Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_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: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 17
Found at i:1658863 original size:37 final size:36
Alignment explanation
Indices: 1658806--1658877 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
1658796 AAACAGGTCA
* *
1658806 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGTAAACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAACC
*
1658842 ATCTATAAGCCTTCACAGAAGATTAGTGAAGCAAAC
1 ATCT-TAAGCCTTCACAGAAGAGTAGTGAAGCAAAC
1658878 TCATTTTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 4 0.12
37 28 0.88
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (36 bp):
ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAACC
Found at i:1658994 original size:51 final size:51
Alignment explanation
Indices: 1658882--1659052 Score: 184
Period size: 51 Copynumber: 3.3 Consensus size: 51
1658872 GCAAACTCAT
*
1658882 TTTA-TGAAGATCGAGTCCTATACTCTCT-AAATGAATAGGGAGCGGACACG
1 TTTATTGAAGATTGAGTCCTATACTCTCTGAAA-GAATAGGGAGCGGACACG
* * **
1658932 TTTGTTCAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACTTG
1 TTTATTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACG
* * * * *
1658983 TTTATTGAAGATTTTCCGAGTTCTATACTCTCTGAAGGAATAGAGAGCTGACCCG
1 TTTATTGAAGA--TT--GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACG
1659038 TTTTATTGAAGATTG
1 -TTTATTGAAGATTG
1659053 TTCAAGTCTT
Statistics
Matches: 101, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
50 3 0.03
51 47 0.47
52 4 0.04
53 2 0.02
54 2 0.02
55 32 0.32
56 11 0.11
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (51 bp):
TTTATTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACG
Found at i:1674603 original size:25 final size:25
Alignment explanation
Indices: 1674572--1674627 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
1674562 ATTATTAATC
1674572 TTATTATTTAATTGGATAAAGTATA
1 TTATTATTTAATTGGATAAAGTATA
1674597 TTATTATTTAATTGGATAAAGTATA
1 TTATTATTTAATTGGATAAAGTATA
1674622 TTATTA
1 TTATTA
1674628 ATCGAATAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (25 bp):
TTATTATTTAATTGGATAAAGTATA
Found at i:1675592 original size:23 final size:21
Alignment explanation
Indices: 1675560--1675603 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
1675550 TGATTGATTA
1675560 TAATTCTAATTATATAAATATAT
1 TAATTCTAATT-TA-AAATATAT
*
1675583 TAATTTTAATTTAAAATATAT
1 TAATTCTAATTTAAAATATAT
1675604 ACATTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 2 0.10
23 10 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATTCTAATTTAAAATATAT
Found at i:1676668 original size:42 final size:42
Alignment explanation
Indices: 1676617--1676887 Score: 454
Period size: 42 Copynumber: 6.5 Consensus size: 42
1676607 CATATTCGCA
* *
1676617 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTTCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1676659 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1676701 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
1676743 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTTCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1676785 TTGCGATAGTCCAAGTTCGTGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1676827 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1676869 TTGCGATTGT-CAAGTTCGC
1 TTGCGATAGTCCAAGTTCGC
1676888 CACGACCACG
Statistics
Matches: 215, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
41 9 0.04
42 206 0.96
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:1677310 original size:12 final size:12
Alignment explanation
Indices: 1677293--1677322 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1677283 TCCCACATAG
1677293 TATTGGAAACAC
1 TATTGGAAACAC
1677305 TATTGGAAACAC
1 TATTGGAAACAC
1677317 TATTGG
1 TATTGG
1677323 GAATGGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (12 bp):
TATTGGAAACAC
Found at i:1677383 original size:6 final size:6
Alignment explanation
Indices: 1677372--1677398 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1677362 CCTCGCCTCG
1677372 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1677399 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1677584 original size:62 final size:62
Alignment explanation
Indices: 1677513--1677632 Score: 179
Period size: 62 Copynumber: 1.9 Consensus size: 62
1677503 GAATTTGGAA
* *
1677513 TAAATCGCAACGCGA-ACTTCGACTATCGCAATGTGAACTTGGACTATCGCAATGCGAATATG
1 TAAATCGCAACGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATG
* * *
1677575 TAAATCGCAATGCGATAGTCGATTATCGCAATGCGACCTTGGACTATCGCAATGCGAA
1 TAAATCGCAACGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAA
1677633 CTTGAACTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
62 51 0.98
63 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (62 bp):
TAAATCGCAACGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATG
Found at i:1677636 original size:21 final size:21
Alignment explanation
Indices: 1677516--1677636 Score: 122
Period size: 21 Copynumber: 5.8 Consensus size: 21
1677506 TTTGGAATAA
* *
1677516 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTGGACT
*
1677537 ATCGCAATGTGAACTTGGACT
1 ATCGCAATGCGAACTTGGACT
* *
1677558 ATCGCAATGCGAA-TATGTA-A
1 ATCGCAATGCGAACT-TGGACT
* * *
1677578 ATCGCAATGCGATA-GTCGATT
1 ATCGCAATGCGA-ACTTGGACT
*
1677599 ATCGCAATGCGACCTTGGACT
1 ATCGCAATGCGAACTTGGACT
1677620 ATCGCAATGCGAACTTG
1 ATCGCAATGCGAACTTG
1677637 AACTTGGTCA
Statistics
Matches: 81, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
20 15 0.19
21 66 0.81
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (21 bp):
ATCGCAATGCGAACTTGGACT
Found at i:1681973 original size:14 final size:14
Alignment explanation
Indices: 1681954--1681981 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1681944 TCGGTAATAT
1681954 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
1681968 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
1681982 ATATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.14, G:0.21, T:0.57
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:1682018 original size:24 final size:25
Alignment explanation
Indices: 1681973--1682030 Score: 91
Period size: 24 Copynumber: 2.3 Consensus size: 25
1681963 TGTTCGTTCG
*
1681973 TTTATGTTCATATTTTTTTGTGTTTA
1 TTTATGTTCA-ATTTTTGTGTGTTTA
1681999 TTTATGTTC-ATTTTTGTGTGTTTA
1 TTTATGTTCAATTTTTGTGTGTTTA
1682023 TTTATGTT
1 TTTATGTT
1682031 TAGCTTAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 22 0.71
26 9 0.29
ACGTcount: A:0.14, C:0.03, G:0.14, T:0.69
Consensus pattern (25 bp):
TTTATGTTCAATTTTTGTGTGTTTA
Found at i:1682310 original size:24 final size:24
Alignment explanation
Indices: 1682207--1682310 Score: 120
Period size: 24 Copynumber: 4.4 Consensus size: 24
1682197 TTCATTTATC
*
1682207 TTCGTTTACGTTCATTTA-TTGTG
1 TTCGTTTATGTTCATTTATTTGTG
* **
1682230 TTCGTTTACGTTTGTTTATTTGTG
1 TTCGTTTATGTTCATTTATTTGTG
* ***
1682254 TTCGTTTATGTTCATTTATATCCA
1 TTCGTTTATGTTCATTTATTTGTG
*
1682278 TTCGTTTATGTTCATTAATTTGTG
1 TTCGTTTATGTTCATTTATTTGTG
1682302 TTCGTTTAT
1 TTCGTTTAT
1682311 TATTTAAATG
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
23 16 0.24
24 50 0.76
ACGTcount: A:0.14, C:0.12, G:0.15, T:0.59
Consensus pattern (24 bp):
TTCGTTTATGTTCATTTATTTGTG
Found at i:1682729 original size:21 final size:21
Alignment explanation
Indices: 1682705--1682746 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1682695 AAACCAACCT
** *
1682705 AAAATCTTTAATTTTCTAAAA
1 AAAATCTCAAATTTCCTAAAA
1682726 AAAATCTCAAATTTCCTAAAA
1 AAAATCTCAAATTTCCTAAAA
1682747 TCCTTTCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATCTCAAATTTCCTAAAA
Found at i:1687159 original size:5 final size:5
Alignment explanation
Indices: 1687149--1687174 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1687139 ACGATGAGTA
1687149 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
1687175 ACGGCTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:1697661 original size:2 final size:2
Alignment explanation
Indices: 1697654--1697689 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1697644 TTTTAATTGA
1697654 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
1697690 TAAAATATTT
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:1704349 original size:23 final size:23
Alignment explanation
Indices: 1704323--1704371 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1704313 TCAATCGTAA
1704323 TAACATAACAAGTTGCACCTATT
1 TAACATAACAAGTTGCACCTATT
* * * *
1704346 TAACGTAACATGTTGCGCCTGTT
1 TAACATAACAAGTTGCACCTATT
1704369 TAA
1 TAA
1704372 AGCTGATGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (23 bp):
TAACATAACAAGTTGCACCTATT
Found at i:1705800 original size:254 final size:251
Alignment explanation
Indices: 1705317--1705869 Score: 780
Period size: 249 Copynumber: 2.2 Consensus size: 251
1705307 TTATTTCGTG
** *
1705317 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCCAGTCGGGTCGGTTTTTTTAAGTGTGATATTC
1 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGATTTTTTTAAGTGTGATATT-
*
1705382 GGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCAAACCGACCCGAAAATATATATAATTT
65 --GTC-GG-CGAGTTCGGGTTTAGGGTGAAAAATACCCAAACCGACCCGAAAAAATATATAATTT
* * * *
1705447 TACCTTATATATTTAGGAATAATTACAATAAACCCCTCTATATATAATTTTTTTAATTAATTCAT
126 TACCTTATATATTTAGAAATAATTACAATAAAACCCTCTATATATAATTTTTTTAATTAAGTCAC
1705512 TATTTTTATTGAATAAAAATATTTTTTTTATTATTTCGAATCGGGTCGGGTTTCTAATTCATATA
191 TATTTTTATTGAATAAAAATATTTTTTTTATTA-TT----TCGGGTCGGGTTTCTAATTCATATA
1705577 T
251 T
*
1705578 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTTCGATTTTTTTAAAGTGTGATA-T
1 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGATTTTTTT-AAGTGTGATATT
* *
1705642 -TC-G-G-G-TCGGGTTTAGGGTG-AAAATACCCGACCCGACCCGGCCCAAAAAATATATAATTT
65 GTCGGCGAGTTCGGGTTTAGGGTGAAAAATACCCAAACCGACCC-G---AAAAAATATATAATTT
*
1705701 TACCTTATATATTTATAAATAATTACAATAATAACCCTCTATATATAATTTTTTTAATTAAGTCA
126 TACCTTATATATTTAGAAATAATTACAATAA-AACCCTCTATATATAATTTTTTTAATTAAGTCA
*
1705766 CTGTTTTTATTGAATAAAAATA-TTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATAT
190 CTATTTTTATTGAATAAAAATATTTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATAT
*
1705827 TCGGGTTGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTC
1 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTC
1705870 TCAGATGGAG
Statistics
Matches: 271, Mismatches: 15, Indels: 24
0.87 0.05 0.08
Matches are distributed among these distances:
249 67 0.25
250 17 0.06
251 15 0.06
252 1 0.00
253 3 0.01
254 55 0.20
255 52 0.19
257 2 0.01
261 49 0.18
262 10 0.04
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (251 bp):
TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGATTTTTTTAAGTGTGATATTG
TCGGCGAGTTCGGGTTTAGGGTGAAAAATACCCAAACCGACCCGAAAAAATATATAATTTTACCT
TATATATTTAGAAATAATTACAATAAAACCCTCTATATATAATTTTTTTAATTAAGTCACTATTT
TTATTGAATAAAAATATTTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATAT
Found at i:1710773 original size:72 final size:71
Alignment explanation
Indices: 1710637--1710848 Score: 227
Period size: 72 Copynumber: 3.0 Consensus size: 71
1710627 TAAAAAAAGT
* * *
1710637 TTGATACTTTGCAATC-TACTCATTTCCTATG-TTTTTTTAATTCGAAAGTATTGATATTTGTGG
1 TTGATACTTTGCAACCTTA-TCATTTTCTATGTTTTTTTTAATTCGAAAGTATCGATATTTGTGG
1710700 AAAAATA
65 AAAAATA
* * *
1710707 TTGAAACTTTGCAACCTTATCATTTTCTATGCTTTTTTTTAATTTGAAATTATCGATATTAT-TG
1 TTGATACTTTGCAACCTTATCATTTTCTATG-TTTTTTTTAATTCGAAAGTATCGATATT-TGTG
*
1710771 GAAAATTA
64 GAAAAATA
* * * * * * * *
1710779 TTTATACTTTGTAGCCTTCTCATTTTC-AT-TTTTTTTAAATTCGAAAGTATCTATACTTGTGAA
1 TTGATACTTTGCAACCTTATCATTTTCTATGTTTTTTTTAATTCGAAAGTATCGATATTTGTGGA
1710842 AAAATA
66 AAAATA
1710848 T
1 T
1710849 CAATACTTAC
Statistics
Matches: 118, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
68 1 0.01
69 32 0.27
70 25 0.21
71 4 0.03
72 55 0.47
73 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (71 bp):
TTGATACTTTGCAACCTTATCATTTTCTATGTTTTTTTTAATTCGAAAGTATCGATATTTGTGGA
AAAATA
Found at i:1711650 original size:2 final size:2
Alignment explanation
Indices: 1711643--1711673 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1711633 TTTGTTTCTA
*
1711643 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1711674 ATTGATCTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1711849 original size:24 final size:25
Alignment explanation
Indices: 1711809--1711855 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1711799 AAGGTGGATG
1711809 ATTATTAATTTTCTTTT-TTTTTAT
1 ATTATTAATTTTCTTTTCTTTTTAT
*
1711833 ATTATGTAA-TTTGTTTTCTTTTT
1 ATTAT-TAATTTTCTTTTCTTTTT
1711856 TTCTTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (25 bp):
ATTATTAATTTTCTTTTCTTTTTAT
Found at i:1711854 original size:25 final size:24
Alignment explanation
Indices: 1711809--1711855 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
1711799 AAGGTGGATG
*
1711809 ATTATTAATTTTCTTTTTTTTTAT
1 ATTATTAATTTTCTTTCTTTTTAT
1711833 ATTATGTAATTTGT-TTTCTTTTT
1 ATTAT-TAATTT-TCTTTCTTTTT
1711856 TTCTTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 14 0.70
26 1 0.05
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (24 bp):
ATTATTAATTTTCTTTCTTTTTAT
Found at i:1715908 original size:22 final size:20
Alignment explanation
Indices: 1715877--1715917 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1715867 ATGACTAAAT
*
1715877 TTATTGAATTGAATTAAAATTA
1 TTATTAAATT-AA-TAAAATTA
1715899 TTATTAAATTAATAAAATT
1 TTATTAAATTAATAAAATT
1715918 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
TTATTAAATTAATAAAATTA
Found at i:1729115 original size:60 final size:60
Alignment explanation
Indices: 1728999--1729115 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
1728989 CCATTGACAC
* * * * *
1728999 GATGCCTTCAAGTTCCAATGGGAGGCATTCAACTGCAAGGTTCTTCGACCTCAATGTAGA
1 GATGCCTTCAAGTTCCAAAGGGAGACATTCAACTACAAGCTTCTTCGACCTAAATGTAGA
* * * *
1729059 GATGCCTTCAAGTT-CAAAGGGAAGACATTCAACTACCAGCTTGTTCTACTTAAATGT
1 GATGCCTTCAAGTTCCAAAGGG-AGACATTCAACTACAAGCTTCTTCGACCTAAATGT
1729116 CGATATCGTG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 6 0.13
60 41 0.87
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (60 bp):
GATGCCTTCAAGTTCCAAAGGGAGACATTCAACTACAAGCTTCTTCGACCTAAATGTAGA
Found at i:1732948 original size:9 final size:8
Alignment explanation
Indices: 1732918--1732983 Score: 55
Period size: 9 Copynumber: 8.0 Consensus size: 8
1732908 TGTATATATT
1732918 AAATAATA
1 AAATAATA
1732926 AAATACATA
1 AAATA-ATA
*
1732935 TAATAATA
1 AAATAATA
1732943 ACAATAA-A
1 A-AATAATA
*
1732951 AAATAGTA
1 AAATAATA
1732959 TAAA-AATA
1 -AAATAATA
*
1732967 AAATAGTA
1 AAATAATA
1732975 TAAATAATA
1 -AAATAATA
1732984 GTATAAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
7 7 0.15
8 17 0.37
9 22 0.48
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (8 bp):
AAATAATA
Found at i:1732969 original size:16 final size:17
Alignment explanation
Indices: 1732945--1732983 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
1732935 TAATAATAAC
1732945 AATAA-AAAATAGTATA
1 AATAATAAAATAGTATA
1732961 AA-AATAAAATAGTATA
1 AATAATAAAATAGTATA
1732977 AATAATA
1 AATAATA
1732984 GTATAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.10
16 15 0.71
17 4 0.19
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (17 bp):
AATAATAAAATAGTATA
Found at i:1732991 original size:12 final size:12
Alignment explanation
Indices: 1732968--1732993 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1732958 ATAAAAATAA
1732968 AATAGTATAAAT
1 AATAGTATAAAT
1732980 AATAGTATAAAT
1 AATAGTATAAAT
1732992 AA
1 AA
1732994 AAACCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (12 bp):
AATAGTATAAAT
Found at i:1733035 original size:18 final size:18
Alignment explanation
Indices: 1733012--1733046 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1733002 AAAAAAATAA
1733012 ATAAAT-ATAAAGATATAT
1 ATAAATGATAAA-ATATAT
1733030 ATAAATGATAAAATATA
1 ATAAATGATAAAATATA
1733047 ATACTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
ATAAATGATAAAATATAT
Found at i:1733073 original size:17 final size:17
Alignment explanation
Indices: 1733053--1733091 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1733043 TATAATACTT
1733053 AAATAAAAAGAA-TAACC
1 AAATAAAAAGAATTAA-C
*
1733070 AAATAAAAATAATTAAC
1 AAATAAAAAGAATTAAC
1733087 AAATA
1 AAATA
1733092 TACATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATAAAAAGAATTAAC
Found at i:1734228 original size:2 final size:2
Alignment explanation
Indices: 1734221--1734258 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1734211 CATGTAAATA
1734221 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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 A
1734259 AATAAAACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1734826 original size:2 final size:2
Alignment explanation
Indices: 1734821--1734873 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1734811 TATACTCAAC
1734821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1734862 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1734874 TCAGTATTGA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1735488 original size:65 final size:64
Alignment explanation
Indices: 1735362--1735553 Score: 178
Period size: 65 Copynumber: 3.0 Consensus size: 64
1735352 CGATGTATCA
* ** ** *
1735362 ATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATTTATTTCA-AGCATCGATGCA
1 ATCCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATTTGATA-CATCGATGCA
*
1735424 -T
63 CC
* *
1735425 ATACCATGCATCGATGCACTCAGGGT-TTTATGAAAACATCGAATGCATTTGATACATTGATGCA
1 AT-CCATGCATCGATGCACTCAGGCTATTT-TG-AAACATCGAATGCATTTGATACATCGATGCA
1735489 CC
63 CC
* * * *
1735491 ATCCATGCATCGATGCACTTAGGCTATTTTGAAATATCGAATGCATTTTATGCATCGATGCAC
1 ATCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTGATACATCGATGCAC
1735554 TCTTAGTGCA
Statistics
Matches: 107, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
62 1 0.01
63 5 0.05
64 46 0.43
65 49 0.46
66 6 0.06
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (64 bp):
ATCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTGATACATCGATGCACC
Found at i:1735568 original size:19 final size:19
Alignment explanation
Indices: 1735541--1735592 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1735531 ATGCATTTTA
*
1735541 TGCATCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
1735560 TGCACCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
1735579 TGCACCGATGCACT
1 TGCACCGATGCACT
1735593 AAGGGTCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (19 bp):
TGCACCGATGCACTCTTAG
Found at i:1741356 original size:25 final size:25
Alignment explanation
Indices: 1741322--1741380 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
1741312 TTTGGGGGAG
1741322 TTTATGTTCTTTGGTGAAAATTAAC
1 TTTATGTTCTTTGGTGAAAATTAAC
1741347 TTTATGTTCTTTGGTGAAAATTAAC
1 TTTATGTTCTTTGGTGAAAATTAAC
1741372 TTTATGTTC
1 TTTATGTTC
1741381 AAATGTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.51
Consensus pattern (25 bp):
TTTATGTTCTTTGGTGAAAATTAAC
Found at i:1741602 original size:23 final size:23
Alignment explanation
Indices: 1741533--1741608 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
1741523 ACACTTAACA
1741533 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACTCCTTGAAT
* * *
1741555 GTGCATCGAT--ACACCATGAAA
1 GTGCATCGATGCACTCCTTGAAT
*
1741576 GTGCACCGATGCACTCCTTGAAT
1 GTGCATCGATGCACTCCTTGAAT
1741599 GTGCATCGAT
1 GTGCATCGAT
1741609 ACACAAGGAC
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
20 1 0.02
21 15 0.35
22 10 0.23
23 17 0.40
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACTCCTTGAAT
Found at i:1741602 original size:44 final size:43
Alignment explanation
Indices: 1741514--1741612 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 43
1741504 TTGTGTTTAA
* *
1741514 TGCATCGATACA-CTTAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACCTGAACAGTGCACCGATGCATCCTTGAATG
1741556 TGCATCGATACACCATGAA-AGTGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACC-TGAACAGTGCACCGATGCA-TCCTTGAATG
1741600 TGCATCGATACAC
1 TGCATCGATACAC
1741613 AAGGACATGC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
42 12 0.23
43 14 0.27
44 26 0.50
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (43 bp):
TGCATCGATACACCTGAACAGTGCACCGATGCATCCTTGAATG
Found at i:1741630 original size:43 final size:43
Alignment explanation
Indices: 1741532--1741632 Score: 141
Period size: 44 Copynumber: 2.3 Consensus size: 43
1741522 TACACTTAAC
* *
1741532 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGAA
1 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACAAGGAA
* *
1741575 AGTGCACCGATGCACTCCTTGAATGTGCATCGATACACAAGGAC
1 AGTGCATCGATGCA-TCCTTGAATGTGCATCGATACACAAGGAA
*
1741619 A-TGCATTGATGCAT
1 AGTGCATCGATGCAT
1741633 TCATCGGGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.02
43 23 0.45
44 27 0.53
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (43 bp):
AGTGCATCGATGCATCCTTGAATGTGCATCGATACACAAGGAA
Found at i:1743869 original size:16 final size:17
Alignment explanation
Indices: 1743843--1743875 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1743833 TTGATTTAAC
1743843 AAAAGGGGGAGAAGTGT
1 AAAAGGGGGAGAAGTGT
1743860 AAAA-GGGGAGAAGTGT
1 AAAAGGGGGAGAAGTGT
1743876 TAGAGTAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.12
Consensus pattern (17 bp):
AAAAGGGGGAGAAGTGT
Found at i:1744391 original size:44 final size:46
Alignment explanation
Indices: 1744297--1744403 Score: 173
Period size: 44 Copynumber: 2.4 Consensus size: 46
1744287 TGCACATACC
* *
1744297 ATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAGGCTATTATGAAAACATCGAATGCATTTG
*
1744343 ATGCATCGATGCACTCAGGCTATT-TG-AAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGCTATTATGAAAACATCGAATGCATTTG
1744387 ATGCATCGATGCACTCA
1 ATGCATCGATGCACTCA
1744404 AATGATTTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 34 0.59
45 2 0.03
46 22 0.38
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (46 bp):
ATGCATCGATGCACTCAGGCTATTATGAAAACATCGAATGCATTTG
Found at i:1745755 original size:34 final size:35
Alignment explanation
Indices: 1745704--1745773 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 35
1745694 TATAACTGCA
* *
1745704 AAAAGTAATAAAAAATTAGTATAA-TAAAATTTAAT
1 AAAAGTAATAAAAAATTA-AATAATTAAAATATAAT
*
1745739 AAAA-TAATAAATAATTAAATAATTAAAATATAAT
1 AAAAGTAATAAAAAATTAAATAATTAAAATATAAT
1745773 A
1 A
1745774 GAGAATACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 4 0.13
34 23 0.74
35 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (35 bp):
AAAAGTAATAAAAAATTAAATAATTAAAATATAAT
Found at i:1747183 original size:13 final size:13
Alignment explanation
Indices: 1747167--1747202 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1747157 TAATAATAAA
1747167 AAAAATAAATATT
1 AAAAATAAATATT
*
1747180 AAAAAT-TATATT
1 AAAAATAAATATT
1747192 AAAAATAAATA
1 AAAAATAAATA
1747203 AAATAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATAAATATT
Found at i:1747222 original size:29 final size:28
Alignment explanation
Indices: 1747156--1747222 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
1747146 TTTTTCAGAT
* *
1747156 ATAATAATAAAAAAAATAAATATTAAAA
1 ATAATATTAAAAAAAATAAATATAAAAA
*
1747184 ATTATATTAAAAATAAATAAA-ATAAACAA
1 ATAATATTAAAAA-AAATAAATATAAA-AA
*
1747213 ATAATTTTAA
1 ATAATATTAA
1747223 TTGTCTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (28 bp):
ATAATATTAAAAAAAATAAATATAAAAA
Found at i:1753148 original size:17 final size:17
Alignment explanation
Indices: 1753110--1753148 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1753100 ATCAAACTTC
1753110 TAATTTTGTTTTTATTT
1 TAATTTTGTTTTTATTT
* *
1753127 CAATTTTGTTTTTTTTT
1 TAATTTTGTTTTTATTT
1753144 TAATT
1 TAATT
1753149 GTCTTTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (17 bp):
TAATTTTGTTTTTATTT
Found at i:1755283 original size:2 final size:2
Alignment explanation
Indices: 1755276--1755368 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
1755266 TCTTCACCCA
1755276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1755318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1755360 AT AT AT AT A
1 AT AT AT AT A
1755369 AACACTGCAT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1757201 original size:34 final size:34
Alignment explanation
Indices: 1757124--1757210 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 34
1757114 AAAACTTTAA
1757124 ATATATATTTAAAAATTATAAAAAAATAAAAATAG
1 ATATATATTTAAAAA-TATAAAAAAATAAAAATAG
* * * * *
1757159 ATAAATATTTTAAAATAT-AAAAGATACATAATAT
1 ATATATATTTAAAAATATAAAAAAATA-AAAATAG
1757193 ATATATATTTAAAAATAT
1 ATATATATTTAAAAATAT
1757211 CACCCAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 7 0.16
34 24 0.55
35 13 0.30
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (34 bp):
ATATATATTTAAAAATATAAAAAAATAAAAATAG
Found at i:1762120 original size:16 final size:16
Alignment explanation
Indices: 1762099--1762131 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1762089 TAAAAAATAA
1762099 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1762115 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1762131 A
1 A
1762132 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1762212 original size:10 final size:10
Alignment explanation
Indices: 1762197--1762271 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1762187 CATTTAATAA
1762197 ATAAACGAAC
1 ATAAACGAAC
1762207 ATAAACGAAC
1 ATAAACGAAC
1762217 ----ACGAAC
1 ATAAACGAAC
1762223 ATAAACGAAC
1 ATAAACGAAC
** *
1762233 ACGAAC-ATAA
1 ATAAACGA-AC
1762243 ATGAACACGAAC
1 AT-AA-ACGAAC
1762255 ATAAACGAAC
1 ATAAACGAAC
1762265 ATAAACG
1 ATAAACG
1762272 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1762222 original size:16 final size:16
Alignment explanation
Indices: 1762201--1762265 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
1762191 TAATAAATAA
1762201 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1762217 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1762233 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1762249 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1762265 A
1 A
1762266 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1763025 original size:10 final size:10
Alignment explanation
Indices: 1763010--1763057 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
1763000 ATAAATGAAT
1763010 GAACATAAAC
1 GAACATAAAC
1763020 GAACATAATCGAAC
1 GAACAT-A---AAC
1763034 GAACATAAAC
1 GAACATAAAC
*
1763044 GAACATAACC
1 GAACATAAAC
1763054 GAAC
1 GAAC
1763058 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1763034 original size:14 final size:14
Alignment explanation
Indices: 1763017--1763047 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1763007 AATGAACATA
*
1763017 AACGAACATAATCG
1 AACGAACATAAACG
1763031 AACGAACATAAACG
1 AACGAACATAAACG
1763045 AAC
1 AAC
1763048 ATAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:1763037 original size:24 final size:24
Alignment explanation
Indices: 1762997--1763058 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
1762987 GATTGTGTTA
*
1762997 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
1763021 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
*
1763045 AACATAACCGAACG
1 AACATAATCGAACG
1763059 TTCACGAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 3 0.09
24 32 0.91
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:1764446 original size:8 final size:8
Alignment explanation
Indices: 1764435--1764468 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
1764425 TTTCAAAATT
1764435 AAAATTAA
1 AAAATTAA
1764443 AAAATTAA
1 AAAATTAA
1764451 AAAATT-A
1 AAAATTAA
1764458 AAAATTAA
1 AAAATTAA
1764466 AAA
1 AAA
1764469 TTCGACAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:1764452 original size:7 final size:7
Alignment explanation
Indices: 1764429--1764470 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
1764419 TTTTTATTTC
1764429 AAAATT-
1 AAAATTA
1764435 AAAATTAA
1 AAAATT-A
1764443 AAAATTAA
1 AAAATT-A
1764451 AAAATTA
1 AAAATTA
1764458 AAAATTA
1 AAAATTA
1764465 AAAATT
1 AAAATT
1764471 CGACAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.18
7 14 0.41
8 14 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAATTA
Found at i:1771172 original size:18 final size:18
Alignment explanation
Indices: 1771134--1771169 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1771124 AATTAACATT
1771134 ATAATGGAGATAAAAACA
1 ATAATGGAGATAAAAACA
*
1771152 ATAA-GGAGATTAAAACA
1 ATAATGGAGATAAAAACA
1771169 A
1 A
1771170 ATATTGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.61, C:0.06, G:0.17, T:0.17
Consensus pattern (18 bp):
ATAATGGAGATAAAAACA
Found at i:1771828 original size:2 final size:2
Alignment explanation
Indices: 1771821--1771868 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1771811 TAACATACAC
*
1771821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1771863 AT AT AT
1 AT AT AT
1771869 GCAATCTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1779402 original size:20 final size:21
Alignment explanation
Indices: 1779365--1779406 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1779355 GTCATGCAAC
1779365 TAATAATAGTTGCATAATGCA
1 TAATAATAGTTGCATAATGCA
*
1779386 TAATAATGGTT-CATAATGCA
1 TAATAATAGTTGCATAATGCA
1779406 T
1 T
1779407 TGTAAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
TAATAATAGTTGCATAATGCA
Found at i:1800048 original size:121 final size:121
Alignment explanation
Indices: 1799827--1800309 Score: 835
Period size: 121 Copynumber: 4.0 Consensus size: 121
1799817 ATGTTCGCAC
* **
1799827 CTTGTT-TTTTTATCAATAGATCTTGTTCGTACATGGTTATATTATCAATCATGATCATTATTCA
1 CTTGTTCTTTTTATCAATAGATCTTGTTCGTACATGGTTATATTATCACTCATGATCATTAGACA
* * *
1799891 AATGAATTATGAATGGT-TGAAGTGTTTTCTCGAGTCGTTCATGGTTACTTGGTGAA
66 AATGAATTATGGAT-GTCTAAAGTGTTTTCTCGAGTCGTTCATGGTTACTTGATGAA
*
1799947 CTTGTTCTTTTTATCAATAGATCTTGTTCGTACATGGTTATATTATCACTCATGATCATTAGATA
1 CTTGTTCTTTTTATCAATAGATCTTGTTCGTACATGGTTATATTATCACTCATGATCATTAGACA
* * *
1800012 AATGAATTATGGATGTCTAAAGTGTTTTCTCTAGTCGTTCATGGTTACATGGTGAA
66 AATGAATTATGGATGTCTAAAGTGTTTTCTCGAGTCGTTCATGGTTACTTGATGAA
1800068 CTTGTTCTTTTTATCAATAGATCTTGTTCGTACATGGTTATATTATCACTCATGATCATTAGACA
1 CTTGTTCTTTTTATCAATAGATCTTGTTCGTACATGGTTATATTATCACTCATGATCATTAGACA
1800133 AATGAATTATGGATGTCTAAAGTGTTTTCTCGAGTCGTTCATGGTTACTTGATGAA
66 AATGAATTATGGATGTCTAAAGTGTTTTCTCGAGTCGTTCATGGTTACTTGATGAA
1800189 CTTGTTCTTTTTATCAATAGATCTTGTTCGTACATGGTTATATTATCACTCATGATCATTAGACA
1 CTTGTTCTTTTTATCAATAGATCTTGTTCGTACATGGTTATATTATCACTCATGATCATTAGACA
**
1800254 AATGAATTATGGATGTCTAAAGTGTTTTCTTAAGTCGTTCATGGTTACTTGATGAA
66 AATGAATTATGGATGTCTAAAGTGTTTTCTCGAGTCGTTCATGGTTACTTGATGAA
1800310 TAAATTTGTT
Statistics
Matches: 347, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
120 8 0.02
121 339 0.98
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (121 bp):
CTTGTTCTTTTTATCAATAGATCTTGTTCGTACATGGTTATATTATCACTCATGATCATTAGACA
AATGAATTATGGATGTCTAAAGTGTTTTCTCGAGTCGTTCATGGTTACTTGATGAA
Found at i:1800337 original size:2 final size:2
Alignment explanation
Indices: 1800326--1800365 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1800316 TGTTATCAAC
1800326 TA TA -A 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 TA TA TA T
1800366 TTTATAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1800766 original size:26 final size:26
Alignment explanation
Indices: 1800694--1800767 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 26
1800684 ATAAAATAAT
*
1800694 ATTTTAATATATTTTAATTTTTTTGAA
1 ATTTTAAAATATTTT-ATTTTTTTGAA
*
1800721 ATTTTAAATTATATTT-TTTTTTTGAA
1 ATTTTAAAATAT-TTTATTTTTTTGAA
1800747 A-TTTAAAATATTTATATTTTT
1 ATTTTAAAATATTT-TATTTTT
1800768 AAAAATATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 2 0.05
25 10 0.24
26 16 0.39
27 10 0.24
28 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.64
Consensus pattern (26 bp):
ATTTTAAAATATTTTATTTTTTTGAA
Found at i:1801254 original size:16 final size:15
Alignment explanation
Indices: 1801233--1801299 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 15
1801223 AATTTTAGTT
1801233 GAACCAAAAGTAACCC
1 GAACCAAAA-TAACCC
* *
1801249 GAACCAAAAACAACTC
1 GAACC-AAAATAACCC
1801265 GAACCAAAATCAACCC
1 GAACCAAAAT-AACCC
**
1801281 GAACTGAAATCAACCC
1 GAACCAAAAT-AACCC
1801297 GAA
1 GAA
1801300 TTGAAATGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
15 4 0.09
16 35 0.81
17 4 0.09
ACGTcount: A:0.51, C:0.31, G:0.10, T:0.07
Consensus pattern (15 bp):
GAACCAAAATAACCC
Found at i:1801304 original size:16 final size:17
Alignment explanation
Indices: 1801271--1801332 Score: 85
Period size: 16 Copynumber: 3.8 Consensus size: 17
1801261 ACTCGAACCA
1801271 AAAT-CAACCCGAACTG
1 AAATGCAACCCGAACTG
*
1801287 AAAT-CAACCCGAATTG
1 AAATGCAACCCGAACTG
*
1801303 AAATGCAACCCGAACCG
1 AAATGCAACCCGAACTG
1801320 -AATGCAACCCGAA
1 AAATGCAACCCGAA
1801333 TTTAATTTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
16 32 0.76
17 10 0.24
ACGTcount: A:0.44, C:0.31, G:0.15, T:0.11
Consensus pattern (17 bp):
AAATGCAACCCGAACTG
Found at i:1801317 original size:33 final size:32
Alignment explanation
Indices: 1801271--1801334 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1801261 ACTCGAACCA
*
1801271 AAATCAACCCGAACTGAAAT-CAACCCGAATTG
1 AAATCAACCCGAACCG-AATGCAACCCGAATTG
1801303 AAATGCAACCCGAACCGAATGCAACCCGAATT
1 AAAT-CAACCCGAACCGAATGCAACCCGAATT
1801335 TAATTTACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 7 0.24
33 22 0.76
ACGTcount: A:0.42, C:0.30, G:0.14, T:0.14
Consensus pattern (32 bp):
AAATCAACCCGAACCGAATGCAACCCGAATTG
Found at i:1804186 original size:16 final size:18
Alignment explanation
Indices: 1804154--1804186 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1804144 GCTACAGGTT
1804154 AAATGAGAAAATGAACAA
1 AAATGAGAAAATGAACAA
1804172 AAATGA-AAAAT-AACA
1 AAATGAGAAAATGAACA
1804187 TAAACTCAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.70, C:0.06, G:0.12, T:0.12
Consensus pattern (18 bp):
AAATGAGAAAATGAACAA
Found at i:1805146 original size:7 final size:7
Alignment explanation
Indices: 1805136--1805160 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1805126 CTGATAGCTG
1805136 ATGGCTA
1 ATGGCTA
1805143 ATGGCTA
1 ATGGCTA
1805150 ATGGCTA
1 ATGGCTA
1805157 ATGG
1 ATGG
1805161 TTTCTGGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (7 bp):
ATGGCTA
Found at i:1808916 original size:2 final size:2
Alignment explanation
Indices: 1808911--1808948 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1808901 AACATATCTC
1808911 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1808949 TGTGTAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1809274 original size:2 final size:2
Alignment explanation
Indices: 1809267--1809295 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1809257 TAAAACCTAA
1809267 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1809296 CCAATTAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1812774 original size:21 final size:21
Alignment explanation
Indices: 1812748--1812792 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1812738 GATTTCTGGG
* *
1812748 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1812769 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1812790 CAA
1 CAA
1812793 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1816912 original size:17 final size:15
Alignment explanation
Indices: 1816898--1816930 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
1816888 TATGATTTGC
1816898 TGTGTATGTTGA-TT
1 TGTGTATGTTGATTT
1816912 TGTGTATGTTGATGTT
1 TGTGTATGTTGAT-TT
1816928 TGT
1 TGT
1816931 TTTTGCTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 12 0.71
16 5 0.29
ACGTcount: A:0.12, C:0.00, G:0.30, T:0.58
Consensus pattern (15 bp):
TGTGTATGTTGATTT
Found at i:1816915 original size:14 final size:14
Alignment explanation
Indices: 1816898--1816924 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1816888 TATGATTTGC
1816898 TGTGTATGTTGATT
1 TGTGTATGTTGATT
1816912 TGTGTATGTTGAT
1 TGTGTATGTTGAT
1816925 GTTTGTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (14 bp):
TGTGTATGTTGATT
Found at i:1817153 original size:31 final size:31
Alignment explanation
Indices: 1817112--1817176 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1817102 TAGGCTATTA
1817112 TATATATATATATATAT-ATATTTGTTGTTTG
1 TATATATATATATATATGA-ATTTGTTGTTTG
* *
1817143 TATATGTATATATTTATGAATTTGTTGTTTG
1 TATATATATATATATATGAATTTGTTGTTTG
1817174 TAT
1 TAT
1817177 GTTATGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.58
Consensus pattern (31 bp):
TATATATATATATATATGAATTTGTTGTTTG
Found at i:1817182 original size:22 final size:22
Alignment explanation
Indices: 1817156--1817242 Score: 135
Period size: 22 Copynumber: 4.1 Consensus size: 22
1817146 ATGTATATAT
*
1817156 TTATGAATTTGTTGTTTGTATG
1 TTATGAATTTGCTGTTTGTATG
1817178 TTATGAATTTGCTGTTTGTATG
1 TTATGAATTTGCTGTTTGTATG
1817200 TTATGAATTTGCTGTTTG-ATG
1 TTATGAATTTGCTGTTTGTATG
*
1817221 TTATGTATTTGCTG--TGTATG
1 TTATGAATTTGCTGTTTGTATG
1817241 TT
1 TT
1817243 GATTTGTGTG
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
19 2 0.03
20 5 0.08
21 16 0.26
22 39 0.63
ACGTcount: A:0.17, C:0.03, G:0.23, T:0.56
Consensus pattern (22 bp):
TTATGAATTTGCTGTTTGTATG
Found at i:1817903 original size:24 final size:24
Alignment explanation
Indices: 1817876--1817926 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1817866 TCTGAACCAA
1817876 CTCTCAATA-ACTCAGTTGATCCAC
1 CTCTCAATACA-TCAGTTGATCCAC
* * *
1817900 CTCTTAGTGCATCAGTTGATCCAC
1 CTCTCAATACATCAGTTGATCCAC
1817924 CTC
1 CTC
1817927 CTGAGTCATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.24, C:0.33, G:0.12, T:0.31
Consensus pattern (24 bp):
CTCTCAATACATCAGTTGATCCAC
Found at i:1817936 original size:24 final size:24
Alignment explanation
Indices: 1817887--1817936 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1817877 TCTCAATAAC
*
1817887 TCAGTTGATCCACCTCTTAGTGCA
1 TCAGTTGATCCACCTCTGAGTGCA
1817911 TCAGTTGATCCACCTCCTGAGT-CA
1 TCAGTTGATCCACCT-CTGAGTGCA
1817935 TC
1 TC
1817937 CCCTACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (24 bp):
TCAGTTGATCCACCTCTGAGTGCA
Found at i:1818329 original size:30 final size:29
Alignment explanation
Indices: 1818295--1818458 Score: 187
Period size: 30 Copynumber: 5.7 Consensus size: 29
1818285 TGATTATATA
1818295 AGAAATATTATATGGTTTGTGGTCTATGTT
1 AGAAATATTATATGGTTTGT-GTCTATGTT
*
1818325 AGAAATATTATATGG-TT-TGTCGATGTT
1 AGAAATATTATATGGTTTGTGTCTATGTT
* *
1818352 CA-AAACATTATATGGTTTGTAGTTTATGTT
1 -AGAAATATTATATGGTTTGT-GTCTATGTT
*
1818382 AGAAATATTATATGG-TT-TGTCGATGTT
1 AGAAATATTATATGGTTTGTGTCTATGTT
* *
1818409 CA-AAACATTTTATGGTTTGTGGTCTATGTT
1 -AGAAATATTATATGGTTTGT-GTCTATGTT
1818439 AGAAATATTATATGGTTTGT
1 AGAAATATTATATGGTTTGT
1818459 ATTAAAGTTA
Statistics
Matches: 112, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
27 38 0.34
28 8 0.07
29 8 0.07
30 58 0.52
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.46
Consensus pattern (29 bp):
AGAAATATTATATGGTTTGTGTCTATGTT
Found at i:1818361 original size:27 final size:27
Alignment explanation
Indices: 1818331--1818428 Score: 126
Period size: 27 Copynumber: 3.5 Consensus size: 27
1818321 TGTTAGAAAT
1818331 ATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTCGATGTTCAAAAC
* *
1818358 ATTATATGGTTTGTAGTTTATGTT-AGAAAT
1 ATTATATGGTTTGTCG---ATGTTCA-AAAC
1818388 ATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTCGATGTTCAAAAC
*
1818415 ATTTTATGGTTTGT
1 ATTATATGGTTTGT
1818429 GGTCTATGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
27 36 0.59
28 1 0.02
29 1 0.02
30 23 0.38
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (27 bp):
ATTATATGGTTTGTCGATGTTCAAAAC
Found at i:1818389 original size:57 final size:57
Alignment explanation
Indices: 1818301--1818458 Score: 289
Period size: 57 Copynumber: 2.8 Consensus size: 57
1818291 TATAAGAAAT
1818301 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
* *
1818358 ATTATATGGTTTGTAGTTTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
*
1818415 ATTTTATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGT
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGT
1818459 ATTAAAGTTA
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 96 1.00
ACGTcount: A:0.27, C:0.05, G:0.21, T:0.47
Consensus pattern (57 bp):
ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
Found at i:1819808 original size:31 final size:31
Alignment explanation
Indices: 1819771--1819829 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1819761 AGTTGTATGG
*
1819771 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTGCAAAACTAAA
1819802 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTGCAAAACT
1819830 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTGCAAAACTAAA
Found at i:1826287 original size:15 final size:17
Alignment explanation
Indices: 1826261--1826292 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1826251 TTCTATGGGA
1826261 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1826277 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1826293 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1826524 original size:24 final size:24
Alignment explanation
Indices: 1826497--1826544 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1826487 GAACATAGGA
1826497 ATATAGATATGGTCGTTTAACAGT
1 ATATAGATATGGTCGTTTAACAGT
1826521 ATATAGATATGGTCGTTTAACAGT
1 ATATAGATATGGTCGTTTAACAGT
1826545 CTGTCCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (24 bp):
ATATAGATATGGTCGTTTAACAGT
Found at i:1827680 original size:21 final size:21
Alignment explanation
Indices: 1827651--1827692 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1827641 GGAATTATTA
*
1827651 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
* *
1827672 TAATTTTTTATAATAAATAAT
1 TAATATTTTAAAATAAATAAT
1827693 ATTAATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:1830373 original size:64 final size:64
Alignment explanation
Indices: 1830272--1830399 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
1830262 CTTGATCATC
1830272 TTGATATGCAATGCCAAAGTGAGAGGAATATGAGAGACCACGAGAAGCACGAACCTCAATAAAA
1 TTGATATGCAATGCCAAAGTGAGAGGAATATGAGAGACCACGAGAAGCACGAACCTCAATAAAA
1830336 TTGATATGCAATGCCAAAGTGAGAGGAATATGAGAGACCACGAGAAGCACGAACCTCAATAAAA
1 TTGATATGCAATGCCAAAGTGAGAGGAATATGAGAGACCACGAGAAGCACGAACCTCAATAAAA
1830400 GTGGCATACA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (64 bp):
TTGATATGCAATGCCAAAGTGAGAGGAATATGAGAGACCACGAGAAGCACGAACCTCAATAAAA
Found at i:1830942 original size:15 final size:15
Alignment explanation
Indices: 1830922--1830953 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1830912 TGTCCCCCGG
1830922 AGAACTATTCATGTT
1 AGAACTATTCATGTT
1830937 AGAACTATTCATGTT
1 AGAACTATTCATGTT
1830952 AG
1 AG
1830954 TACCTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (15 bp):
AGAACTATTCATGTT
Found at i:1831230 original size:137 final size:138
Alignment explanation
Indices: 1830937--1831357 Score: 727
Period size: 138 Copynumber: 3.1 Consensus size: 138
1830927 TATTCATGTT
* * *
1830937 AGAACTATTCATGTTAGTACCTATTATTTCTAAGGGGACTTGGCAAAGTGGTGAAAGTGCGTTCT
1 AGAACTATTCATGTCAGTACCTATTATTTCTAAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCC
*
1831002 CGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
66 CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
*
1831067 TCCCCCAA
131 TCCCCCAG
*
1831075 AGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCC
1 AGAACTATTCATGTCAGTACCTATTATTTCTAAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCC
* *
1831140 CGGGGGTGCGCCTTCCATTATTTT-TCAGAGAATATGTTATCATTGTCCTATTATGTCACTCATG
66 CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
1831204 TCCCCCAG
131 TCCCCCAG
* *
1831212 AGAACTATTCATGTCAGTACCTATTATTTTTTAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCC
1 AGAACTATTCATGTCAGTACCTATTATTTCTAAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCC
*
1831277 CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGATATCATTGCCCTATTATGTCACTCATG
66 CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
*
1831342 TCCCCCGG
131 TCCCCCAG
1831350 AGAACTAT
1 AGAACTAT
1831358 AGATGGATGG
Statistics
Matches: 269, Mismatches: 13, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
137 132 0.49
138 137 0.51
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (138 bp):
AGAACTATTCATGTCAGTACCTATTATTTCTAAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCC
CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
TCCCCCAG
Found at i:1831571 original size:61 final size:59
Alignment explanation
Indices: 1831487--1831608 Score: 201
Period size: 61 Copynumber: 2.0 Consensus size: 59
1831477 GTTATGCGAA
1831487 GTTTGAAATTGGATAAATGTTATGAATAAATTGAATAAATGTGAAGTGATCAA-TTGGTT
1 GTTTGAAATTGGATAAATGTTATGAATAAATTGAATAAATGTGAAGTGAT-AAGTTGGTT
*
1831546 GTTTGAATATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
1 GTTTGAA-ATTGGAT-AAATGTTATGAATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
1831607 GT
1 GT
1831609 GACATTGAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
59 7 0.12
60 9 0.15
61 43 0.73
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.38
Consensus pattern (59 bp):
GTTTGAAATTGGATAAATGTTATGAATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
Found at i:1831847 original size:34 final size:34
Alignment explanation
Indices: 1831808--1831880 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
1831798 TTAAGTTAAA
1831808 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
* *
1831842 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
*
1831876 ATTAA
1 TTTAA
1831881 AAACATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATACCATAATTTGTAT
Found at i:1833495 original size:21 final size:21
Alignment explanation
Indices: 1833469--1833510 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1833459 AACTGTAGCG
1833469 CCCCAACTATATCTTCCAGCT
1 CCCCAACTATATCTTCCAGCT
* *
1833490 CCCCAACTCTATCTTCTAGCT
1 CCCCAACTATATCTTCCAGCT
1833511 TTATCAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.43, G:0.05, T:0.31
Consensus pattern (21 bp):
CCCCAACTATATCTTCCAGCT
Found at i:1834260 original size:20 final size:20
Alignment explanation
Indices: 1834216--1834260 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1834206 ATTAGCACAA
* *
1834216 AAAATAATTAATTAATAAAT
1 AAAATAAATAATAAATAAAT
* *
1834236 TAAATAAATAATAAATATAT
1 AAAATAAATAATAAATAAAT
1834256 AAAAT
1 AAAAT
1834261 TATTTTAATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATAAATAATAAATAAAT
Found at i:1834292 original size:55 final size:53
Alignment explanation
Indices: 1834214--1834329 Score: 121
Period size: 55 Copynumber: 2.2 Consensus size: 53
1834204 TAATTAGCAC
*
1834214 AAAAAATAATTAATTAATAAATTAAATAAATA-ATAAATATATAAAATTATTTTAA
1 AAAAAATAATTAATTAATAAATTAAATAAATATA-AAATATA-AAAACTA-TTTAA
* * * *
1834269 TAAAAAATAA-T-ATTTATATAATTATATTACTATAAAATATAAAAACTATTTAA
1 -AAAAAATAATTAATTAATA-AATTAAATAAATATAAAATATAAAAACTATTTAA
1834322 AAAAAATA
1 AAAAAATA
1834330 CTAACTTACA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
52 8 0.15
53 5 0.09
54 12 0.23
55 18 0.34
56 10 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (53 bp):
AAAAAATAATTAATTAATAAATTAAATAAATATAAAATATAAAAACTATTTAA
Found at i:1834306 original size:30 final size:29
Alignment explanation
Indices: 1834238--1834307 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
1834228 TAATAAATTA
* *
1834238 AATAAATAATAAATATATAAAATTATTTT
1 AATAAAAAATAAATATATAAAATTATATT
* *
1834267 AATAAAAAATAATATTTATATAATTATATT
1 AATAAAAAATAA-ATATATAAAATTATATT
* *
1834297 ACTATAAAATA
1 AATAAAAAATA
1834308 TAAAAACTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 11 0.32
30 23 0.68
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
AATAAAAAATAAATATATAAAATTATATT
Found at i:1839002 original size:52 final size:52
Alignment explanation
Indices: 1838924--1839032 Score: 209
Period size: 52 Copynumber: 2.1 Consensus size: 52
1838914 ACGTGGGACA
*
1838924 CGTATGAGGTTGTGAATGTAGAGAATGTTCGATGAATTGTTTGTGAATAGTT
1 CGTATGAGGTTGTGAATATAGAGAATGTTCGATGAATTGTTTGTGAATAGTT
1838976 CGTATGAGGTTGTGAATATAGAGAATGTTCGATGAATTGTTTGTGAATAGTT
1 CGTATGAGGTTGTGAATATAGAGAATGTTCGATGAATTGTTTGTGAATAGTT
1839028 CGTAT
1 CGTAT
1839033 AATGTTCGTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.28, C:0.05, G:0.29, T:0.39
Consensus pattern (52 bp):
CGTATGAGGTTGTGAATATAGAGAATGTTCGATGAATTGTTTGTGAATAGTT
Found at i:1839406 original size:23 final size:23
Alignment explanation
Indices: 1839377--1839454 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 23
1839367 AACATGTTTG
*
1839377 ATGTTAAATGAATATGTTAACGA
1 ATGTTAAACGAATATGTTAACGA
* * * *
1839400 ATGTTAAACAAACATGTTTATGA
1 ATGTTAAACGAATATGTTAACGA
* ***
1839423 ATATTAAACGAATATGTTTGTGA
1 ATGTTAAACGAATATGTTAACGA
1839446 ATGTTAAAC
1 ATGTTAAAC
1839455 AAATGAACAC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (23 bp):
ATGTTAAACGAATATGTTAACGA
Found at i:1839408 original size:42 final size:45
Alignment explanation
Indices: 1839361--1839456 Score: 117
Period size: 46 Copynumber: 2.2 Consensus size: 45
1839351 TTGTTAAACA
* *
1839361 TTAAACAACATG-TT-TG-ATGTTAAATGAATATGTTAACGAATG
1 TTAAACAACATGTTTATGAATATTAAACGAATATGTTAACGAATG
***
1839403 TTAAACAAACATGTTTATGAATATTAAACGAATATGTTTGTGAATG
1 TTAAAC-AACATGTTTATGAATATTAAACGAATATGTTAACGAATG
1839449 TTAAACAA
1 TTAAACAA
1839457 ATGAACACGA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
42 6 0.13
43 6 0.13
44 2 0.04
45 4 0.09
46 27 0.60
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (45 bp):
TTAAACAACATGTTTATGAATATTAAACGAATATGTTAACGAATG
Found at i:1839479 original size:28 final size:28
Alignment explanation
Indices: 1839439--1839522 Score: 159
Period size: 28 Copynumber: 3.0 Consensus size: 28
1839429 AACGAATATG
1839439 TTTGTGAATGTTAAACAAATGAACACGA
1 TTTGTGAATGTTAAACAAATGAACACGA
1839467 TTTGTGAATGTTAAACAAATGAACACGA
1 TTTGTGAATGTTAAACAAATGAACACGA
*
1839495 TTTGTGAATGTTAAACAAATGGACACGA
1 TTTGTGAATGTTAAACAAATGAACACGA
1839523 ATATATTTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.29
Consensus pattern (28 bp):
TTTGTGAATGTTAAACAAATGAACACGA
Found at i:1841862 original size:180 final size:178
Alignment explanation
Indices: 1841546--1841873 Score: 606
Period size: 180 Copynumber: 1.8 Consensus size: 178
1841536 CAAGGCTTTC
1841546 ACAGTTAGCTTGAATACTGTTTTTTTGTCTTGTGTGCTTTTTGTTGTGTTGAAAAAAAAGGGGAA
1 ACAGTTAGCTTGAATACTGTTTTTTTGTCTTGTGTGCTTTTTGTTGTGTTGAAAAAAAAGGGGAA
1841611 TTTTTCTTGTGAATTTGAAAGCGATTGGCTGATGATTATAACTTGTTTGACTAGCAAGATTTTCT
66 TTTTTCTTGTGAATTTGAAAGCGATTGGCTGATGATTATAACTTGTTTGACTAGCAAGATTTTCT
1841676 TATTTGAAAATATTAATTTCTTTGAGAAATTACCCAACAATTTCTTCA
131 TATTTGAAAATATTAATTTCTTTGAGAAATTACCCAACAATTTCTTCA
1841724 ACAGTTAGCTTGAATACTG-TTTTTTGTCTTGTGTG-TGCTTTTGTTGTGTTGAAAAAAAAAGGG
1 ACAGTTAGCTTGAATACTGTTTTTTTGTCTTGTGTGCT--TTTTGTTGTGTTG-AAAAAAAAGGG
1841787 GAATTTTTCTTGTGAATTTGAAAGCGATTGGGCTGATGATTATAACTTGTTTGACTAGCAAGATT
63 GAATTTTTCTTGTGAATTTGAAAGCGATT-GGCTGATGATTATAACTTGTTTGACTAGCAAGATT
1841852 TTCTTATTTGAAAATATTAATT
127 TTCTTATTTGAAAATATTAATT
1841874 AATTGACAAT
Statistics
Matches: 146, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
176 1 0.01
177 16 0.11
178 32 0.22
179 40 0.27
180 57 0.39
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (178 bp):
ACAGTTAGCTTGAATACTGTTTTTTTGTCTTGTGTGCTTTTTGTTGTGTTGAAAAAAAAGGGGAA
TTTTTCTTGTGAATTTGAAAGCGATTGGCTGATGATTATAACTTGTTTGACTAGCAAGATTTTCT
TATTTGAAAATATTAATTTCTTTGAGAAATTACCCAACAATTTCTTCA
Found at i:1843632 original size:153 final size:152
Alignment explanation
Indices: 1843350--1843654 Score: 560
Period size: 153 Copynumber: 2.0 Consensus size: 152
1843340 GAGAAGAGAG
1843350 AGTGAGATCTTTACCTTTGTGTTGAACAATCGGTGTTAGTGCTTAGGAGGAATCGATCGAGAGAA
1 AGTGAGATCTTTACCTTTGTGTTGAACAATCGGTGTTAGTGCTTAGGAGGAATCGATCGAGAGAA
1843415 CTAGGCTTTGGTGTCGGGTGAAAAACAAAGTGAAGAGAAAGTGAGGCTAGAGTTGTAAGGGGTTC
66 CTAGGCTTTGGTGTCGGGTGAAAAACAAAGTGAAGAGAAAGTGAGGCTAGAGTTGTAAGGGGTTC
1843480 GGGTTTGTCGGTTTGGGTCACC
131 GGGTTTGTCGGTTTGGGTCACC
*
1843502 AGTGAAGATCTTTACC-TTGTGTTGAACTCATCGGTGTTAGTGCTTAGGAGGAATCGATCGAGAG
1 AGTG-AGATCTTTACCTTTGTGTTGAAC-AATCGGTGTTAGTGCTTAGGAGGAATCGATCGAGAG
1843566 AACTAGGCTTTGGTGTCGGGGTGAAAAACAAAGTGAAGAG-AAGTGAGGCTAGAGTTGTAAGGGG
64 AACTAGGCTTTGGTGTC-GGGTGAAAAACAAAGTGAAGAGAAAGTGAGGCTAGAGTTGTAAGGGG
1843630 TTCGGGTTTGTCGGTTTGGGTCACC
128 TTCGGGTTTGTCGGTTTGGGTCACC
1843655 GGACTGTCGG
Statistics
Matches: 149, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
152 15 0.10
153 112 0.75
154 22 0.15
ACGTcount: A:0.25, C:0.12, G:0.34, T:0.28
Consensus pattern (152 bp):
AGTGAGATCTTTACCTTTGTGTTGAACAATCGGTGTTAGTGCTTAGGAGGAATCGATCGAGAGAA
CTAGGCTTTGGTGTCGGGTGAAAAACAAAGTGAAGAGAAAGTGAGGCTAGAGTTGTAAGGGGTTC
GGGTTTGTCGGTTTGGGTCACC
Found at i:1845943 original size:21 final size:22
Alignment explanation
Indices: 1845911--1845955 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1845901 CTTTTAAGAT
1845911 AAAATCTGAA-TTATTT-ATAA
1 AAAATCTGAATTTATTTGATAA
*
1845931 AAAATTCTTAATTTATTTGATAA
1 AAAA-TCTGAATTTATTTGATAA
1845954 AA
1 AA
1845956 TAGAGATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 5 0.24
22 6 0.29
23 6 0.29
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (22 bp):
AAAATCTGAATTTATTTGATAA
Found at i:1848381 original size:23 final size:23
Alignment explanation
Indices: 1848355--1848417 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1848345 AATTTTATAT
* *
1848355 GGCACTACAGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
1848378 GGCACTTTGGTGCAATTCTAGGT
1 GGCACTTCGGTGCAATTCTACGC
1848401 GGCACTTCGGTGCAATT
1 GGCACTTCGGTGCAATT
1848418 TATACGAGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:1848943 original size:21 final size:21
Alignment explanation
Indices: 1848917--1848958 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1848907 ATTTAATGAG
1848917 TTTATATAAATTGGTCGAAAT
1 TTTATATAAATTGGTCGAAAT
*
1848938 TTTATATAAGTTGGTCGAAAT
1 TTTATATAAATTGGTCGAAAT
1848959 ACTGTAGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.43
Consensus pattern (21 bp):
TTTATATAAATTGGTCGAAAT
Found at i:1849446 original size:68 final size:68
Alignment explanation
Indices: 1849337--1849472 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 68
1849327 AAGAGCTAAT
* *
1849337 GGAGGAAGAAAATGGAAATGCCGTGGAAAATAAGAAAATGAGTAGTAATGATGCTGGAAGTTCTG
1 GGAGGAAGAAAAAGGAAATGCCATGGAAAATAAGAAAATGAGTAGTAATGATGCTGGAAGTTCTG
1849402 TTA
66 TTA
*
1849405 GGAGGAAGAAAAAGGTAATGCCATGGAAAATAAGAAAATGAGTAGTAATGATGCTGGAAGTTCTG
1 GGAGGAAGAAAAAGGAAATGCCATGGAAAATAAGAAAATGAGTAGTAATGATGCTGGAAGTTCTG
1849470 TTA
66 TTA
1849473 AGAAGAAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.42, C:0.06, G:0.30, T:0.22
Consensus pattern (68 bp):
GGAGGAAGAAAAAGGAAATGCCATGGAAAATAAGAAAATGAGTAGTAATGATGCTGGAAGTTCTG
TTA
Found at i:1850855 original size:20 final size:21
Alignment explanation
Indices: 1850810--1850855 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
1850800 ACAACAAATC
1850810 ATTTTTGATTTCATTAATAGTT
1 ATTTTTGATTT-ATTAATAGTT
1850832 -TTTTTAGATTT-TTAAT-GTT
1 ATTTTT-GATTTATTAATAGTT
1850851 ATTTT
1 ATTTT
1850856 CCCTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 5 0.23
22 5 0.23
ACGTcount: A:0.24, C:0.02, G:0.09, T:0.65
Consensus pattern (21 bp):
ATTTTTGATTTATTAATAGTT
Found at i:1858966 original size:5 final size:5
Alignment explanation
Indices: 1858956--1858982 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1858946 CCGTATACTT
1858956 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1858983 ATATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1858989 original size:2 final size:2
Alignment explanation
Indices: 1858982--1859034 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1858972 TTTATTTTAT
1858982 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1859024 TA TA TA T- TA TA
1 TA TA TA TA TA TA
1859035 GTTTGCAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1859138 original size:73 final size:71
Alignment explanation
Indices: 1859048--1859301 Score: 253
Period size: 75 Copynumber: 3.5 Consensus size: 71
1859038 TGCAAATGAT
*
1859048 TTTTGAAATAGATATATAATATATAATTTTTGAAAGCA-TTTGAATATATATATATTATATAATT
1 TTTTGAAA-ATATATATAATATATAA-TTTTGAAAGCATTTTGAA-ATATATATATTATATAATT
*
1859112 TTTAAAACA
63 TTTAAAATA
* * *
1859121 TTTTG-AAATATATATATATAATATAGATTTTGAATGCATTTTGAAAAATATATATAATATATAG
1 TTTTGAAAATATATATA-AT-ATATA-ATTTTGAAAGCATTTTG--AAATATATATATTATATAA
*
1859185 TTTTTAAAATG
61 TTTTTAAAATA
* * * * * *
1859196 TTTTGAAAA-CTATATAATATATAATTTTGAAAACATTTTTAAAAATATATATAATATATAGTTT
1 TTTTGAAAATATATATAATATATAATTTTGAAAGCATTTTGAAATATATATATTATATA-ATTTT
1859260 TAAAATA
65 TAAAATA
* **
1859267 TTATTTGAAAATATATATATTATATGGTTTTGAAA
1 -T-TTTGAAAATATATATAATATATAATTTTGAAA
1859302 ATAATTTTTA
Statistics
Matches: 150, Mismatches: 20, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
70 15 0.10
71 17 0.11
72 19 0.13
73 33 0.22
74 26 0.17
75 35 0.23
76 5 0.03
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (71 bp):
TTTTGAAAATATATATAATATATAATTTTGAAAGCATTTTGAAATATATATATTATATAATTTTT
AAAATA
Found at i:1859146 original size:111 final size:108
Alignment explanation
Indices: 1859017--1859291 Score: 301
Period size: 111 Copynumber: 2.5 Consensus size: 108
1859007 ATATATATAT
* * *
1859017 ATATATATATATATTATAGTTTGCAAATGATTTTTGAAATAGATATATAATATATAATTTTTGAA
1 ATATATATATATAATATAGTTTG-AAATGATTTTTGAAA-ATATATATAATATATAATTTTTAAA
* *
1859082 A-GCATTTGAATATA-TATATATTATATAATTTTTAAAACATTTTGAA
64 ATG-ATTTGAA-A-ACTATATAATATATAATTTTGAAAACATTTTGAA
*
1859128 ATATATATATATAATATAGATTTTG-AATGCA-TTTTGAAAAATATATATAATATATAGTTTTTA
1 ATATATATATATAATATAG--TTTGAAATG-ATTTTTG-AAAATATATATAATATATAATTTTTA
* *
1859191 AAATGTTTTGAAAACTATATAATATATAATTTTGAAAACATTTTTAA
62 AAATGATTTGAAAACTATATAATATATAATTTTGAAAACATTTTGAA
* * *
1859238 AAATATATATA-ATATATAGTTTTAAAAT-ATTATTTGAAAATATATATATTATAT
1 ATATATATATATA-ATATAG-TTTGAAATGATT-TTTGAAAATATATATAATATAT
1859292 GGTTTTGAAA
Statistics
Matches: 143, Mismatches: 11, Indels: 22
0.81 0.06 0.12
Matches are distributed among these distances:
108 1 0.01
109 24 0.17
110 53 0.37
111 56 0.39
112 5 0.03
113 4 0.03
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (108 bp):
ATATATATATATAATATAGTTTGAAATGATTTTTGAAAATATATATAATATATAATTTTTAAAAT
GATTTGAAAACTATATAATATATAATTTTGAAAACATTTTGAA
Found at i:1859297 original size:37 final size:37
Alignment explanation
Indices: 1859017--1859341 Score: 240
Period size: 37 Copynumber: 8.7 Consensus size: 37
1859007 ATATATATAT
**
1859017 ATATATATATATATTATAG-TTTGCAAATGATTTTTGAAA
1 ATATATATAT-TA-TATAGTTTTTAAAAT-ATTTTTGAAA
* * * ** *
1859056 TAGATATATAATATATAATTTTTGAAAGCA--TTTGAAT
1 -ATATATATATTATATAGTTTTT-AAAATATTTTTGAAA
* *
1859093 ATATATATATTATATAATTTTTAAAACA-TTTTGAAA
1 ATATATATATTATATAGTTTTTAAAATATTTTTGAAA
* * *
1859129 TATATATATATAATATAGATTTT-GAATGCA-TTTTGAAAA
1 -ATATATATATTATATAGTTTTTAAAAT--ATTTTTG-AAA
* *
1859168 ATATATATAATATATAGTTTTTAAAAT-GTTTTGAAA
1 ATATATATATTATATAGTTTTTAAAATATTTTTGAAA
* * * *
1859204 ACTATATA-A-TATATAATTTTGAAAACATTTTTAAAA
1 A-TATATATATTATATAGTTTTTAAAATATTTTTGAAA
*
1859240 ATATATATAATATATAG-TTTTAAAATATTATTTGAAA
1 ATATATATATTATATAGTTTTTAAAATATT-TTTGAAA
* *
1859277 ATATATATATTATATGGTTTTGAAAATAATTTTT-AAA
1 ATATATATATTATATAGTTTTTAAAAT-ATTTTTGAAA
* *
1859314 AGCATATATAGTATATAGTTTTTAAAAT
1 A-TATATATATTATATAGTTTTTAAAAT
1859342 GTTCTTTTTT
Statistics
Matches: 231, Mismatches: 37, Indels: 36
0.76 0.12 0.12
Matches are distributed among these distances:
35 25 0.11
36 52 0.23
37 67 0.29
38 62 0.27
39 15 0.06
40 10 0.04
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (37 bp):
ATATATATATTATATAGTTTTTAAAATATTTTTGAAA
Found at i:1859402 original size:21 final size:22
Alignment explanation
Indices: 1859352--1859407 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
1859342 GTTCTTTTTT
1859352 TTTATCTTTT-TTTTATATATTA
1 TTTAT-TTTTATTTTATATATTA
*
1859374 TTTA-TTTTATTTTA-CTATTA
1 TTTATTTTTATTTTATATATTA
1859394 TTTATTTTTATTTT
1 TTTATTTTTATTTT
1859408 TTTACTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 13 0.42
21 14 0.45
22 4 0.13
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTATTTTTATTTTATATATTA
Found at i:1860541 original size:2 final size:2
Alignment explanation
Indices: 1860534--1860590 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1860524 ATAGTCACCT
1860534 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1860576 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1860591 GTGTGTGTGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1860595 original size:2 final size:2
Alignment explanation
Indices: 1860590--1860614 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1860580 TATATATATA
1860590 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1860615 TTTTAATATT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1860795 original size:16 final size:16
Alignment explanation
Indices: 1860750--1860805 Score: 51
Period size: 18 Copynumber: 3.4 Consensus size: 16
1860740 TTTATTTAAT
**
1860750 TTTTTTATTTTATGTTT
1 TTTTTTATTTTAT-TCA
1860767 TTATTTTATTTTATCTCA
1 TT-TTTTATTTTAT-TCA
*
1860785 TTTTTTA-TTTATTTA
1 TTTTTTATTTTATTCA
1860800 TTTTTT
1 TTTTTT
1860806 TCCTTTGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 8 0.24
16 5 0.15
17 7 0.21
18 14 0.41
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTTTATTTTATTCA
Found at i:1860804 original size:26 final size:26
Alignment explanation
Indices: 1860737--1860804 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 26
1860727 TAAATTTAAC
* * *
1860737 TTTTTTATTTAATT-TTTTTATTTTA
1 TTTTTTATTTATTTATTTTTATCTCA
1860762 TGTTTTTA--T-TTTA-TTTTATCTCA
1 T-TTTTTATTTATTTATTTTTATCTCA
1860785 TTTTTTATTTATTTATTTTT
1 TTTTTTATTTATTTATTTTT
1860805 TTCCTTTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
22 6 0.18
23 11 0.32
24 2 0.06
25 5 0.15
26 10 0.29
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (26 bp):
TTTTTTATTTATTTATTTTTATCTCA
Found at i:1860847 original size:13 final size:13
Alignment explanation
Indices: 1860673--1860895 Score: 97
Period size: 13 Copynumber: 16.8 Consensus size: 13
1860663 TTGTTTATTT
1860673 TTTTA-TTTTTTA
1 TTTTATTTTTTTA
*
1860685 TTATT-TCTTTTTA
1 TT-TTATTTTTTTA
1860698 TTTCATATTGTTTTTA
1 TTT--TATT-TTTTTA
*
1860714 TTTTAGTACTTTTTAAA
1 TTTTA-T--TTTTT-TA
* *
1860731 TTTAACTTTTTTA
1 TTTTATTTTTTTA
*
1860744 TTTAATTTTTTTA
1 TTTTATTTTTTTA
*
1860757 TTTTATGTTTTTA
1 TTTTATTTTTTTA
*
1860770 TTTTATTTTATCTCA
1 TTTTATTTT-T-TTA
*
1860785 -TTT-TTTATTTA
1 TTTTATTTTTTTA
*
1860796 -TTTATTTTTTTCC
1 TTTTATTTTTTT-A
* *
1860809 TTTGATTTGATTTGA
1 TTTTATTT--TTTTA
*
1860824 TTTGA-TTTTTTA
1 TTTTATTTTTTTA
1860836 TTTTATTTTTTTA
1 TTTTATTTTTTTA
* *
1860849 CTTTA--TTGTT-
1 TTTTATTTTTTTA
*
1860859 TTTTATGTTTTTA
1 TTTTATTTTTTTA
*
1860872 TATTTA-TTTATTA
1 T-TTTATTTTTTTA
1860885 TTATTATTTTT
1 TT-TTATTTTT
1860896 CCTTTTTTTC
Statistics
Matches: 160, Mismatches: 27, Indels: 46
0.69 0.12 0.20
Matches are distributed among these distances:
10 4 0.03
11 9 0.06
12 23 0.14
13 66 0.41
14 27 0.17
15 9 0.06
16 16 0.10
17 6 0.04
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:1860894 original size:24 final size:21
Alignment explanation
Indices: 1860666--1860895 Score: 68
Period size: 22 Copynumber: 10.4 Consensus size: 21
1860656 AATTTGTTTG
1860666 TTTATTTTTTTATTT-TTTAT
1 TTTATTTTTTTATTTATTTAT
* *
1860686 TATT-TCTTTTTATTTCATATTGTT
1 T-TTATTTTTTTATTT-AT-TT-AT
** *
1860710 TTTATTTTAGTACTTT-TTAAAT
1 TTTATTTTTTTA-TTTATT-TAT
* *
1860732 TTAACTTTTTTATTTAATTT-T
1 TTTATTTTTTTATTT-ATTTAT
1860753 TTTATTTTATGTT-TTTATTTTAT
1 TTTATTTT-T-TTATTTA-TTTAT
1860776 TTTATCTCATTTTTTATTTATTTAT
1 TTTA--T--TTTTTTATTTATTTAT
*
1860801 TTT-TTTCCTTTGATTTGATTTGAT
1 TTTATTT--TTTTATTT-ATTT-AT
*
1860825 TTGA-TTTTTTATTTTATTT-T
1 TTTATTTTTTTA-TTTATTTAT
* * *
1860845 TTTACTTTATTGTTT-TTTAT
1 TTTATTTTTTTATTTATTTAT
*
1860865 GTTT-TTATATTTATTTA-TTAT
1 -TTTATT-TTTTTATTTATTTAT
1860886 TATTATTTTT
1 T-TTATTTTT
1860896 CCTTTTTTTC
Statistics
Matches: 153, Mismatches: 25, Indels: 63
0.63 0.10 0.26
Matches are distributed among these distances:
19 3 0.02
20 23 0.15
21 35 0.23
22 36 0.24
23 21 0.14
24 13 0.08
25 14 0.09
26 5 0.03
27 3 0.02
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTATTTTTTTATTTATTTAT
Found at i:1864095 original size:16 final size:16
Alignment explanation
Indices: 1864074--1864116 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1864064 AACTGGTATT
* *
1864074 ACCTGACTTGTTTTCA
1 ACCTGACCTGTTATCA
*
1864090 ACCTGACCTGTTATGA
1 ACCTGACCTGTTATCA
1864106 ACCTGACCTGT
1 ACCTGACCTGT
1864117 AATTGACTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (16 bp):
ACCTGACCTGTTATCA
Found at i:1865165 original size:20 final size:20
Alignment explanation
Indices: 1865140--1865200 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
1865130 AACCCTTACA
**
1865140 AATATCAAGTAGAAGCAAGC
1 AATATCAAACAGAAGCAAGC
*
1865160 AATATCAAACAGAAGCAAAC
1 AATATCAAACAGAAGCAAGC
*
1865180 AATATAAAACAGAAGCAAGC
1 AATATCAAACAGAAGCAAGC
1865200 A
1 A
1865201 GAATTAAGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.57, C:0.16, G:0.15, T:0.11
Consensus pattern (20 bp):
AATATCAAACAGAAGCAAGC
Found at i:1865580 original size:31 final size:31
Alignment explanation
Indices: 1865535--1865650 Score: 178
Period size: 31 Copynumber: 3.7 Consensus size: 31
1865525 TTCGTCCTGG
1865535 TTTATTGTTGTTGATGTAAATGATGTACTGA
1 TTTATTGTTGTTGATGTAAATGATGTACTGA
* * * *
1865566 TTTATTGCTATTGATGTAAATGATGTATTAA
1 TTTATTGTTGTTGATGTAAATGATGTACTGA
*
1865597 TTTATTGTTGTTGGTGTAAATGATGTACTGA
1 TTTATTGTTGTTGATGTAAATGATGTACTGA
*
1865628 TTTATTGTTGTTGTTGTAAATGA
1 TTTATTGTTGTTGATGTAAATGA
1865651 GGTAAACAAC
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.26, C:0.03, G:0.22, T:0.50
Consensus pattern (31 bp):
TTTATTGTTGTTGATGTAAATGATGTACTGA
Found at i:1866207 original size:210 final size:210
Alignment explanation
Indices: 1865733--1867262 Score: 2482
Period size: 210 Copynumber: 7.3 Consensus size: 210
1865723 TATTTTTCAT
* *
1865733 ATTTGATCACTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATATCATATTTGTTCAAT
1 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
*
1865798 TTAGTCCTCCACATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTATT-
66 TTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTT-TTA
* * * * * *
1865862 AATTTGCCCATAACTTTTTAAAT--G----AGTTAGTTCATTTTTGTATTAATTTCAACCTCAAA
130 AATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACA
1865921 ATTTAAAATTATTTCG
195 ATTTAAAATTATTTCG
* * *
1865937 GTTTGATCCCTTTTGTGTTGTTTAGTTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAAT
1 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
1866002 TTAGTCCTCCAAATGTTT-TTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTA
66 TTAGTCCTCCAAAT-TTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTA
1866066 AATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACA
130 AATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACA
1866131 ATTTAAAATTATTTCG
195 ATTTAAAATTATTTCG
* *
1866147 ATTTGATCCCTTTTGTATTTTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
1 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
*
1866212 TTAGTCCTCCAAATTTTATTTGCATCTAAAATTGA-CC---C--A-TACTTATTTCTATTTTTAA
66 TTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTAA
*
1866270 ATTGGTCCATAACTTTTTAAATGGGTATAATTTAGTAC-TTTTTGTATTAATTTCAACATCACAA
131 ATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAA
1866334 TTTAAAATTATTTCG
196 TTTAAAATTATTTCG
*
1866349 ATTTGATCCCTTTTGTGCTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
1 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
* *
1866414 TTAGTCCTCCAATTTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTAA
66 TTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTAA
*
1866479 ATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACATTTTTGTATTAATTTCAACATCACAA
131 ATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAA
*
1866544 TTTAAAATTGTTTCG
196 TTTAAAATTATTTCG
*
1866559 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAAT
1 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
* *
1866624 TTAGTCCTCCAATTTTTATTTGCATCTGAAATTGACCCATGCTTATTACTTATTTCTATTTTTAA
66 TTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTAA
*
1866689 ATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTTTATTAATTTCAACATCACAA
131 ATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAA
1866754 TTTAAAATTATTTCG
196 TTTAAAATTATTTCG
1866769 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
1 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
* *
1866834 TTAGTCCTCCAATTTTTATTTGCATATGAAATTGACCCATACTTATTACTTATTTCTATTTTTAA
66 TTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTAA
* *
1866899 ATTGGACCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCATAA
131 ATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAA
1866964 TTTAAAATTATTTCG
196 TTTAAAATTATTTCG
1866979 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
1 ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
* * * * * *
1867044 TTAGTCCTCCAAATTTTATTTGGATATGAAATTGATCCATACTTTTTACTTAATTCTATTTTTTA
66 TTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTAA
* * *
1867109 ATTGGCCCATATA-TTTTTAAATGGGTATACTTTAGTACTTTTTTGAATTAATTTCAACCTCACA
131 ATTGGCCCATA-ACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACA
*
1867173 ATTTAAAATTATTTCA
195 ATTTAAAATTATTTCG
* *
1867189 ATTTGATCCCTCATCAATGCGTGTTGTTTAATTTATTTAAATTTTTATTTTTAATTTCATATTTG
1 ATTTGATCCCT--T---T-TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTG
*
1867254 TTTAATTTA
60 TTCAATTTA
1867263 ATTCTTAAAT
Statistics
Matches: 1247, Mismatches: 55, Indels: 36
0.93 0.04 0.03
Matches are distributed among these distances:
202 136 0.11
203 60 0.05
204 139 0.11
205 3 0.00
206 3 0.00
208 1 0.00
209 60 0.05
210 790 0.63
211 1 0.00
212 1 0.00
215 1 0.00
216 52 0.04
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (210 bp):
ATTTGATCCCTTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAT
TTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTAA
ATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAA
TTTAAAATTATTTCG
Found at i:1869550 original size:22 final size:22
Alignment explanation
Indices: 1869521--1869582 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
1869511 AGGGTCTACG
*
1869521 AGGTCCTTCGGGACATATACA-
1 AGGTCCTTCGGGACAAATACAT
* *
1869542 ATGGTCCTTTGGGATAAATACAT
1 A-GGTCCTTCGGGACAAATACAT
*
1869565 AGGTCCTTCGGGATAAAT
1 AGGTCCTTCGGGACAAAT
1869583 TTCATATGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (22 bp):
AGGTCCTTCGGGACAAATACAT
Found at i:1871991 original size:59 final size:59
Alignment explanation
Indices: 1871891--1872253 Score: 380
Period size: 59 Copynumber: 6.2 Consensus size: 59
1871881 TGGTACTATA
*
1871891 TGTGCTAAAATGATAAGG-AATCATACTGAATGTATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATGGAGCACTGAG
*
1871949 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATGGAGCACTGAG
* *
1872008 TGTGCTAAAATGATAAGGAAAACATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATGGAGCACTGAG
* * * * * * * *
1872067 TGTGCTAAAATGATAAAGAAATCATATTGAATATATGTATTTCCAGAT-AAGGCA-TTATA
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATGGA-GCACTGA-G
* * * * * *** * *
1872126 TGTGCTAAAATGGTAAGGGAATCATACCGAGTGTAAT-GATTTCCAGAAAAATCACTAAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGT-ATGGATTTCCATATGGAGCACTGAG
* * * * *
1872185 GGTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGG-GCACTTCA-
1 TGTGCTAAAATGATAAGGAAATCATACTGAAT-GTATGGATTTCCATAT-GGAGCAC-TGAG
1872244 TGTGCTAAAA
1 TGTGCTAAAA
1872254 ATGGTAAAGG
Statistics
Matches: 254, Mismatches: 41, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
58 25 0.10
59 221 0.87
60 8 0.03
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATGGAGCACTGAG
Found at i:1872281 original size:60 final size:59
Alignment explanation
Indices: 1872199--1872373 Score: 224
Period size: 60 Copynumber: 2.9 Consensus size: 59
1872189 CTACAAGGAT
*
1872199 AAGGAAATCATACTAATAGTATGGATTTTCATATAGGGCACTTCATGTGCTAAAAATGGTA
1 AAGG-AATCATACTAATGGTATGGATTTTCA-ATAGGGCACTTCATGTGCTAAAAATGGTA
** * *
1872260 AAGGGGTCATACTAATGGTATGGATTCTCGAATAGGGCACTTCAGGTGCTAAAAATGGTA
1 AAGGAATCATACTAATGGTATGGATTTTC-AATAGGGCACTTCATGTGCTAAAAATGGTA
** * * *
1872320 AAGGAATCGCATTAATGGTATGGATTCTTGAATAGGGCACTTCGTGTGCTAAAA
1 AAGGAATCATACTAATGGTATGGATT-TTCAATAGGGCACTTCATGTGCTAAAA
1872374 TGAGAAGGAA
Statistics
Matches: 98, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
60 92 0.94
61 6 0.06
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (59 bp):
AAGGAATCATACTAATGGTATGGATTTTCAATAGGGCACTTCATGTGCTAAAAATGGTA
Found at i:1872593 original size:22 final size:22
Alignment explanation
Indices: 1872526--1872594 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
1872516 TCAGTGATGC
1872526 AAATTATAGTAAGTATATTGGT
1 AAATTATAGTAAGTATATTGGT
* ** **
1872548 AAA-TA-AGCTTACG-AGCTTATT
1 AAATTATAG--TAAGTATATTGGT
1872569 AAATTATAGTAAGTATATTGGT
1 AAATTATAGTAAGTATATTGGT
1872591 AAAT
1 AAAT
1872595 AAGCTTACGA
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
20 2 0.06
21 12 0.38
22 16 0.50
23 2 0.06
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (22 bp):
AAATTATAGTAAGTATATTGGT
Found at i:1872724 original size:44 final size:44
Alignment explanation
Indices: 1872534--1872898 Score: 473
Period size: 44 Copynumber: 8.3 Consensus size: 44
1872524 GCAAATTATA
** * *
1872534 GTAAGTATATTGGT-AAATAAGCTTACGAGCTTATTAAATTATA
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATG
* * *
1872577 GTAAGTATATTGGT-AAATAAGCTTACGAGCTTATGAAATTATA
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATG
* * *
1872620 GTAAGTATATTGATAAAATAAGCTTACGAGCTTAGGGATTTAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA-ATAATG
*
1872665 GTAAGTATATTGGTAAAATAAGCTTACGAGTTTATGGAATAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATG
* *
1872709 GTAAGTATATGGGTAAAATAAGCTTACGAGCTTATAGAATAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATG
* * * *
1872753 GTAAGCATATTGGTAAAATAAGCTTATGAGCATATGTAATAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATG
* * *
1872797 GTAAGTATATTGATAAAATAAGCTTACGAGCTTAGGGATTTAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA-ATAATG
* * *
1872842 GTAAGTATATTGGTAAAATAAGCTTAGGAGCTTATGGATTAAATA
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAAT-AATG
*
1872887 GTATGTATATTG
1 GTAAGTATATTG
1872899 ATAAGAAATT
Statistics
Matches: 286, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
43 55 0.19
44 139 0.49
45 92 0.32
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (44 bp):
GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATG
Done.