Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008316.1 Hibiscus syriacus cultivar Beakdansim tig00111013_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: 2380696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 12
Found at i:1089183 original size:22 final size:21
Alignment explanation
Indices: 1089149--1089191 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1089139 ATTTCATTAA
1089149 TATTATCGACGAACAACTTCAT
1 TATTATCGACGAACAA-TTCAT
*
1089171 TATTAT-GATCGAAGAATTCAT
1 TATTATCGA-CGAACAATTCAT
1089192 AAAATTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (21 bp):
TATTATCGACGAACAATTCAT
Found at i:1094843 original size:58 final size:58
Alignment explanation
Indices: 1094776--1094893 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
1094766 TGAGATATCT
1094776 TTTCTTTCTACAATCTTCTTATTTTGTTGAATTAGAATCTGCAAACTAGAGCAGATTC
1 TTTCTTTCTACAATCTTCTTATTTTGTTGAATTAGAATCTGCAAACTAGAGCAGATTC
*
1094834 TTTCTTTCTATAATCTTCTTATTTTGTTGAATTAGAATCTGCAAACTAGAGCAGATTC
1 TTTCTTTCTACAATCTTCTTATTTTGTTGAATTAGAATCTGCAAACTAGAGCAGATTC
1094892 TT
1 TT
1094894 CCACGTATAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (58 bp):
TTTCTTTCTACAATCTTCTTATTTTGTTGAATTAGAATCTGCAAACTAGAGCAGATTC
Found at i:1100727 original size:27 final size:26
Alignment explanation
Indices: 1100691--1100750 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 26
1100681 ATAATAAAAT
*
1100691 AATAATTATCAATGAATTTTTATTTA
1 AATAATTATCAATGAATTTTTATATA
*
1100717 AATATATTATCGATGAATTTTTATATA
1 AATA-ATTATCAATGAATTTTTATATA
1100744 AATAATT
1 AATAATT
1100751 TTTATTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (26 bp):
AATAATTATCAATGAATTTTTATATA
Found at i:1100752 original size:15 final size:15
Alignment explanation
Indices: 1100732--1100765 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1100722 ATTATCGATG
1100732 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1100747 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1100762 AATT
1 AATT
1100766 AGAATTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1101129 original size:19 final size:19
Alignment explanation
Indices: 1101101--1101144 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1101091 AATGATCAAT
* * *
1101101 AAATTCGCAACGCGATCTC
1 AAATTTGCAACACGAACTC
1101120 AAATTTGCAACACGAACTC
1 AAATTTGCAACACGAACTC
*
1101139 CAATTT
1 AAATTT
1101145 CGTAACCCAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.25
Consensus pattern (19 bp):
AAATTTGCAACACGAACTC
Found at i:1101245 original size:20 final size:20
Alignment explanation
Indices: 1101217--1101267 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1101207 CAACGCGGAA
*
1101217 TTTCAAATTCGTAACTAGAT
1 TTTCGAATTCGTAACTAGAT
1101237 TTTCGAATTCGTAACTAGAT
1 TTTCGAATTCGTAACTAGAT
1101257 TTTCGAATTCG
1 TTTCGAATTCG
1101268 CAACACGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
TTTCGAATTCGTAACTAGAT
Found at i:1101466 original size:14 final size:15
Alignment explanation
Indices: 1101447--1101484 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1101437 TCCCCATCTC
1101447 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1101461 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1101477 TAATTTTT
1 TAATTTTT
1101485 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1102254 original size:24 final size:24
Alignment explanation
Indices: 1102227--1102280 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1102217 GTATTCGAAA
1102227 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1102251 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1102275 TTTGAT
1 TTTGAT
1102281 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1103250 original size:20 final size:20
Alignment explanation
Indices: 1103183--1103265 Score: 94
Period size: 20 Copynumber: 4.1 Consensus size: 20
1103173 AATCATATTG
1103183 CCCAGGGGGTACAGATTCCAC
1 CCCAGGGGGTACAGATTCC-C
* * *
1103204 CCCAGGGGGTACATATTTCT
1 CCCAGGGGGTACAGATTCCC
* * *
1103224 TCTAGGGGGAACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
1103244 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
1103264 CC
1 CC
1103266 TGTCTAACGG
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
20 32 0.65
21 17 0.35
ACGTcount: A:0.20, C:0.33, G:0.28, T:0.19
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:1105160 original size:20 final size:20
Alignment explanation
Indices: 1105135--1105196 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 20
1105125 TCATATTGCA
1105135 CAGGGGGTACAGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
1105155 CAGGGGGTACAGATTCCCCCCC
1 CAGGGGGTACAGATT--CCCCC
*
1105177 CAGGGGGTACCGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
1105197 TGTCTAACGA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
20 20 0.51
22 19 0.49
ACGTcount: A:0.18, C:0.39, G:0.29, T:0.15
Consensus pattern (20 bp):
CAGGGGGTACAGATTCCCCC
Found at i:1105178 original size:22 final size:22
Alignment explanation
Indices: 1105135--1105196 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
1105125 TCATATTGCA
1105135 CAGGGGGTACAGATT--CCCCC
1 CAGGGGGTACAGATTCCCCCCC
1105155 CAGGGGGTACAGATTCCCCCCC
1 CAGGGGGTACAGATTCCCCCCC
*
1105177 CAGGGGGTACCGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
1105197 TGTCTAACGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 15 0.38
22 24 0.62
ACGTcount: A:0.18, C:0.39, G:0.29, T:0.15
Consensus pattern (22 bp):
CAGGGGGTACAGATTCCCCCCC
Found at i:1107919 original size:66 final size:66
Alignment explanation
Indices: 1107837--1108046 Score: 379
Period size: 66 Copynumber: 3.2 Consensus size: 66
1107827 AATTTAAAAC
1107837 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1107902 A
66 A
1107903 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1107968 A
66 A
* * *
1107969 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AACAAATAATTCTTATTTCCTCATC-AATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1108032 A
66 A
1108033 AACAAATCAACTTT
1 AACAAATCAACTTT
1108047 CAATGTAAAA
Statistics
Matches: 141, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
64 19 0.13
65 22 0.16
66 100 0.71
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.30
Consensus pattern (66 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
A
Found at i:1109460 original size:20 final size:21
Alignment explanation
Indices: 1109414--1109511 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
1109404 GCGGGCGGGA
* *
1109414 CCTCTTGAACGATGACAAGGG
1 CCTCTTGAACGATGAGAGGGG
*
1109435 CCTCTTGAACGGTG-GAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
1109455 CTTCTTTAATGATGAGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
1109476 CCTCTTGAATGAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
*
1109497 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
1109512 TAGGTGCATC
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
20 15 0.23
21 48 0.75
22 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:1109477 original size:41 final size:42
Alignment explanation
Indices: 1109414--1109511 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 42
1109404 GCGGGCGGGA
* * * * *
1109414 CCTCTTGAACGATGACAAGGGCCTCTTGAACGGT-GGAGGGG
1 CCTCTTGAATGATGAGAGGGGCCTCTTGAACGATAGGAGGCG
* * *
1109455 CTTCTTTAATGATGAGAGGGGCCTCTTGAATGATAGGAGGCG
1 CCTCTTGAATGATGAGAGGGGCCTCTTGAACGATAGGAGGCG
1109497 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
1109512 TAGGTGCATC
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
41 27 0.59
42 19 0.41
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (42 bp):
CCTCTTGAATGATGAGAGGGGCCTCTTGAACGATAGGAGGCG
Found at i:1111714 original size:19 final size:19
Alignment explanation
Indices: 1111662--1111716 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
1111652 GAGTAGTTTC
* *
1111662 TGAAACTTAAATTCGCAACG
1 TGAAAC-TAAAATCACAACG
* *
1111682 CGAAAATGAAAATCACAACG
1 TGAAACT-AAAATCACAACG
1111702 TGAAACTAAAATCAC
1 TGAAACTAAAATCAC
1111717 GTTGTGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.49, C:0.20, G:0.13, T:0.18
Consensus pattern (19 bp):
TGAAACTAAAATCACAACG
Found at i:1111745 original size:20 final size:21
Alignment explanation
Indices: 1111716--1111763 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
1111706 ACTAAAATCA
*
1111716 CGTTGTGATTTTCATTTTC-T
1 CGTTGCGATTTTCATTTTCGT
1111736 CGTTGCGATTTTCATTTTCGT
1 CGTTGCGATTTTCATTTTCGT
1111757 -GTTGCGA
1 CGTTGCGA
1111764 ATTTAAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.10, C:0.17, G:0.21, T:0.52
Consensus pattern (21 bp):
CGTTGCGATTTTCATTTTCGT
Found at i:1112137 original size:22 final size:22
Alignment explanation
Indices: 1112098--1112143 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1112088 GATGGAGATA
* *
1112098 GACGGATTTCGCCAGAGATGGG
1 GACGAATTTCGCCAGAGATAGG
* *
1112120 GACGAATTTCGTCGGAGATAGG
1 GACGAATTTCGCCAGAGATAGG
1112142 GA
1 GA
1112144 AGGATGTCGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.39, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCAGAGATAGG
Found at i:1112283 original size:20 final size:20
Alignment explanation
Indices: 1112258--1112419 Score: 168
Period size: 20 Copynumber: 8.1 Consensus size: 20
1112248 TAACATTATG
*
1112258 TTTCGCGTTACGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
1112278 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
1112298 TTTTGTGTTGAGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
1112318 TTTTGTGTTGCGAATTTGGC
1 TTTCGCGTTGCGAATTTGAC
*
1112338 TATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
1112358 TTAT-GTGTTGCG-ATTT-AC
1 TT-TCGCGTTGCGAATTTGAC
* *
1112376 AAATTCGCGTTGTGAATTTGAC
1 --TTTCGCGTTGCGAATTTGAC
*
1112398 TATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
1112418 TT
1 TT
1112420 CTGTGTTGCG
Statistics
Matches: 117, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
18 2 0.02
19 5 0.04
20 103 0.88
21 5 0.04
22 2 0.02
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:1112345 original size:60 final size:59
Alignment explanation
Indices: 1112259--1112441 Score: 224
Period size: 60 Copynumber: 3.1 Consensus size: 59
1112249 AACATTATGT
* * * *
1112259 TTCGCGTTACGAATTTGACTTTCGCGTTGCGAATTTGACTTTTGTGTTGAGAATTTGAC-T
1 TTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGAG-ATTT-ACAA
* * * *
1112319 TTTGTGTTGCGAATTTGGCTATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAA
1 TTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGAGATTTAC-AA
* * *
1112379 TTCGCGTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACATA
1 TTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGAGATTTACA-A
1112439 TTC
1 TTC
1112442 AAGTTGCAAA
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
58 2 0.02
59 5 0.05
60 100 0.93
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (59 bp):
TTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGAGATTTACAA
Found at i:1112471 original size:60 final size:60
Alignment explanation
Indices: 1112339--1112457 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
1112329 GAATTTGGCT
** ** * *
1112339 ATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGCGTTGTGAATTTGACT
1 ATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCAAGTTGAAAATTGGACA
* *
1112399 ATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACATATTCAAGTTGCAAAATTGGA
1 ATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCAAGTTG-AAAATTGGA
1112458 AACTGGGTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 45 0.88
61 6 0.12
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.39
Consensus pattern (60 bp):
ATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCAAGTTGAAAATTGGACA
Found at i:1112958 original size:32 final size:31
Alignment explanation
Indices: 1112909--1113016 Score: 119
Period size: 32 Copynumber: 3.4 Consensus size: 31
1112899 TATTTTTAAT
* *
1112909 TTAATTACT-TAACTTTCAAATTACTCATAA
1 TTAATCACTCTAAATTTCAAATTACTCATAA
* *
1112939 CTTAATCACTCTAAATTTCAAATTATTCCTAA
1 -TTAATCACTCTAAATTTCAAATTACTCATAA
* * *
1112971 TTTAATCACTTTAAATTTTAAATTACTCTTAA
1 -TTAATCACTCTAAATTTCAAATTACTCATAA
1113003 TGTAATCACTCTAA
1 T-TAATCACTCTAA
1113017 GGGGCAAATG
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
31 9 0.14
32 56 0.86
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.44
Consensus pattern (31 bp):
TTAATCACTCTAAATTTCAAATTACTCATAA
Found at i:1113025 original size:64 final size:63
Alignment explanation
Indices: 1112905--1113025 Score: 145
Period size: 64 Copynumber: 1.9 Consensus size: 63
1112895 TTATTATTTT
* * ***
1112905 TAATTTAATTACTTAACTTTCAAATTACTCATAACTTAATCACTCTAAATTTCAAATTATTCC
1 TAATTTAATCACTTAAATTTCAAATTACTCATAACTTAATCACTCTAAAGGGCAAATTATTCC
* * *
1112968 TAATTTAATCACTTTAAATTTTAAATTACTCTTAA-TGTAATCACTCTAAGGGGCAAAT
1 TAATTTAATCAC-TTAAATTTCAAATTACTCATAACT-TAATCACTCTAAAGGGCAAAT
1113026 GTTATACCCT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
63 12 0.25
64 36 0.75
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.41
Consensus pattern (63 bp):
TAATTTAATCACTTAAATTTCAAATTACTCATAACTTAATCACTCTAAAGGGCAAATTATTCC
Found at i:1113899 original size:19 final size:19
Alignment explanation
Indices: 1113875--1113911 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1113865 ATGACCAACA
*
1113875 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1113894 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1113912 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1114044 original size:21 final size:21
Alignment explanation
Indices: 1114018--1114154 Score: 174
Period size: 21 Copynumber: 6.6 Consensus size: 21
1114008 GAATATGTAA
1114018 ATCGCAACGCGATAACACGTG
1 ATCGCAACGCGATAACACGTG
1114039 ATCGCAACGCGATAACACGTG
1 ATCGCAACGCGATAACACGTG
1114060 ATCGCAACGCGATAACACGTG
1 ATCGCAACGCGATAACACGTG
**
1114081 ATCGCAACGCGATTATGAC-T-
1 ATCGCAACGCGA-TAACACGTG
* * *
1114101 ATCGCGACGCGATTCAGAC-T-
1 ATCGCAACGCGA-TAACACGTG
*
1114121 ATCGCAACGCGATAATACGTG
1 ATCGCAACGCGATAACACGTG
1114142 ATCGCAACGCGAT
1 ATCGCAACGCGAT
1114155 TCTGACTATC
Statistics
Matches: 105, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
19 4 0.04
20 29 0.28
21 68 0.65
22 4 0.04
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGATAACACGTG
Found at i:1114110 original size:20 final size:20
Alignment explanation
Indices: 1114081--1114206 Score: 157
Period size: 20 Copynumber: 6.2 Consensus size: 20
1114071 ATAACACGTG
1114081 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTATGACT
*
1114101 ATCGCGACGCGATTCA-GACT
1 ATCGCAACGCGATT-ATGACT
*
1114121 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTATGAC-T
*
1114141 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTATGACT
*
1114162 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACT
* *
1114182 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTATGACT
1114202 ATCGC
1 ATCGC
1114207 GTTGCGATAA
Statistics
Matches: 95, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.03
20 74 0.78
21 16 0.17
22 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:1114133 original size:61 final size:61
Alignment explanation
Indices: 1114060--1114190 Score: 226
Period size: 61 Copynumber: 2.1 Consensus size: 61
1114050 ATAACACGTG
*
1114060 ATCGCAACGCGATAACACGTGATCGCAACGCGATTATGACTATCGCGACGCGATTCAGACT
1 ATCGCAACGCGATAACACGTGATCGCAACGCGATTATGACTATCGCAACGCGATTCAGACT
* * *
1114121 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAACACGTGATCGCAACGCGATTATGACTATCGCAACGCGATTCAGACT
1114182 ATCGCAACG
1 ATCGCAACG
1114191 AGATTCTGAC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (61 bp):
ATCGCAACGCGATAACACGTGATCGCAACGCGATTATGACTATCGCAACGCGATTCAGACT
Found at i:1114146 original size:41 final size:41
Alignment explanation
Indices: 1114039--1114206 Score: 175
Period size: 41 Copynumber: 4.1 Consensus size: 41
1114029 ATAACACGTG
* * *
1114039 ATCGCAACGCGATAACACGTGATCGCAACGCGA-TAACACGT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCAGAC-T
* *
1114080 GATCGCAACGCGATTATGAC-T-ATCGCGACGCGATTCAGACT
1 -ATCGCAACGCGATAAT-ACGTGATCGCAACGCGATTCAGACT
*
1114121 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCAGACT
** * *
1114162 ATCGCAACGCGATTCTGAC-T-ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATAAT-ACGTGATCGCAACGCGATTCAGACT
1114202 ATCGC
1 ATCGC
1114207 GTTGCGATAA
Statistics
Matches: 110, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
39 2 0.02
40 40 0.36
41 45 0.41
42 21 0.19
43 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATAATACGTGATCGCAACGCGATTCAGACT
Found at i:1114218 original size:81 final size:82
Alignment explanation
Indices: 1114039--1114206 Score: 243
Period size: 81 Copynumber: 2.1 Consensus size: 82
1114029 ATAACACGTG
*
1114039 ATCGCAACGCGATAACACGTGATCGCAACGCGATAACACGTGATCGCAACGCGATTATGACTATC
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATAACACGTGATCGCAACGCGATTATGACTATC
* *
1114104 GCGACGCGATTCAGACT
66 GCAACGAGATTCAGACT
* *
1114121 ATCGCAACGCGATAATACGTGATCGCAACGCGAT-TCTGAC-T-ATCGCAACGCGATTCTGACTA
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATAAC--ACGTGATCGCAACGCGATTATGACTA
*
1114183 TCGCAACGAGATTCTGACT
64 TCGCAACGAGATTCAGACT
1114202 ATCGC
1 ATCGC
1114207 GTTGCGATAA
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
81 42 0.54
82 34 0.44
83 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (82 bp):
ATCGCAACGCGATAATACGTGATCGCAACGCGATAACACGTGATCGCAACGCGATTATGACTATC
GCAACGAGATTCAGACT
Found at i:1114227 original size:81 final size:81
Alignment explanation
Indices: 1114081--1114236 Score: 204
Period size: 81 Copynumber: 1.9 Consensus size: 81
1114071 ATAACACGTG
* * ***
1114081 ATCGCAACGCGATTATGACTATCGCGACGCGATTCAGACTATCGCAACGCGATAATACGTGATCG
1 ATCGCAACGCGATTATGACTATCGCAACGAGATTCAGACTATCGCAACGCGATAATACAAAATCG
1114146 CAACGCGATTCTGACT
66 CAACGCGATTCTGACT
* * *** *
1114162 ATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACTATCGCGTTGCGATAATATAAAATCG
1 ATCGCAACGCGATTATGACTATCGCAACGAGATTCAGACTATCGCAACGCGATAATACAAAATCG
*
1114227 CAATGCGATT
66 CAACGCGATT
1114237 TTCAAAGCGC
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 63 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (81 bp):
ATCGCAACGCGATTATGACTATCGCAACGAGATTCAGACTATCGCAACGCGATAATACAAAATCG
CAACGCGATTCTGACT
Found at i:1114402 original size:22 final size:22
Alignment explanation
Indices: 1114376--1114448 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
1114366 CTACGGCGAC
* *
1114376 ATCCGTCCTCATCTCTGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* **
1114398 ATCCGTCCCCATTTCCGGTGAA
1 ATCCGTCCCCATCTCCGACGAA
1114420 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
1114442 ATTCGTC
1 ATCCGTC
1114449 TATCTCCTTC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1114827 original size:33 final size:34
Alignment explanation
Indices: 1114778--1114860 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 34
1114768 CGCAACGACG
1114778 AAATTCGCGTTGCGATTATCTCGTTGCGATAG-C
1 AAATTCGCGTTGCGATTATCTCGTTGCGATAGTC
* * *
1114811 CATTTCGCGTTACGATTATCTCGTTGCGATAGTC
1 AAATTCGCGTTGCGATTATCTCGTTGCGATAGTC
1114845 AAATTCGCGTTGCGAT
1 AAATTCGCGTTGCGAT
1114861 AATCATTTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 29 0.67
34 14 0.33
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (34 bp):
AAATTCGCGTTGCGATTATCTCGTTGCGATAGTC
Found at i:1114871 original size:20 final size:20
Alignment explanation
Indices: 1114832--1114900 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
1114822 ACGATTATCT
* **
1114832 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATCATTTTCG
1114852 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCATTTTCG
* * **
1114872 TGTTGCGCTTTTCATTTTCG
1 CGTTGCGATAATCATTTTCG
*
1114892 TGTTGCGAT
1 CGTTGCGAT
1114901 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAATCATTTTCG
Found at i:1114903 original size:20 final size:20
Alignment explanation
Indices: 1114848--1114903 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1114838 GATAGTCAAA
* **
1114848 TTCGCGTTGCGATAATCATT
1 TTCGTGTTGCGATTTTCATT
*
1114868 TTCGTGTTGCGCTTTTCATT
1 TTCGTGTTGCGATTTTCATT
1114888 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
1114904 AAGTTTCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.18, G:0.21, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1114910 original size:20 final size:20
Alignment explanation
Indices: 1114867--1114910 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1114857 CGATAATCAT
* * *
1114867 TTTCGTGTTGCGCTTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1114887 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1114907 TTTC
1 TTTC
1114911 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.16, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1116305 original size:21 final size:20
Alignment explanation
Indices: 1116234--1116306 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
1116224 CTCCACTTCG
1116234 AGAGCCATCACCTCAC--CC
1 AGAGCCATCACCTCACAACC
*
1116252 AGAGCCATCACCTGATCAACC
1 AGAGCCATCACCTCA-CAACC
* * *
1116273 ACA-CTATACACCTCTACAACG
1 AGAGCCAT-CACCTC-ACAACC
1116294 AGAGCCATCACCT
1 AGAGCCATCACCT
1116307 ATTCTGTAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 14 0.33
19 1 0.02
20 3 0.07
21 20 0.48
22 4 0.10
ACGTcount: A:0.33, C:0.41, G:0.11, T:0.15
Consensus pattern (20 bp):
AGAGCCATCACCTCACAACC
Found at i:1116927 original size:20 final size:20
Alignment explanation
Indices: 1116902--1117041 Score: 78
Period size: 20 Copynumber: 7.3 Consensus size: 20
1116892 AGAATAATAG
*
1116902 TCGCAACACGAAAATGATTA
1 TCGCAACACGAAAATGACTA
* **
1116922 TCGCAACGCGAATTTGACTA
1 TCGCAACACGAAAATGACTA
* *
1116942 TCGCAACGC-AAATTTGACTA
1 TCGCAACACGAAA-ATGACTA
**
1116962 TCGC-A-ACG-GGAT-A--A
1 TCGCAACACGAAAATGACTA
** *
1116976 TCGCAATGCGAAAACGACTA
1 TCGCAACACGAAAATGACTA
*
1116996 TCGCAACACGGAAATGACTA
1 TCGCAACACGAAAATGACTA
* * **
1117016 TCGTAACGCGAATTTGACTA
1 TCGCAACACGAAAATGACTA
1117036 TCGCAA
1 TCGCAA
1117042 TGGGATAATC
Statistics
Matches: 89, Mismatches: 23, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
14 5 0.06
15 1 0.01
16 3 0.03
17 2 0.02
18 2 0.02
19 3 0.03
20 73 0.82
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1117024 original size:74 final size:74
Alignment explanation
Indices: 1116910--1117082 Score: 249
Period size: 74 Copynumber: 2.3 Consensus size: 74
1116900 AGTCGCAACA
* * *
1116910 CGAAAATGATTATCGCAACGCGAATTTGACTATCGCAACGCAAATTTGACTATCGCAACGGGATA
1 CGAAAATGACTATCGCAACACGAATATGACTATCGCAACGCAAATTTGACTATCGCAACGGGATA
1116975 ATCGCAATG
66 ATCGCAATG
* * * *
1116984 CGAAAACGACTATCGCAACACGGAA-ATGACTATCGTAACGCGAATTTGACTATCGCAATGGGAT
1 CGAAAATGACTATCGCAACAC-GAATATGACTATCGCAACGCAAATTTGACTATCGCAACGGGAT
1117048 AATCGCAATG
65 AATCGCAATG
* *
1117058 CTAAAATGACTATCGCAACGCGAAT
1 CGAAAATGACTATCGCAACACGAAT
1117083 TTAGTTTCGC
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
73 3 0.03
74 81 0.93
75 3 0.03
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (74 bp):
CGAAAATGACTATCGCAACACGAATATGACTATCGCAACGCAAATTTGACTATCGCAACGGGATA
ATCGCAATG
Found at i:1117099 original size:19 final size:19
Alignment explanation
Indices: 1117086--1117138 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
1117076 CGCGAATTTA
1117086 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
1117105 GTTTCGCGTTGCTATTTTG
1 GTTTCGCGTTGCGATTTTG
1117124 GTTTCGCGTTGCGAT
1 GTTTCGCGTTGCGAT
1117139 AGTCATTTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.06, C:0.17, G:0.30, T:0.47
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:1117147 original size:19 final size:19
Alignment explanation
Indices: 1117125--1117199 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 19
1117115 GCTATTTTGG
1117125 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
*
1117144 TTTCGCATTGCGAT--T-A
1 TTTCGCGTTGCGATAGTCA
*
1117160 --TCTCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTC-A
* * *
1117178 ATTCGCTTTGCGATAATCA
1 TTTCGCGTTGCGATAGTCA
1117197 TTT
1 TTT
1117200 TTGTGTTGCG
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
14 10 0.23
16 2 0.05
17 1 0.02
18 1 0.02
19 16 0.37
20 13 0.30
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:1117225 original size:20 final size:20
Alignment explanation
Indices: 1117202--1117241 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1117192 AATCATTTTT
1117202 GTGTTGCGATTTTAAGTTTC
1 GTGTTGCGATTTTAAGTTTC
1117222 GTGTTGCGATTTTAAGTTTC
1 GTGTTGCGATTTTAAGTTTC
1117242 ATAAACTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.25, T:0.50
Consensus pattern (20 bp):
GTGTTGCGATTTTAAGTTTC
Found at i:1117813 original size:21 final size:21
Alignment explanation
Indices: 1117722--1117818 Score: 104
Period size: 21 Copynumber: 4.6 Consensus size: 21
1117712 AACTCATCTG
*
1117722 TCATCGTTCAAGAGGCCTCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
1117743 TTATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1117764 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
1117785 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
*
1117806 TCATCGTTGAAGA
1 TCATCGTTCAAGA
1117819 CGTCCCTCCC
Statistics
Matches: 59, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1119284 original size:36 final size:30
Alignment explanation
Indices: 1119204--1119269 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
1119194 ATAAGAGTTG
* *
1119204 ATTTGTTTAATTAATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
1119234 ATTTGTTTAATTGATGTGTAAATAATTATT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
1119264 ATTTGT
1 ATTTGT
1119270 GCTTGTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTATT
Found at i:1119446 original size:20 final size:20
Alignment explanation
Indices: 1119419--1119682 Score: 243
Period size: 20 Copynumber: 13.8 Consensus size: 20
1119409 GTGATTTTCT
1119419 CGTTGCGATAGTCAAATTC-
1 CGTTGCGATAGTCAAATTCG
* *
1119438 CTATTGCGATAATCAAATTCG
1 C-GTTGCGATAGTCAAATTCG
* *
1119459 CGTTGTGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
1119478 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1119498 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1119518 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
1119538 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
1119552 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1119572 CGTTGCGATAGTC--ATT--
1 CGTTGCGATAGTCAAATTCG
* * * *
1119588 -TTTGC-ATTG-CAATTATCC
1 CGTTGCGATAGTCAAAT-TCG
* *
1119606 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
1119626 CATTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
1119646 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
1119666 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
1119683 GAATGTGTAA
Statistics
Matches: 197, Mismatches: 31, Indels: 33
0.75 0.12 0.13
Matches are distributed among these distances:
13 1 0.01
14 13 0.07
15 5 0.03
16 2 0.01
18 4 0.02
19 23 0.12
20 144 0.73
21 5 0.03
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1119575 original size:54 final size:54
Alignment explanation
Indices: 1119441--1119654 Score: 259
Period size: 54 Copynumber: 3.9 Consensus size: 54
1119431 CAAATTCCTA
* * * *
1119441 TTGCGATAATCAAATTCGCGTTGTGATAGTCA-TTTCGCGTTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT--T---A-TCCCG
*
1119500 TTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCG
* *
1119554 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTTGCATTGCAATTATCCCG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCG
* * * * *
1119608 TTGCGATATTCAAATTCACATTGCGATAGTCATATTCGCGTTGCGAT
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT
1119655 AGTCATATTC
Statistics
Matches: 139, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
54 95 0.68
55 1 0.01
58 1 0.01
59 29 0.21
60 13 0.09
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (54 bp):
TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCG
Found at i:1122176 original size:24 final size:24
Alignment explanation
Indices: 1122142--1122195 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1122132 CTGAAACATC
1122142 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1122166 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1122190 ATCAAA
1 ATCAAA
1122196 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1123037 original size:20 final size:20
Alignment explanation
Indices: 1123007--1123154 Score: 174
Period size: 20 Copynumber: 7.3 Consensus size: 20
1122997 AATTCAGTTA
*
1123007 TGCGTTAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
*
1123027 TGCAATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
**
1123047 TGCGATCACGT-ATTATCGCGT
1 TGCGAT-A-GTCAGAATCGCGT
*
1123068 TGCGATAGTCAGAATCTCGT
1 TGCGATAGTCAGAATCGCGT
1123088 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
**
1123108 TGCGATCACGT-ATTATCGCGT
1 TGCGAT-A-GTCAGAATCGCGT
*
1123129 TGCGATAGTCCGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
1123149 TGCGAT
1 TGCGAT
1123155 CACGTGTTAT
Statistics
Matches: 108, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
19 4 0.04
20 70 0.65
21 30 0.28
22 4 0.04
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:1123130 original size:41 final size:40
Alignment explanation
Indices: 1123007--1123154 Score: 174
Period size: 41 Copynumber: 3.6 Consensus size: 40
1122997 AATTCAGTTA
* *
1123007 TGCGTTAGTCAGAATCGCGTTGCAATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGT
** *
1123047 TGCGATCACGT-ATTATCGCGTTGCGATAGTCAGAATCTCGT
1 TGCGAT-A-GTCAGAATCGCGTTGCGATAGTCAGAATCGCGT
**
1123088 TGCGATAGTCAGAATCGCGTTGCGATCACGT-ATTATCGCGT
1 TGCGATAGTCAGAATCGCGTTGCGAT-A-GTCAGAATCGCGT
*
1123129 TGCGATAGTCCGAATCGCGTTGCGAT
1 TGCGATAGTCAGAATCGCGTTGCGAT
1123155 CACGTGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
39 2 0.02
40 20 0.22
41 66 0.72
42 4 0.04
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (40 bp):
TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGT
Found at i:1123152 original size:61 final size:61
Alignment explanation
Indices: 1123007--1123154 Score: 260
Period size: 61 Copynumber: 2.4 Consensus size: 61
1122997 AATTCAGTTA
* *
1123007 TGCGTTAGTCAGAATCGCGTTGCAATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
1 TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
*
1123068 TGCGATAGTCAGAATCTCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
1 TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
*
1123129 TGCGATAGTCCGAATCGCGTTGCGAT
1 TGCGATAGTCAGAATCGCGTTGCGAT
1123155 CACGTGTTAT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 82 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (61 bp):
TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
Found at i:1123155 original size:41 final size:41
Alignment explanation
Indices: 1123085--1123175 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 41
1123075 GTCAGAATCT
*
1123085 CGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCG
1 CGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCA
* *
1123126 CGTTGCGATAGTCCGAATCGCGTTGCGATCACGTGTTATCA
1 CGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCA
*
1123167 TGTTGCGAT
1 CGTTGCGAT
1123176 TTACATATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (41 bp):
CGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCA
Found at i:1123253 original size:21 final size:21
Alignment explanation
Indices: 1123184--1123256 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
1123174 ATTTACATAT
* *
1123184 TCGCATTGC-GATTATCTAAAA
1 TCGCAATGCGGATT-TCGAAAA
* *
1123205 TCGCAACGCAGATTTCGAAAA
1 TCGCAATGCGGATTTCGAAAA
*
1123226 TCGCAATGCGGATTTTGAAAA
1 TCGCAATGCGGATTTCGAAAA
1123247 TCGCAATGCG
1 TCGCAATGCG
1123257 ATGGTCAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 41 0.91
22 4 0.09
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGGATTTCGAAAA
Found at i:1129152 original size:4 final size:4
Alignment explanation
Indices: 1129143--1129172 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1129133 AATCAACAAA
1129143 AATT AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
1129173 AACAAAACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:1131094 original size:28 final size:28
Alignment explanation
Indices: 1131063--1131119 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1131053 TTTAATGTTA
1131063 TAAATTTAAAATTATATTTAATATGAAT
1 TAAATTTAAAATTATATTTAATATGAAT
* *
1131091 TAAATTTAGATTTATATTTAATATGAAT
1 TAAATTTAAAATTATATTTAATATGAAT
1131119 T
1 T
1131120 CAGAATAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (28 bp):
TAAATTTAAAATTATATTTAATATGAAT
Found at i:1132777 original size:60 final size:60
Alignment explanation
Indices: 1132650--1132783 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 60
1132640 ATAGTTAGGT
* * * * * * *
1132650 GACCATTTTATGACTTTTAATAGTCGATGGACTCAACAAAGCAACTCCCTATATTTGGGT
1 GACCATTTTGTAACTTTTAATAGTCGAAGGACTCAACAAAACAACTCCCTATAGTCGGGG
* * * * *
1132710 GACCATTTTGTAACTTTTAATAGTCGAAGGAGTTAACAAAACAATTTCTTATAGTCGGGG
1 GACCATTTTGTAACTTTTAATAGTCGAAGGACTCAACAAAACAACTCCCTATAGTCGGGG
*
1132770 GATCATTTGTGTAA
1 GACCATTT-TGTAA
1132784 TTTACCCTAA
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 55 0.92
61 5 0.08
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCGAAGGACTCAACAAAACAACTCCCTATAGTCGGGG
Found at i:1135799 original size:2 final size:2
Alignment explanation
Indices: 1135792--1135821 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1135782 AATAAAAATA
1135792 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
1135822 GCATACTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1146156 original size:2 final size:2
Alignment explanation
Indices: 1146091--1146141 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
1146081 GAAACTTTCA
*
1146091 AT AT AT TT 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
1146133 AT AT A- AT AT
1 AT AT AT AT AT
1146142 CTTTAATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1160422 original size:17 final size:17
Alignment explanation
Indices: 1160400--1160434 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1160390 CACATGTTTG
1160400 ACAAAATTTGATATATA
1 ACAAAATTTGATATATA
1160417 ACAAAATTTGATATATA
1 ACAAAATTTGATATATA
1160434 A
1 A
1160435 AGTCGGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (17 bp):
ACAAAATTTGATATATA
Found at i:1169321 original size:21 final size:21
Alignment explanation
Indices: 1169295--1169336 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1169285 TTATTATTTG
1169295 AAATTTATTATTGATAAAAAT
1 AAATTTATTATTGATAAAAAT
1169316 AAATTTATTATTGATAAAAAT
1 AAATTTATTATTGATAAAAAT
1169337 TTGAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
AAATTTATTATTGATAAAAAT
Found at i:1171706 original size:191 final size:191
Alignment explanation
Indices: 1171355--1171709 Score: 450
Period size: 191 Copynumber: 1.9 Consensus size: 191
1171345 TCGTGGATAT
* * * *
1171355 TGGAATTTGAGTGCCAGGATTTCAGGTAATTTAATTTTGTTTATATTTTCATGTGGAGATGTGTT
1 TGGAATTTGAGTGCCAGGATTTCA-GTAATTTAATTTTGTTAATATTTTCATGTGGAAATGTATA
* *
1171420 ACTAGTGTCACGCTTTTCATGTAATTGCAAATTAGTTGATCAAACCTGTTAATTTGTTTTATCAG
65 ACTAGTGTCACGCTTTTCATGTAATTGCAAATTAGTTGATCAAACATGTAAATTTGTTTTATCAG
* *
1171485 TAACGTTGCTTGCAATCAAGTTGTTCCCCCATTTCGGTCAGTTTTACAAGTTTTAAGAGTAG
130 TAACCTCGCTTGCAATCAAGTTGTTCCCCCATTTCGGTCAGTTTTACAAGTTTTAAGAGTAG
* * * *
1171547 TGGAATTTGAAGTGCTAGTATTTCA-TATTTTAATTTTGTTAATATTTT-ATTTTGGAAATGTAT
1 TGGAATTTG-AGTGCCAGGATTTCAGTAATTTAATTTTGTTAATATTTTCA-TGTGGAAATGTAT
*** * *
1171610 AACTAGTGTTTTGCTTTTCATGTAATTG-AAATTTAGTTGATCAATCATGCTAAATTTGTTTTCT
64 AACTAGTGTCACGCTTTTCATGTAATTGCAAA-TTAGTTGATCAAACATG-TAAATTTGTTTTAT
**
1171674 TTGTAACCTCGTCTT-CAATCAAGTTG-TCCCCCATTT
127 CAGTAACCTCG-CTTGCAATCAAGTTGTTCCCCCATTT
1171710 TCAGTTAGAT
Statistics
Matches: 139, Mismatches: 19, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
190 4 0.03
191 80 0.58
192 39 0.28
193 16 0.12
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (191 bp):
TGGAATTTGAGTGCCAGGATTTCAGTAATTTAATTTTGTTAATATTTTCATGTGGAAATGTATAA
CTAGTGTCACGCTTTTCATGTAATTGCAAATTAGTTGATCAAACATGTAAATTTGTTTTATCAGT
AACCTCGCTTGCAATCAAGTTGTTCCCCCATTTCGGTCAGTTTTACAAGTTTTAAGAGTAG
Found at i:1173305 original size:237 final size:237
Alignment explanation
Indices: 1172890--1173367 Score: 956
Period size: 237 Copynumber: 2.0 Consensus size: 237
1172880 CATATCATTC
1172890 GGATTCAGAATCAAGGCCTTATGCTCATGCTGAGGAGTATTCTAGTGCTATCAATATTGACGAAA
1 GGATTCAGAATCAAGGCCTTATGCTCATGCTGAGGAGTATTCTAGTGCTATCAATATTGACGAAA
1172955 TTGGCTGTGTGTATAAAGTGCATCATGATGGAGAGGATTTTGATTCAAACCCTTTGAAGGGTTCA
66 TTGGCTGTGTGTATAAAGTGCATCATGATGGAGAGGATTTTGATTCAAACCCTTTGAAGGGTTCA
1173020 CCATTAGCTGAGAATTTCAGTATACAAAGTGTAGATGGAATCAAGAAAATTGAGGAAGTAAATGA
131 CCATTAGCTGAGAATTTCAGTATACAAAGTGTAGATGGAATCAAGAAAATTGAGGAAGTAAATGA
1173085 ACATGAGAATGCTGATCAGGATGAAGCTCCTGCTTATGATGT
196 ACATGAGAATGCTGATCAGGATGAAGCTCCTGCTTATGATGT
1173127 GGATTCAGAATCAAGGCCTTATGCTCATGCTGAGGAGTATTCTAGTGCTATCAATATTGACGAAA
1 GGATTCAGAATCAAGGCCTTATGCTCATGCTGAGGAGTATTCTAGTGCTATCAATATTGACGAAA
1173192 TTGGCTGTGTGTATAAAGTGCATCATGATGGAGAGGATTTTGATTCAAACCCTTTGAAGGGTTCA
66 TTGGCTGTGTGTATAAAGTGCATCATGATGGAGAGGATTTTGATTCAAACCCTTTGAAGGGTTCA
1173257 CCATTAGCTGAGAATTTCAGTATACAAAGTGTAGATGGAATCAAGAAAATTGAGGAAGTAAATGA
131 CCATTAGCTGAGAATTTCAGTATACAAAGTGTAGATGGAATCAAGAAAATTGAGGAAGTAAATGA
1173322 ACATGAGAATGCTGATCAGGATGAAGCTCCTGCTTATGATGT
196 ACATGAGAATGCTGATCAGGATGAAGCTCCTGCTTATGATGT
1173364 GGAT
1 GGAT
1173368 GAGACAGATG
Statistics
Matches: 241, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
237 241 1.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.29
Consensus pattern (237 bp):
GGATTCAGAATCAAGGCCTTATGCTCATGCTGAGGAGTATTCTAGTGCTATCAATATTGACGAAA
TTGGCTGTGTGTATAAAGTGCATCATGATGGAGAGGATTTTGATTCAAACCCTTTGAAGGGTTCA
CCATTAGCTGAGAATTTCAGTATACAAAGTGTAGATGGAATCAAGAAAATTGAGGAAGTAAATGA
ACATGAGAATGCTGATCAGGATGAAGCTCCTGCTTATGATGT
Found at i:1176969 original size:16 final size:16
Alignment explanation
Indices: 1176950--1176983 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1176940 GGTTTACTAA
1176950 CCGATTTCCAATTCAC
1 CCGATTTCCAATTCAC
1176966 CCGATTTCCAATTCAC
1 CCGATTTCCAATTCAC
1176982 CC
1 CC
1176984 AGTGAATTCG
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:0.41, G:0.06, T:0.29
Consensus pattern (16 bp):
CCGATTTCCAATTCAC
Found at i:1186192 original size:21 final size:21
Alignment explanation
Indices: 1186150--1186192 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1186140 TTTCTGGGTT
* * *
1186150 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1186171 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1186192 A
1 A
1186193 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1186253 original size:66 final size:67
Alignment explanation
Indices: 1186150--1186321 Score: 215
Period size: 67 Copynumber: 2.6 Consensus size: 67
1186140 TTTCTGGGTT
* * *
1186150 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATG
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATG
1186213 CTAG
64 CTAG
* * *
1186217 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCT
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
*
1186282 TG
66 AG
* *
1186284 AGGGGAATCGATA-CCCCAGGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCA-GGGGGGAACCGATACCCCC
1186322 ATGAGAAAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
65 2 0.02
66 27 0.29
67 64 0.69
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.17
Consensus pattern (67 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
AG
Found at i:1187034 original size:22 final size:22
Alignment explanation
Indices: 1186961--1187026 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
1186951 TATGGACATC
1186961 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
*
1186983 ATTCTACGGGCACTTTGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1187005 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1187027 TTTATACGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:1193099 original size:21 final size:21
Alignment explanation
Indices: 1193057--1193099 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1193047 TTTCTGGGTT
* * *
1193057 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1193078 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1193099 A
1 A
1193100 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1193159 original size:66 final size:67
Alignment explanation
Indices: 1193079--1193228 Score: 207
Period size: 67 Copynumber: 2.3 Consensus size: 67
1193069 ACCCATTCAA
*
1193079 GGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATGCTAGAGGGGAATC-AGTACCCCC
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGA-TA-CCCC
1193142 A-GG
64 AGGG
* * * *
1193145 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCAG
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCAG
1193210 GG
66 GG
*
1193212 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1193229 ATGAGAAAAG
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
66 27 0.36
67 47 0.63
68 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCAG
GG
Found at i:1193940 original size:22 final size:22
Alignment explanation
Indices: 1193867--1193932 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
1193857 TATGGACATC
1193867 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1193889 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1193911 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
1193933 TTTATACGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:1203635 original size:22 final size:21
Alignment explanation
Indices: 1203603--1203677 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 21
1203593 GTGTCATCAG
*
1203603 TAAGTCTTTCGAGCATGATGA
1 TAAGTCCTTCGAGCATGATGA
* *
1203624 TGAAGTCCTTCGGGCCATCA-G-
1 T-AAGTCCTTCGAG-CATGATGA
*
1203645 TAAGTCTTTCGAGCATGATGA
1 TAAGTCCTTCGAGCATGATGA
*
1203666 TTAAATCCTTCG
1 -TAAGTCCTTCG
1203678 GGTAATTTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
19 4 0.10
20 11 0.27
21 2 0.05
22 20 0.49
23 4 0.10
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (21 bp):
TAAGTCCTTCGAGCATGATGA
Found at i:1203655 original size:20 final size:19
Alignment explanation
Indices: 1203597--1203660 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
1203587 CAATAAGTGT
1203597 CATCAGTAAGTCTTTCGAG
1 CATCAGTAAGTCTTTCGAG
* * *
1203616 CATGATGATGAAGTCCTTCGGG
1 CATCA-G-T-AAGTCTTTCGAG
1203638 CCATCAGTAAGTCTTTCGAG
1 -CATCAGTAAGTCTTTCGAG
1203658 CAT
1 CAT
1203661 GATGATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 7 0.20
20 11 0.31
21 2 0.06
22 11 0.31
23 4 0.11
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (19 bp):
CATCAGTAAGTCTTTCGAG
Found at i:1203656 original size:42 final size:42
Alignment explanation
Indices: 1203597--1203679 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
1203587 CAATAAGTGT
*
1203597 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGC
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGC
*
1203639 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
1203680 TAATTTGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGC
Found at i:1203736 original size:13 final size:13
Alignment explanation
Indices: 1203718--1203742 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1203708 TGAAGCAAAT
1203718 CCATCAGTAAGTG
1 CCATCAGTAAGTG
1203731 CCATCAGTAAGT
1 CCATCAGTAAGT
1203743 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:1203736 original size:135 final size:135
Alignment explanation
Indices: 1203491--1203762 Score: 463
Period size: 135 Copynumber: 2.0 Consensus size: 135
1203481 TAAACAATTT
* * *
1203491 AAGTCCTTTGGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAGTCTTTCAGGTAATTTGTAAG
1 AAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAATCCTTCAGGTAATTTGTAAG
*
1203556 CCTTCACCGAAGAGTAGTGAAGCAAACCCATCAATAAGTGTCATCAGTAAGTCTTTCGAGCATGA
66 CCTTCACCGAAGAGTAGTGAAGCAAACCCATCAATAAGTGCCATCAGTAAGTCTTTCGAGCATGA
1203621 TGATG
131 TGATG
* *
1203626 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAG
1 AAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAATCCTTCAGGTAATTTGTAAG
* * *
1203691 CCTTCACTGAAGAGTAGTGAAGCAAATCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGA
66 CCTTCACCGAAGAGTAGTGAAGCAAACCCATCAATAAGTGCCATCAGTAAGTCTTTCGAGCATGA
1203756 TGATG
131 TGATG
1203761 AA
1 AA
1203763 TTCTTTCGAG
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
135 128 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (135 bp):
AAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAATCCTTCAGGTAATTTGTAAG
CCTTCACCGAAGAGTAGTGAAGCAAACCCATCAATAAGTGCCATCAGTAAGTCTTTCGAGCATGA
TGATG
Found at i:1203770 original size:22 final size:21
Alignment explanation
Indices: 1203742--1203870 Score: 86
Period size: 22 Copynumber: 6.0 Consensus size: 21
1203732 CATCAGTAAG
*
1203742 TCTTTCGAGCATGATGATGAAT
1 TCTTTCGAGCATGATGAT-AAA
*
1203764 TCTTTCGAGCATAATGATTAAA
1 TCTTTCGAGCATGATGA-TAAA
* * * *
1203786 TCTTTTGGGTCATCA-G-TAAG
1 TCTTTCGAG-CATGATGATAAA
1203806 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATGATGA-TAAA
* * * *
1203828 TCATTCGGGCCATCA-G-TAAG
1 TCTTTCGAG-CATGATGATAAA
1203848 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATGATGA-TAAA
1203870 T
1 T
1203871 TATTCGGGTC
Statistics
Matches: 80, Mismatches: 18, Indels: 18
0.69 0.16 0.16
Matches are distributed among these distances:
19 8 0.10
20 22 0.28
22 41 0.51
23 9 0.11
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (21 bp):
TCTTTCGAGCATGATGATAAA
Found at i:1203811 original size:42 final size:42
Alignment explanation
Indices: 1203764--1203937 Score: 187
Period size: 42 Copynumber: 4.2 Consensus size: 42
1203754 GATGATGAAT
*
1203764 TCTTTCGAGCATAATGATTAAATCTTTTGGGTCATCAGTAAG
1 TCTTTCGAGCATAATGATTAAATCTTTCGGGTCATCAGTAAG
* * *
1203806 TCTTTCGAGCATGATGATTAAATCATTCGGGCCATCAGTAAG
1 TCTTTCGAGCATAATGATTAAATCTTTCGGGTCATCAGTAAG
* *** *
1203848 TCTTTCGAGCATGATGATTAAAT-TATTCGGGTCATTTTTGAG
1 TCTTTCGAGCATAATGATTAAATCT-TTCGGGTCATCAGTAAG
1203890 TCTTTCGAG-A-AA-GATAATAAATCTTTCGGGTCATCCA-TAAG
1 TCTTTCGAGCATAATGAT--TAAATCTTTCGGGTCAT-CAGTAAG
*
1203931 TCATTCG
1 TCTTTCG
1203938 GGTATGATGT
Statistics
Matches: 112, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
39 3 0.03
40 1 0.01
41 25 0.22
42 83 0.74
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (42 bp):
TCTTTCGAGCATAATGATTAAATCTTTCGGGTCATCAGTAAG
Found at i:1204417 original size:53 final size:53
Alignment explanation
Indices: 1204359--1204688 Score: 416
Period size: 53 Copynumber: 6.2 Consensus size: 53
1204349 GAATCACACC
* *
1204359 AGAAGATTGTTCGAGTTATACTCCCCGAAGCAAGAGGGAGCGAACCCATAGGA
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGA
* * * *
1204412 AGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAAAGGGAGCGAACCCGT-CGA
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGA
1204464 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATA-GA
1 -AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGA
** * * *
1204517 CAGAAGATTGTTCGAGTTCTAAGCCCTGAAGCAAGAAGGAACGAACCCGTAGGA
1 -AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGA
* * * *
1204571 AGAAGATTGTTCGAGTTCTACTCCTTTAAGCAAGAGGGAGTGAACCCGTAGGA
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGA
* * * *
1204624 AGAAGATAT-TTTGAGTTCTATTCCTTGAAGCAAGAGGGAGCGAACCCACT-GGT
1 AGAAGAT-TGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCA-TAGGA
*
1204677 TGAAGATTGTTC
1 AGAAGATTGTTC
1204689 AAAGAAGAGG
Statistics
Matches: 242, Mismatches: 29, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
52 3 0.01
53 235 0.97
54 4 0.02
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (53 bp):
AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGA
Found at i:1204688 original size:159 final size:159
Alignment explanation
Indices: 1204358--1204671 Score: 470
Period size: 159 Copynumber: 2.0 Consensus size: 159
1204348 AGAATCACAC
** * *
1204358 CAGAAGATTGTTCGAGTTATACTCCCCGAAGCAAGAGGGAGCGAACCCATAGGAAGAAGATTGTT
1 CAGAAGATTGTTCGAGTTATAAGCCCCGAAGCAAGAAGGAACGAACCCATAGGAAGAAGATTGTT
1204423 CGAGTTCTACTCCTTGAAGCAAAAGGGAGCGAACCCGTCGACAGAAGATTGTTCGAGTTCTACTC
66 CGAGTTCTACTCCTTGAAGCAAAAGGGAGCGAACCCGTCGACAGAAGATTGTTCGAGTTCTACTC
1204488 CCTGAAGCAAGAGGGAGCGAACCCATAGA
131 CCTGAAGCAAGAGGGAGCGAACCCATAGA
* * *
1204517 CAGAAGATTGTTCGAGTTCTAAGCCCTGAAGCAAGAAGGAACGAACCCGTAGGAAGAAGATTGTT
1 CAGAAGATTGTTCGAGTTATAAGCCCCGAAGCAAGAAGGAACGAACCCATAGGAAGAAGATTGTT
* * * * * *
1204582 CGAGTTCTACTCCTTTAAGCAAGAGGGAGTGAACCCGTAGGA-AGAAGATAT-TTTGAGTTCTAT
66 CGAGTTCTACTCCTTGAAGCAAAAGGGAGCGAACCCGT-CGACAGAAGAT-TGTTCGAGTTCTAC
*
1204645 TCCTTGAAGCAAGAGGGAGCGAACCCA
129 TCCCTGAAGCAAGAGGGAGCGAACCCA
1204672 CTGGTTGAAG
Statistics
Matches: 139, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
159 136 0.98
160 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.20
Consensus pattern (159 bp):
CAGAAGATTGTTCGAGTTATAAGCCCCGAAGCAAGAAGGAACGAACCCATAGGAAGAAGATTGTT
CGAGTTCTACTCCTTGAAGCAAAAGGGAGCGAACCCGTCGACAGAAGATTGTTCGAGTTCTACTC
CCTGAAGCAAGAGGGAGCGAACCCATAGA
Found at i:1215945 original size:2 final size:2
Alignment explanation
Indices: 1215938--1215984 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1215928 CATGATTGTA
1215938 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
1215980 AT AT A
1 AT AT A
1215985 ATAAATTGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1218132 original size:24 final size:25
Alignment explanation
Indices: 1218095--1218152 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 25
1218085 GAAGTGCCGT
1218095 GTAGAAATTTGTCCCGAAGGACCAC
1 GTAGAAATTTGTCCCGAAGGACCAC
1218120 GTAG-AATTTGTCCCGAAGGACCAC
1 GTAGAAATTTGTCCCGAAGGACCAC
* *
1218144 ATATAAATT
1 GTAGAAATT
1218153 CCTTAAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 22 0.73
25 8 0.27
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (25 bp):
GTAGAAATTTGTCCCGAAGGACCAC
Found at i:1218381 original size:30 final size:31
Alignment explanation
Indices: 1218337--1218402 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
1218327 ATTTATATAG
*
1218337 CATAGACATATCA-TTTCCATACCTTTATCA
1 CATAAACATATCATTTTCCATACCTTTATCA
*
1218367 CATAAACATTTCATTTTCCATACCTTTATCA
1 CATAAACATATCATTTTCCATACCTTTATCA
1218398 CATAA
1 CATAA
1218403 TTCATATAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.38
Consensus pattern (31 bp):
CATAAACATATCATTTTCCATACCTTTATCA
Found at i:1224911 original size:24 final size:25
Alignment explanation
Indices: 1224894--1224950 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
1224884 AAATTACACT
*
1224894 GAAGTACCGCGTAGAAATTTATCCC
1 GAAGGACCGCGTAGAAATTTATCCC
*
1224919 GAAGGACCGCGTAG-AATTTGTCCC
1 GAAGGACCGCGTAGAAATTTATCCC
1224943 GAAGGACC
1 GAAGGACC
1224951 ACATATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 17 0.57
25 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (25 bp):
GAAGGACCGCGTAGAAATTTATCCC
Found at i:1225188 original size:30 final size:31
Alignment explanation
Indices: 1225139--1225209 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
1225129 ACATAATTTA
* *
1225139 TATCGCATAGACATATCA-TTTCCATACCTT
1 TATCACATAAACATATCATTTTCCATACCTT
*
1225169 TATCACATAAACATTTCATTTTCCATACCTT
1 TATCACATAAACATATCATTTTCCATACCTT
1225200 TATCACATAA
1 TATCACATAA
1225210 TTCATATAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 15 0.41
31 22 0.59
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (31 bp):
TATCACATAAACATATCATTTTCCATACCTT
Found at i:1225643 original size:21 final size:21
Alignment explanation
Indices: 1225619--1225661 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1225609 TCATATTCGT
* *
1225619 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1225640 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1225661 T
1 T
1225662 AGCCCATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1227610 original size:18 final size:20
Alignment explanation
Indices: 1227561--1227610 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 20
1227551 TACTATAATT
*
1227561 AATTTATATATTTTCTTTAAA
1 AATTTATATA-ATTCTTTAAA
1227582 AATTT-TA-AATTC-TT-AA
1 AATTTATATAATTCTTTAAA
1227598 AATTTATATAATT
1 AATTTATATAATT
1227611 TTTTTTACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 7 0.27
17 4 0.15
18 7 0.27
19 1 0.04
20 2 0.08
21 5 0.19
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTTATATAATTCTTTAAA
Found at i:1228182 original size:7 final size:7
Alignment explanation
Indices: 1228170--1228291 Score: 172
Period size: 7 Copynumber: 17.4 Consensus size: 7
1228160 GAAGATAGAC
1228170 AAGTGAG
1 AAGTGAG
1228177 AAGTGAG
1 AAGTGAG
1228184 AAGTGAG
1 AAGTGAG
1228191 AAGTGAG
1 AAGTGAG
1228198 AAGTGAG
1 AAGTGAG
1228205 AAGTGAG
1 AAGTGAG
1228212 AAGTGAG
1 AAGTGAG
1228219 AAGTGAG
1 AAGTGAG
1228226 AAGTGAG
1 AAGTGAG
*
1228233 AAGAGAG
1 AAGTGAG
*
1228240 AAGAGAG
1 AAGTGAG
*
1228247 AAGAGAG
1 AAGTGAG
*
1228254 AAGAGAG
1 AAGTGAG
*
1228261 AAGAGAG
1 AAGTGAG
*
1228268 AAGAGAG
1 AAGTGAG
*
1228275 AAGAGAG
1 AAGTGAG
*
1228282 AAGAGAG
1 AAGTGAG
1228289 AAG
1 AAG
1228292 GCATGTGAAG
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
7 114 1.00
ACGTcount: A:0.50, C:0.00, G:0.43, T:0.07
Consensus pattern (7 bp):
AAGTGAG
Found at i:1239274 original size:19 final size:19
Alignment explanation
Indices: 1239250--1239286 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1239240 AAAATCAAAG
*
1239250 TCAATGTGCAGGTCAACGA
1 TCAATGAGCAGGTCAACGA
1239269 TCAATGAGCAGGTCAACG
1 TCAATGAGCAGGTCAACG
1239287 GGCATGTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (19 bp):
TCAATGAGCAGGTCAACGA
Found at i:1264763 original size:17 final size:19
Alignment explanation
Indices: 1264743--1264784 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
1264733 AAACTAGACT
*
1264743 AGAAAATAGA-AAAAA-AA
1 AGAAAACAGATAAAAACAA
1264760 AGAAAACAGATTAAAAACAA
1 AGAAAACAGA-TAAAAACAA
1264780 AGAAA
1 AGAAA
1264785 TTATAATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 9 0.43
19 5 0.24
20 7 0.33
ACGTcount: A:0.76, C:0.05, G:0.12, T:0.07
Consensus pattern (19 bp):
AGAAAACAGATAAAAACAA
Found at i:1272184 original size:24 final size:24
Alignment explanation
Indices: 1272073--1272186 Score: 96
Period size: 24 Copynumber: 4.8 Consensus size: 24
1272063 ACAATCTTAT
*
1272073 ATGGCACTACGGTGC-AATTCTAC
1 ATGGCACTTCGGTGCAAATTCTAC
* *
1272096 GTGGCACTTCGGTGC-ATTTCTAC
1 ATGGCACTTCGGTGCAAATTCTAC
*
1272119 ACGGTC-CTTCGG-GACAAATTCTAC
1 ATGG-CACTTCGGTG-CAAATTCTAC
*
1272143 GTGGTC-CTTCGG-GACAAATTCTAC
1 ATGG-CACTTCGGTG-CAAATTCTAC
*
1272167 ATGGCACTACGGTGCAAATT
1 ATGGCACTTCGGTGCAAATT
1272187 TATACGAGCT
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.01
23 30 0.39
24 44 0.58
25 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (24 bp):
ATGGCACTTCGGTGCAAATTCTAC
Found at i:1280120 original size:14 final size:14
Alignment explanation
Indices: 1280103--1280136 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1280093 CTTTAAACCC
* *
1280103 TAAATCTTAAATTT
1 TAAATATTAAACTT
1280117 TAAATATTAAACTT
1 TAAATATTAAACTT
1280131 TAAATA
1 TAAATA
1280137 ATATAATCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAATATTAAACTT
Found at i:1280332 original size:16 final size:16
Alignment explanation
Indices: 1280311--1280341 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1280301 AACTCGAAAT
1280311 AAAAAATTGAAACTCA
1 AAAAAATTGAAACTCA
*
1280327 AAAAAATTTAAACTC
1 AAAAAATTGAAACTC
1280342 GTAGCATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAAAATTGAAACTCA
Found at i:1282204 original size:27 final size:27
Alignment explanation
Indices: 1282162--1282235 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
1282152 CTTGTGGCGC
* *
1282162 AAAACAAATGCTGCAAAAAGC-ACTGCT
1 AAAACAAACGCCGCAAAAAGCTA-TGCT
*
1282189 AAAACAAACGCCGCAAAAAACTATGCT
1 AAAACAAACGCCGCAAAAAGCTATGCT
* *
1282216 AAAACAAACGTCACAAAAAG
1 AAAACAAACGCCGCAAAAAG
1282236 TTGCGACATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 39 0.98
28 1 0.03
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (27 bp):
AAAACAAACGCCGCAAAAAGCTATGCT
Found at i:1294349 original size:2 final size:2
Alignment explanation
Indices: 1294344--1294372 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1294334 TTAAACATGA
1294344 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
1294373 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:1295780 original size:35 final size:36
Alignment explanation
Indices: 1295741--1295820 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 36
1295731 TCGACTTGAA
1295741 AAATGTGAATTGGAGT-CCGATCATTTATTTAAAAC
1 AAATGTGAATTGGAGTCCCGATCATTTATTTAAAAC
*
1295776 AAATGTGGATTGGAGTCGCCACCGATCATTTATTTAAAAC
1 AAATGTGAATTGGAGT---C-CCGATCATTTATTTAAAAC
1295816 AAATG
1 AAATG
1295821 GGTTGAACGG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
35 15 0.38
40 24 0.62
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (36 bp):
AAATGTGAATTGGAGTCCCGATCATTTATTTAAAAC
Found at i:1296329 original size:18 final size:17
Alignment explanation
Indices: 1296294--1296341 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
1296284 AATATAATGA
1296294 AAATAAATAAATAGTAT
1 AAATAAATAAATAGTAT
1296311 AAATAAAATAATATA-TAT
1 AAAT-AAATAA-ATAGTAT
* *
1296329 ATATATATAAATA
1 AAATAAATAAATA
1296342 TAAAAATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.11
17 9 0.33
18 12 0.44
19 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAATAAATAAATAGTAT
Found at i:1296333 original size:22 final size:21
Alignment explanation
Indices: 1296280--1296345 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
1296270 GCAAAGAAAC
*
1296280 TAAAAATAT-AATGAAAATAAA
1 TAAATATATAAAT-AAAATAAA
1296301 TAAATAGTATAAATAAAATAATA
1 TAAATA-TATAAATAAAATAA-A
* *
1296324 TATATATATATATAAATATAAA
1 TAAATATATAAATAAA-ATAAA
1296346 AATGTATGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.13
22 20 0.53
23 13 0.34
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (21 bp):
TAAATATATAAATAAAATAAA
Found at i:1296342 original size:14 final size:14
Alignment explanation
Indices: 1296300--1296345 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1296290 ATGAAAATAA
1296300 ATAAATAGTATAAAT
1 ATAAATA-TATAAAT
*
1296315 A-AAATA-ATATAT
1 ATAAATATATAAAT
*
1296327 ATATATATATAAAT
1 ATAAATATATAAAT
1296341 ATAAA
1 ATAAA
1296346 AATGTATGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
12 6 0.24
13 4 0.16
14 14 0.56
15 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
ATAAATATATAAAT
Found at i:1296549 original size:11 final size:11
Alignment explanation
Indices: 1296530--1296586 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
1296520 GTAAACATAG
*
1296530 ATAAAATAATA
1 ATAATATAATA
1296541 ATAATATAATTA
1 ATAATATAA-TA
1296553 AT-ATATATATA
1 ATAATATA-ATA
1296564 TATAATAGTAA-A
1 -ATAATA-TAATA
1296576 ATAATATAATA
1 ATAATATAATA
1296587 TAACACACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
10 3 0.08
11 22 0.56
12 8 0.21
13 4 0.10
14 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
ATAATATAATA
Found at i:1298165 original size:106 final size:106
Alignment explanation
Indices: 1297942--1299252 Score: 1772
Period size: 106 Copynumber: 12.3 Consensus size: 106
1297932 GCATTATTCC
* * * * * * *
1297942 GAGTCCAATATCCTCCGTCGTAAAGTTGAAATTGGCTCTGGAATCGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAC-A
* * * *
1298007 ACCAGTC-ATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1298049 GAGTCTAATATCCTTTGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
1298114 CCAGTGGTACCTTCGTTGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1298155 GAGTCCAATATCCTTC-TCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1298219 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1298261 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTAACAA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1298326 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1298367 GAGTCGAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCCGAAATTAGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
1298431 ACCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1298473 GAGTCCAATATCTTTCG-CTGTGAAGTTGAAATTTGTTCCGAAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* *
1298537 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1298579 GAGTCCAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1298643 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1298685 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1298750 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1298791 GAGTCCAATATCCTTCGAT-GTGAAGTTAAAATTGCCTCTGAATTTGGGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCG-TCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * ** *
1298855 ACCAACCGTCCATTCGTTGTGAAGTTGAACTTATGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1298897 GAGTGGCACGATATCCTCCGTCGTGGAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGA
1 GAGT--C-CAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGA
*
1298962 CAACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
63 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1299006 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
**
1299071 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1299112 GAATCCAATATCCTACG-CTGTGAAGTTGAAATTGCCTCTGAATTTGGGAACTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * ** *
1299176 ACCAGCCGTCCATTCGTTGTGAAGTTGAACTTATGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1299218 AAGTGGCACGATATCCTCCGTCGTGGAGTTGAAAT
1 GAGT--C-CAATATCCTTCGTCGTGAAGTTGAAAT
1299253 CGCGGATGGC
Statistics
Matches: 1080, Mismatches: 109, Indels: 28
0.89 0.09 0.02
Matches are distributed among these distances:
105 2 0.00
106 907 0.84
107 58 0.05
108 3 0.00
109 109 0.10
110 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1300850 original size:29 final size:32
Alignment explanation
Indices: 1300818--1300880 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 32
1300808 TTTTTGTCCC
1300818 TTTTTCTTTTT-ATTTTTG-TTC-TTTCTTTT
1 TTTTTCTTTTTCATTTTTGCTTCTTTTCTTTT
*
1300847 TTTTTCTTTTTCTTTTTTGCTTCTTTTCTTTT
1 TTTTTCTTTTTCATTTTTGCTTCTTTTCTTTT
1300879 TT
1 TT
1300881 ATTTTTGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 11 0.37
30 6 0.20
31 3 0.10
32 10 0.33
ACGTcount: A:0.02, C:0.13, G:0.03, T:0.83
Consensus pattern (32 bp):
TTTTTCTTTTTCATTTTTGCTTCTTTTCTTTT
Found at i:1300858 original size:16 final size:16
Alignment explanation
Indices: 1300817--1300880 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 16
1300807 TTTTTTGTCC
1300817 CTTTTTCTTTTTATTTTT
1 CTTTTTC-TTTT-TTTTT
*
1300835 GTTCTTTCTTTTTTTTT
1 CTT-TTTCTTTTTTTTT
*
1300852 CTTTTTCTTTTTTGCTT
1 CTTTTTCTTTTTT-TTT
1300869 C-TTTTCTTTTTT
1 CTTTTTCTTTTTT
1300881 ATTTTTGCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
16 21 0.51
17 10 0.24
18 6 0.15
19 4 0.10
ACGTcount: A:0.02, C:0.14, G:0.03, T:0.81
Consensus pattern (16 bp):
CTTTTTCTTTTTTTTT
Found at i:1300873 original size:22 final size:22
Alignment explanation
Indices: 1300846--1300898 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 22
1300836 TTCTTTCTTT
1300846 TTTTTTCTTTTTCT-TTTTTG-C
1 TTTTTTCTTTTT-TATTTTTGCC
1300867 TTCTTTTCTTTTTTATTTTTGCC
1 TT-TTTTCTTTTTTATTTTTGCC
1300890 TTTTTTCTT
1 TTTTTTCTT
1300899 CTGATTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.10
22 23 0.79
23 3 0.10
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTTTTCTTTTTTATTTTTGCC
Found at i:1300879 original size:6 final size:6
Alignment explanation
Indices: 1300817--1300863 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
1300807 TTTTTTGTCC
* *
1300817 CTTTTT CTTTTT ATTTTT GTTCTTT C-TTTT -TTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTT-TTT CTTTTT CTTTTT CTTTTT CTTTTT
1300864 TGCTTCTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
5 7 0.20
6 25 0.71
7 3 0.09
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (6 bp):
CTTTTT
Found at i:1304361 original size:20 final size:20
Alignment explanation
Indices: 1304336--1304381 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1304326 CCGAGTTATC
1304336 CTTGCCGATGCCCCATTGGG
1 CTTGCCGATGCCCCATTGGG
* *
1304356 CTTGCCGGTGCCCCCTTGGG
1 CTTGCCGATGCCCCATTGGG
1304376 CTTGCC
1 CTTGCC
1304382 AGACCCTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.04, C:0.39, G:0.30, T:0.26
Consensus pattern (20 bp):
CTTGCCGATGCCCCATTGGG
Found at i:1307554 original size:31 final size:31
Alignment explanation
Indices: 1307509--1307584 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
1307499 TAAACTTTCT
* *
1307509 AAATGATTATAAAATGGTAATTAAATTTTATCA
1 AAAT-ATTAGAAAATAGTAATTAAA-TTTATCA
* *
1307542 AAATATTA-AAAATAGTCATTAAATTTATTA
1 AAATATTAGAAAATAGTAATTAAATTTATCA
*
1307572 AATTATTAGAAAA
1 AAATATTAGAAAA
1307585 AGAGTCCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 13 0.34
31 17 0.45
32 4 0.11
33 4 0.11
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (31 bp):
AAATATTAGAAAATAGTAATTAAATTTATCA
Found at i:1309866 original size:137 final size:138
Alignment explanation
Indices: 1309707--1309958 Score: 355
Period size: 137 Copynumber: 1.8 Consensus size: 138
1309697 AAATCCTACC
* * * *
1309707 CTAAACCTAGAAGCTCTGAACATATATAATATATTTATAATTGTACATACACTAAAAATCTTAAA
1 CTAAACCTAAAAGCTCTAAACATATATAATATATTTATAACTGAACATACACTAAAAATCTTAAA
* ** *
1309772 ACAATATTTTATCA-CTTGTATGTATTGTATATGTTATTTTT-ATTTTTTACCACATAAGTTCCA
66 ACAATATTGTATCATC-TCCATGTATTGTATATCTTATTTTTAATTTTTTACCACATAAGTTCCA
1309835 TTATAAACT
130 TTATAAACT
* * * * *
1309844 CTAAACCTAAAAGCTGTAAACATATATAATATATTTATAACTGAATATGCACTAAAATTCTTGAA
1 CTAAACCTAAAAGCTCTAAACATATATAATATATTTATAACTGAACATACACTAAAAATCTTAAA
*
1309909 ATAATATTGTATCATCTCCATGTATTGTATATCTTATTTTTAATTTTTTA
66 ACAATATTGTATCATCTCCATGTATTGTATATCTTATTTTTAATTTTTTA
1309959 ATTTAATTTT
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
137 90 0.91
138 9 0.09
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (138 bp):
CTAAACCTAAAAGCTCTAAACATATATAATATATTTATAACTGAACATACACTAAAAATCTTAAA
ACAATATTGTATCATCTCCATGTATTGTATATCTTATTTTTAATTTTTTACCACATAAGTTCCAT
TATAAACT
Found at i:1314159 original size:3 final size:3
Alignment explanation
Indices: 1314151--1314195 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1314141 AAAGTCTTCA
1314151 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1314196 TTCTCTTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1314833 original size:15 final size:16
Alignment explanation
Indices: 1314795--1314835 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1314785 ACAGTGCCTC
*
1314795 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
1314811 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
1314827 T-AATCATTC
1 TGAATCATTC
1314836 TGAAGTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:1317755 original size:2 final size:2
Alignment explanation
Indices: 1317748--1317778 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1317738 ATTACTCATA
1317748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1317779 AAACATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1323698 original size:20 final size:20
Alignment explanation
Indices: 1323673--1323932 Score: 83
Period size: 20 Copynumber: 12.6 Consensus size: 20
1323663 AATGACCAAT
1323673 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1323693 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1323713 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
1323733 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
** * **
1323754 AAGTTCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1323775 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1323798 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
1323818 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * *
1323838 AGAGTCGCAACGCGATCTAGAAG
1 AAAATCGCAACGCGAT-T--TAG
* * *
1323861 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
1323881 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
1323901 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
*
1323921 AGAATCGCAACG
1 AAAATCGCAACG
1323933 TAAAAAAGAA
Statistics
Matches: 192, Mismatches: 37, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
20 127 0.66
21 36 0.19
22 1 0.01
23 28 0.15
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1323763 original size:21 final size:21
Alignment explanation
Indices: 1323737--1323789 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
1323727 CAAAAGAAAA
1323737 TCGCAACGCGAGCTTCCAAGT
1 TCGCAACGCGAGCTTCCAAGT
1323758 TCGCAACGCGAGCTTCCAAGT
1 TCGCAACGCGAGCTTCCAAGT
1323779 TCGCAACGCGA
1 TCGCAACGCGA
1323790 TTTAGAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.34, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAGCTTCCAAGT
Found at i:1323833 original size:43 final size:39
Alignment explanation
Indices: 1323800--1323930 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 39
1323790 TTTAGAAGAA
1323800 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGA-AGAATCGCAATGCGATTGAGAG
* * *
1323840 AGTCGCAACGCGATCTAGAAGAAAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGAT-T-GAAG--AATCGCAATGCGATTGAGAG
* * *
1323883 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGA-AGAATCGCAATGCGATTGAGAG
1323923 AATCGCAA
1 AATCGCAA
1323931 CGTAAAAAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
40 37 0.48
41 5 0.06
42 5 0.06
43 30 0.39
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (39 bp):
AATCGCAATGCGATTGAAGAATCGCAATGCGATTGAGAG
Found at i:1323859 original size:63 final size:63
Alignment explanation
Indices: 1323779--1323916 Score: 222
Period size: 63 Copynumber: 2.2 Consensus size: 63
1323769 GCTTCCAAGT
* * * * *
1323779 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATCTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAA
1323842 TCGCAACGCGATCTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATCTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAA
*
1323905 TCGCAATGCGAT
1 TCGCAACGCGAT
1323917 TTATAGAATC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 69 1.00
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.18
Consensus pattern (63 bp):
TCGCAACGCGATCTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAA
Found at i:1323947 original size:40 final size:40
Alignment explanation
Indices: 1323820--1323950 Score: 109
Period size: 40 Copynumber: 3.2 Consensus size: 40
1323810 CGATTGATAG
* * * *
1323820 AATCGCAATGCGATTGAGAGAGTCGCAACGCGATCTAGAAGAA
1 AATCGCAATGCGACTGAGAGAATCGCAACGC-A--AAAAAGAA
* * *** *
1323863 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGACTGAGAGAATCGCAACGCAAAAAAGAA
* * * *
1323903 AATCGCAATGCGATTTATAGAATCGCAACGTAAAAAAGAA
1 AATCGCAATGCGACTGAGAGAATCGCAACGCAAAAAAGAA
1323943 AATCGCAA
1 AATCGCAA
1323951 CGTTAAAAAG
Statistics
Matches: 69, Mismatches: 19, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
40 41 0.59
43 28 0.41
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.17
Consensus pattern (40 bp):
AATCGCAATGCGACTGAGAGAATCGCAACGCAAAAAAGAA
Found at i:1323979 original size:20 final size:20
Alignment explanation
Indices: 1323923--1323982 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
1323913 CGATTTATAG
1323923 AATCGCAAC-GTAAAAAAGAA
1 AATCGCAACGGT-AAAAAGAA
*
1323943 AATCGCAACGTTAAAAAGAA
1 AATCGCAACGGTAAAAAGAA
*
1323963 AATCGCAACGGTCAAAAGAA
1 AATCGCAACGGTAAAAAGAA
1323983 TAGTTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 35 0.97
21 1 0.03
ACGTcount: A:0.55, C:0.17, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGGTAAAAAGAA
Found at i:1323979 original size:21 final size:20
Alignment explanation
Indices: 1323923--1323972 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1323913 CGATTTATAG
1323923 AATCGCAACGTAAAAAAGAA
1 AATCGCAACGTAAAAAAGAA
*
1323943 AATCGCAACGTTAAAAAGAA
1 AATCGCAACGTAAAAAAGAA
1323963 AATCGCAACG
1 AATCGCAACG
1323973 GTCAAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.54, C:0.18, G:0.16, T:0.12
Consensus pattern (20 bp):
AATCGCAACGTAAAAAAGAA
Found at i:1324081 original size:6 final size:6
Alignment explanation
Indices: 1324072--1324115 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
1324062 CATTACCATT
1324072 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1324116 CGAGACGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1324817 original size:6 final size:6
Alignment explanation
Indices: 1324806--1324898 Score: 186
Period size: 6 Copynumber: 15.5 Consensus size: 6
1324796 TCTCGTCTCG
1324806 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1324854 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1324899 AATACGTGTC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 87 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1325001 original size:20 final size:20
Alignment explanation
Indices: 1324976--1325019 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1324966 TTTTTAACTA
*
1324976 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
1324996 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
1325016 TTCT
1 TTCT
1325020 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:1325046 original size:19 final size:20
Alignment explanation
Indices: 1325006--1325056 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
1324996 TTCTTTTTAA
1325006 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
*
1325026 CGTTGCGATTTT-TATATCG
1 CGTTGCGATTTTCTAAATCG
1325045 CGTTGCGATTTT
1 CGTTGCGATTTT
1325057 ATTGGTCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:1327779 original size:20 final size:20
Alignment explanation
Indices: 1327754--1327865 Score: 120
Period size: 20 Copynumber: 5.5 Consensus size: 20
1327744 TTTTCCTAAT
1327754 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACATAAA
* *
1327774 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACATAAA
*
1327794 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACATAAA
* * *
1327814 TTGCAACGCGATTA-AGTAAA
1 TCGCAATGCGAATACA-TAAA
*
1327834 TCGCAATGCGAATTAGGA-AAA
1 TCGCAATGCGAA-TA-CATAAA
1327855 TCGCAATGCGA
1 TCGCAATGCGA
1327866 TTTACATAGC
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
20 61 0.78
21 16 0.21
23 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACATAAA
Found at i:1327803 original size:40 final size:40
Alignment explanation
Indices: 1327754--1327846 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
1327744 TTTTCCTAAT
*
1327754 TCGCAATGCGAATACATAAATCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACATAAATCGCAACGCGAATAAGTAAA
* * *
1327794 TCGCAATGCGAATACGTAAATTGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACATAAATCGCAACGCGAATAAGTAAA
1327834 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1327847 TAGGAAAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACATAAATCGCAACGCGAATAAGTAAA
Found at i:1328438 original size:14 final size:14
Alignment explanation
Indices: 1328419--1328479 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
1328409 GGAAATGACT
*
1328419 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
1328433 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
*
1328452 ATCGCAACGAGATA
1 ATCGCAACGAGAAA
*
1328466 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
1328480 CCAAAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Done.