Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000520.1 Hibiscus syriacus cultivar Beakdansim tig00000991_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: 1956684
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:1690813 original size:151 final size:151
Alignment explanation
Indices: 1690563--1690842 Score: 447
Period size: 151 Copynumber: 1.9 Consensus size: 151
1690553 TCGCAACGAC
* * *
1690563 ACTGTAGACTATCACAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCGCAATGCGAGA
1 ACTGTACACTATCACAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGAAA
* * *
1690628 TGGAAAATCGCAATGACACTGTACACTATCGCAAC-ACGATTTTCA-ACTATCGCAACGCGAAAT
66 TGGAAAATCGCAACGACACTGTACACTATCGCAACGAC-ACTGT-AGACTATCGCAACGCGAAAT
1690691 GGAAAATCGCAACGATCGCAATG
129 GGAAAATCGCAACGATCGCAATG
* *
1690714 ACTGTACACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAA
1 ACTGTACACTATCACAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGAAA
*
1690779 TGGAAAATCGCAACGACACTGTAGACTATCGCAACGACACTGTAGACTATCGCAACGCGAAATG
66 TGGAAAATCGCAACGACACTGTACACTATCGCAACGACACTGTAGACTATCGCAACGCGAAATG
1690843 CAACGCGAAA
Statistics
Matches: 118, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
150 1 0.01
151 115 0.97
152 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (151 bp):
ACTGTACACTATCACAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGAAA
TGGAAAATCGCAACGACACTGTACACTATCGCAACGACACTGTAGACTATCGCAACGCGAAATGG
AAAATCGCAACGATCGCAATG
Found at i:1690847 original size:12 final size:12
Alignment explanation
Indices: 1690830--1690863 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
1690820 GTAGACTATC
1690830 GCAACGCGAAAT
1 GCAACGCGAAAT
1690842 GCAACGCGAAAT
1 GCAACGCGAAAT
1690854 GCAACGCGAA
1 GCAACGCGAA
1690864 TTTGCGATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.26, G:0.26, T:0.06
Consensus pattern (12 bp):
GCAACGCGAAAT
Found at i:1693067 original size:15 final size:16
Alignment explanation
Indices: 1693034--1693067 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1693024 ATTATTACAC
1693034 TTTAATATTCTAAATT
1 TTTAATATTCTAAATT
1693050 TTTAAT-TTCTTAAATT
1 TTTAATATTC-TAAATT
1693066 TT
1 TT
1693068 GTCACCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAATATTCTAAATT
Found at i:1693123 original size:39 final size:39
Alignment explanation
Indices: 1693017--1693127 Score: 145
Period size: 39 Copynumber: 2.8 Consensus size: 39
1693007 TTGTTCATAA
* * *
1693017 TTCTTAAATTATTACACTTTAATATTCTAAATTTTTAAT
1 TTCTTAAATTATTTCACATTAACATTCTAAATTTTTAAT
1693056 TTCTTAAATT-TTGTCACCA-TAACATTCTAAATTTTTAAT
1 TTCTTAAATTATT-TCA-CATTAACATTCTAAATTTTTAAT
* *
1693095 TTCTTAAATTATTTCACATTAGCGTTCTAAATT
1 TTCTTAAATTATTTCACATTAACATTCTAAATT
1693128 ATTTTTAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
38 4 0.06
39 56 0.89
40 3 0.05
ACGTcount: A:0.33, C:0.14, G:0.03, T:0.50
Consensus pattern (39 bp):
TTCTTAAATTATTTCACATTAACATTCTAAATTTTTAAT
Found at i:1693201 original size:25 final size:25
Alignment explanation
Indices: 1693155--1693202 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1693145 AACTTCAAAA
*
1693155 TATTTTAAATTTAATTATATTTTTT
1 TATTTTAAATTTAATTAAATTTTTT
1693180 TATTTTAAATTTTAA-TAAATTTT
1 TATTTTAAA-TTTAATTAAATTTT
1693203 ATCTTTCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTTTAAATTTAATTAAATTTTTT
Found at i:1693308 original size:12 final size:12
Alignment explanation
Indices: 1693277--1693310 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1693267 AATTTTAAAT
*
1693277 TATATATATATA
1 TATATATTTATA
1693289 TATATATTTATA
1 TATATATTTATA
*
1693301 TTTATATTTA
1 TATATATTTA
1693311 AAAAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATATTTATA
Found at i:1693454 original size:16 final size:15
Alignment explanation
Indices: 1693414--1693462 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1693404 AAGACATGAG
1693414 CCAATATTTTAGTAC
1 CCAATATTTTAGTAC
*
1693429 CCAAAAATTTTAGGTAC
1 CC-AATATTTTA-GTAC
*
1693446 TCAATATTTTGAGTAC
1 CCAATATTTT-AGTAC
1693462 C
1 C
1693463 TGATTTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 2 0.07
16 19 0.70
17 6 0.22
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (15 bp):
CCAATATTTTAGTAC
Found at i:1694694 original size:12 final size:14
Alignment explanation
Indices: 1694654--1694694 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1694644 AACATATTAA
1694654 ATAATAAATATAATT
1 ATAA-AAATATAATT
*
1694669 ATAAAACTATAATT
1 ATAAAAATATAATT
1694683 A-AAAAATA-AATT
1 ATAAAAATATAATT
1694695 TGGGGCTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.17
13 6 0.25
14 10 0.42
15 4 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAAAATATAATT
Found at i:1700479 original size:21 final size:21
Alignment explanation
Indices: 1700437--1700494 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
1700427 AATAGCCAGA
*
1700437 GTGCATCGATGCATG--GCTG
1 GTGCATCGATGCATGAAACTG
1700456 GTGCATCGATGCATGAAACTG
1 GTGCATCGATGCATGAAACTG
1700477 GTGCATCGATGCATGAAA
1 GTGCATCGATGCATGAAA
1700495 TGCATTTGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 15 0.42
21 21 0.58
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (21 bp):
GTGCATCGATGCATGAAACTG
Found at i:1700611 original size:65 final size:66
Alignment explanation
Indices: 1700454--1700620 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 66
1700444 GATGCATGGC
* *
1700454 TGGTGCATCGATGCATGAAACTGGTGCATCGATGCATGAAATGCATTTGATGTTTTCATAAAATC
1 TGGTGCATCGATGCATG-GATTGGTGCATCGATGCATGAAATGCATTTGATG-TTTCATAAAAT-
1700519 CTCA
63 CTCA
* ** **
1700523 --GTGCATCGGTGCATGG-TAAGTGCATCGATGCATGAAATGCATTTGATG-TTCAATTTAAT-T
1 TGGTGCATCGATGCATGGATTGGTGCATCGATGCATGAAATGCATTTGATGTTTC-ATAAAATCT
1700583 CA
65 CA
*
1700585 TGGTGCATCGATGCATGGATTGGTGCATCGGTGCAT
1 TGGTGCATCGATGCATGGATTGGTGCATCGATGCAT
1700621 CACTTTGATA
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 20 0.24
65 43 0.52
67 14 0.17
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (66 bp):
TGGTGCATCGATGCATGGATTGGTGCATCGATGCATGAAATGCATTTGATGTTTCATAAAATCTC
A
Found at i:1700995 original size:52 final size:52
Alignment explanation
Indices: 1700934--1701040 Score: 187
Period size: 52 Copynumber: 2.1 Consensus size: 52
1700924 ATTTGAAATC
*
1700934 AATTTTGAAAAATTTCTCCCCATTACTATAACACATCTCCCTTTTAACACTT
1 AATTTTGAAAAATTACTCCCCATTACTATAACACATCTCCCTTTTAACACTT
* *
1700986 AATTTTGAAAAATTACTCCCCCTTACTATAACACTTCTCCCTTTTAACACTT
1 AATTTTGAAAAATTACTCCCCATTACTATAACACATCTCCCTTTTAACACTT
1701038 AAT
1 AAT
1701041 ATTTCTCCCC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (52 bp):
AATTTTGAAAAATTACTCCCCATTACTATAACACATCTCCCTTTTAACACTT
Found at i:1701129 original size:2 final size:2
Alignment explanation
Indices: 1701122--1701146 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1701112 AATTGATTAA
1701122 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1701147 GCTTAAGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1703371 original size:21 final size:23
Alignment explanation
Indices: 1703316--1703373 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1703306 CATGGCCTTT
1703316 TGCATCGATGCACATTCAAGGCG
1 TGCATCGATGCACATTCAAGGCG
* * *
1703339 TGCATCGGTGCACCTTC-ATG-G
1 TGCATCGATGCACATTCAAGGCG
*
1703360 TGTATCGATGCACA
1 TGCATCGATGCACA
1703374 ATAAAGGATG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 12 0.41
22 2 0.07
23 15 0.52
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGCG
Found at i:1708991 original size:19 final size:19
Alignment explanation
Indices: 1708938--1708983 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1708928 TAAAATCCTC
*
1708938 AGTGGATCAGTGCATGGTA
1 AGTGCATCAGTGCATGGTA
1708957 AGTGCATCAGTGCATGGTA
1 AGTGCATCAGTGCATGGTA
1708976 AGTGCATC
1 AGTGCATC
1708984 GATGCATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (19 bp):
AGTGCATCAGTGCATGGTA
Found at i:1711290 original size:19 final size:19
Alignment explanation
Indices: 1711261--1711311 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1711251 AATCAGTTTT
*
1711261 AGTATCAATACCAAGGGTG
1 AGTATCGATACCAAGGGTG
* * *
1711280 GGTATCGATACTAAAGGGTT
1 AGTATCGATAC-CAAGGGTG
1711300 AGTATCGATACC
1 AGTATCGATACC
1711312 GTCATCCTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (19 bp):
AGTATCGATACCAAGGGTG
Found at i:1711298 original size:20 final size:20
Alignment explanation
Indices: 1711273--1711310 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1711263 TATCAATACC
*
1711273 AAGGGTGGGTATCGATACTA
1 AAGGGTGAGTATCGATACTA
*
1711293 AAGGGTTAGTATCGATAC
1 AAGGGTGAGTATCGATAC
1711311 CGTCATCCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.26
Consensus pattern (20 bp):
AAGGGTGAGTATCGATACTA
Found at i:1714304 original size:2 final size:2
Alignment explanation
Indices: 1714297--1714332 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1714287 CTTTAAAATC
1714297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1714333 GATCAATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1724271 original size:29 final size:28
Alignment explanation
Indices: 1724237--1724329 Score: 98
Period size: 31 Copynumber: 3.1 Consensus size: 28
1724227 TTAATTTTTA
*
1724237 ATTTTTTAATTATATATATATATATATT
1 ATTTTATAATTATATATATATATATATT
*
1724265 ACGTTTTATTATTATTATATATATATATTATT
1 A--TTTTATAATTA-TATATATATATA-TATT
*
1724297 ATTATTGTACATTATATATATATATATA-T
1 ATT-TTATA-ATTATATATATATATATATT
1724326 ATTT
1 ATTT
1724330 CACTTTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
28 2 0.04
29 4 0.07
30 13 0.24
31 27 0.49
32 9 0.16
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTTATAATTATATATATATATATATT
Found at i:1724278 original size:3 final size:3
Alignment explanation
Indices: 1724270--1724375 Score: 56
Period size: 3 Copynumber: 33.7 Consensus size: 3
1724260 ATATTACGTT
* *
1724270 TTA TTA TTA TTA -TA TATA TATA TTA TTA TTA TTG TACA TTA TATA TATA
1 TTA TTA TTA TTA TTA T-TA T-TA TTA TTA TTA TTA T-TA TTA T-TA T-TA
* * ** *
1724319 TATA TATA TT- TCA CTT- TTT TTA TTA TTA TTA TTA TCG TTA TTT TTA
1 T-TA T-TA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1724365 TTA TTA TTA TT
1 TTA TTA TTA TT
1724376 TTTGTTTTAC
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
2 5 0.06
3 54 0.65
4 24 0.29
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1724300 original size:35 final size:34
Alignment explanation
Indices: 1724245--1724347 Score: 110
Period size: 33 Copynumber: 3.1 Consensus size: 34
1724235 TAATTTTTTA
1724245 ATTATATATATATA-TA-TATTACGTTTTATTATT
1 ATTATATATATATATTATTATTAC-TTTTATTATT
* *
1724278 ATTATATATATATATTATTATTA-TTGTA-CATT
1 ATTATATATATATATTATTATTACTTTTATTATT
* *
1724310 A-TATATATATATATATATT-TCACTTTTTTTATT
1 ATTATATATATATAT-TATTATTACTTTTATTATT
1724343 ATTAT
1 ATTAT
1724348 TATTATCGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
31 15 0.26
32 11 0.19
33 22 0.38
34 5 0.09
35 5 0.09
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (34 bp):
ATTATATATATATATTATTATTACTTTTATTATT
Found at i:1724537 original size:26 final size:26
Alignment explanation
Indices: 1724508--1724572 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
1724498 TATTTCATTA
* *
1724508 TTATTTTTCTTTGTT-TTATGTTTGTT
1 TTATTTTTATTTGTTATTA-ATTTGTT
*
1724534 TTATTTTTATTTTTTATTAATTTGTT
1 TTATTTTTATTTGTTATTAATTTGTT
1724560 TTATCTTTTATTT
1 TTAT-TTTTATTT
1724573 ATGTTAGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 23 0.68
27 11 0.32
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (26 bp):
TTATTTTTATTTGTTATTAATTTGTT
Found at i:1724546 original size:11 final size:11
Alignment explanation
Indices: 1724495--1724603 Score: 53
Period size: 11 Copynumber: 9.5 Consensus size: 11
1724485 TTTCTTCCTA
*
1724495 TTTTATTTCAT
1 TTTTATTTTAT
*
1724506 TATTATTTT-T
1 TTTTATTTTAT
* *
1724516 CTTTGTTTTAT
1 TTTTATTTTAT
* *
1724527 GTTTGTTTTAT
1 TTTTATTTTAT
1724538 TTTTATTTTTTAT
1 TTTTA--TTTTAT
*
1724551 TAATTTGTTTTAT
1 T--TTTATTTTAT
1724564 CTTTTA-TTTAT
1 -TTTTATTTTAT
**
1724575 GTTAGCATTTTAT
1 -TT-TTATTTTAT
1724588 TTTTA-TTTAT
1 TTTTATTTTAT
1724598 TTTTAT
1 TTTTAT
1724604 ATTTTCGCTT
Statistics
Matches: 74, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
10 17 0.23
11 29 0.39
12 6 0.08
13 18 0.24
14 1 0.01
15 3 0.04
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:1724608 original size:18 final size:18
Alignment explanation
Indices: 1724533--1724661 Score: 57
Period size: 18 Copynumber: 6.8 Consensus size: 18
1724523 TTATGTTTGT
1724533 TTTATTTTTAT-TTTTTA
1 TTTATTTTTATATTTTTA
* *
1724550 TTAATTTGTTTTATCTTTTA
1 TTTATTT-TTATAT-TTTTA
*
1724570 TTTATGTTAGCATTTTATTTTTA
1 TTTAT-TT----TTATATTTTTA
**
1724593 TTTATTTTTATATTTTCG
1 TTTATTTTTATATTTTTA
* *
1724611 CTTA-TTTTATCATTTTTC
1 TTTATTTTTAT-ATTTTTA
* * *
1724629 CTTATTTTTGTTATGTTTA
1 TTTATTTTT-ATATTTTTA
*
1724648 -TTATTTTCATATTT
1 TTTATTTTTATATTT
1724662 ACACGTTTTC
Statistics
Matches: 86, Mismatches: 16, Indels: 20
0.70 0.13 0.16
Matches are distributed among these distances:
17 16 0.19
18 30 0.35
19 10 0.12
20 10 0.12
21 2 0.02
22 2 0.02
23 10 0.12
24 6 0.07
ACGTcount: A:0.19, C:0.06, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTATTTTTATATTTTTA
Found at i:1735925 original size:65 final size:62
Alignment explanation
Indices: 1735821--1735992 Score: 199
Period size: 65 Copynumber: 2.8 Consensus size: 62
1735811 TAACACCATC
* * * * *
1735821 TACTCGAGATTGGATTTCAACTTTACAACAAAGGATATCCAACTCAAAGCCAA-TTCGGTGAGGA
1 TACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGACAAGTT-GGTGA--A
*
1735885 TTACTCAAGATCGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGACAAGTTGGTGAA
1 -TACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGACAAGTTGGTGAA
* *
1735948 -A--CAATACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAA
1 TACTCAAGA-TTGGATTTCAACTTCACGACGAAGGATATCCAACTCAA
1735993 GGCTTAACTT
Statistics
Matches: 96, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
59 4 0.04
60 36 0.38
61 1 0.01
63 1 0.01
65 52 0.54
66 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (62 bp):
TACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGACAAGTTGGTGAA
Found at i:1736216 original size:64 final size:65
Alignment explanation
Indices: 1736079--1736235 Score: 264
Period size: 64 Copynumber: 2.4 Consensus size: 65
1736069 GTCAAGATTG
1736079 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGACGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGC-CAACTTCACAATGAAGACGCCATCCA
1736144 C
65 C
*
1736145 GATTTCAACTTCACGACGAAGGATATCCAATTCTAGG-CAACTTCACAATGAAGGA-GCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCCAACTTCACAATGAA-GACGCCATCCA
1736208 C
65 C
*
1736209 GATTTCAACTTCACGATGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
1736236 ATGCCCACAA
Statistics
Matches: 88, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
64 50 0.57
65 2 0.02
66 36 0.41
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (65 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCCAACTTCACAATGAAGACGCCATCCAC
Found at i:1736230 original size:32 final size:32
Alignment explanation
Indices: 1736117--1736231 Score: 114
Period size: 32 Copynumber: 3.6 Consensus size: 32
1736107 AATTCAAGGC
1736117 TCAACTTCACAATGAA-GACGCCATCCACGATT
1 TCAACTTCACAATGAAGGA-GCCATCCACGATT
* * *
1736149 TCAACTTCACGACGAAGGA--TATCCA--ATT
1 TCAACTTCACAATGAAGGAGCCATCCACGATT
1736177 CTAGGCAACTTCACAATGAAGGAGCCATCCACGATT
1 -T---CAACTTCACAATGAAGGAGCCATCCACGATT
*
1736213 TCAACTTCACGATGAAGGA
1 TCAACTTCACAATGAAGGA
1736232 TATCATGCCC
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
28 3 0.04
29 1 0.01
30 5 0.07
32 47 0.70
33 2 0.03
34 5 0.07
35 1 0.01
36 3 0.04
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.22
Consensus pattern (32 bp):
TCAACTTCACAATGAAGGAGCCATCCACGATT
Found at i:1737904 original size:3 final size:3
Alignment explanation
Indices: 1737864--1737996 Score: 62
Period size: 3 Copynumber: 43.0 Consensus size: 3
1737854 TTAATTTTTA
* * *
1737864 ATT ATTT ATT -TT ATT TTT A-T ATAT ATT ATGT TTT ATT ATT ATC ATT
1 ATT A-TT ATT ATT ATT ATT ATT AT-T ATT AT-T ATT ATT ATT ATT ATT
* *
1737910 ATAT ATT -TT ATT ATT ATT ATT GTAC ATT A-T ATAT ATAT ATAT ATAT
1 AT-T ATT ATT ATT ATT ATT ATT AT-T ATT ATT AT-T AT-T AT-T AT-T
* * *
1737956 ATT -TC ACCT -TT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1737997 TTACCAAATA
Statistics
Matches: 101, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
2 10 0.10
3 64 0.63
4 27 0.27
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1737911 original size:28 final size:28
Alignment explanation
Indices: 1737880--1737986 Score: 100
Period size: 28 Copynumber: 3.9 Consensus size: 28
1737870 TATTTTATTT
*
1737880 TTATATATATTATGTTTTATTATTAT-CA
1 TTATATATATTAT-TATTATTATTATACA
* *
1737908 TTATATATTTTATTATTATTATTGTACA
1 TTATATATATTATTATTATTATTATACA
*
1737936 TTATATATA-TA-TATATATATATT-TCACC
1 TTATATATATTATTAT-TAT-TATTAT-ACA
1737964 TT-TAT-TATTATTATTATTATTAT
1 TTATATATATTATTATTATTATTAT
1737987 TATTTTTATT
Statistics
Matches: 67, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
26 9 0.13
27 25 0.37
28 33 0.49
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (28 bp):
TTATATATATTATTATTATTATTATACA
Found at i:1737920 original size:21 final size:20
Alignment explanation
Indices: 1737864--1737989 Score: 78
Period size: 21 Copynumber: 6.0 Consensus size: 20
1737854 TTAATTTTTA
* *
1737864 ATTATTTATTTTATTTTTAT
1 ATTATATATTTTATTATTAT
*
1737884 ATATATTATGTTTTATTATTAT
1 AT-TA-TATATTTTATTATTAT
1737906 CATTATATATTTTATTATTATT
1 -ATTATATATTTTATTATTA-T
* * *
1737928 ATTGTACATTATA-TATATAT
1 ATTATATATTTTATTAT-TAT
* *
1737948 ATATATATATTTCACCT-TTATT
1 AT-TATATATTTTA-TTATTA-T
1737970 ATTAT-TATTATTATTATTAT
1 ATTATATATT-TTATTATTAT
1737990 TTTTATTTTA
Statistics
Matches: 82, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
20 14 0.17
21 45 0.55
22 20 0.24
23 3 0.04
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTATATATTTTATTATTAT
Found at i:1738212 original size:19 final size:18
Alignment explanation
Indices: 1738070--1738208 Score: 77
Period size: 19 Copynumber: 7.4 Consensus size: 18
1738060 GTATTATTTC
**
1738070 TTATTCTTTTTTATTTAGG
1 TTATT-TTTTTTATTTATT
*
1738089 TTCTTTTTTTCTATTTAATT
1 TTATTTTTTT-TATTT-ATT
* * *
1738109 TCATTTTTTTTCTTTGTT
1 TTATTTTTTTTATTTATT
1738127 TTATGTTTGTTTTATTT-TT
1 TTAT-TTT-TTTTATTTATT
* *
1738146 TTATTTTTATTAATT-TT
1 TTATTTTTTTTATTTATT
* *
1738163 TT-TGTCTTTTATTTATGT
1 TTATTTTTTTTATTTAT-T
* *
1738181 TAGCATTTTATTTATTTATT
1 T--TATTTTTTTTATTTATT
1738201 TTATTTTT
1 TTATTTTT
1738209 ATTTTCGCTT
Statistics
Matches: 90, Mismatches: 21, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
16 8 0.09
17 11 0.12
18 20 0.22
19 22 0.24
20 18 0.20
21 11 0.12
ACGTcount: A:0.15, C:0.05, G:0.06, T:0.74
Consensus pattern (18 bp):
TTATTTTTTTTATTTATT
Found at i:1739883 original size:2 final size:2
Alignment explanation
Indices: 1739878--1739906 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1739868 TTAAATTCTC
1739878 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 A
1739907 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1740129 original size:23 final size:23
Alignment explanation
Indices: 1740101--1740152 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1740091 ATATATATAA
1740101 TTTAATTTTATATCT-TCAAATT
1 TTTAATTTTATATCTCTCAAATT
*
1740123 TTATAATTTTATATCTCTTAAATT
1 TT-TAATTTTATATCTCTCAAATT
1740147 TTTAAT
1 TTTAAT
1740153 ATGAATTGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.07
23 17 0.63
24 8 0.30
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTAATTTTATATCTCTCAAATT
Found at i:1741303 original size:19 final size:20
Alignment explanation
Indices: 1741266--1741303 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1741256 TTAGGCAACG
*
1741266 AAATCAATATTTTCGATAAA
1 AAATCAATATTTTAGATAAA
*
1741286 AAAT-AATATTTTATATAA
1 AAATCAATATTTTAGATAA
1741304 CACTTTACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (20 bp):
AAATCAATATTTTAGATAAA
Found at i:1742356 original size:39 final size:37
Alignment explanation
Indices: 1742252--1742356 Score: 131
Period size: 39 Copynumber: 2.7 Consensus size: 37
1742242 CATAATCCTC
*
1742252 AAATTATTTCACACTAACATTCTAAAATCCTAATTTCTT
1 AAATTATTTCACA-TAACGTTCT-AAATCCTAATTTCTT
*
1742291 AAATT-TTGACACCATAACGTTCTAAATCCTTAATTTCTT
1 AAATTATT-TCA-CATAACGTTCTAAATCC-TAATTTCTT
1742330 AAATTATTTCACATTAACGTTCTAAAT
1 AAATTATTTCACA-TAACGTTCTAAAT
1742357 TATTTTTTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
38 10 0.17
39 44 0.76
40 4 0.07
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (37 bp):
AAATTATTTCACATAACGTTCTAAATCCTAATTTCTT
Found at i:1742435 original size:35 final size:35
Alignment explanation
Indices: 1742395--1742463 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
1742385 AAAACATTTG
* * * *
1742395 AAATTTAATTATATTTCTTTATTTTAAATTTTAAT
1 AAATTTAATTATAATTATGTAATTTAAATTTTAAT
* *
1742430 AAATTTTATTTTAATTATGTAATTTAAATTTTAA
1 AAATTTAATTATAATTATGTAATTTAAATTTTAA
1742464 ACTTTATGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (35 bp):
AAATTTAATTATAATTATGTAATTTAAATTTTAAT
Found at i:1742847 original size:21 final size:21
Alignment explanation
Indices: 1742823--1743028 Score: 93
Period size: 20 Copynumber: 10.1 Consensus size: 21
1742813 GCAAATTCGC
*
1742823 GTTGCATTTCGCGTTGTGATA
1 GTTGCATTTCGCGTTGCGATA
* **
1742844 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
1742864 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ** ***
1742885 GTTGAAAATCG-AACGCGA-A
1 GTTGCATTTCGCGTTGCGATA
* * * **
1742904 ATGGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
1742924 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* * *
1742945 GTCTACA-GTCACGTTGCGAT-
1 GT-TGCATTTCGCGTTGCGATA
* *
1742965 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* * *
1742986 GTTGAAATTCGCATTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
1743006 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
1743027 GT
1 GT
1743029 CTACAGTTGT
Statistics
Matches: 130, Mismatches: 47, Indels: 16
0.67 0.24 0.08
Matches are distributed among these distances:
19 13 0.10
20 64 0.49
21 50 0.38
22 3 0.02
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:1742935 original size:20 final size:20
Alignment explanation
Indices: 1742912--1743025 Score: 113
Period size: 20 Copynumber: 5.6 Consensus size: 20
1742902 AAATGGAAAA
1742912 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
1742932 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
*
1742953 TCACGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** *
1742973 TCGCGTTGCGATAGTTGAAAT
1 TCGCGTTGCGAT-TTTCCATT
*
1742994 TCGCATTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
1743014 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1743026 AGTCTACAGT
Statistics
Matches: 72, Mismatches: 18, Indels: 8
0.73 0.18 0.08
Matches are distributed among these distances:
19 4 0.06
20 38 0.53
21 26 0.36
22 4 0.06
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:1742972 original size:41 final size:42
Alignment explanation
Indices: 1742915--1743094 Score: 244
Period size: 41 Copynumber: 4.4 Consensus size: 42
1742905 TGGAAAATCG
*
1742915 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG-TCA
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTCT
* *
1742956 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGA-AATTCG
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGTTCT
* *
1742997 CATTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTCT
* *
1743039 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAGTTCT
1743080 CGTTGCGATTTTCCA
1 CGTTGCGATTTTCCA
1743095 AATTCGTTGT
Statistics
Matches: 126, Mismatches: 8, Indels: 11
0.87 0.06 0.08
Matches are distributed among these distances:
40 3 0.02
41 103 0.82
42 17 0.13
43 3 0.02
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (42 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTCT
Found at i:1743045 original size:22 final size:22
Alignment explanation
Indices: 1743017--1743088 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
1743007 TTCCATTTCG
1743017 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
1743039 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
1743058 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1743080 CGTTGCGAT
1 CGTTGCGAT
1743089 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1743062 original size:19 final size:19
Alignment explanation
Indices: 1743038--1743103 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
1743028 TCTACAGTTG
1743038 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
1743057 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
1743078 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
1743098 TCGTTG
1 TCGTTG
1743104 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:1743199 original size:6 final size:6
Alignment explanation
Indices: 1743188--1743236 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
1743178 GACACGTATT
1743188 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1743234 ACC
1 ACC
1743237 CGAGACGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.23
6 33 0.77
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1743770 original size:6 final size:6
Alignment explanation
Indices: 1743734--1743809 Score: 117
Period size: 6 Copynumber: 13.5 Consensus size: 6
1743724 TCTCGTCTCG
1743734 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1743777 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1743810 AATACGTGTC
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 25 0.36
6 45 0.64
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:1743946 original size:20 final size:20
Alignment explanation
Indices: 1743921--1743972 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1743911 ACTGTAGACT
*
1743921 ATCGCAACGTGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1743941 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* *
1743961 ACCACAACGCGA
1 ATCGCAACGCGA
1743973 TTTTCAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1743991 original size:41 final size:41
Alignment explanation
Indices: 1743941--1744127 Score: 187
Period size: 41 Copynumber: 4.4 Consensus size: 41
1743931 GAAATGGAAA
* *
1743941 ATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
* ***
1743982 ATCGCAACGCGAATTTGCGATGATGGAGATCGCGTTGCGA-TTTCAACT
1 ATCGCAACGCGAA-ATG-GA--A---A-ATCGCAACGCGATTTTCAACT
* * *
1744030 ATCGCAACGCGAAATGAAAAATCGCAACGCGATCTCCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
* *
1744071 ATCGCAACGCGAAATGGAAAAACGCAACTCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
*
1744112 ATCGCAATGCGAAATG
1 ATCGCAACGCGAAATG
1744128 TAACGTGAAT
Statistics
Matches: 118, Mismatches: 19, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
40 9 0.08
41 71 0.60
42 2 0.02
43 2 0.02
44 1 0.01
45 1 0.01
46 1 0.01
47 2 0.02
48 22 0.19
49 7 0.06
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
Found at i:1744041 original size:20 final size:20
Alignment explanation
Indices: 1744018--1744082 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1744008 AGATCGCGTT
1744018 GCGATTTCAACTATCGCAAC
1 GCGATTTCAACTATCGCAAC
** * **
1744038 GCGAAATGAAAAATCGCAAC
1 GCGATTTCAACTATCGCAAC
*
1744058 GCGATCTCCAACTATCGCAAC
1 GCGAT-TTCAACTATCGCAAC
1744079 GCGA
1 GCGA
1744083 AATGGAAAAA
Statistics
Matches: 33, Mismatches: 11, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.17
Consensus pattern (20 bp):
GCGATTTCAACTATCGCAAC
Found at i:1744098 original size:20 final size:19
Alignment explanation
Indices: 1744032--1744098 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
1744022 TTTCAACTAT
1744032 CGCAACGCGAAATGAAAAA
1 CGCAACGCGAAATGAAAAA
** * * *
1744051 TCGCAACGCGATCTCCAACTAT
1 -CGCAACGCGAAAT-GAA-AAA
1744073 CGCAACGCGAAATGGAAAAA
1 CGCAACGCGAAAT-GAAAAA
1744093 CGCAAC
1 CGCAAC
1744099 TCGATTTTCA
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
20 18 0.53
21 15 0.44
22 1 0.03
ACGTcount: A:0.42, C:0.28, G:0.19, T:0.10
Consensus pattern (19 bp):
CGCAACGCGAAATGAAAAA
Found at i:1744315 original size:25 final size:26
Alignment explanation
Indices: 1744267--1744325 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
1744257 GGTTATTTTC
* *
1744267 TCATTTAAAAAATACTTTATTTTATTT
1 TCATTT-AAAAATACTATAATTTATTT
1744294 TCATTTAAAAATA-TATAATTTATTT
1 TCATTTAAAAATACTATAATTTATTT
*
1744319 TAATTTA
1 TCATTTA
1744326 TTAAAAGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 16 0.55
26 7 0.24
27 6 0.21
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (26 bp):
TCATTTAAAAATACTATAATTTATTT
Found at i:1750040 original size:23 final size:22
Alignment explanation
Indices: 1750010--1750134 Score: 137
Period size: 23 Copynumber: 5.6 Consensus size: 22
1750000 ACACTACCCA
1750010 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCA-CCCTTGAAT
* * *
1750033 GTGCATCGATTCA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
1750054 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
* * *
1750077 GTGCATCGATTCA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
1750098 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
1750121 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1750135 TCAATTGTGC
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
21 34 0.41
23 48 0.59
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:1750064 original size:44 final size:44
Alignment explanation
Indices: 1750010--1750130 Score: 217
Period size: 44 Copynumber: 2.8 Consensus size: 44
1750000 ACACTACCCA
*
1750010 GTGCATCGATGCATC-CCTTGAATGTGCATCGATTCACCATGAAG
1 GTGCACCGATGCA-CGCCTTGAATGTGCATCGATTCACCATGAAG
1750054 GTGCACCGATGCACGCCTTGAATGTGCATCGATTCACCATGAAG
1 GTGCACCGATGCACGCCTTGAATGTGCATCGATTCACCATGAAG
1750098 GTGCACCGATGCACGCCTTGAATGTGCATCGAT
1 GTGCACCGATGCACGCCTTGAATGTGCATCGAT
1750131 GCACTCAATT
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
43 1 0.01
44 74 0.99
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (44 bp):
GTGCACCGATGCACGCCTTGAATGTGCATCGATTCACCATGAAG
Found at i:1754319 original size:55 final size:55
Alignment explanation
Indices: 1754260--1754620 Score: 198
Period size: 55 Copynumber: 6.6 Consensus size: 55
1754250 TCCTTTTTCT
* * * * *
1754260 TTCAGGGAGTATAAGACTCGAATAATCTTCGACAAATGTATATGTTCCCTATTCA
1 TTCAGGGAGTATAAGACTCAAATAATCTTCAACAAATGGATACGCTCCCTATTCA
* * * *
1754315 TTCAGGGAGTATAAGACTCAAACAATCTTCAATAAATGGGTCCGCTCCCTATTCA
1 TTCAGGGAGTATAAGACTCAAATAATCTTCAACAAATGGATACGCTCCCTATTCA
* * * ** * *
1754370 TTCAGGGAGTAT-AGAACTCAAATAATTTTCATA-AAATGGGTCCATTCTCTAGTCA
1 TTCAGGGAGTATAAG-ACTCAAATAATCTTCA-ACAAATGGATACGCTCCCTATTCA
* * * * * * * * *
1754425 TTCAGAGAGTAT-AGAACTCAAACAATCTTCAGCAAACGGGTCCACTCTCTATTCC
1 TTCAGGGAGTATAAG-ACTCAAATAATCTTCAACAAATGGATACGCTCCCTATTCA
* * * * * * * * *
1754480 TTCAGAGAGTAT-AGAACTCGAACAATCTTCATA-ATACGGGTCCGCTCTCTATTCC
1 TTCAGGGAGTATAAG-ACTCAAATAATCTTCA-ACAAATGGATACGCTCCCTATTCA
* * * * * * *
1754535 TTCAGAGAGTAT-AGAACTCGAACAATCTTCATA-AAATGGGTCCGCTCTCTATTCC
1 TTCAGGGAGTATAAG-ACTCAAATAATCTTCA-ACAAATGGATACGCTCCCTATTCA
* * *
1754590 TTCAGAGAGTAT-AGAACTCGAACAATCTTCA
1 TTCAGGGAGTATAAG-ACTCAAATAATCTTCA
1754621 TAAAACGTGT
Statistics
Matches: 273, Mismatches: 29, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
54 2 0.01
55 270 0.99
56 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (55 bp):
TTCAGGGAGTATAAGACTCAAATAATCTTCAACAAATGGATACGCTCCCTATTCA
Found at i:1754621 original size:55 final size:55
Alignment explanation
Indices: 1754308--1754752 Score: 547
Period size: 55 Copynumber: 8.3 Consensus size: 55
1754298 TATATGTTCC
* * * * *
1754308 CTATTCATTCAGGGAGTATA-AGACTCAAACAATCTTCA-ATAAATGGGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCATA-AAACGGGTCCGCTCT
* * * * * * **
1754363 CTATTCATTCAGGGAGTATAGAACTCAAATAATTTTCATAAAATGGGTCCATTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
* * * ** *
1754418 CTAGTCATTCAGAGAGTATAGAACTCAAACAATCTTCAGCAAACGGGTCCACTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
*
1754473 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAATACGGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
*
1754528 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAATGGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
*
1754583 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
*
1754638 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACAGGTCCG----
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
* *
1754689 ------CTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACAGGTCCTCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCCGCTCT
1754738 CTATTCCTTCAGAGA
1 CTATTCCTTCAGAGA
1754753 TTACAAGACT
Statistics
Matches: 350, Mismatches: 27, Indels: 26
0.87 0.07 0.06
Matches are distributed among these distances:
44 1 0.00
45 42 0.12
55 305 0.87
56 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (55 bp):
CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCT
Found at i:1754708 original size:45 final size:45
Alignment explanation
Indices: 1754644--1754732 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
1754634 CTCTCTATTC
1754644 CTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACAGGTCCG
1 CTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACAGGTCCG
1754689 CTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACAGGTCC
1 CTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACAGGTCC
1754733 TCTCTCTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 1 0.02
45 42 0.98
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (45 bp):
CTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACAGGTCCG
Found at i:1756150 original size:7 final size:7
Alignment explanation
Indices: 1756140--1756267 Score: 83
Period size: 7 Copynumber: 18.7 Consensus size: 7
1756130 TTTTTCTCTT
1756140 TTTTTCA
1 TTTTTCA
1756147 TTTTTCA
1 TTTTTCA
1756154 TTTTTCA
1 TTTTTCA
1756161 TTTTTCA
1 TTTTTCA
*
1756168 TTTTTCTC
1 TTTTTC-A
*
1756176 TTTCTTCT
1 TTT-TTCA
1756184 TTTTTCA
1 TTTTTCA
1756191 TTTTT--
1 TTTTTCA
*
1756196 TGTCTTCA
1 T-TTTTCA
1756204 TTTTTTC-
1 -TTTTTCA
**
1756211 TTTCACAA
1 TTTTTC-A
1756219 TTTTTCA
1 TTTTTCA
1756226 -TTTT--
1 TTTTTCA
*
1756230 TTTCTCA
1 TTTTTCA
1756237 TTTTTC-
1 TTTTTCA
*
1756243 CTTTTC-
1 TTTTTCA
1756249 TTTTTCA
1 TTTTTCA
*
1756256 TTTTTTA
1 TTTTTCA
1756263 TTTTT
1 TTTTT
1756268 TCCTTTTTTT
Statistics
Matches: 95, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
5 4 0.04
6 21 0.22
7 52 0.55
8 14 0.15
9 4 0.04
ACGTcount: A:0.10, C:0.16, G:0.01, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:1756150 original size:8 final size:8
Alignment explanation
Indices: 1756125--1756307 Score: 76
Period size: 7 Copynumber: 24.1 Consensus size: 8
1756115 TTGAACCCCC
1756125 TTTT-ATT
1 TTTTCATT
*
1756132 TTTCTCTTT
1 TTT-TCATT
1756141 TTTTCA-T
1 TTTTCATT
1756148 TTTTCA-T
1 TTTTCATT
1756155 TTTTCA-T
1 TTTTCATT
1756162 TTTTCATT
1 TTTTCATT
1756170 TTTCTC-TT
1 TTT-TCATT
*
1756178 TCTTC-TT
1 TTTTCATT
1756185 TTTTCA-T
1 TTTTCATT
*
1756192 TTTT--TG
1 TTTTCATT
*
1756198 TCTTCATT
1 TTTTCATT
1756206 TTTTC--T
1 TTTTCATT
** *
1756212 TTCACAAT
1 TTTTCATT
1756220 TTTTCATTT
1 TTTTCA-TT
1756229 TTTTC-TCAT
1 TTTTCAT--T
*
1756238 TTTTC--C
1 TTTTCATT
1756244 TTTTC--T
1 TTTTCATT
1756250 TTTTCATT
1 TTTTCATT
1756258 TTTT-ATT
1 TTTTCATT
*
1756265 TTTTCCTT
1 TTTTCATT
*
1756273 TTTTTATTT
1 TTTTCA-TT
*
1756282 TTTTTATT
1 TTTTCATT
*
1756290 TTTTTATTT
1 TTTTCA-TT
1756299 TTTTCATT
1 TTTTCATT
1756307 T
1 T
1756308 CTTCTTCAAG
Statistics
Matches: 139, Mismatches: 19, Indels: 35
0.72 0.10 0.18
Matches are distributed among these distances:
6 17 0.12
7 45 0.32
8 43 0.31
9 34 0.24
ACGTcount: A:0.10, C:0.14, G:0.01, T:0.75
Consensus pattern (8 bp):
TTTTCATT
Found at i:1756195 original size:37 final size:35
Alignment explanation
Indices: 1756125--1756266 Score: 129
Period size: 37 Copynumber: 4.1 Consensus size: 35
1756115 TTGAACCCCC
*
1756125 TTTT-ATTTTTCTCTTTTTTTCATTTTTCATTTTTCAT
1 TTTTCATTTTTCTC-TTTCTTCATTTTTCATTTTT--T
*
1756162 TTTTCATTTTTCTCTTTCTTCTTTTTTCATTTTTT
1 TTTTCATTTTTCTCTTTCTTCATTTTTCATTTTTT
* *
1756197 GTCTTCATTTTT-TCTTTC-ACAATTTTTCA-TTTTT
1 -TTTTCATTTTTCTCTTTCTTC-ATTTTTCATTTTTT
*
1756231 TTCTCATTTTTC-C-TT-TTC-TTTTTCATTTTTT
1 TTTTCATTTTTCTCTTTCTTCATTTTTCATTTTTT
1756262 ATTTT
1 -TTTT
1756267 TTCCTTTTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
30 7 0.08
31 5 0.06
32 6 0.07
33 10 0.11
34 6 0.07
35 14 0.16
36 10 0.11
37 22 0.25
38 9 0.10
ACGTcount: A:0.10, C:0.16, G:0.01, T:0.73
Consensus pattern (35 bp):
TTTTCATTTTTCTCTTTCTTCATTTTTCATTTTTT
Found at i:1756233 original size:9 final size:9
Alignment explanation
Indices: 1756219--1756307 Score: 66
Period size: 8 Copynumber: 10.1 Consensus size: 9
1756209 TCTTTCACAA
1756219 TTTTTCATTT
1 TTTTTCA-TT
1756229 TTTTCTCATT
1 TTTT-TCATT
1756239 TTTCCTT--TT
1 TTT--TTCATT
1756248 CTTTTTCA-T
1 -TTTTTCATT
1756257 TTTTT-A-T
1 TTTTTCATT
*
1756264 TTTTTCCTT
1 TTTTTCATT
1756273 TTTTT-ATT
1 TTTTTCATT
*
1756281 TTTTTTATT
1 TTTTTCATT
1756290 TTTTT-ATT
1 TTTTTCATT
1756298 TTTTTCATT
1 TTTTTCATT
1756307 T
1 T
1756308 CTTCTTCAAG
Statistics
Matches: 67, Mismatches: 2, Indels: 21
0.74 0.02 0.23
Matches are distributed among these distances:
7 7 0.10
8 22 0.33
9 21 0.31
10 12 0.18
11 4 0.06
12 1 0.01
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTCATT
Found at i:1756266 original size:25 final size:25
Alignment explanation
Indices: 1756236--1756307 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 25
1756226 TTTTTTTCTC
1756236 ATTTTTCCTTTTCTTTTTCATTTTTT
1 ATTTTTCCTTTT-TTTTTCATTTTTT
1756262 ATTTTTTCCTTTTTTTATT--TTTTTT
1 A-TTTTTCCTTTTTTT-TTCATTTTTT
1756287 ATTTTT--TTATTTTTTTCATTT
1 ATTTTTCCTT-TTTTTTTCATTT
1756308 CTTCTTCAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
22 4 0.10
23 5 0.12
24 8 0.20
25 7 0.17
26 4 0.10
27 13 0.32
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (25 bp):
ATTTTTCCTTTTTTTTTCATTTTTT
Found at i:1756266 original size:44 final size:43
Alignment explanation
Indices: 1756125--1756283 Score: 128
Period size: 44 Copynumber: 3.6 Consensus size: 43
1756115 TTGAACCCCC
*
1756125 TTTTATTTTTCTCTTTTTTTCATTTTTCATTTTTCATTTTTCA-T
1 TTTTATTTTTCT-TTTTTTTCATTTTTC-CTTTTCATTTTTCATT
* * ** *
1756169 TTTTCTCTTTCTTCTTTTTTCATTTTTTGTCTTCATTTTTTC-TT
1 TTTTATTTTTCTT-TTTTTTCATTTTTCCTTTTCA-TTTTTCATT
***
1756213 TCACAATTTTTCATTTTTTTCTCATTTTTCCTTTTC-TTTTTCATT
1 T-TTTATTTTTC-TTTTTTT-TCATTTTTCCTTTTCATTTTTCATT
*
1756258 TTTTATTTTTTCCTTTTTTT-ATTTTT
1 TTTTA-TTTTTCTTTTTTTTCATTTTT
1756284 TTTATTTTTT
Statistics
Matches: 90, Mismatches: 17, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
42 6 0.07
43 7 0.08
44 44 0.49
45 19 0.21
46 14 0.16
ACGTcount: A:0.09, C:0.16, G:0.01, T:0.74
Consensus pattern (43 bp):
TTTTATTTTTCTTTTTTTTCATTTTTCCTTTTCATTTTTCATT
Found at i:1761948 original size:16 final size:16
Alignment explanation
Indices: 1761927--1761960 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1761917 TATATTCGGC
1761927 TGCTCACTGTCACCAA
1 TGCTCACTGTCACCAA
1761943 TGCTCACTGTCACCAA
1 TGCTCACTGTCACCAA
1761959 TG
1 TG
1761961 ATGACATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (16 bp):
TGCTCACTGTCACCAA
Found at i:1763485 original size:19 final size:18
Alignment explanation
Indices: 1763461--1763504 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1763451 TGAATGAATA
*
1763461 AAATGCGATGCAAAAATTT
1 AAATGC-ATGAAAAAATTT
*
1763480 AAATGCATTAAAAAATTT
1 AAATGCATGAAAAAATTT
1763498 AAATGCA
1 AAATGCA
1763505 AAATGCAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.27
Consensus pattern (18 bp):
AAATGCATGAAAAAATTT
Found at i:1765997 original size:45 final size:47
Alignment explanation
Indices: 1765932--1766029 Score: 137
Period size: 45 Copynumber: 2.1 Consensus size: 47
1765922 TGTTATTCAC
*
1765932 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC-TTGTTCG
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
* * *
1765978 AAAAATAAA-CCTAATCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCG
1766025 AAAAA
1 AAAAA
1766030 CAAAAATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
45 27 0.59
46 8 0.17
47 11 0.24
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
Found at i:1784073 original size:20 final size:20
Alignment explanation
Indices: 1784048--1784086 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1784038 TGATTAATTA
*
1784048 TATAAATTAACTAAAACCAT
1 TATAAATTAACCAAAACCAT
1784068 TATAAATTAACCAAAACCA
1 TATAAATTAACCAAAACCA
1784087 GAAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (20 bp):
TATAAATTAACCAAAACCAT
Found at i:1787864 original size:24 final size:24
Alignment explanation
Indices: 1787832--1787878 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1787822 TTTTCAGAAC
*
1787832 TTTTATAATAATATAATATTATAT
1 TTTTATAATAATATAATAATATAT
* *
1787856 TTTTTTAATATTATAATAATATA
1 TTTTATAATAATATAATAATATA
1787879 CTCAATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTATAATAATATAATAATATAT
Found at i:1788094 original size:24 final size:23
Alignment explanation
Indices: 1788022--1788130 Score: 73
Period size: 24 Copynumber: 4.7 Consensus size: 23
1788012 TTTATGTATT
*
1788022 TATATTAATATAATAATA-TAATAA
1 TATATTAAT-TAATATTATTAA-AA
* * *
1788046 TATTTTAATAAAGA-TATTTAAAA
1 TATATTAATTAATATTA-TTAAAA
*
1788069 TATATTAATTAATATTTTCTAAAA
1 TATATTAATTAATATTAT-TAAAA
* *
1788093 TATAATATAA-TACTATTATTGAAA
1 TAT-AT-TAATTAATATTATTAAAA
1788117 TA-ATTAATTAATAT
1 TATATTAATTAATAT
1788131 AATCTATAAT
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
21 3 0.04
22 9 0.13
23 17 0.25
24 26 0.39
25 9 0.13
26 3 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TATATTAATTAATATTATTAAAA
Found at i:1788110 original size:35 final size:35
Alignment explanation
Indices: 1788027--1788110 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 35
1788017 GTATTTATAT
1788027 TAATATAATA-ATATAATAATATTTTAATAAAGATA
1 TAATATAATATAT-TAATAATATTTTAATAAAGATA
* * *
1788062 T-TTAAAATATATTAATTAATATTTT-CTAAA-ATA
1 TAATATAATATATTAA-TAATATTTTAATAAAGATA
1788095 TAATATAATACTATTA
1 TAATATAATA-TATTA
1788111 TTGAAATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
33 4 0.10
34 19 0.47
35 17 0.43
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (35 bp):
TAATATAATATATTAATAATATTTTAATAAAGATA
Found at i:1796486 original size:143 final size:144
Alignment explanation
Indices: 1796228--1796520 Score: 572
Period size: 143 Copynumber: 2.0 Consensus size: 144
1796218 AAAAGAAATA
1796228 CAATT-AGTGAATTTGTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGT
1 CAATTCAGTGAATTTGTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGT
1796292 TGAGAAAATCGAACCACTCTAAATCGTTGTGCAAATATTTTTAATTTTCTGCTAAAGCTTCCACC
66 TGAGAAAATCGAACCACTCTAAATCGTTGTGCAAATATTTTTAATTTTCTGCTAAAGCTTCCACC
1796357 GAAATTTTTATTGC
131 GAAATTTTTATTGC
1796371 CAATTCAGTG-ATTTGTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGT
1 CAATTCAGTGAATTTGTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGT
1796435 TGAGAAAATCGAACCACTCTAAATCGTTGTGCAAATATTTTTAATTTTCTGCTAAAGCTTCCACC
66 TGAGAAAATCGAACCACTCTAAATCGTTGTGCAAATATTTTTAATTTTCTGCTAAAGCTTCCACC
1796500 GAAATTTTTATTGC
131 GAAATTTTTATTGC
1796514 CAATTCA
1 CAATTCA
1796521 CCTTAATGAC
Statistics
Matches: 149, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
143 145 0.97
144 4 0.03
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (144 bp):
CAATTCAGTGAATTTGTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGGT
TGAGAAAATCGAACCACTCTAAATCGTTGTGCAAATATTTTTAATTTTCTGCTAAAGCTTCCACC
GAAATTTTTATTGC
Found at i:1796692 original size:113 final size:113
Alignment explanation
Indices: 1796551--1796763 Score: 417
Period size: 113 Copynumber: 1.9 Consensus size: 113
1796541 TAAGCACATG
1796551 ATCTTGAAGCATGGATAATAATAAAAAAAAGGATATTCTTCTCCTACAAAGAAGGAAAAGAAGTG
1 ATCTTGAAGCATGGATAATAATAAAAAAAAGGATATTCTTCTCCTACAAAGAAGGAAAAGAAGTG
1796616 GAGTGATTAGGAACAGAAGAAAACTCAACAAAATGATATTCTAAGCAC
66 GAGTGATTAGGAACAGAAGAAAACTCAACAAAATGATATTCTAAGCAC
*
1796664 ATCTTGAAGCATGGATAATAATAAAAAAAAGGATATTCTTCTCCTACAAAGAAGGCAAAGAAGTG
1 ATCTTGAAGCATGGATAATAATAAAAAAAAGGATATTCTTCTCCTACAAAGAAGGAAAAGAAGTG
1796729 GAGTGATTAGGAACAGAAGAAAACTCAACAAAATG
66 GAGTGATTAGGAACAGAAGAAAACTCAACAAAATG
1796764 CAAAGGCTAT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 99 1.00
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (113 bp):
ATCTTGAAGCATGGATAATAATAAAAAAAAGGATATTCTTCTCCTACAAAGAAGGAAAAGAAGTG
GAGTGATTAGGAACAGAAGAAAACTCAACAAAATGATATTCTAAGCAC
Found at i:1797220 original size:117 final size:117
Alignment explanation
Indices: 1797064--1797287 Score: 299
Period size: 117 Copynumber: 1.9 Consensus size: 117
1797054 TAAAAATGGT
* * *
1797064 CTTCTTTTGAAAGCTAAAATAGACTTGGAAAATAAAAATGAAATGTTGAAAAATGAGTTAGAGCT
1 CTTCTTTAGAAAGCTAAAATAGACTTGGAAAATAAAAATGAAATATTGAAAAAGGAGTTAGAGCT
1797129 TTCAAAAATGAAATCTGAAAACT-TTGAAAAAGAAAATTTTGAATTAAACAAA
66 TTCAAAAATGAAATCTG-AAACTGTTGAAAAAGAAAATTTTGAATTAAACAAA
* * * * * *
1797181 CTTCTTCTAGAAA-CTAAAATGGATTTTGAAAATCAAAATGAAATATTGAATAAGGATTTAGAGC
1 CTTCTT-TAGAAAGCTAAAATAGACTTGGAAAATAAAAATGAAATATTGAAAAAGGAGTTAGAGC
* * * *
1797245 TTTTAAAAATGAAATTTGAAAGTGTTGAAAAAGAAATTTTTGA
65 TTTCAAAAATGAAATCTGAAACTGTTGAAAAAGAAAATTTTGA
1797288 TTTAGAAGTT
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
116 4 0.04
117 83 0.90
118 5 0.05
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (117 bp):
CTTCTTTAGAAAGCTAAAATAGACTTGGAAAATAAAAATGAAATATTGAAAAAGGAGTTAGAGCT
TTCAAAAATGAAATCTGAAACTGTTGAAAAAGAAAATTTTGAATTAAACAAA
Found at i:1808858 original size:17 final size:18
Alignment explanation
Indices: 1808838--1808872 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1808828 CCAAAATTTA
1808838 TGTTAAAAGCTAG-AAAG
1 TGTTAAAAGCTAGTAAAG
*
1808855 TGTTAAAATCTAGTAAAG
1 TGTTAAAAGCTAGTAAAG
1808873 ATTCGGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.29
Consensus pattern (18 bp):
TGTTAAAAGCTAGTAAAG
Found at i:1815664 original size:21 final size:20
Alignment explanation
Indices: 1815640--1815680 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1815630 TCAATGGGAT
*
1815640 TAGGAATAGGATTTGGTAGGA
1 TAGGAAGAGGATTTGG-AGGA
*
1815661 TAGGAGGAGGATTTGGAGGA
1 TAGGAAGAGGATTTGGAGGA
1815681 GGGTTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.44, T:0.24
Consensus pattern (20 bp):
TAGGAAGAGGATTTGGAGGA
Found at i:1816408 original size:23 final size:22
Alignment explanation
Indices: 1816364--1816433 Score: 88
Period size: 23 Copynumber: 3.2 Consensus size: 22
1816354 CCCAGGGGTT
* *
1816364 ATCGATTCCCCTAC-AGGGGGA
1 ATCGGTTCCCCTTCAAGGGGGA
1816385 ATCGGTTCCCCTTCAAAGGGGGA
1 ATCGGTTCCCCTTC-AAGGGGGA
* *
1816408 ATCGGTTCTCCTTCAAGGGGGT
1 ATCGGTTCCCCTTCAAGGGGGA
1816430 ATCG
1 ATCG
1816434 ATTTCCTCTG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 12 0.28
22 11 0.26
23 20 0.47
ACGTcount: A:0.20, C:0.26, G:0.30, T:0.24
Consensus pattern (22 bp):
ATCGGTTCCCCTTCAAGGGGGA
Found at i:1825851 original size:20 final size:21
Alignment explanation
Indices: 1825807--1825851 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
1825797 TACTATGCTG
* *
1825807 GAAA-TTAATGTTAGATTGTT
1 GAAATTTAATATTAGAATGTT
1825827 G-AATTTAATATTAGAATG-T
1 GAAATTTAATATTAGAATGTT
1825846 GAAATT
1 GAAATT
1825852 GGACTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (21 bp):
GAAATTTAATATTAGAATGTT
Found at i:1827364 original size:19 final size:19
Alignment explanation
Indices: 1827326--1827364 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1827316 TATGCACTTG
*
1827326 GCTATGAATTTGAAAATAA
1 GCTATGAATCTGAAAATAA
1827345 GCTATGAATCT-AAAAGTAA
1 GCTATGAATCTGAAAA-TAA
1827364 G
1 G
1827365 TTACGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (19 bp):
GCTATGAATCTGAAAATAA
Found at i:1827442 original size:12 final size:13
Alignment explanation
Indices: 1827416--1827448 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1827406 TTATGTAATG
1827416 ATATGAAAGTGAA
1 ATATGAAAGTGAA
1827429 ATATGAAA-TGAA
1 ATATGAAAGTGAA
*
1827441 ATAGGAAA
1 ATATGAAA
1827449 AAAATATCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (13 bp):
ATATGAAAGTGAA
Found at i:1827885 original size:46 final size:46
Alignment explanation
Indices: 1827815--1828515 Score: 833
Period size: 46 Copynumber: 15.5 Consensus size: 46
1827805 AATAACTATA
*
1827815 ATGAAAGGATGCCATAAATGAAAATGTATAACGGTGCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* * *
1827861 ATGAAAGGATGACATAAATAAAAATGCATAAAGGTGCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* * * * *
1827907 ATGAAAGAATGCCAAAAATTAAAATGCATAAC-ATCTCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGT-GCATTATCGGC
* * * *
1827953 ATGAAAGGATGCCATATATGAGAATGCATAACGATGCATTATTGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* *
1827999 ATGAAATGATGCCATAAATGAAAATGCATAACGGTGCATTATCAGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* **
1828045 ATGAAAGGATGCCGTAAATGAAAATGCATAACACTGCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* * * * *
1828091 ATGAAATGTTGTCATAAATGAAAATACATAAAGGTGCATTATC-GC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
*
1828136 AT-AAAGGGATGCC-TAAATGAAAATGC-TAACGGTTCATTATCGGC
1 ATGAAA-GGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
1828180 ATGAAAGGATGCCATAAATG-AAATGCATAACGGTGCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* * *
1828225 ATG-AA-GATGACA-AAAT-AAAATGCATAATGGTGCATTATCAGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* * * * * * *
1828267 ---AAAGAATGACATAAATGAAAATGAATAGCAGTTCAATATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
*
1828310 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGAC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
** **
1828356 ATGAAAGGATTTCATAAATGAAAATGCATAACGGTGCATTATCAAC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* * * **
1828402 ATGAAAGGTTGCCATTAATGAAAATGCATAGCAATGCATTATC-GC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* * *
1828447 ATAAAAGGATGCCATAAATG-AAATGCATAACTGTGCATAATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
1828492 ATGAAAGGATG-C-TACAATGAAAAT
1 ATGAAAGGATGCCATA-AATGAAAAT
1828516 ATATAGCGGT
Statistics
Matches: 555, Mismatches: 82, Indels: 37
0.82 0.12 0.05
Matches are distributed among these distances:
40 2 0.00
41 6 0.01
42 31 0.06
43 40 0.07
44 57 0.10
45 72 0.13
46 345 0.62
47 2 0.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (46 bp):
ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
Found at i:1832274 original size:46 final size:46
Alignment explanation
Indices: 1832207--1832698 Score: 664
Period size: 46 Copynumber: 10.7 Consensus size: 46
1832197 GAGATTCAAA
* * *
1832207 ATGAAAGGATGTCATAAATGAAAATGCATGACGGTGTATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* * *
1832253 ATGAAAGGTTGCCATAAATGAAAATGCATCACGGTGCATTATCGGT
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* * *
1832299 ACGAAAGGATGCCATAAATGAAAATACATAACGGTGCATTATCGAC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* *
1832345 ATGAAATGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGT
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* *
1832391 ATGAAAGGATGCCATAAATGAAAATGCATAACGTTGCATTATCGAC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
** *
1832437 ATGAAAGGATAACATAAATGAAAAATGCATAACAGTGCATTATCGGC
1 ATGAAAGGATGCCATAAATG-AAAATGCATAACGGTGCATTATCGGC
* *
1832484 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTACATTATCGAC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* ** **
1832530 ATAAAAGGATGCCATAAATGAAAATGCATAATAGTATATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
**
1832576 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCTTC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* * * * *
1832622 -CGAAAGGATGCCATAAATGAAAAAGAATAATGGTG-AGTTATCAGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCA-TTATCGGC
* *
1832667 ATGAAAGGATGTCATAAATGAAAATGTATAAC
1 ATGAAAGGATGCCATAAATGAAAATGCATAAC
1832699 TGTTGAAAAC
Statistics
Matches: 390, Mismatches: 53, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
44 1 0.00
45 37 0.09
46 311 0.80
47 41 0.11
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (46 bp):
ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
Found at i:1838824 original size:21 final size:21
Alignment explanation
Indices: 1838798--1838837 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1838788 CCCCCTTTGA
*
1838798 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1838819 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1838838 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1842294 original size:46 final size:46
Alignment explanation
Indices: 1842221--1842602 Score: 493
Period size: 46 Copynumber: 8.3 Consensus size: 46
1842211 TAACTCAACA
* * * *
1842221 ATAACGATGCATTATC-GACTTGAAAGGATGCTATAAATAAAAATGC
1 ATAACGGTGCATTATCTG-CATGAAAGGATGCCATAAATGAAAATGC
** *
1842267 ATAACGGTGCATTATCTGCATTTAAGGATGCAATAAATGAAAATGC
1 ATAACGGTGCATTATCTGCATGAAAGGATGCCATAAATGAAAATGC
1842313 ATAACGGTGCATTAT-TGACATGAAAGGATGCCATAAATGAAAATGC
1 ATAACGGTGCATTATCTG-CATGAAAGGATGCCATAAATGAAAATGC
*
1842359 ATAACAGTGCATTAT-TGACATGAAAGGATGCCATAAATGAAAATGC
1 ATAACGGTGCATTATCTG-CATGAAAGGATGCCATAAATGAAAATGC
* * *
1842405 ATAACGATGCATTATCGGCATGAAAGGATGCCATAAATGGAAATGC
1 ATAACGGTGCATTATCTGCATGAAAGGATGCCATAAATGAAAATGC
* *
1842451 ATAACGGTGCATTATCAGCATGAAAGGATGCCATAAATGAAAATGA
1 ATAACGGTGCATTATCTGCATGAAAGGATGCCATAAATGAAAATGC
* * *
1842497 ATAACAGTGTATTATC-GACATGAAAGGATGCCATAAATGGAAATGC
1 ATAACGGTGCATTATCTG-CATGAAAGGATGCCATAAATGAAAATGC
* * * * *
1842543 ATAACGGTGCATAATCGGCATGAAAGGATGCTACAAATGAAAATAC
1 ATAACGGTGCATTATCTGCATGAAAGGATGCCATAAATGAAAATGC
* *
1842589 ATAATGGTGTATTA
1 ATAACGGTGCATTA
1842603 ATGACATGTT
Statistics
Matches: 299, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
45 3 0.01
46 293 0.98
47 3 0.01
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (46 bp):
ATAACGGTGCATTATCTGCATGAAAGGATGCCATAAATGAAAATGC
Found at i:1842473 original size:138 final size:138
Alignment explanation
Indices: 1842220--1842610 Score: 554
Period size: 138 Copynumber: 2.8 Consensus size: 138
1842210 TTAACTCAAC
* * * *
1842220 AATAAC-GATGCATTATCGACTTGAAAGGATGCTATAAATAAAAATGCATAACGGTGCATTATCT
1 AATAACAG-TGCATTATCGACATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCG
** *
1842284 GCATTTAAGGATGCAATAAATGAAAATGCATAACGGTGCATTATTGACATGAAAGGATGCCATAA
65 GCATGAAAGGATGCAATAAATGAAAATGCATAACGGTGCATTATAGACATGAAAGGATGCCATAA
1842349 ATGAAAATG
130 ATGAAAATG
* * *
1842358 CATAACAGTGCATTATTGACATGAAAGGATGCCATAAATGAAAATGCATAACGATGCATTATCGG
1 AATAACAGTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGG
* *
1842423 CATGAAAGGATGCCATAAATGGAAATGCATAACGGTGCATTATCAG-CATGAAAGGATGCCATAA
66 CATGAAAGGATGCAATAAATGAAAATGCATAACGGTGCATTAT-AGACATGAAAGGATGCCATAA
1842487 ATGAAAATG
130 ATGAAAATG
* * *
1842496 AATAACAGTGTATTATCGACATGAAAGGATGCCATAAATGGAAATGCATAACGGTGCATAATCGG
1 AATAACAGTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGG
* * * * *
1842561 CATGAAAGGATGCTACAAATGAAAATACATAATGGTGTATTA-ATGACATG
66 CATGAAAGGATGCAATAAATGAAAATGCATAACGGTGCATTATA-GACATG
1842611 TTAGGTGCCA
Statistics
Matches: 225, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
136 1 0.00
137 1 0.00
138 221 0.98
139 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (138 bp):
AATAACAGTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGG
CATGAAAGGATGCAATAAATGAAAATGCATAACGGTGCATTATAGACATGAAAGGATGCCATAAA
TGAAAATG
Found at i:1847031 original size:20 final size:20
Alignment explanation
Indices: 1846987--1847031 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1846977 TACTATGCTA
*
1846987 GAAATTAATGTTAGATTGTT
1 GAAATTAATGTTAGAATGTT
1847007 G-AATTAAATGTTAGAATG-T
1 GAAATT-AATGTTAGAATGTT
1847026 GAAATT
1 GAAATT
1847032 GGACTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (20 bp):
GAAATTAATGTTAGAATGTT
Found at i:1848707 original size:19 final size:19
Alignment explanation
Indices: 1848683--1848735 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1848673 TATGCATTGG
*
1848683 GCTATGAATTTGAAAATAA
1 GCTATGAATATGAAAATAA
*
1848702 GCTATGAATATGAAATTAA
1 GCTATGAATATGAAAATAA
* *
1848721 GTTATTAATAT-AAAA
1 GCTATGAATATGAAAA
1848736 GTGAGTTCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 3 0.10
19 26 0.90
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (19 bp):
GCTATGAATATGAAAATAA
Found at i:1855246 original size:12 final size:12
Alignment explanation
Indices: 1855229--1855253 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1855219 CTTTGTTTAT
1855229 TCTAGTTAACAA
1 TCTAGTTAACAA
1855241 TCTAGTTAACAA
1 TCTAGTTAACAA
1855253 T
1 T
1855254 GCTAAACTAC
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:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TCTAGTTAACAA
Found at i:1855348 original size:21 final size:22
Alignment explanation
Indices: 1855300--1855358 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
1855290 TGATTTATTA
*
1855300 TTATGGATTTCAAGTTGGTTTT
1 TTATGGATTTCAAGTTGGTTTG
1855322 TTATGGATTTCAAGATT-G-TTG
1 TTATGGATTTCAAG-TTGGTTTG
*
1855343 TTATGGATGTCAAGTT
1 TTATGGATTTCAAGTT
1855359 TATTAGATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.06
21 15 0.44
22 15 0.44
23 2 0.06
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.49
Consensus pattern (22 bp):
TTATGGATTTCAAGTTGGTTTG
Found at i:1855794 original size:43 final size:42
Alignment explanation
Indices: 1855712--1855794 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 42
1855702 GTCATTTCTC
* * *
1855712 AAAAAAGCCGCTAAATATCATAACATTTACATGCGTTTGTAG
1 AAAAAAGCCGCTAAAAATCATAACATTTACAGGCATTTGTAG
*
1855754 AAAAAATGCCGCTAAAAATCATAACCTTTAGC-GGCATTTGT
1 AAAAAA-GCCGCTAAAAATCATAACATTTA-CAGGCATTTGT
1855795 GGACGATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 6 0.17
43 28 0.80
44 1 0.03
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (42 bp):
AAAAAAGCCGCTAAAAATCATAACATTTACAGGCATTTGTAG
Found at i:1856824 original size:35 final size:35
Alignment explanation
Indices: 1856777--1856856 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
1856767 AACACAGTCA
* *
1856777 TCAATTATATTCTAAACCCCAAAATCCAAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAACACT
* ** *
1856812 TCAATTACATTCTAAACCTCAATTTTCAAAACACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAACACT
*
1856847 TTAATTACAT
1 TCAATTACAT
1856857 GCCCAACCCC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAAATCCAAAACACT
Found at i:1857083 original size:148 final size:148
Alignment explanation
Indices: 1856906--1857195 Score: 463
Period size: 148 Copynumber: 2.0 Consensus size: 148
1856896 ATAACAAAAT
* *
1856906 AGTTTATAAAATAGTTGACTCGAAATTTTTTTGATTTGAGGTTATAAAATTTAAATCAAGTCGAA
1 AGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGGTTATAAAATTTAAATCAAGCCGAA
* * * * *
1856971 TTGAATTTAATTTTCGAGTTTCTGTTTAAATTTAATTACAAATATTTATCATATTATAATATTAT
66 TTGAATTGAATTCTCGAGTTTCTGTTTAAATTTAATTACAAATATTTATAAAACTATAATATTAT
*
1857036 TTGATTCTAATTCAGTTC
131 TTGATTATAATTCAGTTC
* *
1857054 AGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAGATCAAGCCGAA
1 AGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGGTTATAAAATTTAAATCAAGCCGAA
* *
1857119 TTGAATTGAATTCTCGAGTTTTTGTTTAAATTTAATTATAAATATTTATAAAACTATAATATTAT
66 TTGAATTGAATTCTCGAGTTTCTGTTTAAATTTAATTACAAATATTTATAAAACTATAATATTAT
*
1857184 TTTATTATAATT
131 TTGATTATAATT
1857196 TAAATAGTTT
Statistics
Matches: 129, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
148 129 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (148 bp):
AGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGGTTATAAAATTTAAATCAAGCCGAA
TTGAATTGAATTCTCGAGTTTCTGTTTAAATTTAATTACAAATATTTATAAAACTATAATATTAT
TTGATTATAATTCAGTTC
Found at i:1857762 original size:35 final size:36
Alignment explanation
Indices: 1857696--1857774 Score: 108
Period size: 35 Copynumber: 2.2 Consensus size: 36
1857686 GTTGGTCATG
*
1857696 TAATTGAAGTATTTTTTTGAATTTGAGGTTTAGAATA
1 TAATTGAAGTA-TTTTTGGAATTTGAGGTTTAGAATA
*
1857733 TAATTGAAGTA-TTTTGGAATTTG-GAGTTTAGAATG
1 TAATTGAAGTATTTTTGGAATTTGAG-GTTTAGAATA
1857768 TAATTGA
1 TAATTGA
1857775 TGATTGTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
34 1 0.03
35 27 0.69
37 11 0.28
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.46
Consensus pattern (36 bp):
TAATTGAAGTATTTTTGGAATTTGAGGTTTAGAATA
Found at i:1861156 original size:30 final size:33
Alignment explanation
Indices: 1861122--1861191 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
1861112 AACAAAATGC
1861122 TAATAAATAA-AAA-AAA-AATATAA-AAAATAA
1 TAATAAATAAGAAAGAAAGAA-ATAATAAAATAA
1861152 TAAT-AATAATGAAAGAAAGAAATAATAAAATAA
1 TAATAAATAA-GAAAGAAAGAAATAATAAAATAA
1861185 TAATAAA
1 TAATAAA
1861192 AGGTTAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
29 5 0.15
30 4 0.12
31 3 0.09
32 7 0.21
33 13 0.38
34 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (33 bp):
TAATAAATAAGAAAGAAAGAAATAATAAAATAA
Found at i:1862324 original size:15 final size:14
Alignment explanation
Indices: 1862292--1862320 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1862282 CTAAAAAAAC
1862292 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
1862306 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
1862320 A
1 A
1862321 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:1862403 original size:31 final size:32
Alignment explanation
Indices: 1862360--1862531 Score: 104
Period size: 33 Copynumber: 5.2 Consensus size: 32
1862350 ATATAATACA
**
1862360 TATATTTCAAAAATA-TTTTTTAAACTATATAT
1 TATATTTCAAAAA-AGTTTTCAAAACTATATAT
1862392 TATATTT-AAAAAAGTTTTCAAAACTATAT-T
1 TATATTTCAAAAAAGTTTTCAAAACTATATAT
* *
1862422 ATATAGTTTTC-AAAATGTTTT-AAAAATATTATAT
1 -TATA--TTTCAAAAAAGTTTTCAAAACTA-TATAT
* * *
1862456 AAGT-TTTTAAAAAACGTTTTTAAAACTATATATT
1 TA-TATTTCAAAAAA-GTTTTCAAAACTATATA-T
* *
1862490 ATATAATTTATTCAAAAATGTTTTTAAAACTATATAT
1 -TAT-A--T-TTCAAAAAAGTTTTCAAAACTATATAT
1862527 TATAT
1 TATAT
1862532 AAGTTTTTAA
Statistics
Matches: 111, Mismatches: 11, Indels: 35
0.71 0.07 0.22
Matches are distributed among these distances:
30 2 0.02
31 25 0.23
32 17 0.15
33 26 0.23
34 10 0.09
35 2 0.02
36 3 0.03
37 1 0.01
38 18 0.16
39 7 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (32 bp):
TATATTTCAAAAAAGTTTTCAAAACTATATAT
Found at i:1862425 original size:36 final size:34
Alignment explanation
Indices: 1862385--1862627 Score: 137
Period size: 36 Copynumber: 6.8 Consensus size: 34
1862375 TTTTTTAAAC
*
1862385 TATATATTATATTTAAAAAAGTTTTCAAAACTATAT
1 TATATA-TATATTTAAAAATGTTTT-AAAACTATAT
* *
1862421 TATATA-GT-TTTCAAAATGTTTTAAAA--ATAT
1 TATATATATATTTAAAAATGTTTTAAAACTATAT
* *
1862451 TATATA-AGTTTTTAAAAAACGTTTTTAAAACTATATAT
1 TATATATA-TATTT-AAAAATG-TTTTAAAAC--TATAT
* *
1862489 TATATAATTTATTCAAAAATGTTTTTAAAACTATA-
1 TATAT-ATATATTTAAAAATG-TTTTAAAACTATAT
*
1862524 TAT-TATATAAGTTTTTAAAATGATTTTAAAACTATAT
1 TATATATAT-A--TTTAAAAATG-TTTTAAAACTATAT
*
1862561 GT-TATATATATTTTCTAAAATGTTTTAAAAACTATAT
1 -TATATATATA-TTT-AAAAATGTTTT-AAAACTATAT
*
1862598 GT-TATATAGT-TTTCAAAAAATATTTTAAAA
1 -TATATATA-TATTT--AAAAATGTTTTAAAA
1862628 AAACTATATA
Statistics
Matches: 170, Mismatches: 17, Indels: 40
0.75 0.07 0.18
Matches are distributed among these distances:
30 10 0.06
31 1 0.01
32 7 0.04
33 20 0.12
34 11 0.06
35 3 0.02
36 46 0.27
37 36 0.21
38 32 0.19
39 4 0.02
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (34 bp):
TATATATATATTTAAAAATGTTTTAAAACTATAT
Found at i:1862492 original size:38 final size:37
Alignment explanation
Indices: 1862396--1862640 Score: 221
Period size: 38 Copynumber: 6.8 Consensus size: 37
1862386 ATATATTATA
* *
1862396 TTTAAAAAAGTTTTCAAAAC--TATATTATAT-AG-T
1 TTTAAAAATGTTTTTAAAACTATATATTATATAAGTT
*
1862429 TTTCAAAATG-TTTT-AAA--A-ATATTATATAAGTT
1 TTTAAAAATGTTTTTAAAACTATATATTATATAAGTT
*
1862461 TTTAAAAAACGTTTTTAAAACTATATATTATATAA-TT
1 TTT-AAAAATGTTTTTAAAACTATATATTATATAAGTT
1862498 TATTCAAAAATGTTTTTAAAACTATATATTATATAAGTT
1 T-TT-AAAAATGTTTTTAAAACTATATATTATATAAGTT
* *
1862537 TTT-AAAATGATTTTAAAACTATATGTTATATATA-TT
1 TTTAAAAATGTTTTTAAAACTATATATTATATA-AGTT
* *
1862573 TTCT-AAAATGTTTTAAAAACTATATGTTATAT-AGTT
1 TT-TAAAAATGTTTTTAAAACTATATATTATATAAGTT
* * *
1862609 TTCAAAAAATATTTTAAAAAAACTATATATTA
1 TT-TAAAAATGTTTT--TAAAACTATATATTA
1862641 CCCATATTTT
Statistics
Matches: 181, Mismatches: 14, Indels: 28
0.81 0.06 0.13
Matches are distributed among these distances:
30 9 0.05
31 5 0.03
32 7 0.04
33 13 0.07
34 4 0.02
35 4 0.02
36 36 0.20
37 41 0.23
38 45 0.25
39 17 0.09
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (37 bp):
TTTAAAAATGTTTTTAAAACTATATATTATATAAGTT
Found at i:1865049 original size:22 final size:23
Alignment explanation
Indices: 1865021--1865066 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
1865011 TGATACGATT
1865021 AATTTTCAGGGTGGACAC-CATA
1 AATTTTCAGGGTGGACACACATA
1865043 AATTTTCAGGGTGGACACACATA
1 AATTTTCAGGGTGGACACACATA
1865066 A
1 A
1865067 CAATGAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (23 bp):
AATTTTCAGGGTGGACACACATA
Found at i:1867850 original size:24 final size:25
Alignment explanation
Indices: 1867823--1867878 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
1867813 AAATTAATTT
1867823 TTTTAATAATTTAAT-T-TTGTAGTA
1 TTTTAATAATTTAATGTATT-TAGTA
*
1867847 TTTTTAT-ATTTAATGTATTTAGTA
1 TTTTAATAATTTAATGTATTTAGTA
*
1867871 TCTTAATA
1 TTTTAATA
1867879 TTTTTAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 7 0.27
24 17 0.65
25 2 0.08
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (25 bp):
TTTTAATAATTTAATGTATTTAGTA
Found at i:1871974 original size:17 final size:18
Alignment explanation
Indices: 1871954--1871993 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1871944 TAATAATGAG
1871954 TTATATA-AAATATATTT
1 TTATATATAAATATATTT
*
1871971 TTAT-TATAATTATATTT
1 TTATATATAAATATATTT
1871988 TT-TATA
1 TTATATA
1871994 GTTTAAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATATAAATATATTT
Found at i:1872243 original size:13 final size:14
Alignment explanation
Indices: 1872225--1872253 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1872215 AATTCTACAA
1872225 TACTTTT-AAAAGT
1 TACTTTTCAAAAGT
1872238 TACTTTTCAAAAGT
1 TACTTTTCAAAAGT
1872252 TA
1 TA
1872254 TATCAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (14 bp):
TACTTTTCAAAAGT
Found at i:1880455 original size:20 final size:20
Alignment explanation
Indices: 1880430--1880478 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1880420 CGTTAAGGAA
1880430 TGCATCGATACACTGTAGAG
1 TGCATCGATACACTGTAGAG
1880450 TGCATCGATACACTGTAGAG
1 TGCATCGATACACTGTAGAG
1880470 TGCATCGAT
1 TGCATCGAT
1880479 GCATACCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (20 bp):
TGCATCGATACACTGTAGAG
Found at i:1881016 original size:22 final size:22
Alignment explanation
Indices: 1880989--1881065 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
1880979 TTGAGGGTAT
1880989 AGTGGTCCTTCAGGATGTATTC
1 AGTGGTCCTTCAGGATGTATTC
* *
1881011 AATGGTCATTCAGGATGTATTC
1 AGTGGTCCTTCAGGATGTATTC
* * * *
1881033 AGTGTTCCTTCGGGACGTATCC
1 AGTGGTCCTTCAGGATGTATTC
1881055 AGTGGTCCTTC
1 AGTGGTCCTTC
1881066 GGGACAAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (22 bp):
AGTGGTCCTTCAGGATGTATTC
Found at i:1884899 original size:64 final size:64
Alignment explanation
Indices: 1884817--1884973 Score: 169
Period size: 63 Copynumber: 2.5 Consensus size: 64
1884807 TTCAAGGTGT
* ** *
1884817 ATCGATGCA-CATGAAGTGCATCGATGCACTCTGATAAAACAAAAACATCGAATGCCATT-AGTG
1 ATCGATGCATAATGAAGTGCATCGATGCAC-CACATAAAACAAAAACATCGAATACCATTCA-TG
1884880 C
64 C
* * * **
1884881 ATCGATGCATAATG-AGTGCATCGATGCACCACATTAAATACAAACATCGAATATGATTCATGC
1 ATCGATGCATAATGAAGTGCATCGATGCACCACATAAAACAAAAACATCGAATACCATTCATGC
* *
1884944 ACCGATGCATAA-GTAGTGCATCGATGCACC
1 ATCGATGCATAATGAAGTGCATCGATGCACC
1884974 CGTTAAGGAA
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
62 1 0.01
63 51 0.64
64 25 0.31
65 3 0.04
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.23
Consensus pattern (64 bp):
ATCGATGCATAATGAAGTGCATCGATGCACCACATAAAACAAAAACATCGAATACCATTCATGC
Found at i:1885550 original size:22 final size:22
Alignment explanation
Indices: 1885523--1885595 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
1885513 TCGAGGGTAT
*
1885523 AGTGGTCCTTCAAGACGTATTC
1 AGTGGTCCTTCAGGACGTATTC
* * *
1885545 AATGGTCATTCTGGACGTATTC
1 AGTGGTCCTTCAGGACGTATTC
* * *
1885567 AGTGGCCCTTCGGGACGTATCC
1 AGTGGTCCTTCAGGACGTATTC
1885589 AGTGGTC
1 AGTGGTC
1885596 TTTTGGGACA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.30
Consensus pattern (22 bp):
AGTGGTCCTTCAGGACGTATTC
Found at i:1892096 original size:20 final size:21
Alignment explanation
Indices: 1892071--1892122 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1892061 AACCAACAAA
1892071 TTCGCAACGCGA-ATTCCAAT
1 TTCGCAACGCGAGATTCCAAT
* *
1892091 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGAGATTCCAAT
1892111 TTCGCAACGCGA
1 TTCGCAACGCGA
1892123 TAGTCAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (21 bp):
TTCGCAACGCGAGATTCCAAT
Found at i:1892134 original size:20 final size:20
Alignment explanation
Indices: 1892111--1892232 Score: 90
Period size: 20 Copynumber: 6.0 Consensus size: 20
1892101 AGTTTCCAAT
1892111 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* **
1892131 TTCGC-GCTGCGATTTTTCAAA
1 TTCGCAAC-GCGA-TAGTCAAA
* *
1892152 TTCGCAACGGGAATTTGT-AAA
1 TTCGCAACGCG-A-TAGTCAAA
*
1892173 -TCGCAACACAGA-AGTCAAA
1 TTCGCAACGC-GATAGTCAAA
*
1892192 TTCGCAACGCGATAGTGAAA
1 TTCGCAACGCGATAGTCAAA
* *
1892212 TTTGCAACGCGAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
1892232 T
1 T
1892233 GTTTTTACGC
Statistics
Matches: 80, Mismatches: 14, Indels: 16
0.73 0.13 0.15
Matches are distributed among these distances:
18 2 0.03
19 6 0.08
20 49 0.61
21 17 0.21
22 6 0.08
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (20 bp):
TTCGCAACGCGATAGTCAAA
Found at i:1892378 original size:22 final size:22
Alignment explanation
Indices: 1892353--1892406 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
1892343 TCACTCTCTA
*
1892353 CGACGACATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
* *
1892375 CGACGAAATTCGTCCCCATTTC
1 CGACGAAATCCGTCCCCATCTC
1892397 CGACGAAATC
1 CGACGAAATC
1892407 TGTCTATCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.20
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:1892705 original size:19 final size:20
Alignment explanation
Indices: 1892665--1892707 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1892655 CACACCAAAT
*
1892665 TCGCAACGCGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
*
1892685 TCGCAACACGAAACT-AAAA
1 TCGCAACACGAAAATGAAAA
1892704 TCGC
1 TCGC
1892708 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.47, C:0.26, G:0.16, T:0.12
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:1892745 original size:20 final size:20
Alignment explanation
Indices: 1892704--1892745 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1892694 GAAACTAAAA
* * *
1892704 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGAATTTAAGTT
1892724 TCGCGTTGCGAATTTAAGTT
1 TCGCGTTGCGAATTTAAGTT
1892744 TC
1 TC
1892746 AGAAACTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGAATTTAAGTT
Found at i:1896869 original size:19 final size:19
Alignment explanation
Indices: 1896825--1896874 Score: 93
Period size: 18 Copynumber: 2.7 Consensus size: 19
1896815 ACTAAAACCG
1896825 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
1896844 G-TGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
1896862 GTTGCGAATTTGA
1 GTTGCGAATTTGA
1896875 CTTTCGCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:1896888 original size:20 final size:20
Alignment explanation
Indices: 1896863--1896913 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1896853 TGAAATTCAG
*
1896863 TTGCGAATTTGACTTTCGCA
1 TTGCGAATTTGACTATCGCA
*
1896883 TTGCGAATTTGACTATCGCT
1 TTGCGAATTTGACTATCGCA
1896903 TTGCGAATTTG
1 TTGCGAATTTG
1896914 GAAAATCACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCA
Found at i:1896986 original size:20 final size:21
Alignment explanation
Indices: 1896937--1896990 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1896927 TGATTTACAT
*
1896937 ATTCGCGTTGCGAAATTGGAA
1 ATTCGCGTTGCGAAATTAGAA
*
1896958 ATT-GGGTTGCGAAATTAG-A
1 ATTCGCGTTGCGAAATTAGAA
1896977 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
1896991 TTGTTGGTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 22 0.76
21 3 0.10
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.30
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTAGAA
Found at i:1898076 original size:13 final size:13
Alignment explanation
Indices: 1898049--1898090 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
1898039 AGGGTCTATT
1898049 TGTTTTACTGAAAA
1 TGTTTT-CTGAAAA
1898063 TGTTTT-TGGAAAA
1 TGTTTTCT-GAAAA
1898076 TGTTTTCTGAAAA
1 TGTTTTCTGAAAA
1898089 TG
1 TG
1898091 AATTACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.04
13 18 0.69
14 7 0.27
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (13 bp):
TGTTTTCTGAAAA
Found at i:1898201 original size:14 final size:13
Alignment explanation
Indices: 1898184--1898230 Score: 62
Period size: 12 Copynumber: 3.7 Consensus size: 13
1898174 GCAAATTTTC
1898184 TATAAATTATTTAT
1 TATAAA-TATTTAT
1898198 TATAAATATTT-T
1 TATAAATATTTAT
*
1898210 TATTAA-ATTTAT
1 TATAAATATTTAT
1898222 TATAAATAT
1 TATAAATAT
1898231 CAAATACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 4 0.14
12 12 0.41
13 7 0.24
14 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATAAATATTTAT
Found at i:1898216 original size:27 final size:24
Alignment explanation
Indices: 1898178--1898230 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 24
1898168 CAAATGGCAA
1898178 ATTTTCTATAAATTATTTATTATAAAT
1 ATTTTCTAT-AA--ATTTATTATAAAT
1898205 ATTTT-TATTAAATTTATTATAAAT
1 ATTTTCTA-TAAATTTATTATAAAT
1898229 AT
1 AT
1898231 CAAATACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 15 0.60
26 4 0.16
27 6 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTCTATAAATTTATTATAAAT
Found at i:1903010 original size:35 final size:35
Alignment explanation
Indices: 1902971--1903060 Score: 130
Period size: 35 Copynumber: 2.6 Consensus size: 35
1902961 GATATTTCAT
1902971 ACATATATTTCATTGACACTCTTGTCACTCTAAAG
1 ACATATATTTCATTGACACTCTTGTCACTCTAAAG
* *
1903006 ACATATATTGT--TTAAGTACTCTTGTCACTCTAAAG
1 ACATATATT-TCATTGA-CACTCTTGTCACTCTAAAG
1903041 ACATATATTTCATTGACACT
1 ACATATATTTCATTGACACT
1903061 TATCGATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
34 4 0.09
35 39 0.83
36 4 0.09
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (35 bp):
ACATATATTTCATTGACACTCTTGTCACTCTAAAG
Found at i:1904501 original size:18 final size:18
Alignment explanation
Indices: 1904478--1904549 Score: 108
Period size: 18 Copynumber: 4.0 Consensus size: 18
1904468 ACTGAATATT
*
1904478 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
1904496 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
*
1904514 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1904532 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1904550 ATAATCCCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1908015 original size:176 final size:174
Alignment explanation
Indices: 1907723--1908075 Score: 647
Period size: 177 Copynumber: 2.0 Consensus size: 174
1907713 TAGTTCATTA
*
1907723 GGTGAGCAATGTTGGTTAGTTGAGTTCATGAACATATAGTGCTTTCGTGGTAGATATTAGTCTAA
1 GGTGAGCAATGTTGGTTAGTTGAGTTCATGAACATATAGTGCATTCGTGGTAGATATTAGTCTAA
1907788 TGTTTTTAAGCATGAGAGACTTTATAACTCACATAAGACTTTAATAATGCTTAAGGGTCTTAGA-
66 TGTTTTTAAGCATGAGAGACTTTATAACTCACATAAGACTTTAATAATGCTTAAGGGTCTTAGAG
1907852 GGGGCAAATGGGGATAGTTGGGTTAGAATCTCATGCCCAAACAT
131 GGGGCAAATGGGGATAGTTGGGTTAGAATCTCATGCCCAAACAT
1907896 GGTGAGCAATGTTGGTTAGTTGAGTTCATAGAACATATATGTG-ATTCGTGGTAGATATTAGTCA
1 GGTGAGCAATGTTGGTTAGTTGAGTTCAT-GAACATATA-GTGCATTCGTGGTAGATATTAGTC-
1907960 TAATGTTTTTAAGCATGAGAGACTTTAATAACTCACATAAGACTTTAATAATGCTTAAGGGTCTT
63 TAATGTTTTTAAGCATGAGAGACTTT-ATAACTCACATAAGACTTTAATAATGCTTAAGGGTCTT
1908025 AGAGGGGGCAAATGGGGATAGTTGGGTTAGAATCTCATGCCCAAACAT
127 AGAGGGGGCAAATGGGGATAGTTGGGTTAGAATCTCATGCCCAAACAT
1908073 GGT
1 GGT
1908076 ATTTCTGGGT
Statistics
Matches: 174, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
173 29 0.17
174 28 0.16
175 29 0.17
176 41 0.24
177 47 0.27
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.33
Consensus pattern (174 bp):
GGTGAGCAATGTTGGTTAGTTGAGTTCATGAACATATAGTGCATTCGTGGTAGATATTAGTCTAA
TGTTTTTAAGCATGAGAGACTTTATAACTCACATAAGACTTTAATAATGCTTAAGGGTCTTAGAG
GGGGCAAATGGGGATAGTTGGGTTAGAATCTCATGCCCAAACAT
Found at i:1911971 original size:15 final size:15
Alignment explanation
Indices: 1911951--1912005 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
1911941 ATTTTCTAAA
1911951 ATATTTATATCAAAT
1 ATATTTATATCAAAT
***
1911966 ATATTTATATGGGAT
1 ATATTTATATCAAAT
1911981 ATATTTATATCAAAT
1 ATATTTATATCAAAT
*
1911996 ATATTCATAT
1 ATATTTATAT
1912006 GGGAGGGACA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (15 bp):
ATATTTATATCAAAT
Found at i:1911987 original size:30 final size:30
Alignment explanation
Indices: 1911951--1912009 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1911941 ATTTTCTAAA
*
1911951 ATATTTATATCAAATATATTTATATGGGAT
1 ATATTTATATCAAATATATTCATATGGGAT
1911981 ATATTTATATCAAATATATTCATATGGGA
1 ATATTTATATCAAATATATTCATATGGGA
1912010 GGGACAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (30 bp):
ATATTTATATCAAATATATTCATATGGGAT
Found at i:1913728 original size:14 final size:14
Alignment explanation
Indices: 1913693--1913734 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1913683 CGTTTCTGTC
*
1913693 TATATGCAGAGATT
1 TATATGCAGGGATT
*
1913707 TGTATGCAGGGATT
1 TATATGCAGGGATT
*
1913721 TATTTGCAGGGATT
1 TATATGCAGGGATT
1913735 ACTCCCCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.26, C:0.07, G:0.29, T:0.38
Consensus pattern (14 bp):
TATATGCAGGGATT
Found at i:1916950 original size:2 final size:2
Alignment explanation
Indices: 1916943--1916977 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1916933 TATTGTACAT
1916943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1916978 CACCCCTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1917284 original size:81 final size:81
Alignment explanation
Indices: 1917149--1917396 Score: 406
Period size: 81 Copynumber: 3.1 Consensus size: 81
1917139 ACTTTTCATA
*
1917149 TTTTACTCAGCGGTCTTTAACCGTTCATCTAACTGGCATAATTGACATCTTTCTGCCAATTGCAC
1 TTTTACTCAGCGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCAC
1917214 AGTTAGGCCATTATTC
66 AGTTAGGCCATTATTC
* * *
1917230 TTTTACTCAACGGTCTTTAACCGTTCATCTAATTGGCATAATTGACCCCTTTCTGCCAATTGCAC
1 TTTTACTCAGCGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCAC
*
1917295 AGTTAAGCCATTATTC
66 AGTTAGGCCATTATTC
* * * * *
1917311 TTTTATTCAGCGGTCTTTAATCGTTTATCTAACTGGCATAATTGACACATTTCTGTCAATTGCAC
1 TTTTACTCAGCGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCAC
1917376 AGTTAGGCCATTATTC
66 AGTTAGGCCATTATTC
1917392 TTTTA
1 TTTTA
1917397 TTTTGGACTA
Statistics
Matches: 153, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 153 1.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (81 bp):
TTTTACTCAGCGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCAC
AGTTAGGCCATTATTC
Found at i:1919082 original size:27 final size:27
Alignment explanation
Indices: 1919052--1919136 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
1919042 GTGGAACGCA
1919052 AACTTAGTGATTGTACGGTTATTCATC
1 AACTTAGTGATTGTACGGTTATTCATC
* * ** *
1919079 AACTTAGGATGAAT-TCCGTGGAATGCA-C
1 AACTTA-G-TGATTGTACG-GTTATTCATC
*
1919107 -ACTTAGTGCTTGTACGGTTATTCATC
1 AACTTAGTGATTGTACGGTTATTCATC
1919133 AACT
1 AACT
1919137 CATGATGAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 12
0.64 0.17 0.19
Matches are distributed among these distances:
25 8 0.20
26 5 0.12
27 14 0.34
28 5 0.12
29 9 0.22
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (27 bp):
AACTTAGTGATTGTACGGTTATTCATC
Done.