC
57 AAAATAATATCC
* * * *
1609933 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAATTTAAAATA
1609995 TAATGTTTAA
Statistics
Matches: 121, Mismatches: 8, Indels: 21
0.81 0.05 0.14
Matches are distributed among these distances:
68 6 0.05
69 21 0.17
70 27 0.22
71 3 0.02
75 3 0.02
76 37 0.31
77 24 0.20
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.29
Consensus pattern (68 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAATTTAAAATAATA
TCC
Found at i:1609917 original size:44 final size:43
Alignment explanation
Indices: 1609869--1609994 Score: 123
Period size: 44 Copynumber: 3.1 Consensus size: 43
1609859 ATCCTAATTA
1609869 AAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGAT
1 AAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAA-AT
* *
1609913 AAAATA-TAAAA---A--T-AA-T---AT-CCTAAAACTTAATT
1 AAAATACTAAAACCTATTTAAACTAAAATACCTAAAAC-AAAAT
1609945 AAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATAT
1 AAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAA-AT
1609989 AAAATA
1 AAAATA
1609995 TAATGTTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 28
0.67 0.04 0.29
Matches are distributed among these distances:
32 15 0.23
33 9 0.14
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
40 2 0.03
43 9 0.14
44 21 0.33
ACGTcount: A:0.60, C:0.13, G:0.01, T:0.25
Consensus pattern (43 bp):
AAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAT
Found at i:1609969 original size:76 final size:77
Alignment explanation
Indices: 1609844--1609997 Score: 265
Period size: 76 Copynumber: 2.0 Consensus size: 77
1609834 AATAATATTT
* *
1609844 AAAATAATATTCTAAATCCTAATTAAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAA
1 AAAATAATATCCTAAAACCTAATTAAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAA
1609909 AGATAAAATATA
66 AGATAAAATATA
*
1609921 AAAATAATATCCTAAAACTTAATT-AAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAA
1 AAAATAATATCCTAAAACCTAATTAAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAA
*
1609985 ATATAAAATATA
66 AGATAAAATATA
1609997 A
1 A
1609998 TGTTTAAAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
76 52 0.71
77 21 0.29
ACGTcount: A:0.59, C:0.13, G:0.01, T:0.27
Consensus pattern (77 bp):
AAAATAATATCCTAAAACCTAATTAAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAA
AGATAAAATATA
Found at i:1609991 original size:25 final size:24
Alignment explanation
Indices: 1609944--1609991 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1609934 AAAACTTAAT
** *
1609944 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
1609968 TAAAATACCTAAAACAAATATAAA
1 TAAAATA-CTAAAACAAATATAAA
1609992 ATATAATGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Found at i:1617207 original size:13 final size:13
Alignment explanation
Indices: 1617191--1617220 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1617181 AAAAAAAAAC
*
1617191 AGAATTTTCTTTT
1 AGAATTTTCTGTT
1617204 AGAATTTTCTGTT
1 AGAATTTTCTGTT
1617217 AGAA
1 AGAA
1617221 GATATAGGAG
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:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (13 bp):
AGAATTTTCTGTT
Found at i:1623978 original size:24 final size:22
Alignment explanation
Indices: 1623933--1623974 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1623923 ATTTTCCCCA
1623933 CAATAATTACAGAATATATACT
1 CAATAATTACAGAATATATACT
1623955 CAATAATTACAGAATATATA
1 CAATAATTACAGAATATATA
1623975 TACTTGCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (22 bp):
CAATAATTACAGAATATATACT
Done.