Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008184.1 Hibiscus syriacus cultivar Beakdansim tig00110785_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: 1549336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:498900 original size:17 final size:17
Alignment explanation
Indices: 498859--498892 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
498849 AAATTCCAAT
498859 TGACAATAATTTTAATA
1 TGACAATAATTTTAATA
498876 TGACAATAATTTTAATA
1 TGACAATAATTTTAATA
498893 ATACAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
TGACAATAATTTTAATA
Found at i:502444 original size:2 final size:2
Alignment explanation
Indices: 502432--502466 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
502422 GTATAAGTAG
502432 AT AT CAT 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
502467 TAGTACCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:508203 original size:147 final size:142
Alignment explanation
Indices: 507917--508223 Score: 510
Period size: 147 Copynumber: 2.1 Consensus size: 142
507907 TATAATTGCA
*
507917 CCGAAGTACCGCGTTAGAATTGCACCGTAGTGCCATATAAATGTCCATAAGGACCACATATTATC
1 CCGAAGGACCGCG-TAGAATTGCACCGTAGTGCCATATAAATGTCCATAAGGACCACATATTATC
507982 CTTAAGAATCAATACATATACTAGGGATCATTGTGTCTTTCAAGACTTCACACATGTTCCAAAGA
65 CTTAAGAATCAATACATATACTAGGGATCATTGTGTCTTTCAAGACTTCACACATGTTCCAAAGA
508047 ATATACATATGTC
130 ATATACATATGTC
508060 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATA-TAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAA--ATGTCCATAAGGACCACATATTA-
508124 TCCTTAAGAATCATATACATAT-CTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
63 TCCTTAAGAATCA-ATACATATACTAGGGATC-A-T-TGTGTCTTTCAAGACTTCACACATGTTC
508188 CAAAGAATATACATATGTC
124 CAAAGAATATACATATGTC
*
508207 CTGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
508224 CCCTCGCTCT
Statistics
Matches: 155, Mismatches: 2, Indels: 10
0.93 0.01 0.06
Matches are distributed among these distances:
142 26 0.17
143 14 0.09
144 42 0.27
145 9 0.06
146 1 0.01
147 63 0.41
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (142 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAAATGTCCATAAGGACCACATATTATCC
TTAAGAATCAATACATATACTAGGGATCATTGTGTCTTTCAAGACTTCACACATGTTCCAAAGAA
TATACATATGTC
Found at i:508725 original size:2 final size:2
Alignment explanation
Indices: 508718--508749 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
508708 CATATCTATC
508718 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
508750 CTCAAGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:509617 original size:21 final size:21
Alignment explanation
Indices: 509593--509637 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
509583 TGTTGTTCGT
* *
509593 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
509614 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
509635 TTG
1 TTG
509638 CCCAGAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:515801 original size:22 final size:22
Alignment explanation
Indices: 515754--515807 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
515744 CACGTTGATT
*
515754 GTTGACTTTGATCGGCATAACT
1 GTTGACTTTGATCGGCATAACC
* *
515776 GTTGACTTTGA-CTGGTATGACC
1 GTTGACTTTGATC-GGCATAACC
515798 GTTGACTTTG
1 GTTGACTTTG
515808 CCGAAAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.39
Consensus pattern (22 bp):
GTTGACTTTGATCGGCATAACC
Found at i:521476 original size:29 final size:29
Alignment explanation
Indices: 521357--521471 Score: 187
Period size: 29 Copynumber: 4.0 Consensus size: 29
521347 CAGTGGCAAC
521357 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
* *
521386 ATAGGTCGCCATGCACGCACAGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
521415 ATAGGTCGCCATGCACGCCCGGCGTCC-T
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
*
521443 ATAAGGACGCCATGCACGCCCGGCGTCCT
1 AT-AGGTCGCCATGCACGCCCGGCGTCCT
521472 ATAAGTTATT
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
28 3 0.04
29 76 0.96
ACGTcount: A:0.17, C:0.37, G:0.27, T:0.18
Consensus pattern (29 bp):
ATAGGTCGCCATGCACGCCCGGCGTCCTT
Found at i:521523 original size:29 final size:30
Alignment explanation
Indices: 521485--521541 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
521475 AGTTATTTGC
521485 TTGGGGTGGCCGCTGTT-GTGGCCGCTGCT
1 TTGGGGTGGCCGCTGTTGGTGGCCGCTGCT
521514 TTGGGGTGGCCGCTGTTGGTGGCCGCTG
1 TTGGGGTGGCCGCTGTTGGTGGCCGCTG
521542 TTGCTCGTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.00, C:0.23, G:0.47, T:0.30
Consensus pattern (30 bp):
TTGGGGTGGCCGCTGTTGGTGGCCGCTGCT
Found at i:521536 original size:13 final size:13
Alignment explanation
Indices: 521489--521544 Score: 69
Period size: 13 Copynumber: 4.1 Consensus size: 13
521479 ATTTGCTTGG
521489 GGTGGCCGCTGTT
1 GGTGGCCGCTGTT
521502 -GTGGCCGCTGCTTT
1 GGTGGCCGCTG--TT
521516 GGGGTGGCCGCTGTT
1 --GGTGGCCGCTGTT
521531 GGTGGCCGCTGTT
1 GGTGGCCGCTGTT
521544 G
1 G
521545 CTCGTCCATC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
12 10 0.26
13 14 0.37
14 2 0.05
15 2 0.05
17 10 0.26
ACGTcount: A:0.00, C:0.23, G:0.46, T:0.30
Consensus pattern (13 bp):
GGTGGCCGCTGTT
Found at i:521827 original size:12 final size:12
Alignment explanation
Indices: 521810--521834 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
521800 CCGACGACAT
521810 GGTAGGTGGTAG
1 GGTAGGTGGTAG
521822 GGTAGGTGGTAG
1 GGTAGGTGGTAG
521834 G
1 G
521835 TCGCCATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.60, T:0.24
Consensus pattern (12 bp):
GGTAGGTGGTAG
Found at i:521910 original size:35 final size:35
Alignment explanation
Indices: 521871--521938 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
521861 TCCTGCATCG
*
521871 CGACCCAGCTTTAACTGTAGCACTCATGCATGCAA
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
*
521906 CGACCAAGCTTTAACTGTATCACTCATGCATGC
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGC
521939 GTTGCATCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (35 bp):
CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
Found at i:522398 original size:21 final size:21
Alignment explanation
Indices: 522373--522416 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
522363 AATCTAGTTA
*
522373 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTGGTTAGTATAAATT
* *
522394 ATTAGTTGGTTAGTTTAAGTT
1 ATTAGTTGGTTAGTATAAATT
522415 AT
1 AT
522417 ATATTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (21 bp):
ATTAGTTGGTTAGTATAAATT
Found at i:522832 original size:13 final size:13
Alignment explanation
Indices: 522814--522838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
522804 AGTAATTTAT
522814 TATTTTTGTTGTC
1 TATTTTTGTTGTC
522827 TATTTTTGTTGT
1 TATTTTTGTTGT
522839 TGTGTATGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.04, G:0.16, T:0.72
Consensus pattern (13 bp):
TATTTTTGTTGTC
Found at i:522934 original size:18 final size:20
Alignment explanation
Indices: 522910--522963 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
522900 GAGATAATTT
*
522910 TTGTTTAAAAAT-TATATTG
1 TTGTTTAAAAATATATAGTG
*
522929 -TGTTTAAAAATATTTAGTG
1 TTGTTTAAAAATATATAGTG
*
522948 TTGTTTAAAAAAATAT
1 TTGTTTAAAAATATAT
522964 TTTGTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 11 0.38
19 5 0.17
20 13 0.45
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (20 bp):
TTGTTTAAAAATATATAGTG
Found at i:522968 original size:17 final size:18
Alignment explanation
Indices: 522903--522970 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
522893 TTTGTGCGAG
522903 ATAAT-TTTTGTTTAAAA
1 ATAATATTTTGTTTAAAA
* *
522920 ATTATATTGTGTTTAAAA
1 ATAATATTTTGTTTAAAA
* *
522938 ATATTTAGTGTTGTTTAAAA
1 ATA-ATA-TTTTGTTTAAAA
522958 A-AATATTTTGTTT
1 ATAATATTTTGTTT
522971 TATTTATATT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
17 11 0.28
18 15 0.38
19 3 0.08
20 11 0.28
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (18 bp):
ATAATATTTTGTTTAAAA
Found at i:522969 original size:20 final size:19
Alignment explanation
Indices: 522910--522969 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 19
522900 GAGATAATTT
* *
522910 TTGTTTAAAAATTATATTG
1 TTGTTTAAAAAATATTTTG
522929 -TGTTT-AAAAATATTTAGTG
1 TTGTTTAAAAAATATTT--TG
522948 TTGTTTAAAAAAATATTTTG
1 TTGTTT-AAAAAATATTTTG
522968 TT
1 TT
522970 TTATTTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 2 0.06
20 9 0.26
22 10 0.29
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.52
Consensus pattern (19 bp):
TTGTTTAAAAAATATTTTG
Found at i:522976 original size:22 final size:22
Alignment explanation
Indices: 522934--522976 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
522924 TATTGTGTTT
*
522934 AAAAATATTTAGTGTTGTTTAA
1 AAAAATATTTAGTGTTATTTAA
* *
522956 AAAAATATTTTGTTTTATTTA
1 AAAAATATTTAGTGTTATTTA
522977 TATTGTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
AAAAATATTTAGTGTTATTTAA
Found at i:523273 original size:26 final size:26
Alignment explanation
Indices: 523226--523275 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
523216 ATTAAATATC
*
523226 AAATCATTAGATTAATAATAATTATT
1 AAATCATTAGAATAATAATAATTATT
* * *
523252 AAATCATTATAATATTAGTAATTA
1 AAATCATTAGAATAATAATAATTA
523276 ATCAATTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (26 bp):
AAATCATTAGAATAATAATAATTATT
Found at i:526182 original size:26 final size:26
Alignment explanation
Indices: 526153--526423 Score: 190
Period size: 26 Copynumber: 11.0 Consensus size: 26
526143 TTTGATGATT
526153 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
526179 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
526205 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
526231 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
526253 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
526277 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
526303 TAGTAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** * *
526329 TAAAAATGATTTAATAATGAT--TTAA
1 TAGTAATGATTTGATAATAATCATT-A
* *
526354 TATTTAATGATTTG------ATGATT-
1 TA-GTAATGATTTGATAATAATCATTA
526374 TAGTAATGATTTGATAATAATCA-T-
1 TAGTAATGATTTGATAATAATCATTA
* *
526398 TA-TAATGATTTTATAATAATTATTA
1 TAGTAATGATTTGATAATAATCATTA
526423 T
1 T
526424 GTTATTATTT
Statistics
Matches: 202, Mismatches: 19, Indels: 49
0.75 0.07 0.18
Matches are distributed among these distances:
19 11 0.05
20 9 0.04
22 5 0.02
23 29 0.14
24 15 0.07
25 17 0.08
26 109 0.54
27 7 0.03
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:526281 original size:98 final size:97
Alignment explanation
Indices: 526179--526423 Score: 433
Period size: 98 Copynumber: 2.5 Consensus size: 97
526169 ATAATCATTA
526179 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
526244 ATAATGATTTAAATATTTAATGATTTGATGATT
66 ATAATGATTT-AATATTTAATGATTTGATGATT
*
526277 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTAGTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
526342 ATAATGATTTAATATTTAATGATTTGATGATT
66 ATAATGATTTAATATTTAATGATTTGATGATT
* *
526374 TAGTAATGATTTGATAATAATCATTATAATGAT--TTTA-TAATAATTATTAT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTAT
526424 GTTATTATTT
Statistics
Matches: 143, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
94 12 0.08
95 4 0.03
97 53 0.37
98 74 0.52
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (97 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
ATAATGATTTAATATTTAATGATTTGATGATT
Found at i:526321 original size:124 final size:124
Alignment explanation
Indices: 526098--526346 Score: 464
Period size: 124 Copynumber: 2.0 Consensus size: 124
526088 ATGTATTTAT
526098 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* *
526163 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAAAAATGATTTAATAA
526222 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
526287 TTGATAATAATCATTATAGTAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAA
66 TTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAAAAATGATTTAATAA
526346 T
1 T
526347 GATTTAATAT
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
123 1 0.01
124 121 0.99
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.43
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAAAAATGATTTAATAA
Found at i:526366 original size:8 final size:8
Alignment explanation
Indices: 526343--526375 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
526333 AATGATTTAA
526343 TAATGATT
1 TAATGATT
526351 TAAT-ATT
1 TAATGATT
526358 TAATGATT
1 TAATGATT
*
526366 TGATGATT
1 TAATGATT
526374 TA
1 TA
526376 GTAATGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TAATGATT
Found at i:526468 original size:14 final size:14
Alignment explanation
Indices: 526436--526477 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
526426 TATTATTTAG
*
526436 TAATTATTT-ATAA
1 TAATGATTTAATAA
*
526449 TAATGATTTAATAC
1 TAATGATTTAATAA
526463 TAATGATTTAATAA
1 TAATGATTTAATAA
526477 T
1 T
526478 TATTACTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:526500 original size:38 final size:38
Alignment explanation
Indices: 526430--526503 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
526420 TTATGTTATT
* **
526430 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
526468 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
526504 CAAAGTAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:526598 original size:14 final size:13
Alignment explanation
Indices: 526579--526643 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
526569 TTTAAATATT
526579 TAATGATTTGATAC
1 TAATGATTT-ATAC
526593 TAATGA-TT-TAC
1 TAATGATTTATAC
*
526604 TAAT--TAT-TAC
1 TAATGATTTATAC
526614 TAATGATTTAATAC
1 TAATGATTT-ATAC
*
526628 TAATTATTTGATAC
1 TAATGATTT-ATAC
526642 TA
1 TA
526644 GTAATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 8 0.19
11 7 0.17
12 2 0.05
13 2 0.05
14 23 0.55
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TAATGATTTATAC
Found at i:526615 original size:10 final size:11
Alignment explanation
Indices: 526590--526623 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
526580 AATGATTTGA
526590 TACTAATGATT
1 TACTAATGATT
*
526601 TACTAATTA-T
1 TACTAATGATT
526611 TACTAATGATT
1 TACTAATGATT
526622 TA
1 TA
526624 ATACTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
TACTAATGATT
Found at i:526633 original size:21 final size:21
Alignment explanation
Indices: 526590--526633 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
526580 AATGATTTGA
* *
526590 TACTAATGATTTACTAATTAT
1 TACTAATGATTTAATAATAAT
*
526611 TACTAATGATTTAATACTAAT
1 TACTAATGATTTAATAATAAT
526632 TA
1 TA
526634 TTTGATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
TACTAATGATTTAATAATAAT
Found at i:526650 original size:17 final size:17
Alignment explanation
Indices: 526628--526660 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
526618 GATTTAATAC
526628 TAATTATTTGATACTAG
1 TAATTATTTGATACTAG
526645 TAATTATTTGATACTA
1 TAATTATTTGATACTA
526661 AACATCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (17 bp):
TAATTATTTGATACTAG
Found at i:528827 original size:15 final size:14
Alignment explanation
Indices: 528804--528834 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
528794 TACAACACTA
528804 AACTTTAATATAAT
1 AACTTTAATATAAT
528818 AACTTATAATATAAT
1 AACTT-TAATATAAT
528833 AA
1 AA
528835 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:528842 original size:16 final size:16
Alignment explanation
Indices: 528809--528855 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
528799 CACTAAACTT
*
528809 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
528824 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
528840 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
528856 ATTTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:528970 original size:32 final size:34
Alignment explanation
Indices: 528895--528976 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
528885 CCAAACCCTT
* *
528895 AAAC-AACTAATAAAATATTTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTCATATAACTA
528928 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTTCA-TATAACTA
*
528961 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
528977 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
32 11 0.25
33 8 0.18
34 20 0.45
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTTTTTCATATAACTA
Found at i:529083 original size:42 final size:43
Alignment explanation
Indices: 529034--529145 Score: 122
Period size: 42 Copynumber: 2.6 Consensus size: 43
529024 AACTATTTAA
529034 CTAACAAAACTAATTAAATAATTTTTTTT-A-TATAACTAACTAT
1 CTAACAAAACTAATTAAATAATTTTTTTTAACTAT-A-TAACTAT
* * * *
529077 -TAACAAAACAAACTAATTAATTATTTTTAACTATATAACTAT
1 CTAACAAAACTAATTAAATAATTTTTTTTAACTATATAACTAT
* *
529119 CAAACATATACTAATTAAATAATTTTT
1 CTAACA-AAACTAATTAAATAATTTTT
529146 AATTTATGTA
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
42 31 0.56
43 6 0.11
44 18 0.33
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (43 bp):
CTAACAAAACTAATTAAATAATTTTTTTTAACTATATAACTAT
Found at i:529094 original size:46 final size:47
Alignment explanation
Indices: 529015--529104 Score: 123
Period size: 46 Copynumber: 1.9 Consensus size: 47
529005 CAACAAACAA
*
529015 ATATAACTTAACTATTTAACTAACAAAACTAATTAAATAATTTTTTTT
1 ATATAACTTAACTATTTAACAAACAAAACTAATT-AATAATTTTTTTT
*
529063 ATATAAC-TAACTA-TTAACAAA-ACAAACTAATTAATTATTTTT
1 ATATAACTTAACTATTTAACAAACA-AAACTAATTAATAATTTTT
529105 AACTATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 10 0.26
46 16 0.41
47 6 0.15
48 7 0.18
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (47 bp):
ATATAACTTAACTATTTAACAAACAAAACTAATTAATAATTTTTTTT
Found at i:529112 original size:46 final size:47
Alignment explanation
Indices: 529015--529117 Score: 122
Period size: 46 Copynumber: 2.2 Consensus size: 47
529005 CAACAAACAA
* **
529015 ATATAACTTAACTATTTAACTAACAAAACTAATTAAATAATTTTTTTT
1 ATATAAC-TAACTATTTAACAAACAAAACTAATTAAATAATTTTTACT
*
529063 ATATAACTAACTA-TTAACAAA-ACAAACTAATT-AATTATTTTTAACT
1 ATATAACTAACTATTTAACAAACA-AAACTAATTAAATAATTTTT-ACT
529109 ATATAACTA
1 ATATAACTA
529118 TCAAACATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
45 10 0.20
46 26 0.53
47 6 0.12
48 7 0.14
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (47 bp):
ATATAACTAACTATTTAACAAACAAAACTAATTAAATAATTTTTACT
Found at i:529173 original size:41 final size:39
Alignment explanation
Indices: 529086--529173 Score: 88
Period size: 41 Copynumber: 2.2 Consensus size: 39
529076 TTAACAAAAC
*
529086 AAACTAATTAATTATTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
529126 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATT-AATAATTTTTAA-CTATATA-ACTATAAACAT
529167 AAACTAA
1 AAACTAA
529174 CAATCATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
40 8 0.21
41 21 0.54
42 5 0.13
43 5 0.13
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (39 bp):
AAACTAATTAATAATTTTTAACTATATAACTATAAACAT
Found at i:529238 original size:16 final size:18
Alignment explanation
Indices: 529209--529247 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
529199 ACTAATTAAC
*
529209 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
529227 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
529243 ATTTA
1 ATTTA
529248 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:529578 original size:50 final size:50
Alignment explanation
Indices: 529461--529568 Score: 186
Period size: 50 Copynumber: 2.2 Consensus size: 50
529451 TAGGATCACA
*
529461 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
529510 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTAT-T
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
529559 TGGC-TGCATG
1 TGGCATGCATG
529569 TGCATGCATG
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
48 6 0.11
49 13 0.23
50 38 0.67
ACGTcount: A:0.22, C:0.19, G:0.39, T:0.20
Consensus pattern (50 bp):
TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
Found at i:529636 original size:29 final size:29
Alignment explanation
Indices: 529603--529697 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
529593 GGGATGCCGG
529603 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
529632 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
** *
529661 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
529690 GGCGACCT
1 GGCGACCT
529698 CTCTATTGGC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:529726 original size:32 final size:32
Alignment explanation
Indices: 529684--529755 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
529674 GTCGCCCAGA
*
529684 CTGCATGGCGACCTCTCTATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
* *
529716 TTGCATGGCGACCTCTCCGTTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
529748 CTGCATGG
1 CTGCATGG
529756 TGAGTATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.08, C:0.31, G:0.31, T:0.31
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:529820 original size:24 final size:19
Alignment explanation
Indices: 529770--529807 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
529760 TATATGGCTT
529770 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
529789 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
529808 TGAGTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.37, T:0.32
Consensus pattern (19 bp):
GTATGGCTCGTCTGCATGG
Found at i:533118 original size:25 final size:25
Alignment explanation
Indices: 533085--533140 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
533075 AACAAGTTAA
*
533085 ATTATTAATATTAAAATA-AAAATAT
1 ATTATTAATA-AAAAATATAAAATAT
533110 -TTATATAATAAAAAATATAAAATAT
1 ATTAT-TAATAAAAAATATAAAATAT
533135 ATTATT
1 ATTATT
533141 TCATTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 10 0.37
25 13 0.48
26 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
ATTATTAATAAAAAATATAAAATAT
Found at i:538171 original size:31 final size:32
Alignment explanation
Indices: 538131--538211 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 32
538121 TTAAGGATTG
* *
538131 TTTTATAATAGTATGATAAA-TTGAATGATCA
1 TTTTATAATAGTTTGATAAAGTTGAATGACCA
* *
538162 TTTTTTAATAGTTTGATAAAGTTTAATGACCA
1 TTTTATAATAGTTTGATAAAGTTGAATGACCA
*
538194 CTTTATAATAGTTTGATA
1 TTTTATAATAGTTTGATA
538212 CATTTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 18 0.42
32 25 0.58
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (32 bp):
TTTTATAATAGTTTGATAAAGTTGAATGACCA
Found at i:538945 original size:11 final size:11
Alignment explanation
Indices: 538929--538958 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
538919 AATACTTTCA
*
538929 ATAAATTTTTT
1 ATAAATTTTAT
538940 ATAAATTTTAT
1 ATAAATTTTAT
538951 ATAAATTT
1 ATAAATTT
538959 ACTCAGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATAAATTTTAT
Found at i:539155 original size:18 final size:17
Alignment explanation
Indices: 539132--539166 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
539122 TTATTTTGTA
539132 CAATTTAATATTAAATTT
1 CAATTTAAT-TTAAATTT
539150 CAATTTAATTTAAATTT
1 CAATTTAATTTAAATTT
539167 ATAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
CAATTTAATTTAAATTT
Found at i:548965 original size:21 final size:20
Alignment explanation
Indices: 548937--549010 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 20
548927 TTTCGTCCCA
548937 TATATATTTATTTATT-TATT
1 TATATATTTATTT-TTATATT
*
548957 TACTATATTTCTTTTTATATT
1 TA-TATATTTATTTTTATATT
*
548978 TATATTATATTATTTTTAT-TA
1 TATA-TAT-TTATTTTTATATT
548999 TATATATCTTAT
1 TATATAT-TTAT
549011 ATCATTCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
20 13 0.28
21 24 0.52
22 9 0.20
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (20 bp):
TATATATTTATTTTTATATT
Found at i:548977 original size:25 final size:25
Alignment explanation
Indices: 548943--549040 Score: 76
Period size: 25 Copynumber: 3.8 Consensus size: 25
548933 CCCATATATA
548943 TTTATT-TATTTAT-TTACTA-TATT
1 TTTATTATATTTATATTA-TATTATT
*
548966 TCTTTTTATATTTATATTATATTATT
1 T-TTATTATATTTATATTATATTATT
* * *
548992 TTTATTATATATATCTTATATCATT
1 TTTATTATATTTATATTATATTATT
* *
549017 CTATATATATATATATATATATAT
1 -TTTAT-TATATTTATAT-TATAT
549041 ATGTGTATAG
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.02
24 4 0.07
25 29 0.48
26 12 0.20
27 10 0.16
28 5 0.08
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTATTATATTTATATTATATTATT
Found at i:549004 original size:2 final size:2
Alignment explanation
Indices: 548972--549042 Score: 53
Period size: 2 Copynumber: 37.5 Consensus size: 2
548962 TATTTCTTTT
* * * *
548972 TA TA TT TA TA T- TA TA T- TA TT TT TA T- TA TA TA TA TC T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
549010 TA TCA T- TC TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
549043 GTGTATAGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
1 5 0.09
2 50 0.88
3 2 0.04
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:549198 original size:45 final size:46
Alignment explanation
Indices: 549069--549207 Score: 114
Period size: 45 Copynumber: 3.1 Consensus size: 46
549059 ATTTTTCTCC
* * * * *
549069 ATTTACTATGTATATA-TATTTTTTCTTAATATTA-TATTTTATATGT
1 ATTTA-TATATATATATTATTTTTACTTTATTTTATTTTTTTATAT-T
*
549115 -TTT-TATATATATATT-TTTTAATA-TTCTATTTT-TGTTTTTAT-TT
1 ATTTATATATATATATTATTTT--TACTT-TATTTTATTTTTTTATATT
*
549158 ATTTATATATATATATTATTTTTACTTTATTTTATTTTTTTCTATT
1 ATTTATATATATATATTATTTTTACTTTATTTTATTTTTTTATATT
549204 ATTT
1 ATTT
549208 TTTTCTTAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
43 14 0.19
44 15 0.20
45 35 0.47
46 10 0.14
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (46 bp):
ATTTATATATATATATTATTTTTACTTTATTTTATTTTTTTATATT
Found at i:549205 original size:18 final size:19
Alignment explanation
Indices: 549171--549208 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
549161 TATATATATA
549171 TATTATTTTTACTTTATTT
1 TATTATTTTTACTTTATTT
549190 TATT-TTTTT-CTATTATTT
1 TATTATTTTTACT-TTATTT
549208 T
1 T
549209 TTTCTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 12 0.67
19 4 0.22
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTATTTTTACTTTATTT
Found at i:549207 original size:13 final size:13
Alignment explanation
Indices: 549189--549213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
549179 TTACTTTATT
549189 TTATTTTTTTCTA
1 TTATTTTTTTCTA
549202 TTATTTTTTTCT
1 TTATTTTTTTCT
549214 TAATATCATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTCTA
Found at i:549239 original size:30 final size:31
Alignment explanation
Indices: 549200--549267 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
549190 TATTTTTTTC
549200 TATTATTTTTTT-CTTAATATCATATATCT-T
1 TATT-TTTTTTTACTTAATATCATATATCTAT
* * *
549230 TATTTTTTTTTACTTAGTATTATATATTTAT
1 TATTTTTTTTTACTTAATATCATATATCTAT
549261 TATTTTT
1 TATTTTT
549268 ATTTGTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 7 0.21
30 18 0.55
31 8 0.24
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (31 bp):
TATTTTTTTTTACTTAATATCATATATCTAT
Found at i:549253 original size:28 final size:28
Alignment explanation
Indices: 549200--549267 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
549190 TATTTTTTTC
*
549200 TATTATTTTTTTCTTAATATCATATATCTT
1 TATT-TTTTTTTCTTAATAT-ATATATATT
*
549230 TATTTTTTTTTACTTAGTAT-TATATATT
1 TATTTTTTTTT-CTTAATATATATATATT
*
549258 TATTATTTTT
1 TATTTTTTTT
549268 ATTTGTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 16 0.47
29 7 0.21
30 11 0.32
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (28 bp):
TATTTTTTTTTCTTAATATATATATATT
Found at i:549343 original size:18 final size:18
Alignment explanation
Indices: 549316--549350 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
549306 TTTTTATTCA
549316 TTTTTAATTTCTTTTACC
1 TTTTTAATTTCTTTTACC
* *
549334 TTTTTTATTTTTTTTAC
1 TTTTTAATTTCTTTTAC
549351 TCCATTAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTAATTTCTTTTACC
Found at i:549417 original size:19 final size:19
Alignment explanation
Indices: 549395--549436 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
549385 TTTTTTAACA
549395 TTTTATTCATTTTGT-TTAT
1 TTTTATTCATTTT-TATTAT
* *
549414 TTTTGTTTATTTTTATTAT
1 TTTTATTCATTTTTATTAT
549433 TTTT
1 TTTT
549437 TACGTGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (19 bp):
TTTTATTCATTTTTATTAT
Found at i:549455 original size:9 final size:10
Alignment explanation
Indices: 549404--549436 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
549394 ATTTTATTCA
549404 TTTTGTTTAT
1 TTTTGTTTAT
549414 TTTTGTTTAT
1 TTTTGTTTAT
*
549424 TTTT-ATTAT
1 TTTTGTTTAT
549433 TTTT
1 TTTT
549437 TACGTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (10 bp):
TTTTGTTTAT
Found at i:549477 original size:26 final size:26
Alignment explanation
Indices: 549419--549481 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
549409 TTTATTTTTG
549419 TTTATTT-TTATTATTTTTTACGTGT
1 TTTATTTATTATTATTTTTTACGTGT
* * *
549444 TTT-GTTATTTTTCATTTTTT-CTTGT
1 TTTATTTATTATT-ATTTTTTACGTGT
549469 TTTATTTATTATT
1 TTTATTTATTATT
549482 CTCACGTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
24 2 0.07
25 14 0.47
26 14 0.47
ACGTcount: A:0.14, C:0.05, G:0.06, T:0.75
Consensus pattern (26 bp):
TTTATTTATTATTATTTTTTACGTGT
Found at i:554294 original size:36 final size:37
Alignment explanation
Indices: 554236--554305 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
554226 TAAAAAGAAG
*
554236 TTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTATCTCGCTTGAGACAGTTTCCCTTGAAACAAAA
* * *
554273 TTTTGTCTC-CTTGATACAGTTTCTCTTGAAACA
1 TTTTATCTCGCTTGAGACAGTTTCCCTTGAAACA
554306 TAAACATTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 21 0.72
37 8 0.28
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (37 bp):
TTTTATCTCGCTTGAGACAGTTTCCCTTGAAACAAAA
Found at i:554376 original size:37 final size:37
Alignment explanation
Indices: 554334--554508 Score: 103
Period size: 36 Copynumber: 5.0 Consensus size: 37
554324 CTTTGAAATG
* *
554334 AATTTTGTCT-CTCTTGAGATAGTTTCCCTTGAAACAA
1 AATTTTGCCTCCT-TTGAGACAGTTTCCCTTGAAACAA
*
554371 AATTTTGCCTCCTTTGAGACAGTTTCTCTTGAAACATA
1 AATTTTGCCTCCTTTGAGACAGTTTCCCTTGAAACA-A
* * * *
554409 AA-ATTG--------AAAACA-TTTCCCTTGAAA-TA
1 AATTTTGCCTCCTTTGAGACAGTTTCCCTTGAAACAA
* *
554435 AATTTCGTCT-CTCTTGAGACAGTTTCCCTTGAAAC-A
1 AATTTTGCCTCCT-TTGAGACAGTTTCCCTTGAAACAA
*
554471 AATTTT--CTCTCTCTTGAGACAGTTTTCCTTGAAACAA
1 AATTTTGCCTC-CT-TTGAGACAGTTTCCCTTGAAACAA
554508 A
1 A
554509 TTATTTGAAT
Statistics
Matches: 108, Mismatches: 14, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
26 3 0.03
27 2 0.02
28 11 0.10
29 4 0.04
34 2 0.02
35 4 0.04
36 42 0.39
37 35 0.32
38 5 0.05
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (37 bp):
AATTTTGCCTCCTTTGAGACAGTTTCCCTTGAAACAA
Found at i:554419 original size:100 final size:101
Alignment explanation
Indices: 554236--554506 Score: 392
Period size: 100 Copynumber: 2.7 Consensus size: 101
554226 TAAAAAGAAG
* * *
554236 TTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC-TTGATACAGTTTCTCTT
1 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTG-CTCCTTTGAGACAGTTTCTCTT
* *
554300 GAAACATAAACATTGAAAACATTT-CTTTGAAATGAA
65 GAAACATAAACATTGAAAACATTTCCCTTGAAATAAA
554336 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGCCTCCTTTGAGACAGTTTCTCTT
1 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTG-CTCCTTTGAGACAGTTTCTCTT
554401 GAAACATAAA-ATTGAAAACATTTCCCTTGAAATAAA
65 GAAACATAAACATTGAAAACATTTCCCTTGAAATAAA
* *
554437 TTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTT-CTCTCTCTTGAGACAGTTT-TCC
1 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGCTC-CT-TTGAGACAGTTTCT-C
554499 TTGAAACA
63 TTGAAACA
554507 AATTATTTGA
Statistics
Matches: 158, Mismatches: 8, Indels: 10
0.90 0.05 0.06
Matches are distributed among these distances:
98 3 0.02
99 3 0.02
100 85 0.54
101 67 0.42
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.39
Consensus pattern (101 bp):
TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGCTCCTTTGAGACAGTTTCTCTTG
AAACATAAACATTGAAAACATTTCCCTTGAAATAAA
Found at i:554459 original size:101 final size:100
Alignment explanation
Indices: 554241--554605 Score: 395
Period size: 101 Copynumber: 3.6 Consensus size: 100
554231 AGAAGTTTTA
* *
554241 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC-TTGATACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTG-CTCCTTTGAGACAGTTTCTCTTGAAAC
* * *
554305 ATAAACATTGAAAACATTTCTTTGAAATGAATTTTG
65 ATAAACATTGAAAACATTTCCTTGAAATAAATTTCG
554341 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGCCTCCTTTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTG-CTCCTTTGAGACAGTTTCTCTTGAAAC
554406 ATAAA-ATTGAAAACATTTCCCTTGAAATAAATTTCG
65 ATAAACATTGAAAACATTT-CCTTGAAATAAATTTCG
*
554442 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTT-CTCTCTCTTGAGACAGTTT-TCCTTGAA
1 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGCTC-CT-TTGAGACAGTTTCT-CTTGAA
** *** ** * *
554504 ACA-AATTATTTGAATATGTTTTATTTGAAACAAATTTCA
63 ACATAAACA-TTGAA-AACATTTCCTTGAAATAAATTTCG
* ** * * *
554543 TCTCCCTTGA-ATAGTTTCTTTTGGAACTAAGTTTTG-TCTCTCTTGAGACAGTTTCTCTTGAAA
1 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGCTC-CT-TTGAGACAGTTTCTCTTGAAA
554606 TAAATTTCGT
Statistics
Matches: 233, Mismatches: 21, Indels: 21
0.85 0.08 0.08
Matches are distributed among these distances:
98 3 0.01
99 5 0.02
100 95 0.41
101 125 0.54
102 5 0.02
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (100 bp):
TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGCTCCTTTGAGACAGTTTCTCTTGAAACA
TAAACATTGAAAACATTTCCTTGAAATAAATTTCG
Found at i:554468 original size:36 final size:36
Alignment explanation
Indices: 554421--554645 Score: 200
Period size: 36 Copynumber: 6.4 Consensus size: 36
554411 ATTGAAAACA
*
554421 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
554457 TTTCCCTTGAAACAAATTTTC-TCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAA-TTTCGTCTCTCTTGAGACAG
* * *
554493 TTTTCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** * * *
554522 TTTTATTTGAAACAAATTTCATCTCCCTTGA-ATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * * *
554557 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
554594 TTTCTCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
554630 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
554646 ATATTCGAAT
Statistics
Matches: 155, Mismatches: 23, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
28 2 0.01
29 19 0.12
30 2 0.01
31 1 0.01
34 1 0.01
35 12 0.08
36 101 0.65
37 17 0.11
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:554591 original size:201 final size:201
Alignment explanation
Indices: 554241--554605 Score: 461
Period size: 201 Copynumber: 1.8 Consensus size: 201
554231 AGAAGTTTTA
* * *
554241 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCTTGATACAGTTTCTCTTGAAACA
1 TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATTTTCTCTCCTTGAGACAGTTTCTCTTGAAACA
* ** ** *
554306 TAAACATTGAAAACATTTCTTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
66 TAAACATTGAAAACATTTATTTGAAACAAATTTCATCTCCCTTGAGATAGTTTCCCTTGAAACAA
554371 AATTTTGCCTCCTTTGAGACAGTTTCTCTTGAAACATAAAATTGAAAACATTTCCCTTGAAATAA
131 AATTTTGCCTCCTTTGAGACAGTTTCTCTTGAAACATAAAATTGAAAACATTTCCCTTGAAATAA
554436 ATTTCG
196 ATTTCG
*
554442 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTCTCTCTCTTGAGACAGTTT-TCCTTGAAA
1 TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATTTTCTCTC-CTTGAGACAGTTTCT-CTTGAAA
** *** ** *
554505 CA-AATTATTTGAATATGTTTTATTTGAAACAAATTTCATCTCCCTTGA-ATAGTTTCTTTTGGA
64 CATAAACA-TTGAA-AACATTTATTTGAAACAAATTTCATCTCCCTTGAGATAGTTTCCCTTGAA
* * *
554568 ACTAAGTTTTGTCT-CTCTTGAGACAGTTTCTCTTGAAA
127 ACAAAATTTTGCCTCCT-TTGAGACAGTTTCTCTTGAAA
554606 TAAATTTCGT
Statistics
Matches: 138, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
200 17 0.12
201 96 0.70
202 25 0.18
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (201 bp):
TCTCGCTTGAGACAGTTTCCCTTGAAACAAAATTTTCTCTCCTTGAGACAGTTTCTCTTGAAACA
TAAACATTGAAAACATTTATTTGAAACAAATTTCATCTCCCTTGAGATAGTTTCCCTTGAAACAA
AATTTTGCCTCCTTTGAGACAGTTTCTCTTGAAACATAAAATTGAAAACATTTCCCTTGAAATAA
ATTTCG
Found at i:554672 original size:137 final size:137
Alignment explanation
Indices: 554441--554689 Score: 356
Period size: 137 Copynumber: 1.8 Consensus size: 137
554431 AATAAATTTC
*
554441 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTCTCTCTCTTGAGACAGTTTTCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTCTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * * ** *
554506 AAATTATTTGAATATGTTTTATTTGAAACAAATTTCATCTCCCTTGAATAGTTTCTTTTGGAACT
66 AAAATATTCGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAATAGTTTCTTTTGGAACT
554571 AAGTTTT
131 AAGTTTT
* *
554578 GTCTCTCTTGAGACAGTTTCTCTTGAAATAAA-TTTCGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTC-TCTCTCTTGAGACAGTTTCCCTTGAAA
* * **
554642 CAAAATATTCGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGA
65 CAAAATATTCGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGA
554690 GACAATTTCT
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
136 4 0.04
137 93 0.96
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (137 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTCTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATATTCGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAATAGTTTCTTTTGGAACT
AAGTTTT
Found at i:554773 original size:67 final size:67
Alignment explanation
Indices: 554607--554775 Score: 182
Period size: 67 Copynumber: 2.6 Consensus size: 67
554597 CTCTTGAAAT
* * * * * * *
554607 AAATTTCGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATATTCGAATTTATTTCCCCTAAA
1 AAATTTTGTCTCCCTTGACACAATTTCTCATGAAACACAAAATATTCAAATTTATTTCCCCTAAA
554670 AC
66 AC
* * * *
554672 AAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAA
1 AAATTTTGTCTCCCTTGACACAATTTCTCATGAAACACAAAATATTCAAATTTATTTCCCCTAAA
554737 AC
66 AC
* **
554739 AAAATTTTGTTTCCCTTGACACCGTTT-TCATGAAACA
1 -AAATTTTGTCTCCCTTGACACAATTTCTCATGAAACA
554776 ACAGATATCT
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 28 0.31
66 2 0.02
67 37 0.42
68 22 0.25
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (67 bp):
AAATTTTGTCTCCCTTGACACAATTTCTCATGAAACACAAAATATTCAAATTTATTTCCCCTAAA
AC
Found at i:555732 original size:19 final size:19
Alignment explanation
Indices: 555708--555744 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
555698 CACATGGATT
*
555708 TCAACTTCACGATGAAGGA
1 TCAACTTCACGACGAAGGA
555727 TCAACTTCACGACGAAGG
1 TCAACTTCACGACGAAGG
555745 GGCCACCCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (19 bp):
TCAACTTCACGACGAAGGA
Found at i:557006 original size:16 final size:16
Alignment explanation
Indices: 556985--557026 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
556975 TCGTCCCCTA
556985 TATATATATTTTTAAT
1 TATATATATTTTTAAT
*
557001 TATATATATTTTTTAT
1 TATATATATTTTTAAT
557017 T-TACTATATT
1 TATA-TATATT
557027 CCTTTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATATATTTTTAAT
Found at i:557053 original size:14 final size:14
Alignment explanation
Indices: 557034--557073 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
557024 ATTCCTTTTT
557034 TTATTTATATTATA
1 TTATTTATATTATA
*
557048 TTATTTTTATTATA
1 TTATTTATATTATA
557062 TATATCTTATAT
1 T-TAT-TTATAT
557074 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:557054 original size:21 final size:22
Alignment explanation
Indices: 556995--557068 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 22
556985 TATATATATT
*
556995 TTTA-ATTATATATATTTTTTA
1 TTTATATTATATCTATTTTTTA
557016 TTTACTA-TAT-TCCT-TTTTTTA
1 TTTA-TATTATAT-CTATTTTTTA
557037 TTTATATTATAT-TA-TTTTTA
1 TTTATATTATATCTATTTTTTA
557057 -TTATA-TATATCT
1 TTTATATTATATCT
557069 TATATCATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 16
0.73 0.02 0.26
Matches are distributed among these distances:
18 5 0.11
19 6 0.13
20 9 0.20
21 19 0.42
22 5 0.11
23 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTATATTATATCTATTTTTTA
Found at i:557345 original size:33 final size:35
Alignment explanation
Indices: 557276--557345 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
557266 ATGTATATAT
* *
557276 TTATTTTTATTTGTTTTACTTAGTATTATATATTTA
1 TTATTTTTATTTGTTTTACGTAG-AATATATATTTA
557312 TTATTTTTATTTGTTTTA-GTA-AATAT-TACTTTA
1 TTATTTTTATTTGTTTTACGTAGAATATATA-TTTA
557345 T
1 T
557346 ATGTACACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 2 0.06
33 9 0.29
35 2 0.06
36 18 0.58
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (35 bp):
TTATTTTTATTTGTTTTACGTAGAATATATATTTA
Found at i:557406 original size:18 final size:19
Alignment explanation
Indices: 557369--557407 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
557359 TTTTATTATT
557369 TTTTAATTTCTTTTACCTA
1 TTTTAATTTCTTTTACCTA
557388 TTTT-ATTT-TTTTACTCTA
1 TTTTAATTTCTTTTAC-CTA
557406 TT
1 TT
557408 AATATTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 9 0.47
19 4 0.21
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTAATTTCTTTTACCTA
Found at i:557450 original size:19 final size:18
Alignment explanation
Indices: 557428--557526 Score: 55
Period size: 19 Copynumber: 5.4 Consensus size: 18
557418 TTTATCTGTG
557428 TATTTATTTTTTAATATTT
1 TATTTATTTTTTAAT-TTT
* *
557447 TATTCATTTTGTTTATTTT
1 TATTTATTTT-TTAATTTT
*
557466 TA-TTATTTTTATTATTTTT
1 TATTTA-TTTT-TTAATTTT
**
557485 TACGTATTTTGTT-ATTTT
1 TATTTATTTT-TTAATTTT
*
557503 TCA-TTATTTTTT--GTTT
1 T-ATTTATTTTTTAATTTT
557519 TATTTATT
1 TATTTATT
557527 ATTCTCACGT
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.02
16 9 0.14
17 2 0.03
18 13 0.20
19 33 0.52
20 6 0.09
ACGTcount: A:0.19, C:0.03, G:0.04, T:0.74
Consensus pattern (18 bp):
TATTTATTTTTTAATTTT
Found at i:557461 original size:28 final size:27
Alignment explanation
Indices: 557430--557483 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
557420 TATCTGTGTA
557430 TTTATTTTTTAATA-TTTTATTCATTTTG
1 TTTA-TTTTTAATATTTTTATT-ATTTTG
*
557458 TTTATTTTTATTATTTTTATTATTTT
1 TTTATTTTTAATATTTTTATTATTTT
557484 TTACGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTATTTTTAATATTTTTATTATTTTG
Found at i:557463 original size:18 final size:17
Alignment explanation
Indices: 557430--557512 Score: 62
Period size: 19 Copynumber: 4.6 Consensus size: 17
557420 TATCTGTGTA
*
557430 TTTATT-TTTTAATA-T
1 TTTATTATTTTATTATT
*
557445 TTTATTCATTTTGTTTATT
1 TTTATT-ATTTT-ATTATT
557464 TTTATTATTTTTATTATTT
1 TTTATTA-TTTTATTA-TT
* *
557483 TTTACGTATTTTGTTATT
1 TTTA-TTATTTTATTATT
557501 TTTCATTATTTT
1 TTT-ATTATTTT
557513 TTGTTTTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
15 6 0.11
17 4 0.07
18 17 0.31
19 25 0.46
20 2 0.04
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (17 bp):
TTTATTATTTTATTATT
Found at i:557484 original size:9 final size:9
Alignment explanation
Indices: 557435--557513 Score: 65
Period size: 9 Copynumber: 8.6 Consensus size: 9
557425 GTGTATTTAT
*
557435 TTTTTAATA
1 TTTTTATTA
557444 -TTTTATTCA
1 TTTTTATT-A
557453 TTTTGT-TTA
1 TTTT-TATTA
557462 TTTTTATTA
1 TTTTTATTA
557471 TTTTTATTA
1 TTTTTATTA
*
557480 TTTTTTACGTA
1 -TTTTTA-TTA
*
557491 -TTTTGTTA
1 TTTTTATTA
557499 TTTTTCATTA
1 TTTTT-ATTA
557509 TTTTT
1 TTTTT
557514 TGTTTTATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
8 9 0.16
9 26 0.46
10 19 0.33
11 3 0.05
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (9 bp):
TTTTTATTA
Found at i:557527 original size:19 final size:19
Alignment explanation
Indices: 557453--557529 Score: 54
Period size: 20 Copynumber: 4.0 Consensus size: 19
557443 ATTTTATTCA
557453 TTTTG-TTTATTT-TTATT
1 TTTTGTTTTATTTATTATT
* * *
557470 ATTTT-TATTATTTTTTACGTA
1 -TTTTGTTTTATTTATTA--TT
557491 TTTTGTTATT-TTTCATTATT
1 TTTTGTT-TTATTT-ATTATT
557511 TTTTGTTTTATTTATTATT
1 TTTTGTTTTATTTATTATT
557530 CTCACGTTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 15
0.70 0.08 0.23
Matches are distributed among these distances:
18 10 0.22
19 11 0.24
20 15 0.33
21 5 0.11
22 5 0.11
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (19 bp):
TTTTGTTTTATTTATTATT
Found at i:557528 original size:29 final size:27
Alignment explanation
Indices: 557434--557529 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 27
557424 TGTGTATTTA
*
557434 TTTTTTAATA-TTTTATTCATTTTGTT-T
1 TTTTTTATTATTTTTATT-ATTTT-TTGT
*
557461 ATTTTTATTATTTTTATTATTTTTTACG-
1 TTTTTTATTATTTTTATTATTTTTT--GT
* *
557489 TATTTTGTTATTTTTCATTATTTTTTGT
1 TTTTTTATTATTTTT-ATTATTTTTTGT
557517 TTTATTTATTATT
1 TTT-TTTATTATT
557530 CTCACGTTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
26 2 0.04
27 14 0.25
28 21 0.38
29 18 0.33
ACGTcount: A:0.19, C:0.03, G:0.04, T:0.74
Consensus pattern (27 bp):
TTTTTTATTATTTTTATTATTTTTTGT
Found at i:570366 original size:19 final size:19
Alignment explanation
Indices: 570342--570378 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
570332 ATTCTCATTA
570342 TAATTATAAATA-CATTATT
1 TAATTA-AAATATCATTATT
570361 TAATTAAAATATCATTAT
1 TAATTAAAATATCATTAT
570379 AAATTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATTAAAATATCATTATT
Found at i:585460 original size:32 final size:32
Alignment explanation
Indices: 585109--585460 Score: 487
Period size: 32 Copynumber: 11.1 Consensus size: 32
585099 CCAAGAGTCG
585109 AGAATTACCTATGTCTTTCGGGACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGAC
*
585141 A-ATATTACCTATGTCTTTTGGGACATATGGAC
1 AGA-ATTACCTATGTCTTTCGGGACATATGGAC
*
585173 AGAATTACCTATGTTTTTCGGGACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGAC
** *
585205 ATTATTACCTATGTCTTTTGGGACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGAC
*
585237 AGAATTACCTATGTTTTTCGGGACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGAC
*
585269 AGTATTACCTATGTCTTTCGGGACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGAC
*
585301 AAAATTACC--TGTCTTTCGGGACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGAC
* * * *
585331 AAAATTACCTATATCTTTCGGGATACATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGAC
** *
585363 A-ATATTATATACGTCTTTCGGGACATATGGAC
1 AGA-ATTACCTATGTCTTTCGGGACATATGGAC
* **
585395 ATAATTACCTATGTCTTTCGACACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGAC
*
585427 AGAATTACCTATGTCTTTCGGGGCATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGAC
585459 AG
1 AG
585461 TGACCTATGT
Statistics
Matches: 281, Mismatches: 33, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
30 30 0.11
31 2 0.01
32 247 0.88
33 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (32 bp):
AGAATTACCTATGTCTTTCGGGACATATGGAC
Found at i:586041 original size:21 final size:21
Alignment explanation
Indices: 586015--586058 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
586005 TGCTGAAATT
* *
586015 ACTGTAGCAGTGTATCGGTAC
1 ACTGTAGCAGTGCATCGCTAC
586036 ACTGTAGCAGTGCATCGCTAC
1 ACTGTAGCAGTGCATCGCTAC
586057 AC
1 AC
586059 ATTTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGCTAC
Found at i:588266 original size:39 final size:38
Alignment explanation
Indices: 588202--588309 Score: 128
Period size: 39 Copynumber: 2.8 Consensus size: 38
588192 CCTAATTCCC
* * *
588202 AAATTATTTTACCTAACATTCTAAATTCTTAATTTCTT
1 AAATTATTTCACCTAAAATTCTAAATTATTAATTTCTT
*
588240 AAATTATTTCACTGTAAAATTCTAAATTATTAATTTCTT
1 AAATTATTTCAC-CTAAAATTCTAAATTATTAATTTCTT
* *
588279 AAATTATTTTACTCTAACCATT-TAAATTATT
1 AAATTATTTCAC-CTAA-AATTCTAAATTATT
588310 TCTCAAATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
38 11 0.18
39 47 0.77
40 3 0.05
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (38 bp):
AAATTATTTCACCTAAAATTCTAAATTATTAATTTCTT
Found at i:594067 original size:21 final size:22
Alignment explanation
Indices: 594043--594085 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
594033 TTACGTAGTC
594043 TTAAATTTTAATTTT-TTTATG
1 TTAAATTTTAATTTTATTTATG
* *
594064 TTAATTTTTTATTTTATTTATG
1 TTAAATTTTAATTTTATTTATG
594086 AAGTTTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (22 bp):
TTAAATTTTAATTTTATTTATG
Found at i:595934 original size:2 final size:2
Alignment explanation
Indices: 595882--595916 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
595872 TATAATAAAG
595882 AT AT AT AT AT 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 AT AT AT AT AT A
595917 ATTATAACAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:603637 original size:24 final size:24
Alignment explanation
Indices: 603610--603697 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
603600 TTCTATTATA
* *
603610 ATACCTGACCTTGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* *
603634 ATACTTGACCTGGATTCTGATTGA
1 ATACTTGACCTGGATTCTGATCGG
* * *
603658 ATACTTGACATGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
603682 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
603698 ATTTTATGAT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:609217 original size:3 final size:3
Alignment explanation
Indices: 609209--609252 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
609199 TAAATTTCAA
609209 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
609253 ATTAAAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:609264 original size:11 final size:11
Alignment explanation
Indices: 609212--609269 Score: 53
Period size: 12 Copynumber: 5.0 Consensus size: 11
609202 ATTTCAAAAT
*
609212 AATAATAATAAT
1 AATAA-AATAAA
*
609224 AATAATAATAAT
1 AATAA-AATAAA
*
609236 AATAATAATAAT
1 AATAA-AATAAA
*
609248 AATAAATTAAA
1 AATAAAATAAA
609259 AATAAAATAAA
1 AATAAAATAAA
609270 GACCCGAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
11 14 0.33
12 29 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:609489 original size:2 final size:2
Alignment explanation
Indices: 609484--609508 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
609474 ATATATATAT
609484 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
609509 AAGATAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:616607 original size:23 final size:23
Alignment explanation
Indices: 616535--616599 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
616525 ATATTTTACA
*
616535 ATATAAACACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
616558 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
616581 ATATAAGCGCTACCTATTA
1 ATATAAACGCTACCTATTA
616600 TATCATATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:617051 original size:489 final size:488
Alignment explanation
Indices: 616133--618447 Score: 3740
Period size: 489 Copynumber: 4.8 Consensus size: 488
616123 TTATAATATG
* *
616133 TTGAAAGTGTTCATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAATTATGTAATTTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
616198 TTTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
65 TTTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
*
616263 C-AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAT
*
616327 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
* * ** ** *
616392 ACCGTAACATAACAAATAAATCATTAGATACAAATAATTACTAAATTGATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
* *
616457 CAAAAGATAACCTTAAATTAATGTTTTTCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGAA
325 CAAAA-ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
* * *
616522 TATATATTTTACAATATAAACACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
389 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
*
616587 GCGCTACCTATTATATCATATTTTTACCTATTATA
454 GCGCTACCTATTACATCATATTTTTACCTATTATA
*
616622 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATATTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
* *
616687 TCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
66 TTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
616752 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTA-ACATTTAAATTTAACAATAT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGA-ATTTAAATTTAACAATAT
*
616816 TAACTAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
616881 ACCGTAACGTAAAAAATAAATTATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
* *
616946 CAAAATATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACATTTTTATAAAAATGA
325 CAAAA-ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
617011 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
389 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
*
617076 GTGCTACCTATTACATCATATTTTTACCTATTATA
454 GCGCTACCTATTACATCATATTTTTACCTATTATA
*
617111 TTGAAA--G-------------T------G-TCGATACTTTTTATAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
617154 TTAATTTTTTTAATAGTGTTTCATGTTTTCAACCTACAATATTAATTTAATAATTTCATTTACAC
66 TTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
*
617219 -AAAAATTATTTGATCGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
617283 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
* * *
617348 CCGTAACATAAAAAATAAATCATTAGACACCTATAATAACTAAATTAATATCTT--AA-T-A--C
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
* *
617407 -----TAACCTTAAATTAATGTTTTCTACAGTGAAAAAAGTATGGACACATTTATAAAAAGGATA
326 AAAAATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATA
617467 GATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGC
391 GATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGC
617532 GCTACCTATTACATCATATTTTTACCTATTATA
456 GCTACCTATTACATCATATTTTTACCTATTATA
* *
617565 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGACACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
* * * *
617630 TCAA-TTTTTTAATAGTGTTTCATGTTTTCTACATACAATATTAATTTAATAATTTTATTTACAC
66 TTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
617694 AAAAAATTATTTGATTGTTTTGATATTTTA-AAAATATTATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
*
617758 AACCAAAGATAATAATAAATATTTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
*
617823 TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTT-AAA---A--C
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
617882 -----TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATA
326 AAAAATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATA
*
617942 GATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGG
391 GATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGC
* *
618007 GCTATCTATTACATTATATTTTTACCTATTATA
456 GCTACCTATTACATCATATTTTTACCTATTATA
* *
618040 TTGAAAGTGTCCATATTTTTTATAAAAATGATCGATA-TTTTTTTAAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTT-AAAGTTATGTAATTTATGT
*
618104 TTTAATTTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTACA
65 TTTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
*
618169 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAATAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAT
*
618234 TAACCAAAAATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
618299 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
* *
618364 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGAACACTTTTATAAAAATGA
325 CAAAA-ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
*
618429 TAGATATTTTACAATATAA
389 TAGATACTTTACAATATAA
618448 CAGATAAAAA
Statistics
Matches: 1713, Mismatches: 71, Indels: 84
0.92 0.04 0.04
Matches are distributed among these distances:
454 159 0.09
456 1 0.00
460 1 0.00
462 1 0.00
463 1 0.00
464 2 0.00
466 175 0.10
467 95 0.06
468 1 0.00
469 1 0.00
474 8 0.00
475 419 0.24
476 153 0.09
477 150 0.09
478 3 0.00
481 1 0.00
483 1 0.00
487 1 0.00
488 110 0.06
489 430 0.25
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (488 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATA
GATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGC
GCTACCTATTACATCATATTTTTACCTATTATA
Found at i:617059 original size:23 final size:23
Alignment explanation
Indices: 617024--617096 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
617014 ATACTTTACA
*
617024 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
617047 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
617070 ATATAAGTGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
617093 ATAT
1 ATAT
617097 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:617513 original size:23 final size:23
Alignment explanation
Indices: 617478--617550 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
617468 ATACTTTACA
*
617478 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
617501 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
617524 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
617547 ATAT
1 ATAT
617551 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:617988 original size:23 final size:23
Alignment explanation
Indices: 617953--618025 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
617943 ATACTTTACA
*
617953 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
617976 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
617999 ATATAAGGGCTATCTATTACATT
1 ATATAAGCGCTACCTATTACATT
618022 ATAT
1 ATAT
618026 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:621566 original size:30 final size:30
Alignment explanation
Indices: 621530--621586 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
621520 AACACCTTAA
** *
621530 AAAAATAAATAAGTGAATATAAATACATTC
1 AAAAATAAATAAACGAATACAAATACATTC
621560 AAAAATAAATAAACGAATACAAATACA
1 AAAAATAAATAAACGAATACAAATACA
621587 ACACTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.65, C:0.09, G:0.05, T:0.21
Consensus pattern (30 bp):
AAAAATAAATAAACGAATACAAATACATTC
Found at i:622504 original size:15 final size:15
Alignment explanation
Indices: 622484--622514 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
622474 CAACAAATAG
622484 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
622499 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
622514 A
1 A
622515 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:624219 original size:24 final size:24
Alignment explanation
Indices: 624189--624297 Score: 121
Period size: 24 Copynumber: 4.6 Consensus size: 24
624179 TGTTAATTTA
*
624189 TTGTGTTCGTTTACGTTCGTTCAT
1 TTGTGTTCGTTTATGTTCGTTCAT
* * *
624213 TTGTGTTTGTTTATGTTCTTTTA-
1 TTGTGTTCGTTTATGTTCGTTCAT
* * *
624236 TTGTGTTCGTTTATGTTAGTTTAC
1 TTGTGTTCGTTTATGTTCGTTCAT
* **
624260 ATCCGTTCGTTTATGTTCGTTCAT
1 TTGTGTTCGTTTATGTTCGTTCAT
624284 TTGTGTTCGTTTAT
1 TTGTGTTCGTTTAT
624298 CATTTAAATT
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
23 20 0.29
24 48 0.71
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.59
Consensus pattern (24 bp):
TTGTGTTCGTTTATGTTCGTTCAT
Found at i:624272 original size:47 final size:47
Alignment explanation
Indices: 624185--624297 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
624175 TTTGTGTTAA
* * ** ** * *
624185 TTTATTGTGTTCGTTTACGTTCGTTCATTTGTGTTTGTTTATGTTCT
1 TTTATTGTGTTCGTTTATGTTAGTTCACATCCGTTCGTTTATGTTCG
*
624232 TTTATTGTGTTCGTTTATGTTAGTTTACATCCGTTCGTTTATGTTCG
1 TTTATTGTGTTCGTTTATGTTAGTTCACATCCGTTCGTTTATGTTCG
*
624279 TTCATTTGTGTTCGTTTAT
1 TTTA-TTGTGTTCGTTTAT
624298 CATTTAAATT
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 41 0.75
48 14 0.25
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.59
Consensus pattern (47 bp):
TTTATTGTGTTCGTTTATGTTAGTTCACATCCGTTCGTTTATGTTCG
Found at i:624686 original size:19 final size:21
Alignment explanation
Indices: 624648--624686 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
624638 AATTTTAAAA
*
624648 TAAATATAAACTAGTATAATT
1 TAAATATAAACTAATATAATT
624669 TAAAT-TAAA-TAATATAAT
1 TAAATATAAACTAATATAAT
624687 CTATTTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 4 0.24
21 5 0.29
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TAAATATAAACTAATATAATT
Found at i:628575 original size:24 final size:24
Alignment explanation
Indices: 628547--628610 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
628537 CATCAATGCA
*
628547 TAAGGAGTGCATCGATGCACACGT
1 TAAGGAGTGCATCGATGCACACGG
628571 TAAGG-GATGCATCGAT--ACACGG
1 TAAGGAG-TGCATCGATGCACACGG
628593 T-AGGA-TGCATCGATGCAC
1 TAAGGAGTGCATCGATGCAC
628611 TTCAAGGGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
20 9 0.26
21 3 0.09
22 8 0.23
23 1 0.03
24 14 0.40
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (24 bp):
TAAGGAGTGCATCGATGCACACGG
Found at i:641136 original size:6 final size:6
Alignment explanation
Indices: 641125--641158 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
641115 CCCTCTATCT
641125 AATCCC AATCCC AATCCC AAT--C AATCCC AATCCC
1 AATCCC AATCCC AATCCC AATCCC AATCCC AATCCC
641159 CATTTGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
6 22 0.85
ACGTcount: A:0.35, C:0.47, G:0.00, T:0.18
Consensus pattern (6 bp):
AATCCC
Found at i:642733 original size:19 final size:21
Alignment explanation
Indices: 642695--642733 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
642685 AATTTTAAAA
*
642695 TAAATATAAACTAGTATAATT
1 TAAATATAAACTAATATAATT
642716 TAAAT-TAAA-TAATATAAT
1 TAAATATAAACTAATATAAT
642734 CTATTTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 4 0.24
21 5 0.29
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TAAATATAAACTAATATAATT
Found at i:644077 original size:20 final size:20
Alignment explanation
Indices: 644054--644133 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
644044 GTTTCCAGAT
*
644054 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
* * *
644074 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
*
644094 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
*
644115 TCGCAACGCGATTCTGACT
1 TCGCAACGCGATTATGACT
644134 GTTGCAACAC
Statistics
Matches: 45, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
18 1 0.02
20 26 0.58
21 16 0.36
22 2 0.04
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:645013 original size:24 final size:24
Alignment explanation
Indices: 644956--645015 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
644946 TAGTTAGTAT
644956 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
644980 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
645004 TCGAATTTTGAT
1 TCGAAATTTGAT
645016 GATGTTTCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:645223 original size:12 final size:13
Alignment explanation
Indices: 645208--645240 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
645198 AAAAGAAAAA
645208 GAAGAAA-TCCCC
1 GAAGAAAGTCCCC
645220 GAAGAAAAGTCCCC
1 GAAG-AAAGTCCCC
645234 GAAGAAA
1 GAAGAAA
645241 ATGCCACGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 6 0.32
14 9 0.47
ACGTcount: A:0.48, C:0.24, G:0.21, T:0.06
Consensus pattern (13 bp):
GAAGAAAGTCCCC
Found at i:645234 original size:14 final size:14
Alignment explanation
Indices: 645215--645241 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
645205 AAAGAAGAAA
645215 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
645229 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
645242 TGCCACGAGA
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:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:646300 original size:20 final size:20
Alignment explanation
Indices: 646275--646389 Score: 176
Period size: 20 Copynumber: 5.8 Consensus size: 20
646265 TTACACATTC
*
646275 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
646295 ATTTGATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
646315 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
646335 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
646355 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
646375 ATTTGACTATCGCAA
1 ATTTGACTATCGCAA
646390 TGAGAAAATC
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 88 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:646368 original size:60 final size:60
Alignment explanation
Indices: 646275--646389 Score: 194
Period size: 60 Copynumber: 1.9 Consensus size: 60
646265 TTACACATTC
646275 ATTTGAATATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACGCGA
* * * *
646335 ATTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGTATTTGACTATCGCAA
1 ATTTGAATATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAA
646390 TGAGAAAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (60 bp):
ATTTGAATATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACGCGA
Found at i:646459 original size:20 final size:21
Alignment explanation
Indices: 646430--646487 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
646420 GCAACGCGAA
646430 TTGA-CTTTCGCGTTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
646450 TTG-GCTTTCGCATTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
646470 TTGAG-TTTAGCGTTGCGA
1 TTGAGCTTTCGCGTTGCGA
646488 AAGTGTACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.12, C:0.17, G:0.28, T:0.43
Consensus pattern (21 bp):
TTGAGCTTTCGCGTTGCGATT
Found at i:646625 original size:29 final size:29
Alignment explanation
Indices: 646591--646646 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
646581 ATAAGAATTA
*
646591 TTTACACATCAATATTAAACAAATCAACT
1 TTTACAAATCAATATTAAACAAATCAACT
* **
646620 TTTACAAATCAATTTTTTACAAATCAA
1 TTTACAAATCAATATTAAACAAATCAA
646647 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (29 bp):
TTTACAAATCAATATTAAACAAATCAACT
Found at i:646639 original size:15 final size:15
Alignment explanation
Indices: 646586--646648 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 15
646576 CACAAATAAG
* *
646586 AATTATTTACACATC
1 AATTTTTTACAAATC
* **
646601 AATATTAAACAAATC
1 AATTTTTTACAAATC
*
646616 AA-CTTTTACAAATC
1 AATTTTTTACAAATC
646630 AATTTTTTACAAATC
1 AATTTTTTACAAATC
646645 AATT
1 AATT
646649 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
14 11 0.29
15 27 0.71
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTTTTTACAAATC
Found at i:648093 original size:21 final size:21
Alignment explanation
Indices: 648033--648126 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
648023 ATGAATCGGG
* * *
648033 CTCTTGAATGGTGTGAGGGAC
1 CTCTTGAACGGTGAGAGGGGC
* * *
648054 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGAGAGGGGC
* *
648075 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGAGAGGGGC
* *
648096 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGAGAGGGGC
648117 CTCTTGAACG
1 CTCTTGAACG
648127 ATAGGATAGG
Statistics
Matches: 55, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 50 0.91
22 2 0.04
ACGTcount: A:0.20, C:0.19, G:0.37, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGAGAGGGGC
Found at i:648093 original size:42 final size:42
Alignment explanation
Indices: 648033--648126 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
648023 ATGAATCGGG
* *
648033 CTCTTGAATGGTGTGA-GGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCAACGATGACAGGGGC
* ** *
648075 CTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGGGGC
648117 CTCTTGAACG
1 CTCTTGAACG
648127 ATAGGATAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 41 0.91
43 4 0.09
ACGTcount: A:0.20, C:0.19, G:0.37, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGGGGC
Found at i:648131 original size:18 final size:19
Alignment explanation
Indices: 648108--648145 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
648098 CTTGAGGGAT
648108 GATAGG-GGCCTCTTGAAC
1 GATAGGAGGCCTCTTGAAC
648126 GATAGGATAGGCCTCTTGAA
1 GATAGG--AGGCCTCTTGAA
648146 TGATGACAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
21 11 0.65
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (19 bp):
GATAGGAGGCCTCTTGAAC
Found at i:648142 original size:42 final size:42
Alignment explanation
Indices: 648063--648155 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
648053 CCTCTTCAAC
* * *
648063 GATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATAGGAGAGGACTCTTGAGG
* * * **
648105 GATGATAGGGGCCTCTTGAACGATAGGATAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGATAGGAGAGGACTCTTGAGG
648147 GATGACAGG
1 GATGACAGG
648156 TGAGTCGGAC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.16, G:0.39, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATAGGAGAGGACTCTTGAGG
Found at i:648656 original size:20 final size:19
Alignment explanation
Indices: 648631--648702 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
648621 AATAGTTTCT
*
648631 GAAACTTAAAATCGCAACAC
1 GAAA-TTAAAATCGCAACGC
648651 GAAACTT-AAATCGCAACGC
1 GAAA-TTAAAATCGCAACGC
* *
648670 GAAATAAAAATCGTAACGC
1 GAAATTAAAATCGCAACGC
*
648689 GAAATTAAATTCGC
1 GAAATTAAAATCGC
648703 GTTGCGATAG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 1 0.02
19 37 0.82
20 7 0.16
ACGTcount: A:0.47, C:0.21, G:0.14, T:0.18
Consensus pattern (19 bp):
GAAATTAAAATCGCAACGC
Found at i:650740 original size:20 final size:19
Alignment explanation
Indices: 650701--650816 Score: 107
Period size: 20 Copynumber: 6.2 Consensus size: 19
650691 GAAACTTAAA
650701 ATCGCAACACGAAATGACT
1 ATCGCAACACGAAATGACT
* *
650720 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAA-ATGACT
*
650740 ATCGC-A-ACGAGAT-A--
1 ATCGCAACACGAAATGACT
* **
650754 ATCGCAACGCGAAATGAAA
1 ATCGCAACACGAAATGACT
650773 ATCGCAACACGAAAATGACT
1 ATCGCAACACG-AAATGACT
*
650793 ATCGCAACACGAATTTGACT
1 ATCGCAACACGAA-ATGACT
650813 ATCG
1 ATCG
650817 TTGCGATTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
14 5 0.06
15 1 0.01
16 6 0.08
17 2 0.03
18 3 0.04
19 25 0.32
20 36 0.46
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:650780 original size:53 final size:53
Alignment explanation
Indices: 650700--650800 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 53
650690 TGAAACTTAA
** * **
650700 AATCGCAACACGAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGAT
1 AATCGCAACACGAAATGAAAATCGCAACACGAAAATGACTATCGCAACGAGAT
*
650753 AATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACTATCGCAAC
1 AATCGCAACACGAAATGAAAATCGCAACACGAAAATGACTATCGCAAC
650801 ACGAATTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.42, C:0.25, G:0.18, T:0.16
Consensus pattern (53 bp):
AATCGCAACACGAAATGAAAATCGCAACACGAAAATGACTATCGCAACGAGAT
Found at i:651227 original size:22 final size:22
Alignment explanation
Indices: 651195--651246 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
651185 AGATAGACAT
651195 ATTTCGCCGGAGATAGGGACGG
1 ATTTCGCCGGAGATAGGGACGG
* *
651217 ATTTCGTCGGAGATGGGGACGG
1 ATTTCGCCGGAGATAGGGACGG
*
651239 ATGTCGCC
1 ATTTCGCC
651247 TTAGAGAGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.40, T:0.21
Consensus pattern (22 bp):
ATTTCGCCGGAGATAGGGACGG
Found at i:651456 original size:20 final size:20
Alignment explanation
Indices: 651406--651478 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
651396 ATTTTGTATT
* *
651406 ATCGCGTTGCAATAGTCAGA
1 ATCGCGTTGCGATAGTCAAA
651426 ATCGCGTTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAAA
* ** *
651446 ATCGCGTTGCGATACTGGAG
1 ATCGCGTTGCGATAGTCAAA
651466 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
651479 TTAGAGATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAAA
Found at i:651487 original size:19 final size:19
Alignment explanation
Indices: 651446--651499 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
651436 GATAGTCAAA
* *
651446 ATCGCGTTGCGATACTGGAG
1 ATCGCGTTGCGAT-TTAGAG
651466 ATCGCGTTGCGATTTAGAG
1 ATCGCGTTGCGATTTAGAG
*
651485 ATCGCATTGCGATTT
1 ATCGCGTTGCGATTT
651500 TGTTGGTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (19 bp):
ATCGCGTTGCGATTTAGAG
Found at i:656806 original size:29 final size:29
Alignment explanation
Indices: 656763--656843 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
656753 CAACTAAATT
*
656763 GATGTCA-TGCTTACATTATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
656791 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
656820 GATGACATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
656844 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
28 7 0.15
29 36 0.75
30 5 0.10
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:661550 original size:29 final size:29
Alignment explanation
Indices: 661508--661589 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
661498 AAACTAAATT
661508 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
661537 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
661566 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
661590 GTTAGGTGAG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 46 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Done.