Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006710.1 Hibiscus syriacus cultivar Beakdansim tig00016725_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: 2941931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:2342622 original size:10 final size:11
Alignment explanation
Indices: 2342585--2342623 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2342575 AAAGGAAAAG
*
2342585 CAAAAAAAAAA
1 CAAAAAAAATA
*
2342596 CACAAAAAATA
1 CAAAAAAAATA
*
2342607 CAAAAAAAATT
1 CAAAAAAAATA
2342618 CAAAAA
1 CAAAAA
2342624 TCACAACAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.79, C:0.13, G:0.00, T:0.08
Consensus pattern (11 bp):
CAAAAAAAATA
Found at i:2345818 original size:20 final size:20
Alignment explanation
Indices: 2345788--2345839 Score: 95
Period size: 20 Copynumber: 2.5 Consensus size: 20
2345778 TAGTTAGAGG
2345788 AGCTAAGATGGAGCTAAAGTA
1 AGCT-AGATGGAGCTAAAGTA
2345809 AGCTAGATGGAGCTAAAGTA
1 AGCTAGATGGAGCTAAAGTA
2345829 AGCTAGATGGA
1 AGCTAGATGGA
2345840 CTATTTGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.40, C:0.10, G:0.31, T:0.19
Consensus pattern (20 bp):
AGCTAGATGGAGCTAAAGTA
Found at i:2346701 original size:3 final size:3
Alignment explanation
Indices: 2346693--2346718 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2346683 CATTTTCTAC
2346693 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
2346719 ACGTAGGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:2348049 original size:81 final size:81
Alignment explanation
Indices: 2347953--2348358 Score: 562
Period size: 81 Copynumber: 5.1 Consensus size: 81
2347943 AGTTCTAAAA
* *
2347953 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAAAAATATGTTAATAATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAAAAATGTGTCAATAATGCCAGTTAGATGAAAG
2348018 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
2348034 TAAAAGATTAATGGCCTAGCTGTGCATTTGGAAAAAATGTGTCAATAATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAAAAATGTGTCAATAATGCCAGTTAGATGAAAG
2348099 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
2348115 TAAAAGATTAATGG--TA----T-C---TGGCAGAAAGGAGTCAATAATGTCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAAAAATGTGTCAATAATGCCAGTTAGATGAAAG
2348170 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
2348186 TAAAAGATTAATGGCATAGCTGTGCATTTGGCAGAAAGGTGTCAATAATGCCAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAAAAATGTGTCAATAATGCCAGTTAGATGAAAG
**
2348251 GTTAAATACCTTTTTG
66 GTTAAATACCTTTGAG
* * * * * *
2348267 TAAAAGATTAATGGCCTAGTTGTGTATTCGGCAAAAATGTGTCAATTATTCCAGTTAGAGGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAAAAATGTGTCAATAATGCCAGTTAGATGAAAG
2348332 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
2348348 TAAAAGATTAA
1 TAAAAGATTAA
2348359 CAGCCTAATT
Statistics
Matches: 288, Mismatches: 27, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
71 61 0.21
73 2 0.01
74 1 0.00
75 1 0.00
77 1 0.00
78 1 0.00
79 2 0.01
81 219 0.76
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAAAAATGTGTCAATAATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:2348228 original size:152 final size:152
Alignment explanation
Indices: 2347996--2348358 Score: 492
Period size: 152 Copynumber: 2.3 Consensus size: 152
2347986 AAAATATGTT
*
2347996 AATAATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCAT
1 AATAATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCATAGCTGTGCAT
* *
2348061 TTGGAAAAAATGTGTCAATAATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
66 TTGGAAAAAAGGTGTCAATAATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
2348126 TGGTATCTGGCAGAAAGGAGTC
131 TGGTATCTGGCAGAAAGGAGTC
*
2348148 AATAATGTCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCATAGCTGTGCAT
1 AATAATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCATAGCTGTGCAT
* * * **
2348213 TTGGCAGAAAGGTGTCAATAATGCCAGTTAGATGAAATGTTAAATACCTTTTTGTAAAAGATTAA
66 TTGGAAAAAAGGTGTCAATAATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
* * * *
2348278 TGGCCTAGTTGTGTATTCGGCAAAAATGTGTC
131 TGG--TA------T-CT-GGCAGAAAGGAGTC
* * *
2348310 AATTATTCCAGTTAGAGGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
1 AATAATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
2348359 CAGCCTAATT
Statistics
Matches: 184, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
152 124 0.67
154 2 0.01
160 1 0.01
161 1 0.01
162 56 0.30
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (152 bp):
AATAATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCATAGCTGTGCAT
TTGGAAAAAAGGTGTCAATAATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
TGGTATCTGGCAGAAAGGAGTC
Found at i:2348404 original size:81 final size:81
Alignment explanation
Indices: 2348128--2348392 Score: 334
Period size: 81 Copynumber: 3.3 Consensus size: 81
2348118 AAGATTAATG
* * * *
2348128 GTATCTGGCAGAAAGGAGTCAATAATGTCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGA
1 GTATTTGGCAGAAAAGTGTCAATAATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGA
* *
2348193 TTAATGGCATAGCTGT
66 TTAATGGCCTAGTTGT
* * * **
2348209 GCATTTGGCAGAAAGGTGTCAATAATGCCAGTTAGATGAAATGTTAAATACCTTTTTGTAAAAGA
1 GTATTTGGCAGAAAAGTGTCAATAATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGA
2348274 TTAATGGCCTAGTTGT
66 TTAATGGCCTAGTTGT
* * * *
2348290 GTATTCGGCA-AAAATGTGTCAATTATTCCAGTTAGAGGAAAGGTTAAATACCTTTGAGTAAAAG
1 GTATTTGGCAGAAAA-GTGTCAATAATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
** * *
2348354 ATTAACAGCCTAATTAT
65 ATTAATGGCCTAGTTGT
*
2348371 GTATTTGGCAGAAAAGTATCAA
1 GTATTTGGCAGAAAAGTGTCAA
2348393 CCATGCAAGT
Statistics
Matches: 158, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
80 3 0.02
81 151 0.96
82 4 0.03
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.31
Consensus pattern (81 bp):
GTATTTGGCAGAAAAGTGTCAATAATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGA
TTAATGGCCTAGTTGT
Found at i:2353716 original size:81 final size:81
Alignment explanation
Indices: 2353607--2354095 Score: 662
Period size: 81 Copynumber: 6.1 Consensus size: 81
2353597 TTCTAAAATA
* * ** * *
2353607 AAAAAATTAATGACCTAGTTGTGCATTTGGTGGAATGGTGTCAATAATGTAAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATAATGTCAGTTAGATGAAAGG
2353672 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* *
2353688 AAAAGATTAATGGCCTAGCTGTGAATTTGGCAGAAAGGTGTCAATAATG-CAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATAATGTCAGTTAGATGAAAGG
2353752 TT-AATACCTTTGAGT
66 TTAAATACCTTTGAGT
* ** * *
2353767 AAAATATTAATGGAATAGTTGTGCATTTGGCAGTAAGGTGTCAATAATGCCAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATAATGTCAGTTAGATGAAAGG
2353832 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * * *
2353848 AAAACATTAATAGCCTAGTTGTGCATTTGGTAGAAAAGTGTCAATAATGTCAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATAATGTCAGTTAGATGAAAGG
2353913 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * * * * *
2353929 AAAATATTAATGGTCGAGTTGTGCATTCGGCAGAAAGGTTTCAATTATG-CTAGTTAGATGAAAG
1 AAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATAATGTC-AGTTAGATGAAAG
2353993 GTTAAATACCTTTGAGT
65 GTTAAATACCTTTGAGT
* * * **
2354010 AAAAGATTAATGGCCTAGTTTTGCATTTGGCAGAAAAGTGTCAATCATGGAAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATAATGTCAGTTAGATGAAAGG
* *
2354075 CTAAATGCCTTTG-GCT
66 TTAAATACCTTTGAG-T
2354091 AAAAG
1 AAAAG
2354096 GCCAATGGAT
Statistics
Matches: 361, Mismatches: 42, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
79 56 0.16
80 35 0.10
81 270 0.75
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.31
Consensus pattern (81 bp):
AAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATAATGTCAGTTAGATGAAAGG
TTAAATACCTTTGAGT
Found at i:2357908 original size:17 final size:17
Alignment explanation
Indices: 2357878--2357939 Score: 88
Period size: 17 Copynumber: 3.6 Consensus size: 17
2357868 CTTCATTCAG
*
2357878 TAAAGCTAGTTCACTAAT
1 TAAA-CTAGCTCACTAAT
2357896 TAAACTAGCTCACTAAT
1 TAAACTAGCTCACTAAT
* *
2357913 TAAACTAGTTCATTAAT
1 TAAACTAGCTCACTAAT
2357930 TAAACTAGCT
1 TAAACTAGCT
2357940 TATTTAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 36 0.90
18 4 0.10
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (17 bp):
TAAACTAGCTCACTAAT
Found at i:2361581 original size:17 final size:18
Alignment explanation
Indices: 2361547--2361588 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
2361537 CATAAATTAA
2361547 TAAGCATGCTACTTCATT
1 TAAGCATGCTACTTCATT
*
2361565 TAAGCATG-TATTTCATT
1 TAAGCATGCTACTTCATT
2361582 TAAGCAT
1 TAAGCAT
2361589 CAGTTCGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (18 bp):
TAAGCATGCTACTTCATT
Found at i:2365310 original size:16 final size:17
Alignment explanation
Indices: 2365289--2365323 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2365279 AGAATGCTAC
*
2365289 TTCATTTAAGCATG-AG
1 TTCATTAAAGCATGTAG
2365305 TTCATTAAAGCATGTAG
1 TTCATTAAAGCATGTAG
2365322 TT
1 TT
2365324 TTTTATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (17 bp):
TTCATTAAAGCATGTAG
Found at i:2365392 original size:17 final size:17
Alignment explanation
Indices: 2365370--2365407 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2365360 TTCAAGAAAG
2365370 CTAGTTCACTAATTAAA
1 CTAGTTCACTAATTAAA
* *
2365387 CTAGTTCATTCATTAAA
1 CTAGTTCACTAATTAAA
2365404 CTAG
1 CTAG
2365408 CTCATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (17 bp):
CTAGTTCACTAATTAAA
Found at i:2365412 original size:17 final size:17
Alignment explanation
Indices: 2365381--2365413 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2365371 TAGTTCACTA
*
2365381 ATTAAACTAGTTCATTC
1 ATTAAACTAGCTCATTC
2365398 ATTAAACTAGCTCATT
1 ATTAAACTAGCTCATT
2365414 TAATGTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (17 bp):
ATTAAACTAGCTCATTC
Found at i:2381030 original size:11 final size:12
Alignment explanation
Indices: 2381009--2381057 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
2380999 TTGAGAATTT
2381009 GGTGATGATATA
1 GGTGATGATATA
2381021 GGTG-TGATAT-
1 GGTGATGATATA
*
2381031 GATGATGGACTAT-
1 GGTGAT-GA-TATA
2381044 GGTGATGATATA
1 GGTGATGATATA
2381056 GG
1 GG
2381058 CGTGATAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 3 0.10
11 10 0.32
12 10 0.32
13 8 0.26
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.33
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:2385816 original size:23 final size:23
Alignment explanation
Indices: 2385789--2385842 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
2385779 AAAATTCAGA
2385789 TTGCACTCCACTCACTCTCGTGT
1 TTGCACTCCACTCACTCTCGTGT
2385812 TTGCACTCCACTCACTCTCGTGT
1 TTGCACTCCACTCACTCTCGTGT
2385835 TTGCACTC
1 TTGCACTC
2385843 GAGGATATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.13, C:0.39, G:0.13, T:0.35
Consensus pattern (23 bp):
TTGCACTCCACTCACTCTCGTGT
Found at i:2398356 original size:30 final size:31
Alignment explanation
Indices: 2398304--2398363 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
2398294 CTTAGCTTTA
**
2398304 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
2398334 TATTATGTTTGCATCTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
2398364 GGCAGTATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:2399297 original size:19 final size:20
Alignment explanation
Indices: 2399273--2399323 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2399263 CAGCCAAGAG
* *
2399273 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
2399292 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
2399312 CATGTATTTTCA
1 CATGTATTTTCA
2399324 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:2410884 original size:22 final size:21
Alignment explanation
Indices: 2410849--2410889 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2410839 GGTGCAGAAT
2410849 TGATGGTCTGGATGGATGAAGA
1 TGATGGTCTGGAT-GATGAAGA
* *
2410871 TGATGGTGTTGATGATGAA
1 TGATGGTCTGGATGATGAA
2410890 ATAGAGATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.27, C:0.02, G:0.39, T:0.32
Consensus pattern (21 bp):
TGATGGTCTGGATGATGAAGA
Found at i:2414739 original size:17 final size:17
Alignment explanation
Indices: 2414717--2414769 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
2414707 AATTAAGAGT
2414717 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* **
2414734 TAGTTTGACGAATGAAC
1 TAGTTTAATAAATGAAC
*
2414751 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
2414768 TA
1 TA
2414770 CTTCCCTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.36
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:2415083 original size:19 final size:20
Alignment explanation
Indices: 2415059--2415108 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
2415049 GGTCAAGAGC
2415059 ATGTATTTTCATTA-AAATA
1 ATGTATTTTCATTATAAATA
* *
2415078 ATGTATTTCCATTATAAATC
1 ATGTATTTTCATTATAAATA
*
2415098 ATGTATATTCA
1 ATGTATTTTCA
2415109 AAGGGATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (20 bp):
ATGTATTTTCATTATAAATA
Found at i:2423443 original size:22 final size:23
Alignment explanation
Indices: 2423391--2423444 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
2423381 TCTCCAAACA
*
2423391 TTCTTCTGTTGCATTGTCTTTAAG
1 TTCTTCT-TTGCATTGTCTTCAAG
*
2423415 TTGTTCTTT-CATTG-CTTCAATG
1 TTCTTCTTTGCATTGTCTTCAA-G
2423437 TTCTTCTT
1 TTCTTCTT
2423445 CAAGGTGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.19
22 13 0.50
23 2 0.08
24 6 0.23
ACGTcount: A:0.11, C:0.19, G:0.13, T:0.57
Consensus pattern (23 bp):
TTCTTCTTTGCATTGTCTTCAAG
Found at i:2424450 original size:19 final size:19
Alignment explanation
Indices: 2424428--2424478 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
2424418 GAATTTCTTT
*
2424428 TTCTTTTCTTTTTTTCTGA
1 TTCTTTTCTTTTTGTCTGA
**
2424447 TTCTTTTCTTTTTGTCTTT
1 TTCTTTTCTTTTTGTCTGA
2424466 TTCTTTTCTTTTT
1 TTCTTTTCTTTTT
2424479 ACACTCCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (19 bp):
TTCTTTTCTTTTTGTCTGA
Found at i:2425243 original size:19 final size:20
Alignment explanation
Indices: 2425196--2425245 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
2425186 GAAACCCCTT
**
2425196 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
2425216 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2425235 TGAAGATACAT
1 TGAAAATACAT
2425246 TGTCTTGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2432786 original size:19 final size:19
Alignment explanation
Indices: 2432747--2432800 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
2432737 TCTTCTTCTT
*
2432747 TTTTTCTTCTTTTC-TGAA
1 TTTTTCTTCTTTTCTTTAA
*
2432765 TTTTTCTTCTTTTCTTTTA
1 TTTTTCTTCTTTTCTTTAA
2432784 TTTTT-TGTCTTTTCTTT
1 TTTTTCT-TCTTTTCTTT
2432801 CTTTTTGTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTTTCTTCTTTTCTTTAA
Found at i:2432787 original size:18 final size:17
Alignment explanation
Indices: 2432736--2432805 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 17
2432726 CTTTATGAAA
2432736 TTCTTCTTCTTT-TTTTC
1 TTCTT-TTCTTTATTTTC
**
2432753 TTCTTTTCTGAATTTTTC
1 TTCTTTTCTTTA-TTTTC
*
2432771 TTCTTTTCTTTTATTTTT
1 TTCTTTTC-TTTATTTTC
*
2432789 TGTCTTTTCTTTCTTTT
1 T-TCTTTTCTTTATTTT
2432806 TGTTCTCCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
16 4 0.09
17 5 0.12
18 25 0.58
19 9 0.21
ACGTcount: A:0.04, C:0.17, G:0.03, T:0.76
Consensus pattern (17 bp):
TTCTTTTCTTTATTTTC
Found at i:2433015 original size:24 final size:23
Alignment explanation
Indices: 2432987--2433037 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
2432977 GATGTCCTTG
2432987 AATATGGGAATAATAAATAAGAAT
1 AATATGGGAATAATAAAT-AGAAT
*
2433011 AATATGGGAATAATAAATGGAAT
1 AATATGGGAATAATAAATAGAAT
2433034 AATA
1 AATA
2433038 AGATAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.57, C:0.00, G:0.18, T:0.25
Consensus pattern (23 bp):
AATATGGGAATAATAAATAGAAT
Found at i:2439331 original size:24 final size:25
Alignment explanation
Indices: 2439285--2439339 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
2439275 ACAGTTATGC
*
2439285 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
2439309 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
2439334 CA-TTGA
1 CACTTGA
2439340 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:2442758 original size:24 final size:25
Alignment explanation
Indices: 2442712--2442766 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
2442702 ACAGTTATGC
*
2442712 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
2442736 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
2442761 CA-TTGA
1 CACTTGA
2442767 GGCTACAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:2446107 original size:24 final size:24
Alignment explanation
Indices: 2446058--2446108 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
2446048 AGGTACAAGT
* *
2446058 GCCATACATCAAGTGGCATCATAA
1 GCCATACATCAAGCGGAATCATAA
2446082 GCCATACATCAAGCGGTAATCA-AA
1 GCCATACATCAAGCGG-AATCATAA
2446106 GCC
1 GCC
2446109 TTGGTGGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (24 bp):
GCCATACATCAAGCGGAATCATAA
Found at i:2446175 original size:12 final size:12
Alignment explanation
Indices: 2446158--2446182 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2446148 AAATAGAAAA
2446158 TGAAGTGCAAAG
1 TGAAGTGCAAAG
2446170 TGAAGTGCAAAG
1 TGAAGTGCAAAG
2446182 T
1 T
2446183 CAAAGAAATT
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:0.40, C:0.08, G:0.32, T:0.20
Consensus pattern (12 bp):
TGAAGTGCAAAG
Found at i:2450160 original size:23 final size:23
Alignment explanation
Indices: 2450125--2450169 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2450115 AAATCCAGCA
2450125 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATCAAAGCACTCAAAAG
* *
2450148 AAGAAATTGAAAGCACTCAAAA
1 AAGAAAATCAAAGCACTCAAAA
2450170 AGAAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.16, G:0.13, T:0.11
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCAAAAG
Found at i:2459512 original size:13 final size:12
Alignment explanation
Indices: 2459497--2459539 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
2459487 GATTAATATG
2459497 GAAATAATAAAT
1 GAAATAATAAAT
*
2459509 GGAATAATAAGAT
1 GAAATAATAA-AT
2459522 -AAATAATGAAAT
1 GAAATAAT-AAAT
2459534 GAAATA
1 GAAATA
2459540 GTAGGGATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (12 bp):
GAAATAATAAAT
Found at i:2462569 original size:13 final size:12
Alignment explanation
Indices: 2462554--2462596 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
2462544 GATTAATATG
2462554 GAAATAATAAAT
1 GAAATAATAAAT
*
2462566 GGAATAATAAGAT
1 GAAATAATAA-AT
2462579 -AAATAATGAAAT
1 GAAATAAT-AAAT
2462591 GAAATA
1 GAAATA
2462597 GTAGGGATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (12 bp):
GAAATAATAAAT
Found at i:2465626 original size:13 final size:12
Alignment explanation
Indices: 2465611--2465653 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
2465601 GATTAATATG
2465611 GAAATAATAAAT
1 GAAATAATAAAT
*
2465623 GGAATAATAAGAT
1 GAAATAATAA-AT
2465636 -AAATAATGAAAT
1 GAAATAAT-AAAT
2465648 GAAATA
1 GAAATA
2465654 GTAGGGATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (12 bp):
GAAATAATAAAT
Found at i:2472627 original size:33 final size:33
Alignment explanation
Indices: 2472585--2472653 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2472575 GTTGATGAAT
*
2472585 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
2472618 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
2472651 GAA
1 GAA
2472654 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:2472658 original size:13 final size:12
Alignment explanation
Indices: 2472639--2472724 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
2472629 TTATTGGCGT
2472639 GATATGGTGATG
1 GATATGGTGATG
2472651 GAATATGGTGAT-
1 G-ATATGGTGATG
*
2472663 GATATAGGCG-T-
1 GATAT-GGTGATG
2472674 GATAATGGTGATG
1 GAT-ATGGTGATG
2472687 GACTATGGTGAT-
1 GA-TATGGTGATG
*
2472699 GATATAGGCG-T-
1 GATAT-GGTGATG
2472710 GATAATGGTGATG
1 GAT-ATGGTGATG
2472723 GA
1 GA
2472725 CAGATTATGT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:2472694 original size:36 final size:36
Alignment explanation
Indices: 2472624--2472725 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
2472614 AATGGAAGGA
* * *
2472624 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
2472659 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
2472695 TGATGATATAGGCGTGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
2472726 AGATTATGTC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 16 0.25
36 47 0.75
ACGTcount: A:0.26, C:0.05, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:2474363 original size:15 final size:16
Alignment explanation
Indices: 2474312--2474364 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
2474302 AGATAGTGAA
2474312 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
2474329 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
2474346 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
2474361 ATAA
1 ATAA
2474365 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:2474604 original size:10 final size:10
Alignment explanation
Indices: 2474554--2474608 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
2474544 GTTGTAGTAG
2474554 TCTTTTTCTT
1 TCTTTTTCTT
*
2474564 TC-TCTTCTT
1 TCTTTTTCTT
2474573 GT-TTTTTC-T
1 -TCTTTTTCTT
2474582 TCTTTCTTCTT
1 TCTTT-TTCTT
*
2474593 TCTTTTTGTT
1 TCTTTTTCTT
2474603 TCTTTT
1 TCTTTT
2474609 ATTGTAGTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
8 1 0.03
9 10 0.27
10 20 0.54
11 6 0.16
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (10 bp):
TCTTTTTCTT
Found at i:2485736 original size:19 final size:21
Alignment explanation
Indices: 2485712--2485763 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2485702 CGGCCAAGAG
*
2485712 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
2485731 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
2485752 CATGTATTTTCA
1 CATGTATTTTCA
2485764 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:2486198 original size:19 final size:20
Alignment explanation
Indices: 2486174--2486213 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
2486164 TATCCTTTCT
2486174 TTATTTCATTTT-ATT-CTTA
1 TTATTT-ATTTTCATTACTTA
2486193 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
2486213 T
1 T
2486214 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:2488438 original size:91 final size:90
Alignment explanation
Indices: 2488272--2488443 Score: 222
Period size: 91 Copynumber: 1.9 Consensus size: 90
2488262 CACATATGCC
* *
2488272 TTGCATATGACCAACCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGACCAACCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGATGAAGAGATCT
*
2488337 CTCCTTATTCGGCCAAGACATGTGTT
66 ATCC-TATTCGGCCAAGACATGTGTT
* * * * *
2488363 TTGCATGTGATCAGCCCCCATGTGCCTTGCATATGGTTCATTTAGGTGCCAAGATGAATG-GCCA
1 TTGCATATGACCAACCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGATGAA-GAG--A
2488427 TCTATCC-ATTCGGCCAA
63 TCTATCCTATTCGGCCAA
2488444 TCACCATTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
91 63 0.90
92 1 0.01
93 6 0.09
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.30
Consensus pattern (90 bp):
TTGCATATGACCAACCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGATGAAGAGATCT
ATCCTATTCGGCCAAGACATGTGTT
Found at i:2494578 original size:13 final size:12
Alignment explanation
Indices: 2494557--2494611 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 12
2494547 TTTTGAATTC
2494557 TTTTTCTTTTCT
1 TTTTTCTTTTCT
2494569 TTTATTCTTTTCT
1 TTT-TTCTTTTCT
*
2494582 GATTTTTCTCTTCT
1 --TTTTTCTTTTCT
2494596 TTTTGTCTTTTTCT
1 TTTT-TC-TTTTCT
2494610 TT
1 TT
2494612 CTTTTTTCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
12 7 0.19
13 11 0.31
14 15 0.42
15 3 0.08
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:2494595 original size:19 final size:18
Alignment explanation
Indices: 2494573--2494617 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
2494563 TTTTCTTTTA
2494573 TTCTTTTCTG-ATTTTTCT
1 TTCTTTT-TGTATTTTTCT
*
2494591 CTTCTTTTTGTCTTTTTCT
1 -TTCTTTTTGTATTTTTCT
2494610 TTCTTTTT
1 TTCTTTTT
2494618 TCACTCCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (18 bp):
TTCTTTTTGTATTTTTCT
Found at i:2496366 original size:35 final size:37
Alignment explanation
Indices: 2496297--2496376 Score: 101
Period size: 35 Copynumber: 2.2 Consensus size: 37
2496287 ATACTATTTC
* * *
2496297 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCATCCATTATCACACCTATAT
* *
2496334 CATTACCATAGTCCATCAT-CA-TATCACACCTATAT
1 CATCACCATAATCCATCATCCATTATCACACCTATAT
2496369 CATCACCA
1 CATCACCA
2496377 AATTCTCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
35 20 0.54
36 2 0.05
37 15 0.41
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (37 bp):
CATCACCATAATCCATCATCCATTATCACACCTATAT
Found at i:2507032 original size:30 final size:30
Alignment explanation
Indices: 2506998--2507057 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2506988 GGTGTGCTGG
* *
2506998 CACGCACATGGGTGCTGTTTTGTTCCAAAT
1 CACGCACACGGGAGCTGTTTTGTTCCAAAT
2507028 CACGCACACGGGAGCTGTTTTGTTCCAAAT
1 CACGCACACGGGAGCTGTTTTGTTCCAAAT
2507058 GGTGAGTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (30 bp):
CACGCACACGGGAGCTGTTTTGTTCCAAAT
Found at i:2507734 original size:52 final size:52
Alignment explanation
Indices: 2507671--2507791 Score: 188
Period size: 52 Copynumber: 2.3 Consensus size: 52
2507661 AATTATAATT
* * *
2507671 AAATGAAAAACATGCTGTTATGTGAATGTGAGTGCACGTAAATTAACAAAAC
1 AAATGATAAACATGCTGTTATGTGAATGTGAGTGAACATAAATTAACAAAAC
* *
2507723 AAATGATAAACATGCTGTTATGTGAATGTGAGTGAACATGAATTAACAAAAT
1 AAATGATAAACATGCTGTTATGTGAATGTGAGTGAACATAAATTAACAAAAC
*
2507775 AAATGATAGACATGCTG
1 AAATGATAAACATGCTG
2507792 ATGTAAGTCT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (52 bp):
AAATGATAAACATGCTGTTATGTGAATGTGAGTGAACATAAATTAACAAAAC
Found at i:2512433 original size:23 final size:23
Alignment explanation
Indices: 2512400--2512444 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2512390 TTTCTTTTCT
*
2512400 TTTTGAGTGCTTTCAATTTCTTC
1 TTTTGAATGCTTTCAATTTCTTC
* *
2512423 TTTTGAATGCTTTGATTTTCTT
1 TTTTGAATGCTTTCAATTTCTT
2512445 TGCTAGATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.60
Consensus pattern (23 bp):
TTTTGAATGCTTTCAATTTCTTC
Found at i:2520623 original size:36 final size:36
Alignment explanation
Indices: 2520544--2520638 Score: 120
Period size: 36 Copynumber: 2.7 Consensus size: 36
2520534 TTTATAAGTG
* * * * *
2520544 GGTGATAATATAGGTGTGAT-ATGGTGGTGGAATAT
1 GGTGATGATATAGGCGTGATAATGGAGATAGAATAT
*
2520579 GGTGATGATATAGGCGTGATAATGGAGATAGACTAT
1 GGTGATGATATAGGCGTGATAATGGAGATAGAATAT
*
2520615 GGTGATGATAAAGGCGTGATAATG
1 GGTGATGATATAGGCGTGATAATG
2520639 ATGATGGACA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
35 18 0.35
36 34 0.65
ACGTcount: A:0.32, C:0.03, G:0.36, T:0.29
Consensus pattern (36 bp):
GGTGATGATATAGGCGTGATAATGGAGATAGAATAT
Found at i:2522768 original size:24 final size:24
Alignment explanation
Indices: 2522702--2522768 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2522692 TGGCAATGCA
*
2522702 CTTGGAATTTC-AACGAACGCAACT
1 CTTGGAACTTCAAACG-ACGCAACT
* ** **
2522726 CTTGGCACTTCAAGTGACGCTTCT
1 CTTGGAACTTCAAACGACGCAACT
2522750 CTTGGAACTTCAAACGACG
1 CTTGGAACTTCAAACGACG
2522769 TTATCTTTGA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (24 bp):
CTTGGAACTTCAAACGACGCAACT
Found at i:2524608 original size:36 final size:36
Alignment explanation
Indices: 2524529--2524623 Score: 129
Period size: 36 Copynumber: 2.7 Consensus size: 36
2524519 TTTATAAGTG
* * * *
2524529 GGTGATAATATAGGCGTGAT-ATGGTGGTGGAATAT
1 GGTGATGATATAGGCGTGATAATGGAGATAGAATAT
*
2524564 GGTGATGATATAGGCGTGATAATGGAGATAGACTAT
1 GGTGATGATATAGGCGTGATAATGGAGATAGAATAT
*
2524600 GGTGATGATAAAGGCGTGATAATG
1 GGTGATGATATAGGCGTGATAATG
2524624 ATGATGGACA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 19 0.36
36 34 0.64
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.28
Consensus pattern (36 bp):
GGTGATGATATAGGCGTGATAATGGAGATAGAATAT
Found at i:2525018 original size:19 final size:20
Alignment explanation
Indices: 2524971--2525021 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2524961 GAAACCCCTT
**
2524971 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
2524991 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2525010 TGAAGATACATG
1 TGAAAATACATG
2525022 CTCTGGCCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2553164 original size:30 final size:30
Alignment explanation
Indices: 2553123--2553182 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2553113 GGTGTGCTGG
* * *
2553123 CACGTACATGGGTGCTGTTTTGTTCCAAAT
1 CACGCACATGGGTGATGTTTTGTTACAAAT
2553153 CACGCACATGGGTGATGTTTTGTTACAAAT
1 CACGCACATGGGTGATGTTTTGTTACAAAT
2553183 GGTGAGTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (30 bp):
CACGCACATGGGTGATGTTTTGTTACAAAT
Found at i:2554985 original size:19 final size:20
Alignment explanation
Indices: 2554961--2555011 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2554951 CGGCCAAGAG
* *
2554961 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
2554980 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
2555000 CATGTATTTTCA
1 CATGTATTTTCA
2555012 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:2558948 original size:20 final size:20
Alignment explanation
Indices: 2558909--2558978 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
2558899 CGGCCAAGAG
* *
2558909 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
2558928 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
2558948 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
2558968 CATGTATTTTC
1 CATGTATTTTC
2558979 GAAAGGGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 12 0.25
20 36 0.75
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:2569205 original size:20 final size:20
Alignment explanation
Indices: 2569166--2569235 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
2569156 CGGCCAAGAG
* *
2569166 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
2569185 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
2569205 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
2569225 CATGTATTTTC
1 CATGTATTTTC
2569236 GAAGGGGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 12 0.25
20 36 0.75
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:2569674 original size:13 final size:13
Alignment explanation
Indices: 2569658--2569700 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2569648 TTTATTTCAT
2569658 TTTATTTTTATTA
1 TTTATTTTTATTA
*
2569671 TTTATTTTCATTA
1 TTTATTTTTATTA
*
2569684 CTTATATTATTATTA
1 -TT-TATTTTTATTA
2569699 TT
1 TT
2569701 CACTTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 12 0.48
14 4 0.16
15 9 0.36
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATTTTTATTA
Found at i:2569999 original size:28 final size:28
Alignment explanation
Indices: 2569968--2570029 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
2569958 CAAAAAGAAA
*
2569968 AGAAAAGACA-AAAAGAAGAAAAAATTTC
1 AGAAAAGAAAGAAAAGAA-AAAAAATTTC
*
2569996 AGAAAA-AAAGAAAAGAAAAAGAATTTC
1 AGAAAAGAAAGAAAAGAAAAAAAATTTC
2570023 -GAAAAGA
1 AGAAAAGA
2570030 GAAAGCAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 5 0.17
27 12 0.40
28 13 0.43
ACGTcount: A:0.69, C:0.05, G:0.16, T:0.10
Consensus pattern (28 bp):
AGAAAAGAAAGAAAAGAAAAAAAATTTC
Found at i:2573216 original size:20 final size:20
Alignment explanation
Indices: 2573169--2573219 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
2573159 CGGCCAAGAG
*
2573169 CATGTATCTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
2573189 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
2573209 CATGTATTTTC
1 CATGTATTTTC
2573220 GAAGGGGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:2577172 original size:19 final size:20
Alignment explanation
Indices: 2577148--2577198 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2577138 CGGCCAAGAG
* *
2577148 CATGTATATTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
2577167 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
2577187 CATGTATTTTCA
1 CATGTATTTTCA
2577199 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:2577899 original size:52 final size:51
Alignment explanation
Indices: 2577821--2577954 Score: 175
Period size: 52 Copynumber: 2.6 Consensus size: 51
2577811 TCTTACATCA
*
2577821 GTGAGTGCACGTA-AATTAACAAAACAAATGATAAACATATTGTTATGTGAAT
1 GTGAGTGCACGTAGAATTAACAAAACAAATGATAAACATACTGTTA--TGAAT
* * *
2577873 GTGAGTGGAC-TAGAATTAACAAAACAAATGATAGACATGCTGTTATGAAT
1 GTGAGTGCACGTAGAATTAACAAAACAAATGATAAACATACTGTTATGAAT
*
2577923 GTGAATGCACGT-GAAATTAACAAAACAAATGA
1 GTGAGTGCACGTAG-AATTAACAAAACAAATGA
2577955 ATTCAAATAT
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
50 14 0.19
51 21 0.29
52 38 0.52
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.25
Consensus pattern (51 bp):
GTGAGTGCACGTAGAATTAACAAAACAAATGATAAACATACTGTTATGAAT
Found at i:2581910 original size:20 final size:19
Alignment explanation
Indices: 2581875--2581934 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 19
2581865 AATTGGAGTG
*
2581875 CAAAAAGAAAAGAAAAAGA
1 CAAAAAGAAAAAAAAAAGA
*
2581894 CAAAAAGAAGAAAAAAAA-T
1 CAAAAAGAA-AAAAAAAAGA
2581913 CAGAAAAGAATAAAAGAAAAGA
1 CA-AAAAGAA-AAAA-AAAAGA
2581935 AATTCAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 11 0.33
20 18 0.55
21 4 0.12
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (19 bp):
CAAAAAGAAAAAAAAAAGA
Found at i:2590810 original size:21 final size:22
Alignment explanation
Indices: 2590778--2590820 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2590768 AAGAAGCAAC
2590778 GTGCAACATC-AACAAAAAGAA
1 GTGCAACATCAAACAAAAAGAA
*
2590799 GTGCAA-AGTCAAAGAAAAAGAA
1 GTGCAACA-TCAAACAAAAAGAA
2590821 AATCAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 8 0.42
22 10 0.53
ACGTcount: A:0.58, C:0.14, G:0.19, T:0.09
Consensus pattern (22 bp):
GTGCAACATCAAACAAAAAGAA
Found at i:2590877 original size:27 final size:27
Alignment explanation
Indices: 2590828--2590884 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2590818 GAAAATCAAA
*
2590828 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAATTGAAGCACTCAAAAAG-AAG
* *
2590856 AAAGAAATT-TAGCATTCAAAAAGAAG
1 AAAGAAATTGAAGCACTCAAAAAGAAG
2590882 AAA
1 AAA
2590885 AACAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
27 11 0.42
28 9 0.35
ACGTcount: A:0.60, C:0.11, G:0.16, T:0.14
Consensus pattern (27 bp):
AAAGAAATTGAAGCACTCAAAAAGAAG
Found at i:2604039 original size:24 final size:24
Alignment explanation
Indices: 2603990--2604039 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2603980 TGTCCTTTGA
*
2603990 TTGAAGAGTCACATCCTTATATTC
1 TTGAAGAGTCACATCCTTATACTC
*
2604014 TTGAAGAGTCACGTCCTT-TAGCTC
1 TTGAAGAGTCACATCCTTATA-CTC
2604038 TT
1 TT
2604040 TTCCTTGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (24 bp):
TTGAAGAGTCACATCCTTATACTC
Found at i:2605630 original size:30 final size:30
Alignment explanation
Indices: 2605596--2605653 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2605586 TTTGAGTGTA
2605596 CTTTGCAACTTT-TTCTTCTCTTTTCTTTTG
1 CTTTG-AACTTTATTCTTCTCTTTTCTTTTG
* *
2605626 CTTTGAATTTTATTCTTTTCTTTTCTTT
1 CTTTGAACTTTATTCTTCTCTTTTCTTT
2605654 CTTTTGCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.09, C:0.19, G:0.05, T:0.67
Consensus pattern (30 bp):
CTTTGAACTTTATTCTTCTCTTTTCTTTTG
Found at i:2605733 original size:14 final size:14
Alignment explanation
Indices: 2605714--2605745 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2605704 TTCTTTTTCT
2605714 CTTTTGTTGTAGCA
1 CTTTTGTTGTAGCA
2605728 CTTTTGTTGTAGCA
1 CTTTTGTTGTAGCA
2605742 CTTT
1 CTTT
2605746 GAATGTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.19, T:0.53
Consensus pattern (14 bp):
CTTTTGTTGTAGCA
Found at i:2605939 original size:15 final size:16
Alignment explanation
Indices: 2605919--2605952 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2605909 TATATTGGAA
*
2605919 ATAAGAAATGAAA-GG
1 ATAAGAAATAAAATGG
2605934 ATAAGAAATAAAATGG
1 ATAAGAAATAAAATGG
2605950 ATA
1 ATA
2605953 GAGATGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (16 bp):
ATAAGAAATAAAATGG
Found at i:2606508 original size:19 final size:20
Alignment explanation
Indices: 2606466--2606508 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2606456 GAAACCCCTT
*
2606466 TGAAAACACATGATTTTCAA
1 TGAAAACACATAATTTTCAA
*
2606486 TGAAAATACATAATTTT-AA
1 TGAAAACACATAATTTTCAA
2606505 TGAA
1 TGAA
2606509 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATAATTTTCAA
Found at i:2607441 original size:36 final size:36
Alignment explanation
Indices: 2607362--2607465 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 36
2607352 TTTATAAGTG
* * * *
2607362 GGTGATAATATAGGCGTGAT-ATGGTGGTGGAATAT
1 GGTGATGATATAGGCGTGATAATGGAGATGGACTAT
2607397 GGTGATGATATAGGCGTGATAATGGAGATGGACTAT
1 GGTGATGATATAGGCGTGATAATGGAGATGGACTAT
*
2607433 GGTGATGATAAAGGCGTGATAAT-GATGATGGAC
1 GGTGATGATATAGGCGTGATAATGGA-GATGGAC
2607466 AGATTGTATC
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.34
36 41 0.66
ACGTcount: A:0.31, C:0.05, G:0.37, T:0.28
Consensus pattern (36 bp):
GGTGATGATATAGGCGTGATAATGGAGATGGACTAT
Found at i:2609594 original size:24 final size:24
Alignment explanation
Indices: 2609528--2609594 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2609518 TGGCAATGCA
*
2609528 CTTGGAATTTC-AACGAACGCAACT
1 CTTGGAACTTCAAACG-ACGCAACT
* ** **
2609552 CTTGGCACTTCAAGTGACGCTTCT
1 CTTGGAACTTCAAACGACGCAACT
2609576 CTTGGAACTTCAAACGACG
1 CTTGGAACTTCAAACGACG
2609595 TTATCTTTGA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (24 bp):
CTTGGAACTTCAAACGACGCAACT
Found at i:2610895 original size:15 final size:15
Alignment explanation
Indices: 2610862--2610899 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2610852 CACTTTTCTT
2610862 TTTCTTTTGATTTTC
1 TTTCTTTTGATTTTC
**
2610877 -TTCTTTTTCTTTTC
1 TTTCTTTTGATTTTC
2610891 TTTCTTTTG
1 TTTCTTTTG
2610900 CACTCCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTCTTTTGATTTTC
Found at i:2611425 original size:36 final size:36
Alignment explanation
Indices: 2611346--2611449 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 36
2611336 TTTATAAGTG
* * * *
2611346 GGTGATAATATAGGCGTGAT-ATGGTGGTGGAATAT
1 GGTGATGATATAGGCGTGATAATGGAGATGGACTAT
2611381 GGTGATGATATAGGCGTGATAATGGAGATGGACTAT
1 GGTGATGATATAGGCGTGATAATGGAGATGGACTAT
*
2611417 GGTGATGATAAAGGCGTGATAAT-GATGATGGAC
1 GGTGATGATATAGGCGTGATAATGGA-GATGGAC
2611450 AGATTGTATC
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.34
36 41 0.66
ACGTcount: A:0.31, C:0.05, G:0.37, T:0.28
Consensus pattern (36 bp):
GGTGATGATATAGGCGTGATAATGGAGATGGACTAT
Found at i:2611837 original size:19 final size:20
Alignment explanation
Indices: 2611790--2611840 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2611780 GAAACCCCTT
**
2611790 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
2611810 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2611829 TGAAGATACATG
1 TGAAAATACATG
2611841 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2622765 original size:15 final size:15
Alignment explanation
Indices: 2622732--2622765 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2622722 CTTGATAACA
* *
2622732 ATTCTTTCCATTTCT
1 ATTCTTTCCAATTCC
2622747 ATTCTTTCCAATTCC
1 ATTCTTTCCAATTCC
2622762 ATTC
1 ATTC
2622766 ACTTTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTCTTTCCAATTCC
Found at i:2627811 original size:45 final size:45
Alignment explanation
Indices: 2627746--2627831 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
2627736 AAGATACGTT
* **
2627746 CTTTGAATGAAAAATGGTGTCCCTTTTCTGTTTGATGGACAAGTC
1 CTTTGAATGAAAAATGGTGTCCATTTTCTGTTCAATGGACAAGTC
*
2627791 CTTTGAATGAAAAATTGTGTCCATTTTCTGTTCAATGGACA
1 CTTTGAATGAAAAATGGTGTCCATTTTCTGTTCAATGGACA
2627832 CATATTTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (45 bp):
CTTTGAATGAAAAATGGTGTCCATTTTCTGTTCAATGGACAAGTC
Found at i:2630194 original size:20 final size:19
Alignment explanation
Indices: 2630169--2630217 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
2630159 GCTTCACTTT
2630169 TTCTTTTGCTTTGAATTTTC
1 TTCTTTT-CTTTGAATTTTC
***
2630189 TTCTTTTCTTTTCTTTTTC
1 TTCTTTTCTTTGAATTTTC
2630208 TTC-TTTCTTT
1 TTCTTTTCTTT
2630218 TTCTCTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 7 0.27
19 12 0.46
20 7 0.27
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.73
Consensus pattern (19 bp):
TTCTTTTCTTTGAATTTTC
Found at i:2630219 original size:19 final size:20
Alignment explanation
Indices: 2630184--2630226 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2630174 TTGCTTTGAA
2630184 TTTTCTTCTTTTCTTTTCT-
1 TTTTCTTCTTTTCTTTTCTC
2630203 TTTTCTTC-TTTCTTTTTCTC
1 TTTTCTTCTTTTC-TTTTCTC
2630223 TTTT
1 TTTT
2630227 TGTTGCATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.18
19 14 0.64
20 4 0.18
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTCTTCTTTTCTTTTCTC
Found at i:2632203 original size:45 final size:45
Alignment explanation
Indices: 2632120--2632205 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 45
2632110 AATATACGTT
* * **
2632120 CTTTGAATGAAAAATGGTGTCCCTTTGCTATTTGATGGACAAGTC
1 CTTTGAATGAAAAATGGTGTCCATTTGCTACTCAATGGACAAGTC
* * *
2632165 CTTTGAATGAAAATTTGTGTCCATTTGCTGCTCAATGGACA
1 CTTTGAATGAAAAATGGTGTCCATTTGCTACTCAATGGACA
2632206 CATCTTTTGG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (45 bp):
CTTTGAATGAAAAATGGTGTCCATTTGCTACTCAATGGACAAGTC
Found at i:2632268 original size:17 final size:17
Alignment explanation
Indices: 2632246--2632288 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
2632236 CTAATTCTTC
2632246 CTTTTGGCAAATGGCGT
1 CTTTTGGCAAATGGCGT
*
2632263 CTTTTGGCAAATGGTGT
1 CTTTTGGCAAATGGCGT
2632280 CTTTTGGCA
1 CTTTTGGCA
2632289 CATCCTGCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (17 bp):
CTTTTGGCAAATGGCGT
Found at i:2634639 original size:6 final size:6
Alignment explanation
Indices: 2634628--2634671 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
2634618 GATGTAGGAG
*
2634628 TCTTTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
2634672 TGTTGCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:2634651 original size:12 final size:12
Alignment explanation
Indices: 2634628--2634671 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
2634618 GATGTAGGAG
2634628 TCTTTTTC-TTT
1 TCTTTTTCTTTT
*
2634639 TCTTTTTGTTTT
1 TCTTTTTCTTTT
2634651 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
2634664 TCTCTTTT
1 TCT-TTTT
2634672 TGTTGCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 7 0.25
13 13 0.46
14 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:2652339 original size:11 final size:11
Alignment explanation
Indices: 2652310--2652339 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2652300 TCCATGTGTT
*
2652310 TGAGCTGAAGA
1 TGAGCTGGAGA
2652321 TGAGCTGGAGA
1 TGAGCTGGAGA
2652332 TGAGCTGG
1 TGAGCTGG
2652340 CCATAGATGA
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:0.27, C:0.10, G:0.43, T:0.20
Consensus pattern (11 bp):
TGAGCTGGAGA
Found at i:2654931 original size:15 final size:15
Alignment explanation
Indices: 2654884--2654941 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
2654874 AGGATAAGGT
*
2654884 AATGAAATAAGAA-A
1 AATGAAATAATAAGA
*
2654898 AGATGAAAGAATAAAGA
1 A-ATGAAATAAT-AAGA
2654915 AATGAAATAATAAGAA
1 AATGAAATAATAAG-A
2654931 AATGAAGATAA
1 AATGAA-ATAA
2654942 CTTACAACTC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 1 0.03
15 11 0.31
16 18 0.50
17 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.16
Consensus pattern (15 bp):
AATGAAATAATAAGA
Found at i:2655085 original size:30 final size:30
Alignment explanation
Indices: 2655051--2655108 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2655041 TGTGAGTGTA
2655051 CTTTGCAACTTT-TTATTCTCTTTTCTTTTG
1 CTTTG-AACTTTCTTATTCTCTTTTCTTTTG
* * *
2655081 CTTTGAATTTTCTTCTTTTCTTTTCTTT
1 CTTTGAACTTTCTTATTCTCTTTTCTTT
2655109 CTTTTGCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.09, C:0.19, G:0.05, T:0.67
Consensus pattern (30 bp):
CTTTGAACTTTCTTATTCTCTTTTCTTTTG
Found at i:2655380 original size:15 final size:16
Alignment explanation
Indices: 2655360--2655393 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2655350 TATATTGGAA
*
2655360 ATAAGAAATGAAA-GG
1 ATAAGAAATAAAATGG
2655375 ATAAGAAATAAAATGG
1 ATAAGAAATAAAATGG
2655391 ATA
1 ATA
2655394 GAGATGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (16 bp):
ATAAGAAATAAAATGG
Found at i:2655903 original size:19 final size:20
Alignment explanation
Indices: 2655863--2655905 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2655853 GAAACCCCTT
*
2655863 TGAAAAAACATGATTTTCAA
1 TGAAAAAACATAATTTTCAA
*
2655883 TGAAAATACATAATTTT-AA
1 TGAAAAAACATAATTTTCAA
2655902 TGAA
1 TGAA
2655906 GGTAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAAAACATAATTTTCAA
Found at i:2659631 original size:26 final size:26
Alignment explanation
Indices: 2659577--2659634 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
2659567 TTTATTTATT
* *
2659577 TCATTTCATTTCATTCCTTATCTTTA
1 TCATTTCATTTCATTCCTTATATTAA
2659603 TCATTTCATTAATC-TTCCTT-TATTAA
1 TCATTTCATT--TCATTCCTTATATTAA
2659629 TCATTT
1 TCATTT
2659635 TCCTTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 20 0.71
27 6 0.21
28 2 0.07
ACGTcount: A:0.22, C:0.21, G:0.00, T:0.57
Consensus pattern (26 bp):
TCATTTCATTTCATTCCTTATATTAA
Found at i:2665821 original size:15 final size:15
Alignment explanation
Indices: 2665785--2665814 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2665775 AGTGCTTCAC
2665785 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
2665799 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
2665814 T
1 T
2665815 CTTTTTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:2665897 original size:11 final size:11
Alignment explanation
Indices: 2665881--2665905 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2665871 TTGTTTTTCT
2665881 TTCACTTGCAC
1 TTCACTTGCAC
2665892 TTCACTTGCAC
1 TTCACTTGCAC
2665903 TTC
1 TTC
2665906 TTTTTGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:2680335 original size:11 final size:11
Alignment explanation
Indices: 2680319--2680363 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
2680309 TTTCAATTCA
2680319 TTTATCTT-TT
1 TTTATCTTATT
*
2680329 CTTTATCTTGTT
1 -TTTATCTTATT
*
2680341 TTAATCTTATT
1 TTTATCTTATT
2680352 TTTATCTTATT
1 TTTATCTTATT
2680363 T
1 T
2680364 CCAGCACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 28 0.93
12 2 0.07
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTATCTTATT
Found at i:2684504 original size:23 final size:20
Alignment explanation
Indices: 2684460--2684498 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2684450 GTTTTATATT
2684460 TTTATTT-TTATTATTATAA
1 TTTATTTATTATTATTATAA
2684479 TTTATTTATTATTATTATAA
1 TTTATTTATTATTATTATAA
2684499 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTTATTATTATTATAA
Found at i:2689772 original size:106 final size:106
Alignment explanation
Indices: 2689585--2690643 Score: 1721
Period size: 106 Copynumber: 10.0 Consensus size: 106
2689575 ATTTTGCTCG
*
2689585 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
2689650 CGAAGGGACCACTGGTTGTCAATAAACAATTTC-CTAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC-AATTTC
* *
2689691 ATAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * *
2689756 CGAAGGGACCGCTGGTTGTCAAAAAATAACTTCCCAATTTT
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* *
2689797 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAAATTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
2689862 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* * *
2689903 AGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCCAGACAACGCATGTTC-ACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
2689967 CGAAGAGACCGCTGGTTGTCAACAAATAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* *
2690008 AGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
2690073 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
*
2690114 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
2690179 CGAAGGGACCGCTGGCTGTCAACAAACAACTT-TCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCT-CAATTTC
* * *
2690220 AGAGTCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGCCAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
2690285 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
*
2690326 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACACCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
2690391 CGATGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* * *
2690432 AGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACGCAAGTTCGACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
2690497 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* * *
2690538 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
2690603 CGAAGGGACCGATGGTTGTCAATAAACAACTT-TCAACTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
2690643 A
1 A
2690644 CGACGGAAGA
Statistics
Matches: 887, Mismatches: 62, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
105 104 0.12
106 781 0.88
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
Found at i:2690873 original size:84 final size:84
Alignment explanation
Indices: 2690742--2691169 Score: 463
Period size: 84 Copynumber: 5.1 Consensus size: 84
2690732 CAAATACCCC
* * * * * * * * *
2690742 CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAGCTCAAGGCTAGAAGGGTT
1 CGAGTTCGACTACGCTCAGC-TCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
*
2690807 ATCTGTC-ACCAAAAGACCTT
65 ATCTGCCAACC-AAAGACCTT
* * *
2690827 TGAGTTCGACTACGCTCAGCTCTAAGGAACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTA
1 CGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
*
2690892 TCTG----CCAAAGACCCT
66 TCTGCCAACCAAAGACCTT
* * * * * *
2690907 CGAGTTCGATTACACTCAGCT-TCGAGTGCACGTCATTTGCAGCATAACTTAAGTCGAGAAGGGT
1 CGAGTTCGACTACGCTCAGCTCT-AAG-GCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
2690971 TATCTGCCAACCAAAGACCTT
64 TATCTGCCAACCAAAGACCTT
* * * * * * * * *
2690992 TGAGTTCGACTACGCTCAGCTCCAAGGTACATTATTTGTAACATAGCTCAAGGCAAGAAGGGCTA
1 CGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
*
2691057 TTTGCCAACCAAAGACCTT
66 TCTGCCAACCAAAGACCTT
* * *
2691076 CGAGTTTGACTACGCTCAGCTCTGAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTA
1 CGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
*
2691141 TCTGCCAACCAAAGACCTGA
66 TCTGCCAACCAAAGACCT-T
2691161 CGAGTTCGA
1 CGAGTTCGA
2691170 TTTCATTCAG
Statistics
Matches: 281, Mismatches: 54, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
79 1 0.00
80 28 0.10
81 40 0.14
84 157 0.56
85 55 0.20
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (84 bp):
CGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
TCTGCCAACCAAAGACCTT
Found at i:2690994 original size:165 final size:164
Alignment explanation
Indices: 2690715--2691158 Score: 579
Period size: 165 Copynumber: 2.7 Consensus size: 164
2690705 GGTATCAAAC
* *
2690715 TCGAGAA-GGCTATCTGCCAAATACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
1 TCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGA-GGCACATCATT
* * * * * *
2690779 TACAGCATAGCTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTTGAGTTCGACTACGCT
65 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTTGAGTTCGACTACGCT
* ** *
2690843 CAGCTCTAAGGAACATCATTTGCAGTATAGCTTAAG
129 CAGCTCCAAGGAACATCATTTGCAACATAGCTCAAG
*
2690879 TCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGTGCACGTCATT
1 TCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAG-GCACATCATT
2690944 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTC
65 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTC
* * *
2691009 AGCTCCAAGGTACATTATTTGTAACATAGCTCAAG
130 AGCTCCAAGGAACATCATTTGCAACATAGCTCAAG
* * * * * * *
2691044 GCAAGAAGGGCTATTTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGC-TCTGAGGCACAT
1 TCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTACACTCAGCTTC-GAGGCACAT
*
2691108 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCT
61 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCT
2691159 GACGAGTTCG
Statistics
Matches: 247, Mismatches: 25, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
164 8 0.03
165 149 0.60
166 3 0.01
168 57 0.23
169 30 0.12
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
TCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGCACATCATTT
GCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCA
GCTCCAAGGAACATCATTTGCAACATAGCTCAAG
Found at i:2691415 original size:20 final size:20
Alignment explanation
Indices: 2691399--2691435 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2691389 GTTTTATATT
2691399 TTTATTT-TTATTATTATAA
1 TTTATTTATTATTATTATAA
2691418 TTTATTTATTATTATTAT
1 TTTATTTATTATTATTAT
2691436 TAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTATTTATTATTATTATAA
Found at i:2691425 original size:23 final size:22
Alignment explanation
Indices: 2691397--2691453 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
2691387 GGGTTTTATA
2691397 TTTTTATTTTTATTATT-ATAAT
1 TTTTTATTTTTATTATTAAT-AT
*
2691419 TTATTTATTATTATTATTAATAT
1 TT-TTTATTTTTATTATTAATAT
2691442 TTTTTAATTTTT
1 TTTTT-ATTTTT
2691454 TTGCAGGTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 5 0.17
23 23 0.77
24 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTATTTTTATTATTAATAT
Found at i:2694518 original size:23 final size:23
Alignment explanation
Indices: 2694492--2694536 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2694482 AAATCCAGCA
2694492 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATCAAAGCACTCAAAAG
* *
2694515 AAGAAATTGAAAGCACTCAAAA
1 AAGAAAATCAAAGCACTCAAAA
2694537 AGAAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.16, G:0.13, T:0.11
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCAAAAG
Found at i:2720161 original size:17 final size:18
Alignment explanation
Indices: 2720129--2720163 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2720119 CTTGGCTTGC
*
2720129 TTTCTTTTTTGAATTTTT
1 TTTCTTTTCTGAATTTTT
2720147 TTTCTTTTCTG-ATTTTT
1 TTTCTTTTCTGAATTTTT
2720164 CACTTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTCTTTTCTGAATTTTT
Found at i:2720493 original size:20 final size:20
Alignment explanation
Indices: 2720456--2720496 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
2720446 GAATAATAAT
2720456 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
2720476 ATAAG-AATGAAAATGAAATA
1 ATAAGTAATGAAAA-GAAATA
2720496 A
1 A
2720497 AGAAAGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:2728262 original size:26 final size:26
Alignment explanation
Indices: 2728233--2728319 Score: 122
Period size: 26 Copynumber: 3.3 Consensus size: 26
2728223 TAGGGTCTAG
*
2728233 AAATGGTTATGATAGGGGTAGTATAA
1 AAATGGTTATGATAGGGGTAGGATAA
* *
2728259 AAATGGTTATGATAGGGTTAGGATAG
1 AAATGGTTATGATAGGGGTAGGATAA
*
2728285 AAATGTTTATGATAGGGGTAGGATAGA
1 AAATGGTTATGATAGGGGTAGGATA-A
2728312 AAA-GGTTA
1 AAATGGTTA
2728320 AGAAATGGAT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
26 50 0.94
27 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (26 bp):
AAATGGTTATGATAGGGGTAGGATAA
Found at i:2731644 original size:19 final size:20
Alignment explanation
Indices: 2731597--2731647 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2731587 GAAACCCCTT
**
2731597 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
2731617 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2731636 TGAAGATACATG
1 TGAAAATACATG
2731648 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2732971 original size:22 final size:21
Alignment explanation
Indices: 2732934--2732974 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2732924 CCATCTCCAT
2732934 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
2732955 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
2732975 ATTCCACGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:2733289 original size:6 final size:6
Alignment explanation
Indices: 2733274--2733351 Score: 58
Period size: 6 Copynumber: 13.5 Consensus size: 6
2733264 GTGCAAAAAG
* * *
2733274 AAAGAA AAAGAC AAAG-A AAA-AA AAAGAAA AAAGAA GAA-AA GAAG-A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA AAAGAA AAAGAA AAAGAA
**
2733319 AAAG-A AAAGAA AAAGAA AATCAA AAAGAGA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGA-A AAA
2733352 CAAGCCAAGG
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
5 21 0.36
6 27 0.47
7 10 0.17
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (6 bp):
AAAGAA
Found at i:2733291 original size:16 final size:15
Alignment explanation
Indices: 2733269--2733337 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 15
2733259 TTGGAGTGCA
2733269 AAAAGAAAGAAAAAG
1 AAAAGAAAGAAAAAG
*
2733284 ACAAAGAAAAAAAAAG
1 A-AAAGAAAGAAAAAG
*
2733300 AAAAAAGAAGAAAAGAAG
1 AAAAGA-AAG-AAA-AAG
2733318 AAAAGAAAAGAAAAAG
1 AAAAG-AAAGAAAAAG
2733334 AAAA
1 AAAA
2733338 TCAAAAAGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
15 5 0.11
16 23 0.51
17 6 0.13
18 10 0.22
19 1 0.02
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAAG
Found at i:2733343 original size:11 final size:11
Alignment explanation
Indices: 2733268--2733337 Score: 73
Period size: 10 Copynumber: 6.9 Consensus size: 11
2733258 ATTGGAGTGC
2733268 AAAAAG-AAAG
1 AAAAAGAAAAG
2733278 AAAAAGACAAAG
1 AAAAAGA-AAAG
2733290 AAAAA-AAAAG
1 AAAAAGAAAAG
*
2733300 AAAAA-AGAAG
1 AAAAAGAAAAG
2733310 -AAAAG--AAG
1 AAAAAGAAAAG
2733318 -AAAAGAAAAG
1 AAAAAGAAAAG
2733328 AAAAAGAAAA
1 AAAAAGAAAA
2733338 TCAAAAAGAG
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
8 8 0.15
9 4 0.08
10 22 0.42
11 10 0.19
12 9 0.17
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:2733346 original size:23 final size:23
Alignment explanation
Indices: 2733268--2733336 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 23
2733258 ATTGGAGTGC
2733268 AAAAAG-AAAGAAAAAGACAAAGAAAA
1 AAAAAGAAAAGAAAAAG--AAAG--AA
*
2733294 AAAAAGAAAA-AAGAAGAAAAGAA
1 AAAAAGAAAAGAAAAAG-AAAGAA
*
2733317 GAAAAGAAAAGAAAAAGAAA
1 AAAAAGAAAAGAAAAAGAAA
2733337 ATCAAAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 14 0.38
24 5 0.14
25 4 0.11
26 11 0.30
27 3 0.08
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAGAAAAAGAAAGAA
Found at i:2734354 original size:22 final size:22
Alignment explanation
Indices: 2734312--2734355 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2734302 AAAACACCTT
* *
2734312 AAAGAAGAACATTGAAGCAATG
1 AAAGAACAACATTAAAGCAATG
2734334 AAAGAACAAC-TTAAAGACAATG
1 AAAGAACAACATTAAAG-CAATG
2734356 CAACCGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.57, C:0.11, G:0.18, T:0.14
Consensus pattern (22 bp):
AAAGAACAACATTAAAGCAATG
Found at i:2738156 original size:34 final size:33
Alignment explanation
Indices: 2738109--2738173 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 33
2738099 TTCATCTTGA
2738109 AAAAAAAAGAATTCCAAAAATTTAAAAACAAAAAC
1 AAAAAAAAGAATTCCAAAAA-TTAAAAA-AAAAAC
* **
2738144 AAAAACAA-AATTCTGAAAATTAAAAAAAAA
1 AAAAAAAAGAATTCCAAAAATTAAAAAAAAA
2738174 TAGTTCTGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.15
33 7 0.26
34 9 0.33
35 7 0.26
ACGTcount: A:0.72, C:0.09, G:0.03, T:0.15
Consensus pattern (33 bp):
AAAAAAAAGAATTCCAAAAATTAAAAAAAAAAC
Found at i:2746100 original size:35 final size:37
Alignment explanation
Indices: 2746031--2746110 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
2746021 ATACTATTTC
* *
2746031 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
2746068 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
2746103 CATCACCA
1 CATCACCA
2746111 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.33, C:0.38, G:0.03, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:2746104 original size:11 final size:11
Alignment explanation
Indices: 2746064--2746110 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
2746054 TATCACGCCT
2746064 ATATCATCACC
1 ATATCATCACC
2746075 ATAGTCCATCACC
1 ATA-T-CATCACC
2746088 ATATCA-CACC
1 ATATCATCACC
2746098 TATATCATCACC
1 -ATATCATCACC
2746110 A
1 A
2746111 AATTCTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 12 0.38
12 6 0.19
13 10 0.31
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:2746108 original size:22 final size:24
Alignment explanation
Indices: 2746064--2746110 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2746054 TATCACGCCT
2746064 ATATCATCACCATAGTCCATCACC
1 ATATCATCACCATAGTCCATCACC
2746088 ATATCA-CACCTATA-T-CATCACC
1 ATATCATCACC-ATAGTCCATCACC
2746110 A
1 A
2746111 AATTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATCATCACCATAGTCCATCACC
Found at i:2750190 original size:35 final size:37
Alignment explanation
Indices: 2750121--2750200 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
2750111 ATACTATTTC
* *
2750121 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
**
2750158 CATCACCATTGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
2750193 CATCACCA
1 CATCACCA
2750201 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 3 0.08
37 15 0.38
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:2750194 original size:11 final size:11
Alignment explanation
Indices: 2750154--2750200 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
2750144 TATCACGCCT
2750154 ATATCATCACC
1 ATATCATCACC
*
2750165 ATTGTCCATCACC
1 A-TAT-CATCACC
2750178 ATATCA-CACC
1 ATATCATCACC
2750188 TATATCATCACC
1 -ATATCATCACC
2750200 A
1 A
2750201 AATTCTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 4 0.13
11 10 0.33
12 8 0.27
13 8 0.27
ACGTcount: A:0.34, C:0.36, G:0.02, T:0.28
Consensus pattern (11 bp):
ATATCATCACC
Found at i:2754281 original size:35 final size:37
Alignment explanation
Indices: 2754212--2754296 Score: 120
Period size: 35 Copynumber: 2.4 Consensus size: 37
2754202 ATATTATTTC
* * *
2754212 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAGTCCATCTACCATTATCACACCTATAT
2754249 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAGTCCATCTACCATTATCACACCTATAT
*
2754284 CATCACCAAAGTC
1 CATCACCATAGTC
2754297 TCAAATTTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 25 0.57
36 3 0.07
37 16 0.36
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (37 bp):
CATCACCATAGTCCATCTACCATTATCACACCTATAT
Found at i:2754285 original size:11 final size:11
Alignment explanation
Indices: 2754245--2754291 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
2754235 TATCACGCCT
2754245 ATATCATCACC
1 ATATCATCACC
2754256 ATAGTCCATCACC
1 ATA-T-CATCACC
2754269 ATATCA-CACC
1 ATATCATCACC
2754279 TATATCATCACC
1 -ATATCATCACC
2754291 A
1 A
2754292 AAGTCTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 12 0.38
12 6 0.19
13 10 0.31
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:2754289 original size:22 final size:24
Alignment explanation
Indices: 2754245--2754291 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2754235 TATCACGCCT
2754245 ATATCATCACCATAGTCCATCACC
1 ATATCATCACCATAGTCCATCACC
2754269 ATATCA-CACCTATA-T-CATCACC
1 ATATCATCACC-ATAGTCCATCACC
2754291 A
1 A
2754292 AAGTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATCATCACCATAGTCCATCACC
Found at i:2770318 original size:24 final size:21
Alignment explanation
Indices: 2770283--2770325 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2770273 GGCTCATTCT
*
2770283 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
2770306 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
2770326 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:2771054 original size:24 final size:23
Alignment explanation
Indices: 2771013--2771059 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2771003 TAGATGCTTA
*
2771013 TTTCATATGTTATAATATAATTAT
1 TTTCATATATTATAATAT-ATTAT
2771037 TTTCATATA-TATATATATATTAT
1 TTTCATATATTATA-ATATATTAT
2771060 ACCTATAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTCATATATTATAATATATTAT
Found at i:2787128 original size:24 final size:25
Alignment explanation
Indices: 2787101--2787148 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
2787091 GCCTATTTTT
* * *
2787101 GATGAGGAACCTGAA-ACAATGCAA
1 GATGAAGAAACTGAACAAAATGCAA
2787125 GATGAAGAAACTGAACAAAATGCA
1 GATGAAGAAACTGAACAAAATGCA
2787149 GATCATGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.50, C:0.15, G:0.23, T:0.12
Consensus pattern (25 bp):
GATGAAGAAACTGAACAAAATGCAA
Found at i:2791229 original size:20 final size:19
Alignment explanation
Indices: 2791189--2791230 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
2791179 TCTTTATTTC
*
2791189 ATTTCATTCTTATTCTTTT
1 ATTTCATTCTTATTCTATT
2791208 ATTTCATTACTTATAT-TATT
1 ATTTCATT-CTTAT-TCTATT
2791228 ATT
1 ATT
2791231 CCCTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 11 0.55
21 1 0.05
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTCATTCTTATTCTATT
Done.