Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 9 of 770
Found at i:2384302 original size:20 final size:20
Alignment explanation
Indices: 2384277--2384316 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2384267 TTGTTTTTAC
2384277 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
2384297 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
2384317 TTTAAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:2384321 original size:16 final size:18
Alignment explanation
Indices: 2384272--2384316 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
2384262 GAAAGTTGTT
* *
2384272 TTTACATATATTAATAAA
1 TTTATATATTTTAATAAA
2384290 TTTATATATATATTAATAAA
1 TTTATATAT-T-TTAATAAA
2384310 TTTATAT
1 TTTATAT
2384317 TTTAAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATTTTAATAAA
Found at i:2385307 original size:24 final size:24
Alignment explanation
Indices: 2385275--2385327 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
2385265 GAGTACCTCA
2385275 CACACTCATCTCTAACATTCAACC
1 CACACTCATCTCTAACATTCAACC
2385299 CACACTCATCTCTAACATTCAACC
1 CACACTCATCTCTAACATTCAACC
2385323 CACAC
1 CACAC
2385328 CATAAGAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.34, C:0.43, G:0.00, T:0.23
Consensus pattern (24 bp):
CACACTCATCTCTAACATTCAACC
Found at i:2387247 original size:29 final size:32
Alignment explanation
Indices: 2387200--2387258 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
2387190 AAATTATCAT
2387200 CATATAAATTTTAATTTTG-TACAATTTTATA
1 CATATAAATTTTAATTTTGATACAATTTTATA
*
2387231 CATA-AAATTTTAA-TTTGATCCAATTTTA
1 CATATAAATTTTAATTTTGATACAATTTTA
2387259 ATTTAATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 4 0.15
30 18 0.69
31 4 0.15
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.49
Consensus pattern (32 bp):
CATATAAATTTTAATTTTGATACAATTTTATA
Found at i:2395951 original size:91 final size:90
Alignment explanation
Indices: 2395829--2396005 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
2395819 GAGTTGAGGT
* * * *
2395829 TACAAAATTAATGCGACGAATAACATGTAACTCATAAATGATAAGTTTTTGAATGGTCGTTTCCA
1 TACAAAATTAATGCAACAAATAACATATAACTCATAAATGATAAG-TTCTGAATGGTCGTTTCCA
2395894 TCCAACATATGTTGCTTTTGTAGTCC
65 TCCAACATATGTTGCTTTTGTAGTCC
* *
2395920 TACAAAATTAATGCAACAAATAACATATAACTCGTAAATGATAAGTTCTGAATGGTCTTTTCCAT
1 TACAAAATTAATGCAACAAATAACATATAACTCATAAATGATAAGTTCTGAATGGTCGTTTCCAT
2395985 CCAACATATGTTGCTTTTGTA
66 CCAACATATGTTGCTTTTGTA
2396006 ATCCGGGTAC
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 39 0.49
91 41 0.51
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (90 bp):
TACAAAATTAATGCAACAAATAACATATAACTCATAAATGATAAGTTCTGAATGGTCGTTTCCAT
CCAACATATGTTGCTTTTGTAGTCC
Found at i:2407956 original size:9 final size:9
Alignment explanation
Indices: 2407942--2407969 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2407932 ATCAGGGACT
2407942 AAATTGTAA
1 AAATTGTAA
2407951 AAATTGTAA
1 AAATTGTAA
2407960 AAATTGTAA
1 AAATTGTAA
2407969 A
1 A
2407970 TTTTAGGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (9 bp):
AAATTGTAA
Found at i:2408425 original size:31 final size:30
Alignment explanation
Indices: 2408374--2408432 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
2408364 TGTGAAATGT
*
2408374 AAGACCATAATGGATCTATGGCATAGTGTGA
1 AAGACCATAATGGA-CTATGGCACAGTGTGA
2408405 AAGACCATAACTGAGA-TATGGCACAGTG
1 AAGACCATAA-TG-GACTATGGCACAGTG
2408433 AAAGTGAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 21 0.84
32 2 0.08
33 2 0.08
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.22
Consensus pattern (30 bp):
AAGACCATAATGGACTATGGCACAGTGTGA
Found at i:2413054 original size:30 final size:31
Alignment explanation
Indices: 2413019--2413084 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
2413009 CTACTTGGTA
* *
2413019 TTTTAGTTTGGGT-AATATTAGTCATTTTAT
1 TTTTAGATTCGGTCAATATTAGTCATTTTAT
* *
2413049 TTTTAGATTCGGTCAATTTTAGTCTTTTTAT
1 TTTTAGATTCGGTCAATATTAGTCATTTTAT
2413080 TTTTA
1 TTTTA
2413085 AAATTTTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.21, C:0.06, G:0.14, T:0.59
Consensus pattern (31 bp):
TTTTAGATTCGGTCAATATTAGTCATTTTAT
Found at i:2417504 original size:40 final size:40
Alignment explanation
Indices: 2417445--2417586 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
2417435 AAATTGAATG
* * *
2417445 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
2417485 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
2417525 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
2417565 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
2417587 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:2417587 original size:40 final size:39
Alignment explanation
Indices: 2417484--2417612 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
2417474 TGCTGGAAAT
* * *
2417484 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
2417524 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
2417564 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
2417604 TATATCCGG
1 TATATCCGG
2417613 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:2419485 original size:23 final size:23
Alignment explanation
Indices: 2419450--2419494 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2419440 AAAAATAATT
*
2419450 TTTTTACTGTTTTCTTATTGTTG
1 TTTTTACTATTTTCTTATTGTTG
* *
2419473 TTTTTGCTATTTTCTTGTTGTT
1 TTTTTACTATTTTCTTATTGTT
2419495 TTCACTATTA
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:0.07, C:0.09, G:0.13, T:0.71
Consensus pattern (23 bp):
TTTTTACTATTTTCTTATTGTTG
Found at i:2419664 original size:24 final size:24
Alignment explanation
Indices: 2419633--2419678 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
2419623 AAGTATACAT
2419633 ATTTTTAA-AAAAAATTATTTTCA
1 ATTTTTAAGAAAAAATTATTTTCA
* *
2419656 ATTTGTTAAGAAACATTTATTTT
1 ATTT-TTAAGAAAAAATTATTTT
2419679 ATTTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 4 0.21
25 11 0.58
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (24 bp):
ATTTTTAAGAAAAAATTATTTTCA
Found at i:2426790 original size:31 final size:31
Alignment explanation
Indices: 2426739--2426808 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
2426729 TTAAATTAGT
2426739 AATGAT-AAAATTACACTTTAATCTCCTTAAA
1 AATGATAAAAATTACACTTTAATCTCC-TAAA
* *
2426770 AATGATAAAAATTTA-A-TTTAATTTTCTAAA
1 AATGATAAAAA-TTACACTTTAATCTCCTAAA
*
2426800 AATTATAAA
1 AATGATAAA
2426809 GATATAGGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 12 0.35
31 14 0.41
32 5 0.15
33 3 0.09
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.39
Consensus pattern (31 bp):
AATGATAAAAATTACACTTTAATCTCCTAAA
Found at i:2431188 original size:43 final size:42
Alignment explanation
Indices: 2431127--2431242 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 42
2431117 ATAATTTCGT
*
2431127 TGAACTTGAGTGATTCAGATTGTGATTAATATATATTTTCAGA
1 TGAACTTAAGTGATTCAGATTGTGATTAATATATATTTT-AGA
* * *
2431170 TGAACTTAAGTGATTCAGATTGTGATCAAATATGTATTTTTGA
1 TGAACTTAAGTGATTCAGATTGTGAT-TAATATATATTTTAGA
*
2431213 TGAACTTTAAGTGATTCA-TTTGTGATTAAT
1 TGAAC-TTAAGTGATTCAGATTGTGATTAAT
2431243 TTTGGGGTTG
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
42 3 0.05
43 39 0.60
44 23 0.35
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (42 bp):
TGAACTTAAGTGATTCAGATTGTGATTAATATATATTTTAGA
Found at i:2438818 original size:3 final size:3
Alignment explanation
Indices: 2438797--2438852 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
2438787 TTGAACACCT
* * *
2438797 GCA GCA GGA GGA GCT GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
2438845 GCA GCA GC
1 GCA GCA GC
2438853 TTTTCTTGGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.30, C:0.30, G:0.38, T:0.02
Consensus pattern (3 bp):
GCA
Found at i:2449149 original size:30 final size:30
Alignment explanation
Indices: 2449115--2449182 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
2449105 TGGCCCAAGA
* *
2449115 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAATTGAAGGACTAATAGT
*
2449145 GTAAATATGAAAAATTGAAGGACTAATAGT
1 GTAAATATCAAAAATTGAAGGACTAATAGT
*
2449175 GCAAATAT
1 GTAAATAT
2449183 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAATTGAAGGACTAATAGT
Found at i:2449457 original size:8 final size:8
Alignment explanation
Indices: 2449444--2449480 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
2449434 TTTTAAATGA
2449444 TATTTTAT
1 TATTTTAT
2449452 TATTTTAT
1 TATTTTAT
2449460 TATTTTAT
1 TATTTTAT
2449468 TATTATT-T
1 TATT-TTAT
2449476 TATTT
1 TATTT
2449481 AATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 1 0.04
8 25 0.89
9 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:2450540 original size:2 final size:2
Alignment explanation
Indices: 2450533--2450565 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2450523 TAAAAGTAAA
2450533 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 A
2450566 GATAATGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2451696 original size:46 final size:46
Alignment explanation
Indices: 2451629--2451810 Score: 276
Period size: 46 Copynumber: 4.0 Consensus size: 46
2451619 AGTGTGCTCT
*
2451629 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
2451675 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
2451721 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATAGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
2451767 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
2451811 TCATGTTAAA
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.01
46 125 0.99
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:2457157 original size:43 final size:43
Alignment explanation
Indices: 2457093--2457178 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
2457083 TATGTGATTG
* *
2457093 ATATTGAAATGGTAAAGATGAGAAATGAATACGAGATGAGAAA
1 ATATTGAAATGGAAAAAATGAGAAATGAATACGAGATGAGAAA
*
2457136 ATATTGAAATGGAAAAAATGAGAAATGAATATGAGATGAGAAA
1 ATATTGAAATGGAAAAAATGAGAAATGAATACGAGATGAGAAA
2457179 TGTAATATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.53, C:0.01, G:0.24, T:0.21
Consensus pattern (43 bp):
ATATTGAAATGGAAAAAATGAGAAATGAATACGAGATGAGAAA
Found at i:2457187 original size:19 final size:18
Alignment explanation
Indices: 2457151--2457201 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 18
2457141 GAAATGGAAA
2457151 AAATGAGAAATGAATATG
1 AAATGAGAAATGAATATG
*
2457169 AGATGAGAAATGTAATATG
1 AAATGAGAAATG-AATATG
2457188 AAATGATGAAATGA
1 AAATGA-GAAATGA
2457202 GATGTGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 11 0.38
19 12 0.41
20 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (18 bp):
AAATGAGAAATGAATATG
Found at i:2457739 original size:24 final size:24
Alignment explanation
Indices: 2457693--2457739 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2457683 GGTTTAAGCT
*
2457693 ATGTTTTGGTATGTAGTTTAGTTA
1 ATGTTTTGGTATGTAGTTAAGTTA
*
2457717 ATGTTTTTGTATGT-GTATAAGTT
1 ATGTTTTGGTATGTAGT-TAAGTT
2457740 TTAAAGGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.21, C:0.00, G:0.23, T:0.55
Consensus pattern (24 bp):
ATGTTTTGGTATGTAGTTAAGTTA
Found at i:2459027 original size:46 final size:44
Alignment explanation
Indices: 2458968--2459082 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
2458958 ACAGGACAGA
* *
2458968 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
2459014 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
2459058 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
2459083 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:2459063 original size:44 final size:45
Alignment explanation
Indices: 2458968--2459101 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
2458958 ACAGGACAGA
* *
2458968 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
2459014 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
2459058 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2459102 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:2464978 original size:46 final size:44
Alignment explanation
Indices: 2464919--2465033 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
2464909 ACAGGACAGA
* *
2464919 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
2464965 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
2465009 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
2465034 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:2465014 original size:44 final size:45
Alignment explanation
Indices: 2464919--2465052 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
2464909 ACAGGACAGA
* *
2464919 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
2464965 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
2465009 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2465053 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:2469272 original size:44 final size:44
Alignment explanation
Indices: 2469192--2469282 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
2469182 AACTCTGTTT
* * *
2469192 TTAGTTTTCCACTTAAACTCTAATTAGTGTAAGTTATTTTAATA
1 TTAGTTTCCCACTTAAACCCTAATTAATGTAAGTTATTTTAATA
* *
2469236 TTAGTTTCCCACTTAAACCCTGATTAATGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACCCTAATTAATGTAAGTTATTTTAATA
2469280 TTA
1 TTA
2469283 TTTGACCTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACCCTAATTAATGTAAGTTATTTTAATA
Found at i:2470482 original size:49 final size:48
Alignment explanation
Indices: 2470426--2470592 Score: 128
Period size: 49 Copynumber: 3.4 Consensus size: 48
2470416 ATGTAAAGAA
2470426 AACATAATTGATGCAGTTCAAATGTTCAATACAAGCATTTAAGCATAAT
1 AACATAATTGATGCAGTTCAAATGTT-AATACAAGCATTTAAGCATAAT
* * * * * *
2470475 ATCATAATCGATGCA----AAATGAGTTAGCATA-AAGGATTTAAGTAAAAAA
1 AACATAATTGATGCAGTTCAAAT--GTTA--ATACAAGCATTTAAG-CATAAT
* * *
2470523 AACATAATTAATGCAATTCAAATGTTTAATACAAGCATCTAAGCATAAT
1 AACATAATTGATGCAGTTCAAATG-TTAATACAAGCATTTAAGCATAAT
* * *
2470572 ACCATGATTGATGTAGTTCAA
1 AACATAATTGATGCAGTTCAA
2470593 TACAAGCATC
Statistics
Matches: 88, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
45 4 0.05
46 1 0.01
47 13 0.15
48 18 0.20
49 35 0.40
50 10 0.11
51 3 0.03
52 4 0.05
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (48 bp):
AACATAATTGATGCAGTTCAAATGTTAATACAAGCATTTAAGCATAAT
Found at i:2470519 original size:97 final size:97
Alignment explanation
Indices: 2470323--2470572 Score: 376
Period size: 97 Copynumber: 2.6 Consensus size: 97
2470313 TAAAAAAAAA
*
2470323 AAAAAAAACATAATTAATGCAGCTCAAATGTTCAATACAAGCATCTAAGCATAATAGAATAATCG
1 AAAAAAAACATAATTAATGCAGTTCAAATGTTCAATACAAGCATCTAAGCATAATAGAATAATCG
*
2470388 ATGCAAATGAGTTACCACAAAGGCATCTATGT
66 ATGCAAATGAGTTACCACAAAGGCATCTAAGT
* * * **
2470420 AAAGAAAACATAATTGATGCAGTTCAAATGTTCAATACAAGCATTTAAGCATAATATCATAATCG
1 AAAAAAAACATAATTAATGCAGTTCAAATGTTCAATACAAGCATCTAAGCATAATAGAATAATCG
* * *
2470485 ATGCAAAATGAGTTAGCATAAAGG-ATTTAAGT
66 ATGC-AAATGAGTTACCACAAAGGCATCTAAGT
* *
2470517 AAAAAAAACATAATTAATGCAATTCAAATGTTTAATACAAGCATCTAAGCATAATA
1 AAAAAAAACATAATTAATGCAGTTCAAATGTTCAATACAAGCATCTAAGCATAATA
2470573 CCATGATTGA
Statistics
Matches: 137, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
97 120 0.88
98 17 0.12
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.26
Consensus pattern (97 bp):
AAAAAAAACATAATTAATGCAGTTCAAATGTTCAATACAAGCATCTAAGCATAATAGAATAATCG
ATGCAAATGAGTTACCACAAAGGCATCTAAGT
Found at i:2471686 original size:15 final size:16
Alignment explanation
Indices: 2471656--2471688 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2471646 ATATTAATGT
*
2471656 TATTTAATCTTTAAAA
1 TATTTAATCATTAAAA
2471672 TATTTAAT-ATTAAAA
1 TATTTAATCATTAAAA
2471687 TA
1 TA
2471689 ATACAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAATCATTAAAA
Found at i:2473734 original size:61 final size:61
Alignment explanation
Indices: 2473636--2473816 Score: 247
Period size: 62 Copynumber: 3.0 Consensus size: 61
2473626 CTGCCCTACC
* * * *
2473636 GCTATTA-TTTTTTTAGAGCAACTGTTTTGCTGTCTCTTCACGTCTCTTTGCAACCCTTGCT
1 GCTATTATTTTTTTTAG-GCAACTGCTTTGCTGCCTCTTCACGTCTCTCTGCAACCCCTGCT
* * *
2473697 GCTATTATTTTTTTTTGGCAACTGCTTTGCTGCCTCTTCACGTATCTCTGCAACCCCTGTT
1 GCTATTATTTTTTTTAGGCAACTGCTTTGCTGCCTCTTCACGTCTCTCTGCAACCCCTGCT
* * *
2473758 GCTATTATATTTTTTTCGACAACTACTTTGCTGCCTCTTCACGTCTCTCTGCAACCCCT
1 GCTATTAT-TTTTTTTAGGCAACTGCTTTGCTGCCTCTTCACGTCTCTCTGCAACCCCT
2473817 ACTGATTTGC
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
61 53 0.50
62 54 0.50
ACGTcount: A:0.15, C:0.28, G:0.13, T:0.44
Consensus pattern (61 bp):
GCTATTATTTTTTTTAGGCAACTGCTTTGCTGCCTCTTCACGTCTCTCTGCAACCCCTGCT
Found at i:2479071 original size:2 final size:2
Alignment explanation
Indices: 2479064--2479107 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
2479054 CTTGCTTTGT
*
2479064 TA TA TA TA TA AA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
2479107 T
1 T
2479108 TAAAATTGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2480557 original size:16 final size:16
Alignment explanation
Indices: 2480522--2480551 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2480512 CATAAAAAAT
2480522 ATAAAAACATGACAAA
1 ATAAAAACATGACAAA
2480538 ATAAAAA-ATGACAA
1 ATAAAAACATGACAA
2480552 TGATAATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.10, G:0.07, T:0.13
Consensus pattern (16 bp):
ATAAAAACATGACAAA
Found at i:2480788 original size:19 final size:19
Alignment explanation
Indices: 2480751--2480789 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2480741 AAGTAATAGT
** *
2480751 AATAATAATGGTAATAATA
1 AATAATAATACTAACAATA
2480770 AATAATAATACTAACAATA
1 AATAATAATACTAACAATA
2480789 A
1 A
2480790 CAAAAATAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (19 bp):
AATAATAATACTAACAATA
Found at i:2481110 original size:3 final size:3
Alignment explanation
Indices: 2480565--2481093 Score: 269
Period size: 3 Copynumber: 177.3 Consensus size: 3
2480555 TAATGAGAAC
* * *
2480565 AAT AAT AAT AAT ATT AAT AAT AAT AAT AAC AAT AAT AGT AA- AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
2480611 AAT AAT ACT AAT GAT AAT AAT AAT AGT AAT AAT AAG AAT ATT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
2480659 AGT AAT AAT AAT AAT GAT AAT AGT AAT AGAA AAT AAA AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
*
2480704 AAT AAT -AT AAT AAT -AT AAT AAT AGT AAAT AA- AAGT AA- AAGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA-T AAT AA-T AAT
* ** * * * *
2480748 AGT AAT AAT AAT GGT AAT AAT AAAT AAT AAT ACT AAC AAT AAC AAA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
* * * ** * * *
2480794 AAT AGT AAT AAT -GT ATT AAAT GGT AA- AAG AAT AAT AGT AAC AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * * * *
2480838 AAT TTT AAA AAA AAT GAT AAT AGT AAT AA- AAT AA- GAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
2480884 AAT ATT AAT AAT AAA AAT GAA- CAT AAA AAA AGAT AGT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* * * ** *
2480930 AAT AAT AAT AGT AAT AGT AA- AAGG AAT AAT AAT AGC AAT AAT AAG
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
** ** ** * * * ** *
2480975 AGC GTT AAT TCT AGT AAA AAT ACA- AAT AAT AAT ATAT ATGT ACG AAA
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT A-AT AAT AAT
*
2481022 AAT AAT AAT AGT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2481069 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
2481094 GAAGTAGTAA
Statistics
Matches: 388, Mismatches: 113, Indels: 50
0.70 0.21 0.09
Matches are distributed among these distances:
2 26 0.07
3 336 0.87
4 26 0.07
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2487413 original size:12 final size:12
Alignment explanation
Indices: 2487396--2487429 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2487386 CGGCCCGCCC
2487396 ATATTAATTTTT
1 ATATTAATTTTT
*
2487408 ATATTATTTTTT
1 ATATTAATTTTT
2487420 ATA-TAATTTT
1 ATATTAATTTT
2487430 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:2487586 original size:30 final size:30
Alignment explanation
Indices: 2487550--2487614 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
2487540 CAACTTAACA
*
2487550 AACAAATAT-TTCTAAAATAATAACAAAATT
1 AACAAATATCTT-TAAAATAATAAAAAAATT
*
2487580 AACAAATGTCTTTAAAATAATAAAAAAATT
1 AACAAATATCTTTAAAATAATAAAAAAATT
2487610 AACAA
1 AACAA
2487615 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.28
Consensus pattern (30 bp):
AACAAATATCTTTAAAATAATAAAAAAATT
Found at i:2489892 original size:11 final size:11
Alignment explanation
Indices: 2489876--2489915 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
2489866 ATTAAAGTAG
2489876 ATTTTAATGTA
1 ATTTTAATGTA
*
2489887 ATTTTAAAGTA
1 ATTTTAATGTA
2489898 GATTTTAATGTA
1 -ATTTTAATGTA
2489910 ATTTTA
1 ATTTTA
2489916 TTGTCCTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (11 bp):
ATTTTAATGTA
Found at i:2489894 original size:23 final size:23
Alignment explanation
Indices: 2489867--2489915 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2489857 AAACCTTATA
2489867 TTAAAGTAGATTTTAATGTAATT
1 TTAAAGTAGATTTTAATGTAATT
2489890 TTAAAGTAGATTTTAATGTAATT
1 TTAAAGTAGATTTTAATGTAATT
2489913 TTA
1 TTA
2489916 TTGTCCTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (23 bp):
TTAAAGTAGATTTTAATGTAATT
Found at i:2489904 original size:12 final size:11
Alignment explanation
Indices: 2489867--2489915 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 11
2489857 AAACCTTATA
2489867 TTAAAGTAGATT
1 TTAAAGTA-ATT
*
2489879 TTAATGTAATT
1 TTAAAGTAATT
2489890 TTAAAGTAGATT
1 TTAAAGTA-ATT
*
2489902 TTAATGTAATT
1 TTAAAGTAATT
2489913 TTA
1 TTA
2489916 TTGTCCTAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 16 0.48
12 17 0.52
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (11 bp):
TTAAAGTAATT
Found at i:2495158 original size:27 final size:26
Alignment explanation
Indices: 2495127--2495190 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 26
2495117 TTTATCAAGG
*
2495127 TTATTAGTTTATCGATAAA-TAAATATT
1 TTATTAATTTATCGATAAAGT-AATA-T
2495154 TTATTAATTTATCGATAAAGTAATAT
1 TTATTAATTTATCGATAAAGTAATAT
2495180 TTATTAATTTA
1 TTATTAATTTA
2495191 GAGAATATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 12 0.34
27 22 0.63
28 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (26 bp):
TTATTAATTTATCGATAAAGTAATAT
Found at i:2495225 original size:3 final size:3
Alignment explanation
Indices: 2495217--2495243 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2495207 TTATTCATGG
2495217 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
2495244 CAAAATCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2498720 original size:2 final size:2
Alignment explanation
Indices: 2498715--2498744 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2498705 TAAAAAATAC
*
2498715 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2498745 CGAAGTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2498807 original size:20 final size:20
Alignment explanation
Indices: 2498761--2498810 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2498751 TTAATTGATT
*
2498761 TATATTTTTTTTAAATTTAA
1 TATATTTTTTTTAAAATTAA
* *
2498781 GAGATTTTTTTTAAAAATT-A
1 TATATTTTTTTT-AAAATTAA
2498801 TATATTTTTT
1 TATATTTTTT
2498811 AATTTGCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TATATTTTTTTTAAAATTAA
Found at i:2499604 original size:29 final size:29
Alignment explanation
Indices: 2499572--2499634 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
2499562 TAGATTCCTC
* *
2499572 AAAAGTTGGGAAAAAAATTTAGGTCCCTT
1 AAAAGTAGGGAAAAAAATTTAGGGCCCTT
* *
2499601 AAAAGTAGGTAAAAAAATTTTGGGCCCTT
1 AAAAGTAGGGAAAAAAATTTAGGGCCCTT
2499630 AAAAG
1 AAAAG
2499635 CTAAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (29 bp):
AAAAGTAGGGAAAAAAATTTAGGGCCCTT
Found at i:2507362 original size:30 final size:30
Alignment explanation
Indices: 2507328--2507392 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
2507318 ATAAGTCAAT
* *
2507328 AAAATTAGTCCTTTTTCGGTAAATA-ATTTA
1 AAAATTAATCCATTTTC-GTAAATATATTTA
*
2507358 AAAATTAATTCATTTTCGTAAATATATTTA
1 AAAATTAATCCATTTTCGTAAATATATTTA
2507388 AAAAT
1 AAAAT
2507393 GGGCCTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (30 bp):
AAAATTAATCCATTTTCGTAAATATATTTA
Found at i:2518452 original size:16 final size:17
Alignment explanation
Indices: 2518430--2518473 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
2518420 CATCTCATAA
2518430 TCATTTCTCATATTTTC
1 TCATTTCTCATATTTTC
*
2518447 -CATTTC-AATATTTTC
1 TCATTTCTCATATTTTC
2518462 TCA--TCTCATATT
1 TCATTTCTCATATT
2518474 CATTTATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 2 0.09
15 13 0.57
16 8 0.35
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (17 bp):
TCATTTCTCATATTTTC
Found at i:2518467 original size:43 final size:43
Alignment explanation
Indices: 2518416--2518497 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
2518406 CATATTTCAA
* *
2518416 TTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATATT
1 TTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATATT
* *
2518459 TTCTCATCTCATATTCATTTATCATCTTTGCCATTTCAA
1 TTCTCATCTCATAATCATTTATCATATTTGCCATTTCAA
2518498 AATCAATCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.24, C:0.24, G:0.01, T:0.50
Consensus pattern (43 bp):
TTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATATT
Found at i:2519437 original size:30 final size:30
Alignment explanation
Indices: 2519401--2519460 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2519391 TTCCCGAGCC
2519401 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
* *
2519431 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
2519461 CGTATTAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:2519939 original size:47 final size:46
Alignment explanation
Indices: 2519881--2520012 Score: 158
Period size: 47 Copynumber: 2.8 Consensus size: 46
2519871 ATGGTTGAAC
**
2519881 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGT-GGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGAACTAGGA
* ** * *
2519926 ATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGC
1 A--TCCGAACTCGTTGAGTTGAGTCCGAGTTCAT-TTATGGAACTAGGA
*
2519975 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGG
2520013 GCGGGTTACA
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
45 1 0.01
46 3 0.04
47 59 0.83
48 5 0.07
49 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (46 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGAACTAGGA
Found at i:2522463 original size:16 final size:17
Alignment explanation
Indices: 2522444--2522484 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
2522434 ACAATTTATT
2522444 TATTATAACAT-ATATA
1 TATTATAACATAATATA
2522460 TATTATTAACATAATATA
1 TATTA-TAACATAATATA
*
2522478 TAATATA
1 TATTATA
2522485 TATACACGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 8 0.36
18 9 0.41
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTATAACATAATATA
Found at i:2525061 original size:20 final size:20
Alignment explanation
Indices: 2525036--2525075 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2525026 CAAAGTGAAC
2525036 ATGGAGACTATGAGTGATAG
1 ATGGAGACTATGAGTGATAG
2525056 ATGGAGACTATGAGTGATAG
1 ATGGAGACTATGAGTGATAG
2525076 TGATGAAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.25
Consensus pattern (20 bp):
ATGGAGACTATGAGTGATAG
Found at i:2531773 original size:19 final size:20
Alignment explanation
Indices: 2531730--2531773 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
2531720 TCGTTTCAGC
*
2531730 TGTTTTGTTTCTTTTAGTTA
1 TGTTTTCTTTCTTTTAGTTA
*
2531750 T-TTTTCTTTCTTTTA-TTT
1 TGTTTTCTTTCTTTTAGTTA
2531768 TGTTTT
1 TGTTTT
2531774 AGTTATTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 17 0.81
20 1 0.05
ACGTcount: A:0.07, C:0.07, G:0.09, T:0.77
Consensus pattern (20 bp):
TGTTTTCTTTCTTTTAGTTA
Found at i:2535474 original size:21 final size:21
Alignment explanation
Indices: 2535448--2535489 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2535438 CTGAGAGTTT
2535448 GTAATTTCTGGGATTCTCTGG
1 GTAATTTCTGGGATTCTCTGG
2535469 GTAATTTCTGGGATTCTCTGG
1 GTAATTTCTGGGATTCTCTGG
2535490 ACTTTATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (21 bp):
GTAATTTCTGGGATTCTCTGG
Found at i:2536272 original size:21 final size:21
Alignment explanation
Indices: 2536243--2536282 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2536233 CATTTAAAAT
* *
2536243 ATCACTATTATTTATTATTTA
1 ATCAATATTATTAATTATTTA
2536264 ATCAATATTATTAATTATT
1 ATCAATATTATTAATTATT
2536283 ATCAAGAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
ATCAATATTATTAATTATTTA
Found at i:2539603 original size:26 final size:26
Alignment explanation
Indices: 2539567--2539673 Score: 178
Period size: 26 Copynumber: 4.1 Consensus size: 26
2539557 TGAAATGCCC
* *
2539567 ATCATGGAACATTTACCTAAACAATT
1 ATCATGGAACATTTACCTAACCCATT
2539593 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
2539619 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
2539645 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2539671 ATC
1 ATC
2539674 CTAACCCATT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2539684 original size:13 final size:13
Alignment explanation
Indices: 2539660--2539686 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2539650 GGAACATTTA
2539660 CCTAACCCATTAT
1 CCTAACCCATTAT
2539673 CCTAACCCATTAT
1 CCTAACCCATTAT
2539686 C
1 C
2539687 ATGGAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.30
Consensus pattern (13 bp):
CCTAACCCATTAT
Found at i:2539688 original size:39 final size:39
Alignment explanation
Indices: 2539634--2539712 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
2539624 GGAATATTTA
*
2539634 CCTAATCCATTATCATGGAACATTTACCTAACCCATTAT
1 CCTAACCCATTATCATGGAACATTTACCTAACCCATTAT
* *
2539673 CCTAACCCATTATCATGGAATATTTACCTAATCCATTAT
1 CCTAACCCATTATCATGGAACATTTACCTAACCCATTAT
2539712 C
1 C
2539713 ATGGAACATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (39 bp):
CCTAACCCATTATCATGGAACATTTACCTAACCCATTAT
Found at i:2539702 original size:26 final size:26
Alignment explanation
Indices: 2539673--2539739 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
2539663 AACCCATTAT
*
2539673 CCTAACCCATTATCATGGAATATTTA
1 CCTAACCCATTATCATGGAACATTTA
*
2539699 CCTAATCCATTATCATGGAACATTTA
1 CCTAACCCATTATCATGGAACATTTA
2539725 CCTAACCCATTATCA
1 CCTAACCCATTATCA
2539740 ATTTGTACCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (26 bp):
CCTAACCCATTATCATGGAACATTTA
Found at i:2539712 original size:65 final size:65
Alignment explanation
Indices: 2539608--2539738 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
2539598 GGAACATTTA
2539608 CCTAACCCATTATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATTAT
1 CCTAACCCATTATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATTAT
2539673 CCTAACCCATTATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATTAT
1 CCTAACCCATTATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATTAT
2539738 C
1 C
2539739 AATTTGTACC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.34
Consensus pattern (65 bp):
CCTAACCCATTATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATTAT
Found at i:2542481 original size:35 final size:35
Alignment explanation
Indices: 2542437--2542603 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
2542427 TTCCCATTGA
** *
2542437 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
2542472 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
2542512 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
2542547 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
2542582 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
2542604 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:2542528 original size:75 final size:73
Alignment explanation
Indices: 2542432--2542603 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
2542422 TGGTTTTCCC
** * * **
2542432 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
2542496 TCAGTATGG
65 TCAGTATGG
*
2542505 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
2542570 CTCAGTATGG
64 CTCAGTATGG
2542580 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
2542604 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:2549971 original size:35 final size:35
Alignment explanation
Indices: 2549927--2550093 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
2549917 TCCTCATTGA
** *
2549927 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
2549962 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
2550002 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
2550037 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
2550072 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
2550094 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:2550010 original size:75 final size:73
Alignment explanation
Indices: 2549922--2550093 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
2549912 GGTTTTCCTC
** * * **
2549922 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
2549986 TCAGTATGG
65 TCAGTATGG
*
2549995 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
2550060 CTCAGTATGG
64 CTCAGTATGG
2550070 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
2550094 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:2560912 original size:35 final size:35
Alignment explanation
Indices: 2560837--2560913 Score: 84
Period size: 37 Copynumber: 2.2 Consensus size: 35
2560827 ATTGAAATTT
* * * *
2560837 ATTTTAAATATAAAATATTATATATTTATTGGTTAT
1 ATTTTAAATATAAAATAGTATATATTCA-TAGTTAA
*
2560873 ATTTTAATATTTAAAATAGTATATATTCA-AGTTAA
1 ATTTTAA-ATATAAAATAGTATATATTCATAGTTAA
2560908 ATTTTA
1 ATTTTA
2560914 TAAATAATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
35 10 0.29
36 7 0.20
37 18 0.51
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (35 bp):
ATTTTAAATATAAAATAGTATATATTCATAGTTAA
Found at i:2561776 original size:12 final size:13
Alignment explanation
Indices: 2561759--2561787 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2561749 TCACTTTGTC
2561759 GGGGTTGGGG-TT
1 GGGGTTGGGGTTT
2561771 GGGGTTGGGGTTT
1 GGGGTTGGGGTTT
2561784 GGGG
1 GGGG
2561788 GGGGGGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (13 bp):
GGGGTTGGGGTTT
Found at i:2562479 original size:16 final size:16
Alignment explanation
Indices: 2562448--2562477 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2562438 TGTATCTTTC
2562448 TTTTTTTAAATATTTA
1 TTTTTTTAAATATTTA
2562464 TTTTTTT-AATATTT
1 TTTTTTTAAATATTT
2562478 TACTACACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:2576859 original size:26 final size:25
Alignment explanation
Indices: 2576829--2576889 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
2576819 AATCATATAA
2576829 CATTTCAATAACCAT-ATAAACATATC
1 CATTTCAAT-ACC-TCATAAACATATC
* *
2576855 CATTTTCCATGCCTCATAAACATATC
1 CA-TTTCAATACCTCATAAACATATC
*
2576881 CTTTTCAAT
1 CATTTCAAT
2576890 TTATCTCATG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 7 0.24
26 16 0.55
27 6 0.21
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (25 bp):
CATTTCAATACCTCATAAACATATC
Found at i:2582501 original size:11 final size:10
Alignment explanation
Indices: 2582484--2582509 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2582474 TTACCCGCAA
2582484 ATTTTTTTTT
1 ATTTTTTTTT
2582494 ATTTTTTTTT
1 ATTTTTTTTT
2582504 ATTTTT
1 ATTTTT
2582510 GGTTCAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:2589071 original size:21 final size:20
Alignment explanation
Indices: 2589032--2589071 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2589022 ATTTTAGTCA
* *
2589032 CACAATTTTTTTAATTTAAT
1 CACAAATTTTTCAATTTAAT
2589052 CACAAATTTTTCAATATTAA
1 CACAAATTTTTCAAT-TTAA
2589072 ATATTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (20 bp):
CACAAATTTTTCAATTTAAT
Found at i:2590401 original size:31 final size:29
Alignment explanation
Indices: 2590344--2590434 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 29
2590334 TATATATTTT
* * *
2590344 TAAAATTTTTATAGTTAGGACAAAATTGA
1 TAAATTTTTTATATTTAGGACCAAATTGA
*
2590373 TAAATTTTTTAAATATTTAGGACCAAATTTA
1 TAAATTTTTT--ATATTTAGGACCAAATTGA
** * *
2590404 TTGATTTTTTATATTTATGATCAAATTGA
1 TAAATTTTTTATATTTAGGACCAAATTGA
2590433 TA
1 TA
2590435 GAATGTGTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
29 26 0.52
31 24 0.48
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (29 bp):
TAAATTTTTTATATTTAGGACCAAATTGA
Found at i:2590572 original size:31 final size:30
Alignment explanation
Indices: 2590529--2590589 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
2590519 TTTTGTGATT
* *
2590529 AAATTGAAAAAAT-TAATAGTTGGGTAACCA
1 AAATAGAAAAAATGT-ATAGTTAGGTAACCA
*
2590559 AAATAGAATAAAATGTATAGTTAGGTGACCA
1 AAATAGAA-AAAATGTATAGTTAGGTAACCA
2590590 TTTTTATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 7 0.27
31 18 0.69
32 1 0.04
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (30 bp):
AAATAGAAAAAATGTATAGTTAGGTAACCA
Found at i:2591452 original size:20 final size:20
Alignment explanation
Indices: 2591416--2591459 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2591406 TTTGGTCTAT
2591416 AAACATTTAAAAGTCATTTA
1 AAACATTTAAAAGTCATTTA
* *
2591436 AAACACTTTAGAA-TCATTTT
1 AAACA-TTTAAAAGTCATTTA
2591456 AAAC
1 AAAC
2591460 TAAGTTCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (20 bp):
AAACATTTAAAAGTCATTTA
Found at i:2595157 original size:22 final size:23
Alignment explanation
Indices: 2595132--2595177 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2595122 CAACCAAATC
2595132 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
2595154 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
2595177 A
1 A
2595178 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:2595183 original size:23 final size:23
Alignment explanation
Indices: 2595139--2595183 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2595129 ATCAATTCAA
*
2595139 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
2595162 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
2595184 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:2601003 original size:30 final size:28
Alignment explanation
Indices: 2600948--2601009 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 28
2600938 CTTATTTAAT
2600948 TAATAAATATCTTTTACTTAATAATAAA
1 TAATAAATATCTTTTACTTAATAATAAA
*
2600976 TAATAAATATCTATTTACTTAAATAATAAG
1 TAATAAATATCT-TTTACTT-AATAATAAA
2601006 TAAT
1 TAAT
2601010 TTAAATCCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 12 0.39
29 7 0.23
30 12 0.39
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (28 bp):
TAATAAATATCTTTTACTTAATAATAAA
Found at i:2608455 original size:126 final size:126
Alignment explanation
Indices: 2608194--2608713 Score: 681
Period size: 126 Copynumber: 4.1 Consensus size: 126
2608184 GGCCAAACAT
* * *
2608194 GAACTACTATAGAAAAAGAGCATCCACGTGGGAGCTTTTTTTAGT-AATTTTGCTGACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAACTTTTTTTA-TCAATTTTGCTGACAGTGCAT
*
2608258 CTTGCTTGAAGCGTTTTTTGACACTATTTGTTCAGAAACGTCTTTTCAAAATTATTTTTTCAG
65 CTTGCTTGAAGCG-TTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
* * * *
2608321 AAACTACTGTAGAAAAAGAGCGTACACGTGGGAACTTTTTTTATCAATTTTGCTGACAGTGTATT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAACTTTTTTTATCAATTTTGCTGACAGTGCATC
* * * *
2608386 TTGCTTGAAGCGTGTTTAACACTATTTGTTTAGAAATGTCTTCTCAAAATTATTTTTTCAG
66 TTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
* * *
2608447 GAACTACTGTAGAAAAAGAGCGTCCATGTGGG-AGTTTTTTTCATCAATTTTGCTGACAGTACAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAACTTTTTTT-ATCAATTTTGCTGACAGTGCAT
* * * * * * *
2608511 CCTGTTTGAAGCATTTTTGATACTATTTGTTCAGAATCGTCTTCTCAAAATCATTTTTTTAG
65 CTTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
* * * * *
2608573 GAACTACTGTAGAAAAATAGCGTCCACAT-GAAAGCTTTTTTCATCAATTTGGCTGACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAA-CTTTTTTTATCAATTTTGCTGACAGTGCAT
* * * * *
2608637 CTTGCTTAAAGCTTTTTTGACACTATTTATTCTGAACCGTCTTCTC-AAATT-TTTTTTCAG
65 CTTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
2608697 GAACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
2608714 AAACCAAAAT
Statistics
Matches: 341, Mismatches: 48, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
124 25 0.07
125 13 0.04
126 229 0.67
127 74 0.22
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAACTTTTTTTATCAATTTTGCTGACAGTGCATC
TTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
Found at i:2608960 original size:41 final size:41
Alignment explanation
Indices: 2608908--2608989 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
2608898 TAAAACCGAA
* * *
2608908 AACCTTAAATTATTTTAACAAAACCTTAACCCTACAAACCT
1 AACCCTAAATTATTTTAACAAAACCCTAACCCTAAAAACCT
2608949 AACCCTAAATTATTTTAACAAAACCCTAACCCTAAAAACCT
1 AACCCTAAATTATTTTAACAAAACCCTAACCCTAAAAACCT
2608990 TAAACTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (41 bp):
AACCCTAAATTATTTTAACAAAACCCTAACCCTAAAAACCT
Found at i:2608998 original size:41 final size:41
Alignment explanation
Indices: 2608913--2608998 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
2608903 CCGAAAACCT
* * *
2608913 TAAATTATTTTAACAAAACCTTAACCCTACAAACCTAACCC
1 TAAATTATTTTAACAAAACCCTAACCCTAAAAACCTAACAC
2608954 TAAATTATTTTAACAAAACCCTAACCCTAAAAACCTTAA-AC
1 TAAATTATTTTAACAAAACCCTAACCCTAAAAACC-TAACAC
2608995 TAAA
1 TAAA
2608999 AAACCTTAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 38 0.93
42 3 0.07
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.27
Consensus pattern (41 bp):
TAAATTATTTTAACAAAACCCTAACCCTAAAAACCTAACAC
Found at i:2609560 original size:16 final size:18
Alignment explanation
Indices: 2609529--2609574 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
2609519 TAATATATTA
2609529 TATTTATTT-TGTATTT-
1 TATTTATTTATGTATTTG
2609545 TATTTATTTATG-ATTTG
1 TATTTATTTATGTATTTG
*
2609562 TGTTATATTTATG
1 TATT-TATTTATG
2609575 GTACTGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 13 0.50
17 5 0.19
18 8 0.31
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (18 bp):
TATTTATTTATGTATTTG
Found at i:2609561 original size:22 final size:20
Alignment explanation
Indices: 2609522--2609573 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
2609512 ATATAATTAA
2609522 TATATTATATTTATTTTGTAT
1 TATATT-TATTTATTTTGTAT
* *
2609543 TTTATTTATTTATGATTTGTGT
1 TATATTTATTTAT--TTTGTAT
2609565 TATATTTAT
1 TATATTTAT
2609574 GGTACTGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.27
21 5 0.19
22 14 0.54
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (20 bp):
TATATTTATTTATTTTGTAT
Found at i:2615731 original size:17 final size:18
Alignment explanation
Indices: 2615702--2615736 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2615692 GAACTTTTAA
2615702 AAAAATTATAAAAAAATT
1 AAAAATTATAAAAAAATT
*
2615720 AAAAATTA-AAAATAATT
1 AAAAATTATAAAAAAATT
2615737 TTTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATTATAAAAAAATT
Found at i:2619001 original size:24 final size:24
Alignment explanation
Indices: 2618965--2619017 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2618955 CCGTGCCTGG
2618965 GGTTGCTGCTGCTGCTGCTG-TGGT
1 GGTTGCTGCTGCTGCTGCTGCT-GT
* *
2618989 GGTTGTTGTTGCTGCTGCTGCTGT
1 GGTTGCTGCTGCTGCTGCTGCTGT
2619013 GGTTG
1 GGTTG
2619018 AGGTTGTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.00, C:0.17, G:0.42, T:0.42
Consensus pattern (24 bp):
GGTTGCTGCTGCTGCTGCTGCTGT
Found at i:2619023 original size:24 final size:24
Alignment explanation
Indices: 2618974--2619023 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2618964 GGGTTGCTGC
**
2618974 TGCTGCTGCTGTGGTGGTTGTTGT
1 TGCTGCTGCTGTGGTGGTTGAGGT
2618998 TGCTGCTGCTGCT-GTGGTTGAGGT
1 TGCTGCTGCTG-TGGTGGTTGAGGT
2619022 TG
1 TG
2619024 TGAGGATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.02, C:0.14, G:0.42, T:0.42
Consensus pattern (24 bp):
TGCTGCTGCTGTGGTGGTTGAGGT
Found at i:2619023 original size:27 final size:27
Alignment explanation
Indices: 2618965--2619024 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
2618955 CCGTGCCTGG
* *
2618965 GGTTGCTGCTGCTGCTGCTGTGGTGGT
1 GGTTGTTGCTGCTGCTGCTGTGGTGGA
* *
2618992 TGTTGTTGCTGCTGCTGCTGTGGTTGA
1 GGTTGTTGCTGCTGCTGCTGTGGTGGA
2619019 GGTTGT
1 GGTTGT
2619025 GAGGATTTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.02, C:0.15, G:0.42, T:0.42
Consensus pattern (27 bp):
GGTTGTTGCTGCTGCTGCTGTGGTGGA
Found at i:2621207 original size:12 final size:12
Alignment explanation
Indices: 2621190--2621225 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
2621180 ATACGGCATG
2621190 TTTATATTAATT
1 TTTATATTAATT
2621202 TTTATATT-ATT
1 TTTATATTAATT
2621213 TTTATA-TAATT
1 TTTATATTAATT
2621224 TT
1 TT
2621226 AAAATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 14 0.61
12 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTATATTAATT
Found at i:2621249 original size:26 final size:28
Alignment explanation
Indices: 2621204--2621261 Score: 84
Period size: 26 Copynumber: 2.1 Consensus size: 28
2621194 TATTAATTTT
* *
2621204 TATATTATTTTTATATAATTTTAAAATA
1 TATATTATTATTATATAATTTTAAAAAA
2621232 TATATTA-TATTATA-AATTTTAAAAAA
1 TATATTATTATTATATAATTTTAAAAAA
2621258 TATA
1 TATA
2621262 AATATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 15 0.54
27 6 0.21
28 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TATATTATTATTATATAATTTTAAAAAA
Found at i:2621335 original size:30 final size:30
Alignment explanation
Indices: 2621301--2621360 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2621291 ACTTAACAAG
2621301 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
** *
2621331 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
2621361 TAGTAAAATA
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:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:2627825 original size:46 final size:46
Alignment explanation
Indices: 2627773--2627867 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
2627763 AGTGTGCTCT
2627773 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
2627819 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
2627865 CTG
1 CTG
2627868 GTTGAAAGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:2627870 original size:24 final size:24
Alignment explanation
Indices: 2627842--2627891 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2627832 TGTAAGACCA
2627842 TGGTTGAAAGATACCATGGCAACC
1 TGGTTGAAAGATACCATGGCAACC
2627866 TGGTTGAAAGATACCATGGCAACC
1 TGGTTGAAAGATACCATGGCAACC
2627890 TG
1 TG
2627892 ATATGAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (24 bp):
TGGTTGAAAGATACCATGGCAACC
Found at i:2627909 original size:70 final size:70
Alignment explanation
Indices: 2627796--2627934 Score: 278
Period size: 70 Copynumber: 2.0 Consensus size: 70
2627786 TGTAAGACCA
2627796 TGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGG
1 TGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGG
2627861 CAACC
66 CAACC
2627866 TGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGG
1 TGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGG
2627931 CAAC
66 CAAC
2627935 GTGATATGAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (70 bp):
TGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGG
CAACC
Found at i:2627916 original size:46 final size:46
Alignment explanation
Indices: 2627866--2628213 Score: 475
Period size: 46 Copynumber: 7.6 Consensus size: 46
2627856 CATGGCAACC
* * **
2627866 TGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCA
1 TGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCA
* *
2627912 TGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCA
1 TGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCA
**
2627958 TGGTTGAAAGATACCATGGCAACATGACGGGAAATGAATAAGACCA
1 TGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCA
* *
2628004 TGGTTGAAAGATACCATGGCAGCGTGACATGAAATGAATAAGACCA
1 TGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCA
*
2628050 TGGTTGAAAGATACCATGGCAACATGACA-GAAAATAAATAAGACCA
1 TGGTTGAAAGATACCATGGCAACATGACATG-AAATGAATAAGACCA
* ***
2628096 TAGTTGAAAGATACCATGGCAGTGTGACATGAAATGAATAAGACCA
1 TGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCA
* *
2628142 TGGTTGAAAGATGCCATGGCAACATGACA-GAAAATGAGTAAGACCA
1 TGGTTGAAAGATACCATGGCAACATGACATG-AAATGAATAAGACCA
* * * *
2628188 TAGTTGAAAGACACTATGGCATCATG
1 TGGTTGAAAGATACCATGGCAACATG
2628214 TCAAAGATAA
Statistics
Matches: 269, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
45 2 0.01
46 266 0.99
47 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
TGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCA
Found at i:2627977 original size:92 final size:92
Alignment explanation
Indices: 2627866--2628208 Score: 526
Period size: 92 Copynumber: 3.7 Consensus size: 92
2627856 CATGGCAACC
* * ** *
2627866 TGGTTGAAAGATACCATGGCAACCTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATG
1 TGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAATAAGACCATAGTTGAAAGATACCATG
* *
2627930 GCAACGTGATATGAAATGAATAAGACCA
65 GCAGCGTGACATGAAATGAATAAGACCA
* * *
2627958 TGGTTGAAAGATACCATGGCAACATGACGGGAAATGAATAAGACCATGGTTGAAAGATACCATGG
1 TGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCATAGTTGAAAGATACCATGG
2628023 CAGCGTGACATGAAATGAATAAGACCA
66 CAGCGTGACATGAAATGAATAAGACCA
*
2628050 TGGTTGAAAGATACCATGGCAACATGACAGAAAATAAATAAGACCATAGTTGAAAGATACCATGG
1 TGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCATAGTTGAAAGATACCATGG
*
2628115 CAGTGTGACATGAAATGAATAAGACCA
66 CAGCGTGACATGAAATGAATAAGACCA
* * * *
2628142 TGGTTGAAAGATGCCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACTATGG
1 TGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCATAGTTGAAAGATACCATGG
2628207 CA
66 CA
2628209 TCATGTCAAA
Statistics
Matches: 233, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
91 1 0.00
92 232 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (92 bp):
TGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAGACCATAGTTGAAAGATACCATGG
CAGCGTGACATGAAATGAATAAGACCA
Found at i:2628513 original size:16 final size:17
Alignment explanation
Indices: 2628492--2628524 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2628482 ATGATGGTGC
2628492 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
2628508 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
2628525 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:2643314 original size:33 final size:33
Alignment explanation
Indices: 2643272--2643337 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2643262 TGTATGAAAG
2643272 TACAACTCGAAATCACTTTATACAAAGTTTAAA
1 TACAACTCGAAATCACTTTATACAAAGTTTAAA
2643305 TACAACTCGAAATCACTTTATACAAAGTTTAAA
1 TACAACTCGAAATCACTTTATACAAAGTTTAAA
2643338 CAAAAGAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.30
Consensus pattern (33 bp):
TACAACTCGAAATCACTTTATACAAAGTTTAAA
Found at i:2644821 original size:23 final size:23
Alignment explanation
Indices: 2644795--2644848 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
2644785 TCATTCTTGC
*
2644795 TTAGTTTTA-TTTCTATTTGTAAT
1 TTAGTTTTATTTTC-AGTTGTAAT
*
2644818 TTAGGTTTATTTTCAGTTGTAAT
1 TTAGTTTTATTTTCAGTTGTAAT
2644841 TGTAGTTT
1 T-TAGTTT
2644849 AGTTTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.20, C:0.04, G:0.15, T:0.61
Consensus pattern (23 bp):
TTAGTTTTATTTTCAGTTGTAAT
Found at i:2646150 original size:12 final size:11
Alignment explanation
Indices: 2646121--2646153 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
2646111 CTCATATTTT
2646121 TCGTTTTTCAC
1 TCGTTTTTCAC
2646132 TCGTTTTTCAC
1 TCGTTTTTCAC
*
2646143 TTGTTTTTCAC
1 TCGTTTTTCAC
2646154 CCCTTTTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.24, G:0.09, T:0.58
Consensus pattern (11 bp):
TCGTTTTTCAC
Found at i:2649026 original size:38 final size:40
Alignment explanation
Indices: 2648972--2649138 Score: 185
Period size: 46 Copynumber: 3.9 Consensus size: 40
2648962 TCTGATATGA
2648972 AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
2649012 -A-GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
**
2649050 ATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTG
1 ------AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
*
2649096 ATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 A-ATG---TG--TAAGACCATGGTTGAAAGATACCATGGCAAC
2649139 ATGACAGAAA
Statistics
Matches: 109, Mismatches: 4, Indels: 22
0.81 0.03 0.16
Matches are distributed among these distances:
38 37 0.34
39 1 0.01
40 1 0.01
41 3 0.03
44 2 0.02
45 1 0.01
46 64 0.59
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (40 bp):
AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:2649080 original size:46 final size:46
Alignment explanation
Indices: 2649015--2649187 Score: 220
Period size: 46 Copynumber: 3.8 Consensus size: 46
2649005 CAACCTGAGT
* *
2649015 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATGT
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATAAAATGA
** *
2649061 GTAAGACCATGGTTGAAAGATACCATGGCAATGTGATATGAAATGA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATAAAATGA
** * *
2649107 ACAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATAAAATGA
* * * * *
2649153 GTAAGACCATAGTTAAAAGACACTATGGCATCATG
1 GTAAGACCATGGTTGAAAGATACCATGGCAACATG
2649188 TCAAAGATAA
Statistics
Matches: 109, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 109 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
GTAAGACCATGGTTGAAAGATACCATGGCAACATGATATAAAATGA
Found at i:2650223 original size:46 final size:46
Alignment explanation
Indices: 2650171--2650264 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
2650161 GGATTAGGAT
* * *
2650171 TAGTTTAGTCTTGCCTCCCTTGGGTATGATCATCGGAGTACTTCCA
1 TAGTTTAGTCTCGCCTCCCCTGGGTACGATCATCGGAGTACTTCCA
*
2650217 TAGTTTAGTCTCGCCTCCCCTGGGTACGATCTTCGGAGTACTTCCA
1 TAGTTTAGTCTCGCCTCCCCTGGGTACGATCATCGGAGTACTTCCA
2650263 TA
1 TA
2650265 CTTCATTGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (46 bp):
TAGTTTAGTCTCGCCTCCCCTGGGTACGATCATCGGAGTACTTCCA
Found at i:2651977 original size:50 final size:50
Alignment explanation
Indices: 2651902--2652001 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
2651892 GCGATCTGCC
* *
2651902 ATCTATTAGTCCATGACATCATCCACCATGTATGTTTAAAGTATGTAAAT
1 ATCTATTAGTCCAAGACATCATCCACCACGTATGTTTAAAGTATGTAAAT
2651952 ATCTATTAGTCCACAG-CATCATCCACCACGTATGTTTAAAGTATGTAAAT
1 ATCTATTAGTCCA-AGACATCATCCACCACGTATGTTTAAAGTATGTAAAT
2652002 GTTTTAAGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 46 0.98
51 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (50 bp):
ATCTATTAGTCCAAGACATCATCCACCACGTATGTTTAAAGTATGTAAAT
Found at i:2653008 original size:17 final size:17
Alignment explanation
Indices: 2652986--2653019 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2652976 TTTCTCAGGT
2652986 AAAATTTTGAAGACGAA
1 AAAATTTTGAAGACGAA
2653003 AAAATTTTGAAGACGAA
1 AAAATTTTGAAGACGAA
2653020 TTTTCTTAAG
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:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (17 bp):
AAAATTTTGAAGACGAA
Found at i:2653588 original size:26 final size:26
Alignment explanation
Indices: 2653552--2653687 Score: 229
Period size: 26 Copynumber: 5.2 Consensus size: 26
2653542 TGATACAAAT
2653552 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
2653578 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
2653604 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
2653630 TGATAAT-GAGTTAGGTAAATGTTTCA
1 TGATAATAG-GTTAGGTAAATGTTTCA
*
2653656 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
2653682 TGATAA
1 TGATAA
2653688 GAATTTCATG
Statistics
Matches: 106, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
25 1 0.01
26 104 0.98
27 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:2657765 original size:20 final size:20
Alignment explanation
Indices: 2657740--2657785 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2657730 TCTTTATTTA
*
2657740 GCACTTCGATGTCTCTGATT
1 GCACTTCAATGTCTCTGATT
*
2657760 GCACTTCAATGTCTCTGTTT
1 GCACTTCAATGTCTCTGATT
2657780 GCACTT
1 GCACTT
2657786 AAGCGCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.26, G:0.17, T:0.41
Consensus pattern (20 bp):
GCACTTCAATGTCTCTGATT
Found at i:2660682 original size:18 final size:19
Alignment explanation
Indices: 2660637--2660683 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2660627 TCTAACCAAT
2660637 ATTAATTTGT-ATATTTTAA
1 ATTAATTT-TAATATTTTAA
2660656 ATTAATTTTAATATTTT-A
1 ATTAATTTTAATATTTTAA
*
2660674 ATTATTTTTA
1 ATTAATTTTA
2660684 TTTTTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTAATTTTAATATTTTAA
Found at i:2660693 original size:18 final size:19
Alignment explanation
Indices: 2660637--2660693 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 19
2660627 TCTAACCAAT
2660637 ATTAATTTGT-ATATTTTA-A
1 ATTAATTT-TAAT-TTTTATA
*
2660656 ATTAATTTTAATATTT-TA
1 ATTAATTTTAATTTTTATA
*
2660674 ATT-ATTTTTATTTTTATA
1 ATTAATTTTAATTTTTATA
2660692 AT
1 AT
2660694 CACATTTAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 10 0.31
18 12 0.38
19 10 0.31
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTAATTTTAATTTTTATA
Found at i:2660789 original size:2 final size:2
Alignment explanation
Indices: 2660782--2660822 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2660772 CATATAATTA
2660782 AT AT AT 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 AT AT AT A
2660823 ACTGATGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2671626 original size:24 final size:24
Alignment explanation
Indices: 2671598--2671646 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2671588 GAATCTAGAA
2671598 TGATAAAAAGAAAAATGAAAAACT
1 TGATAAAAAGAAAAATGAAAAACT
*
2671622 TGATAAAAGGAAAAATGAAAAACT
1 TGATAAAAAGAAAAATGAAAAACT
2671646 T
1 T
2671647 CTAAGAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.63, C:0.04, G:0.14, T:0.18
Consensus pattern (24 bp):
TGATAAAAAGAAAAATGAAAAACT
Found at i:2673779 original size:11 final size:11
Alignment explanation
Indices: 2673765--2673790 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2673755 TAGAGGAGTT
2673765 CTTAAGGAATC
1 CTTAAGGAATC
2673776 CTTAAGGAATC
1 CTTAAGGAATC
2673787 CTTA
1 CTTA
2673791 CTTGAGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (11 bp):
CTTAAGGAATC
Found at i:2674814 original size:22 final size:23
Alignment explanation
Indices: 2674789--2674834 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2674779 CAACCAAATC
2674789 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
2674811 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
2674834 A
1 A
2674835 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:2674840 original size:23 final size:23
Alignment explanation
Indices: 2674796--2674840 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2674786 ATCAATTCAA
*
2674796 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
2674819 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
2674841 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:2679541 original size:23 final size:25
Alignment explanation
Indices: 2679515--2679562 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
2679505 CTAAGGAAAA
* *
2679515 CAAATCAACAATC-GAA-ATTAACT
1 CAAATAAACAAACAGAAGATTAACT
2679538 CAAATAAACAAACAGAAGATTAACT
1 CAAATAAACAAACAGAAGATTAACT
2679563 GACGTTAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.52
24 3 0.14
25 7 0.33
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.19
Consensus pattern (25 bp):
CAAATAAACAAACAGAAGATTAACT
Found at i:2685674 original size:14 final size:15
Alignment explanation
Indices: 2685655--2685687 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2685645 AATGATGAGA
*
2685655 ATAATAGTAAT-AAT
1 ATAATAATAATAAAT
2685669 ATAATAATAATAAAT
1 ATAATAATAATAAAT
2685684 ATAA
1 ATAA
2685688 AAAAACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
ATAATAATAATAAAT
Found at i:2686316 original size:18 final size:19
Alignment explanation
Indices: 2686287--2686322 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2686277 TTCTTTTTCT
*
2686287 TTTTTTATTTTTTTATATG
1 TTTTTTATTTTTATATATG
2686306 TTTTTTA-TTTTATATAT
1 TTTTTTATTTTTATATAT
2686323 TTGTGGGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTTTTATTTTTATATATG
Found at i:2686914 original size:24 final size:25
Alignment explanation
Indices: 2686883--2686930 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
2686873 TATTTGGTTC
2686883 TTGGGTTAGTGGT-TA-TTGGGTTTT
1 TTGGGTTAG-GGTATATTTGGGTTTT
2686907 TTGGGTTAGGGTATATTTGGGTTT
1 TTGGGTTAGGGTATATTTGGGTTT
2686931 GATTGTTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 11 0.50
25 8 0.36
ACGTcount: A:0.10, C:0.00, G:0.38, T:0.52
Consensus pattern (25 bp):
TTGGGTTAGGGTATATTTGGGTTTT
Found at i:2687096 original size:46 final size:46
Alignment explanation
Indices: 2687046--2687393 Score: 405
Period size: 46 Copynumber: 7.6 Consensus size: 46
2687036 CCATAGTGTT
* * *
2687046 TTTCAACTATGGTCTTACTCATTT-ACTGTCAGGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCA-TATCATGTTGCCATGGTATC
** * * **
2687092 TTTCAACCATGGTCTTGTTCATTTCATGTTACATTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
* * ** * *
2687138 TTTCAACCATGGTCTAATTCA-TTCCCATCATTTTACCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
* * * * * *
2687183 TTTCAACCATGGTCTTATTCTTTTCATGTCACGTTGTCATGCTATC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
* *
2687229 TTTCAACCATGGTCTTACACATTTTATATTC-TGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCATA-TCATGTTGCCATGGTATC
* *
2687275 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTGTC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
*
2687321 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
* *
2687367 TTTCAACCATGGTCTTACACTTTTCAT
1 TTTCAACCATGGTCTTACTCATTTCAT
2687394 TTCAGAAAGC
Statistics
Matches: 261, Mismatches: 37, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
45 38 0.15
46 220 0.84
47 3 0.01
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (46 bp):
TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
Found at i:2689176 original size:36 final size:36
Alignment explanation
Indices: 2689136--2689225 Score: 171
Period size: 36 Copynumber: 2.5 Consensus size: 36
2689126 CTCAATTGAG
2689136 GCAAGCTATTTATTATCATTTTTCTCCAATTTTAGT
1 GCAAGCTATTTATTATCATTTTTCTCCAATTTTAGT
2689172 GCAAGCTATTTATTATCATTTTTCTCCAATTTTAGT
1 GCAAGCTATTTATTATCATTTTTCTCCAATTTTAGT
*
2689208 GCAAGCTGTTTATTATCA
1 GCAAGCTATTTATTATCA
2689226 ATTTAGATGC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.48
Consensus pattern (36 bp):
GCAAGCTATTTATTATCATTTTTCTCCAATTTTAGT
Found at i:2691792 original size:30 final size:30
Alignment explanation
Indices: 2691758--2691818 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
2691748 ATAATAAACA
* * *
2691758 TAAAAGGAAC-AAAATTTAATTGAATTAAAG
1 TAAAAGAAACAAAAATAT-ATTAAATTAAAG
2691788 TAAAAGAAACAAAAATATATTAAATTAAAG
1 TAAAAGAAACAAAAATATATTAAATTAAAG
2691818 T
1 T
2691819 TAGAAATGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.61, C:0.03, G:0.10, T:0.26
Consensus pattern (30 bp):
TAAAAGAAACAAAAATATATTAAATTAAAG
Found at i:2696904 original size:18 final size:18
Alignment explanation
Indices: 2696881--2696917 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2696871 AACGGAGAAG
* *
2696881 AAGAAAAGGAAAATAAAA
1 AAGAAAAGAAAAAGAAAA
2696899 AAGAAAAGAAAAAGAAAA
1 AAGAAAAGAAAAAGAAAA
2696917 A
1 A
2696918 TAAATTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (18 bp):
AAGAAAAGAAAAAGAAAA
Found at i:2696911 original size:24 final size:24
Alignment explanation
Indices: 2696876--2696921 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2696866 AAACTAACGG
*
2696876 AGAAGAAGAAAAGGAAAATAAAAA
1 AGAAGAAGAAAAGAAAAATAAAAA
2696900 AGAA-AAGAAAAAGAAAAATAAA
1 AGAAGAAG-AAAAGAAAAATAAA
2696922 TTGTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.04
Consensus pattern (24 bp):
AGAAGAAGAAAAGAAAAATAAAAA
Done.