Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008489.1 Hibiscus syriacus cultivar Beakdansim tig00111331_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: 1108073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:932642 original size:337 final size:335
Alignment explanation
Indices: 932027--932657 Score: 1106
Period size: 337 Copynumber: 1.9 Consensus size: 335
932017 TCTTGATGAG
*
932027 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
* * *
932092 GTAATGTTGATCCATCAACTGATGATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
66 GAAACGATGATCCATCAACTGATGATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
932157 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCATCAA
131 CTTCTTCCTTCTTCAGATGAGTTCTTCTC--TATGAACCTTCTCTGGAAAAGAATGATCCATCAA
*
932222 GTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
194 GTGATGAATTTAAACAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*
932287 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGGTGATCCACCAAATGATGGATTCAGGTAA
259 ATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAGGGTGATCCACCAAATGATGGATTCAGGTAA
932352 AAGGTGAACAAA
324 AAGGTGAACAAA
932364 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
* *
932428 GGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGA
65 GGAAACGATGATCCATCAA-CTGATG-A-TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
932493 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC-ATGAACCTTCTCTGGAAAAGAATGATCCATC
127 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCTATGAACCTTCTCTGGAAAAGAATGATCCATC
932557 AAGTGATGAATTTAAACAAAAGGTCGAAACAAGTTCTTCTCATTATGAACTT-TTCTTCCTTCTT
192 AAGTGATGAATTTAAACAAAAGGTCG-AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
932621 CAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAA
256 CAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAA
932658 CAATGATCCA
Statistics
Matches: 281, Mismatches: 8, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
336 1 0.00
337 181 0.64
338 30 0.11
339 1 0.00
340 68 0.24
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (335 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
GAAACGATGATCCATCAACTGATGATCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTCTATGAACCTTCTCTGGAAAAGAATGATCCATCAAGT
GATGAATTTAAACAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
GAGTTCTTCTCATTATGAACCTTCTCTGGAAAGGGTGATCCACCAAATGATGGATTCAGGTAAAA
GGTGAACAAA
Found at i:932876 original size:123 final size:126
Alignment explanation
Indices: 932725--932974 Score: 463
Period size: 123 Copynumber: 2.0 Consensus size: 126
932715 AAAAATTCAA
932725 CATAGATGAAAATGAATGAAAATGCACCTATTTTTGTAAATACCTAAAATATGATGCATGTATAT
1 CATAGATGAAAATGAATGAAAATGCACCTATTTTTGTAAATACCTAAAATATGATGCATGTATAT
932790 TAAGTTATTTGATTTCAGATGAGTGAATTG-A-ATTT-TTCAATTGTAG-AACCCAATATAT
66 TAAGTTATTTGATTTCAGATGA-TGAATTGAATATTTCTTCAATTGTAGAAACCCAATATAT
932848 CATAGATGAAAATGAATGAAAATGCACCTATTTTTGTAAATACCTAAAATATGATGCATGTATAT
1 CATAGATGAAAATGAATGAAAATGCACCTATTTTTGTAAATACCTAAAATATGATGCATGTATAT
932913 TAAGTTATTTGATTTCAGATGATGAATTGAATATTTCTTCAATTGTAGAAACCCAATATAT
66 TAAGTTATTTGATTTCAGATGATGAATTGAATATTTCTTCAATTGTAGAAACCCAATATAT
932974 C
1 C
932975 TGTCTTCTTC
Statistics
Matches: 123, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
122 7 0.06
123 88 0.72
124 4 0.03
125 11 0.09
126 13 0.11
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (126 bp):
CATAGATGAAAATGAATGAAAATGCACCTATTTTTGTAAATACCTAAAATATGATGCATGTATAT
TAAGTTATTTGATTTCAGATGATGAATTGAATATTTCTTCAATTGTAGAAACCCAATATAT
Found at i:933612 original size:83 final size:83
Alignment explanation
Indices: 933361--933720 Score: 681
Period size: 83 Copynumber: 4.4 Consensus size: 83
933351 GCACTTCTTT
* *
933361 AGATCAAATAACTCAAAGAACGCTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAAT
933426 GCTTGATTCTGTCTAATC
66 GCTTGATTCTGTCTAATC
933444 AGATCAGATAACTC-AAGAACACTTCCAG-A-ATGCTATTGGCAAATTCATCTTCTAAACTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAAT
933506 GCTTGATTCTGTCTAATC
66 GCTTGATTCTGTCTAATC
933524 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAAT
933589 GCTTGATTCTGTCTAATC
66 GCTTGATTCTGTCTAATC
933607 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAAT
933672 GCTTGATTCTGTCTAATC
66 GCTTGATTCTGTCTAATC
933690 AGATCAGATAACTCAAAGAACACTTCCAGAA
1 AGATCAGATAACTCAAAGAACACTTCCAGAA
933721 AATACTATGT
Statistics
Matches: 272, Mismatches: 2, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
80 65 0.24
81 15 0.06
82 14 0.05
83 178 0.65
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (83 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAAT
GCTTGATTCTGTCTAATC
Found at i:933756 original size:52 final size:52
Alignment explanation
Indices: 933669--933993 Score: 512
Period size: 52 Copynumber: 6.3 Consensus size: 52
933659 TTCTAAACTC
* *
933669 AATGCT-TGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAA
1 AATGCTATG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
* *
933721 AATACTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCTAGAA
1 AATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
* *
933773 GATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCTAG-A
1 AATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
933824 AATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
1 AATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
* * *
933876 GATGCTATGTTATGAT-CAACCAGATCAGATAACTCAAAGAACATTTCCAGAA
1 AATGCTATGTTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
*
933928 AATGCTATGTTCTGTCCAACCAGATCAGATAACTTAAAGAACACTTCCAGAA
1 AATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
*
933980 GATGCTATGTTCTG
1 AATGCTATGTTCTG
933994 ATGATTTTCC
Statistics
Matches: 253, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
51 50 0.20
52 200 0.79
53 3 0.01
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (52 bp):
AATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
Found at i:933951 original size:155 final size:155
Alignment explanation
Indices: 933669--933993 Score: 519
Period size: 155 Copynumber: 2.1 Consensus size: 155
933659 TTCTAAACTC
* * *
933669 AATGCT-TGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAAATACTATGTTC
1 AATGCTATG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATACTATGTTA
* *
933733 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGTTCTGTCCAACCAGAT
65 TGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGTTCTGTCCAACCAGAT
*
933798 CAGATAACTCAAAGAACACTTCTAGA
130 CAGATAACTCAAAGAACACTTCCAGA
* *
933824 AATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTAT
1 AATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATACTATGTTAT
*
933889 GAT-CAACCAGATCAGATAACTCAAAGAACATTTCCAGAAAATGCTATGTTCTGTCCAACCAGAT
66 G-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGTTCTGTCCAACCAGAT
*
933953 CAGATAACTTAAAGAACACTTCCAGA
130 CAGATAACTCAAAGAACACTTCCAGA
933979 AGATGCTATGTTCTG
1 A-ATGCTATGTTCTG
933994 ATGATTTTCC
Statistics
Matches: 157, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
155 141 0.90
156 16 0.10
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (155 bp):
AATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATACTATGTTAT
GTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGTTCTGTCCAACCAGATC
AGATAACTCAAAGAACACTTCCAGA
Found at i:934649 original size:16 final size:16
Alignment explanation
Indices: 934613--934650 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
934603 TGAATTTCCA
934613 AAAATAAATTGAATCT
1 AAAATAAATTGAATCT
*
934629 CAAATAAATTGAA-CTT
1 AAAATAAATTGAATC-T
934645 AAAATA
1 AAAATA
934651 GATAGAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAATAAATTGAATCT
Found at i:934980 original size:1 final size:1
Alignment explanation
Indices: 934969--935054 Score: 118
Period size: 1 Copynumber: 86.0 Consensus size: 1
934959 TTGACCCCTC
* * * *
934969 TTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTCTTTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
935034 TTTTTTTTTTCTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTT
935055 AAGCATAATA
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:945813 original size:24 final size:21
Alignment explanation
Indices: 945784--945831 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 21
945774 AATTACTATT
*
945784 ATATTTATTTATGAATATATAAAA
1 ATATTTATTCAT-AA-A-ATAAAA
945808 ATATTTATTCATAAAATAAAA
1 ATATTTATTCATAAAATAAAA
945829 ATA
1 ATA
945832 CTATTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 1 0.04
23 2 0.09
24 11 0.48
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
ATATTTATTCATAAAATAAAA
Found at i:947230 original size:3 final size:3
Alignment explanation
Indices: 947222--947320 Score: 135
Period size: 3 Copynumber: 33.0 Consensus size: 3
947212 TTAATATATT
* *
947222 TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** * *
947270 TGA TAA TAA TGT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
947318 TAA
1 TAA
947321 AATGGATAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:951154 original size:138 final size:138
Alignment explanation
Indices: 950906--951186 Score: 553
Period size: 138 Copynumber: 2.0 Consensus size: 138
950896 GAAAGACAAT
950906 CTTCAAACTAACAACTGCAACACATCCATTTTTTTAAACAATTTAAATTAATAAGATAACAAATG
1 CTTCAAACTAACAACTGCAACACATCCATTTTTTTAAACAATTTAAATTAATAAGATAACAAATG
*
950971 GGAATATGGAGTAATTATTAACATGCTAACTTAAGCATATAAAGTTATTAGTGATTCAATAATAA
66 GGAATATGGAGTAATTATTAACATGCTAACTTAAACATATAAAGTTATTAGTGATTCAATAATAA
951036 AAATTCCC
131 AAATTCCC
951044 CTTCAAACTAACAACTGCAACACATCCATTTTTTTAAACAATTTAAATTAATAAGATAACAAATG
1 CTTCAAACTAACAACTGCAACACATCCATTTTTTTAAACAATTTAAATTAATAAGATAACAAATG
951109 GGAATATGGAGTAATTATTAACATGCTAACTTAAACATATAAAGTTATTAGTGATTCAATAATAA
66 GGAATATGGAGTAATTATTAACATGCTAACTTAAACATATAAAGTTATTAGTGATTCAATAATAA
951174 AAATTCCC
131 AAATTCCC
951182 CTTCA
1 CTTCA
951187 GCATATCGGA
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 142 1.00
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (138 bp):
CTTCAAACTAACAACTGCAACACATCCATTTTTTTAAACAATTTAAATTAATAAGATAACAAATG
GGAATATGGAGTAATTATTAACATGCTAACTTAAACATATAAAGTTATTAGTGATTCAATAATAA
AAATTCCC
Found at i:967434 original size:22 final size:21
Alignment explanation
Indices: 967376--967445 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
967366 ATACCATGGG
*
967376 ACTTTAGTATTAGTGTATAAGC
1 ACTTTAGTAATAGTGT-TAAGC
* **
967398 ACTTTCGTACCAGTGTTAAGAC
1 ACTTTAGTAATAGTGTTAAG-C
967420 ACTTTAGTAATAGTGTTAAGGC
1 ACTTTAGTAATAGTGTTAA-GC
967442 ACTT
1 ACTT
967446 CAGTGATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 4 0.10
22 35 0.88
23 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (21 bp):
ACTTTAGTAATAGTGTTAAGC
Found at i:979015 original size:21 final size:21
Alignment explanation
Indices: 978977--979031 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
978967 AGAGGGAATT
978977 GATACCCCCCTTGAAGGGGAACC
1 GATA-CCCCC-TGAAGGGGAACC
* * *
979000 GATTCCCCCTGTAGGGGAATC
1 GATACCCCCTGAAGGGGAACC
979021 GATACCCCCTG
1 GATACCCCCTG
979032 GAGGTTCTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 20 0.71
22 5 0.18
23 3 0.11
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (21 bp):
GATACCCCCTGAAGGGGAACC
Found at i:986460 original size:20 final size:20
Alignment explanation
Indices: 986435--986492 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
986425 ATGTGAAATT
* *
986435 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGAACCTATATA
*
986455 TGTCCCGAA-ATACCTCTATA
1 TGTCCCGAAGA-ACCTATATA
986475 TGTCCCGAAGAACCTATA
1 TGTCCCGAAGAACCTATA
986493 AACCCTCGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
TGTCCCGAAGAACCTATATA
Found at i:990613 original size:17 final size:17
Alignment explanation
Indices: 990571--990620 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
990561 TATATTATGT
*
990571 ATAATGTATCATTTTAA
1 ATAATTTATCATTTTAA
*
990588 A-AATATTATTATTTTAA
1 ATAAT-TTATCATTTTAA
*
990605 ATAATTTATCACTTTA
1 ATAATTTATCATTTTA
990621 TAGTTTATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 3 0.11
17 21 0.78
18 3 0.11
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (17 bp):
ATAATTTATCATTTTAA
Found at i:990753 original size:22 final size:22
Alignment explanation
Indices: 990702--990759 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
990692 ATATATATTT
*
990702 AATAGTTTATTTTTATTTTTAG
1 AATAGTTTATATTTATTTTTAG
** * *
990724 TGT-TTTTATATTTATTTTTTG
1 AATAGTTTATATTTATTTTTAG
990745 AATAGTTTATATTTA
1 AATAGTTTATATTTA
990760 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (22 bp):
AATAGTTTATATTTATTTTTAG
Found at i:990771 original size:23 final size:22
Alignment explanation
Indices: 990728--990781 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
990718 TTTTAGTGTT
* ** *
990728 TTTATATTTATTTTTTGAATAG
1 TTTATATTTAATTTTAAAATAA
990750 TTTATATTTAAATTTTAAAATAA
1 TTTATATTT-AATTTTAAAATAA
*
990773 TTTTTATTT
1 TTTATATTT
990782 GAAAAATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (22 bp):
TTTATATTTAATTTTAAAATAA
Found at i:994344 original size:3 final size:3
Alignment explanation
Indices: 994336--994388 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
994326 TGTAATTATT
* *
994336 TAA TAA TAA TATA TAA TAA TAAA TAA AAA T-A TAA TAA T-A TAT TAA
1 TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
994381 TAA TAA TA
1 TAA TAA TA
994389 TTAAAAACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.10
3 32 0.76
4 6 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:994351 original size:10 final size:10
Alignment explanation
Indices: 994338--994385 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
994328 TAATTATTTA
994338 ATAATAATAT
1 ATAATAATAT
*
994348 ATAATAATAA
1 ATAATAATAT
994358 ATAA-AA-AT
1 ATAATAATAT
994366 ATAATAATAT
1 ATAATAATAT
994376 ATTAATAATA
1 A-TAATAATA
994386 ATATTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 5 0.15
9 4 0.12
10 16 0.48
11 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
ATAATAATAT
Found at i:994375 original size:28 final size:31
Alignment explanation
Indices: 994338--994395 Score: 95
Period size: 28 Copynumber: 2.0 Consensus size: 31
994328 TAATTATTTA
994338 ATAATAATATA-TAATAATAA-A-TAAAAAT
1 ATAATAATATATTAATAATAATATTAAAAAT
994366 ATAATAATATATTAATAATAATATTAAAAA
1 ATAATAATATATTAATAATAATATTAAAAA
994396 CAAATGGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 11 0.41
29 9 0.33
30 1 0.04
31 6 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
ATAATAATATATTAATAATAATATTAAAAAT
Found at i:994951 original size:236 final size:235
Alignment explanation
Indices: 994642--995161 Score: 916
Period size: 236 Copynumber: 2.2 Consensus size: 235
994632 CTGCTACTTA
* *
994642 TTCTTCAGATGAGTTCTTCTCATTATGAACATTTCT-GAAAATGTTGATGCTGGTCTATCTCCTT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTGGAAAA-GTTGATGCTGATCTATCTCCTT
* * * *
994706 CTTTGATAGAGTCATGCAAAATGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCA
65 CTGTGATAGAGTCACGAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCA
994771 GATAAGTTCTTCTCATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAA
130 GATAAGTTCTTCTCATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAA
*
994836 AAGGTTTGACCAAATTCTTCTCATTATGAATTTGTTTTTCC
195 AAGGTTTGACCAAATTCTTCTCATTATGAATTTGTTCTTCC
* *
994877 TTCTTCAGATGAGTTCTTCTTATTATGAACTCTTTCTGGAAAAGTTGATGTTGATCTATCTCCTT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACT-TTTCTGGAAAAGTTGATGCTGATCTATCTCCTT
994942 CTGTGATAGAGTCACGAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCA
65 CTGTGATAGAGTCACGAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCA
995007 GATAAGTTCTTCTCATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAA
130 GATAAGTTCTTCTCATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAA
995072 AAGGTTTGACCAAATTCTTCTCATTATGAATTTGTTCTTCC
195 AAGGTTTGACCAAATTCTTCTCATTATGAATTTGTTCTTCC
*
995113 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGAT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTT-TCTGGAAAAGTTGAT
995162 CCATCGAATG
Statistics
Matches: 271, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
235 31 0.11
236 235 0.87
237 5 0.02
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (235 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTC
TGTGATAGAGTCACGAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAG
ATAAGTTCTTCTCATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAA
AGGTTTGACCAAATTCTTCTCATTATGAATTTGTTCTTCC
Found at i:996351 original size:18 final size:18
Alignment explanation
Indices: 996328--996378 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
996318 AAATAAAAAG
996328 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
*
996346 AATAAATTGAATCTCAAA
1 AATAAATTGAATTTCAAA
996364 ATATAAATTGAATTT
1 A-ATAAATTGAATTT
996379 AGAGAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Found at i:996753 original size:16 final size:16
Alignment explanation
Indices: 996732--996790 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
996722 TTGACCCTCC
996732 TTTTTTATTTTCTTCT
1 TTTTTTATTTTCTTCT
*
996748 TTTTTTCTTTT-TCTCTT
1 TTTTTTATTTTCT-TC-T
* *
996765 TTTTTTCTTTTCCTCT
1 TTTTTTATTTTCTTCT
996781 TTTTTTATTT
1 TTTTTTATTT
996791 CATTTTTTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 1 0.03
16 22 0.59
17 14 0.38
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTATTTTCTTCT
Found at i:996759 original size:17 final size:16
Alignment explanation
Indices: 996732--996786 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 16
996722 TTGACCCTCC
*
996732 TTTTTTATTTTCT-TCT
1 TTTTTTCTTTTCTCT-T
996748 TTTTTTCTTTTTCTCTT
1 TTTTTTC-TTTTCTCTT
996765 TTTTTTCTTTTCCTCTT
1 TTTTTTCTTTT-CTCTT
996782 TTTTT
1 TTTTT
996787 ATTTCATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
16 10 0.29
17 24 0.69
18 1 0.03
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTCTTTTCTCTT
Found at i:1004137 original size:15 final size:15
Alignment explanation
Indices: 1004114--1004145 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1004104 TGCAATGAAT
1004114 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1004129 AATGCATGTATGCAA
1 AATGAATGTATGCAA
1004144 AA
1 AA
1004146 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1007471 original size:26 final size:26
Alignment explanation
Indices: 1007448--1007503 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
1007438 AAACATTAAT
*
1007448 AAAATAATATACATATAAATATTATG
1 AAAATAATAAACATATAAATATTATG
* * *
1007474 AAAATAATAAATATATAAAAATTTTG
1 AAAATAATAAACATATAAATATTATG
1007500 AAAA
1 AAAA
1007504 GAAAGAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (26 bp):
AAAATAATAAACATATAAATATTATG
Found at i:1008333 original size:18 final size:17
Alignment explanation
Indices: 1008307--1008348 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1008297 AATATATTAC
1008307 AAATAAACATA-TAAAATT
1 AAATAAACA-ACTAAAA-T
*
1008325 AAATCAACAACTAAAAT
1 AAATAAACAACTAAAAT
1008342 AAATAAA
1 AAATAAA
1008349 ATTAAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAAACAACTAAAAT
Found at i:1009643 original size:10 final size:10
Alignment explanation
Indices: 1009630--1009669 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
1009620 TAATTATTTA
1009630 ATAATAATAT
1 ATAATAATAT
*
1009640 ATAATAATAA
1 ATAATAATAT
1009650 ATAA-AA-AT
1 ATAATAATAT
1009658 ATAATAATAT
1 ATAATAATAT
1009668 AT
1 AT
1009670 TAACAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 5 0.19
9 4 0.15
10 17 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
ATAATAATAT
Found at i:1029520 original size:3 final size:3
Alignment explanation
Indices: 1029512--1029567 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
1029502 TGTTAAATTG
1029512 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1029560 TTA TTA TT
1 TTA TTA TT
1029568 TGGATTGAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1030637 original size:3 final size:3
Alignment explanation
Indices: 1030629--1030656 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1030619 ATGAGGTGAC
1030629 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1030657 AATCCAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1030964 original size:3 final size:3
Alignment explanation
Indices: 1030958--1031047 Score: 180
Period size: 3 Copynumber: 30.0 Consensus size: 3
1030948 TTTTTATCCA
1030958 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1031006 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1031048 AAATATATTA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1031073 original size:14 final size:13
Alignment explanation
Indices: 1031046--1031083 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
1031036 TATTATTATT
1031046 ATAAATATATTAA
1 ATAAATATATTAA
1031059 ATAAATATATATAA
1 ATAAATATAT-TAA
1031073 ATAAATA-ATTA
1 ATAAATATATTA
1031084 CAGACCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 2 0.08
13 12 0.50
14 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAAATATATTAA
Found at i:1032505 original size:13 final size:13
Alignment explanation
Indices: 1032489--1032534 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
1032479 ATATAATAAA
1032489 TAAATATTTATTT
1 TAAATATTTATTT
*
1032502 TAAATAAATTATTT
1 TAAAT-ATTTATTT
1032516 T-AATATTTATTT
1 TAAATATTTATTT
*
1032528 TTAATAT
1 TAAATAT
1032535 CGAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:1033197 original size:28 final size:29
Alignment explanation
Indices: 1033154--1033219 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
1033144 AAAAATTCAT
*
1033154 ATATTTA-ATTTAATTT-TATCTTTTCAAA
1 ATATTTATATTTAATTTAT-TATTTTCAAA
* *
1033182 ATTTTTATATTT-ATTTATTATTTTCATA
1 ATATTTATATTTAATTTATTATTTTCAAA
1033210 ATATTTATAT
1 ATATTTATAT
1033220 GTTTCATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (29 bp):
ATATTTATATTTAATTTATTATTTTCAAA
Found at i:1033232 original size:18 final size:18
Alignment explanation
Indices: 1033191--1033233 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1033181 AATTTTTATA
1033191 TTTATTTATTATTTTCAT
1 TTTATTTATTATTTTCAT
**
1033209 AATATTTA-TATGTTTCAT
1 TTTATTTATTAT-TTTCAT
1033227 TTTATTT
1 TTTATTT
1033234 GCAATTATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTATTATTTTCAT
Found at i:1033255 original size:13 final size:15
Alignment explanation
Indices: 1033225--1033257 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1033215 TATATGTTTC
1033225 ATTTTATTTGCAATT
1 ATTTTATTTGCAATT
1033240 ATTTTATTT-C-ATT
1 ATTTTATTTGCAATT
1033253 ATTTT
1 ATTTT
1033258 TCTGTCAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 1 0.06
15 9 0.50
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (15 bp):
ATTTTATTTGCAATT
Found at i:1043875 original size:10 final size:9
Alignment explanation
Indices: 1043860--1043902 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
1043850 ATGCTTGAAG
1043860 AAAAGAAAGA
1 AAAAGAAA-A
1043870 AAAAGAAAA
1 AAAAGAAAA
1043879 AAAAGGAAAA
1 AAAA-GAAAA
*
1043889 AAGAGAAAA
1 AAAAGAAAA
1043898 GAAAA
1 -AAAA
1043903 AGGAGGGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 10 0.34
10 19 0.66
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:1043877 original size:15 final size:15
Alignment explanation
Indices: 1043857--1043904 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1043847 ATTATGCTTG
1043857 AAGAAAAGAAAGAAA
1 AAGAAAAGAAAGAAA
* *
1043872 AAGAAAAAAAAGGAA
1 AAGAAAAGAAAGAAA
*
1043887 AA-AAGAGAAAAGAAA
1 AAGAAAAG-AAAGAAA
1043902 AAG
1 AAG
1043905 GAGGGTCAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.12
15 23 0.88
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAAAGAAA
Found at i:1043895 original size:19 final size:20
Alignment explanation
Indices: 1043857--1043902 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1043847 ATTATGCTTG
1043857 AAGAAAAGAAAGAAAAAGAA
1 AAGAAAAGAAAGAAAAAGAA
*
1043877 AA-AAAAGGAAA-AAAGAGAA
1 AAGAAAA-GAAAGAAAAAGAA
1043896 AAGAAAA
1 AAGAAAA
1043903 AGGAGGGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
AAGAAAAGAAAGAAAAAGAA
Found at i:1045322 original size:83 final size:84
Alignment explanation
Indices: 1045032--1045591 Score: 994
Period size: 83 Copynumber: 6.8 Consensus size: 84
1045022 AAACATTAAC
* *
1045032 TAGAAGATGAATTTGCTC-ATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGG
1 TAGAAGATGAATTTG-TCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1045095 ACAGAA-CAATCATTGAATT
65 ACAGAACCAATCATTGAATT
1045114 TAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGA
1 TAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGA
1045178 CAGAA-CAATCATTGAATT
66 CAGAACCAATCATTGAATT
1045196 TAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-
1 TAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGA
1045260 CAGAACCAATCATTGAATT
66 CAGAACCAATCATTGAATT
1045279 TAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-
1 TAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGA
1045343 CAGAACCAATCATTGAATT
66 CAGAACCAATCATTGAATT
1045362 TAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-
1 TAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGA
1045426 CAGAACCAATCATTGAATT
66 CAGAACCAATCATTGAATT
*
1045445 TAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGA
1 TAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGA
*
1045509 CAGAACCAATCATTGAGTT
66 CAGAACCAATCATTGAATT
* *
1045528 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1045592 TAGGAACTAC
Statistics
Matches: 468, Mismatches: 5, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
81 2 0.00
82 145 0.31
83 317 0.68
84 4 0.01
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (84 bp):
TAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGA
CAGAACCAATCATTGAATT
Found at i:1046661 original size:113 final size:113
Alignment explanation
Indices: 1046318--1046987 Score: 1139
Period size: 113 Copynumber: 5.9 Consensus size: 113
1046308 GATTCAAATC
* * *
1046318 CATCACTTGATGGAGCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
1046382 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
* * * * *
1046430 CATCATTTGATGGATTAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1 CATCATTTGATGGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGA
1046494 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
62 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
*
1046546 CATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1046611 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
1046659 CATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1046724 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
1046772 CATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1046837 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
* * * *
1046885 CATCAATTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCAGAAGAAGAA
1 CATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
1046949 AGAAGAAGTTCATAATAAGAAGAATTTATTCAACCTTTT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
1046988 GAATGACTCT
Statistics
Matches: 533, Mismatches: 19, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
111 1 0.00
112 91 0.17
113 333 0.62
114 1 0.00
115 1 0.00
116 105 0.20
117 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
CATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
Found at i:1047312 original size:3 final size:3
Alignment explanation
Indices: 1047306--1047431 Score: 225
Period size: 3 Copynumber: 41.7 Consensus size: 3
1047296 TTTTTATCCA
1047306 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1047354 TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1047402 TAT TAT TAT TAT TAT TAT TAA TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
1047432 AATAAATATA
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
3 115 0.97
4 3 0.03
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1047449 original size:14 final size:15
Alignment explanation
Indices: 1047421--1047453 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1047411 TATTATTATT
1047421 AATATATATTAAATA
1 AATATATATTAAATA
1047436 AATATATA-TAAATA
1 AATATATATTAAATA
1047450 AATA
1 AATA
1047454 ATTACAGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATATATTAAATA
Found at i:1047897 original size:24 final size:24
Alignment explanation
Indices: 1047863--1047934 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
1047853 ACCCGAACCT
1047863 GAAAAAG-AAAAAAAACAGACAGA
1 GAAAAAGAAAAAAAAACAGACAGA
1047886 GAAAAAGAAAAAAAAACAGACAGA
1 GAAAAAGAAAAAAAAACAGACAGA
* *
1047910 GAGACAA-AAAAAAAGA-AGACAGA
1 GA-AAAAGAAAAAAAAACAGACAGA
1047933 GA
1 GA
1047935 CTACACAGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.36
24 26 0.58
25 3 0.07
ACGTcount: A:0.72, C:0.08, G:0.19, T:0.00
Consensus pattern (24 bp):
GAAAAAGAAAAAAAAACAGACAGA
Found at i:1048908 original size:13 final size:13
Alignment explanation
Indices: 1048892--1048937 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
1048882 ATATAATAAA
1048892 TAAATATTTATTT
1 TAAATATTTATTT
*
1048905 TAAATAAATTATTT
1 TAAAT-ATTTATTT
1048919 T-AATATTTATTT
1 TAAATATTTATTT
*
1048931 TTAATAT
1 TAAATAT
1048938 CGAAGAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:1052837 original size:2 final size:2
Alignment explanation
Indices: 1052832--1052863 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1052822 TCACACACAA
1052832 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
1052864 TAAATACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1056238 original size:76 final size:76
Alignment explanation
Indices: 1056115--1056303 Score: 337
Period size: 76 Copynumber: 2.5 Consensus size: 76
1056105 CGTTACACAG
1056115 GGGGGAATCGGTACCCCCTT--GGGGGAATCGGTTCCCTCCGAGCAATCTGTTATTTCTCAGAGA
1 GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTCCGAGCAATCTGTTATTTCTCAGAGA
1056178 TAAACCATTTA
66 TAAACCATTTA
* * *
1056189 GGGGGAATCAGTACCCCCTTGGGGGGGAATCGGTTCCCTCTGAGCAATCTGTTATTTCTCAGAGC
1 GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTCCGAGCAATCTGTTATTTCTCAGAGA
1056254 TAAACCATTTA
66 TAAACCATTTA
1056265 GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCT
1 GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCT
1056304 TTGGACAATC
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
74 19 0.17
76 90 0.83
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (76 bp):
GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTCCGAGCAATCTGTTATTTCTCAGAGA
TAAACCATTTA
Found at i:1056303 original size:20 final size:21
Alignment explanation
Indices: 1056265--1056307 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1056255 AAACCATTTA
1056265 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTA-CCCCTTGG
* *
1056287 GGGGGAATCGGTTCCCTTTGG
1 GGGGGAATCGGTACCCCTTGG
1056308 ACAATCTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.12, C:0.23, G:0.42, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCTTGG
Found at i:1058659 original size:19 final size:19
Alignment explanation
Indices: 1058637--1058673 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1058627 TTTGAAAGCT
1058637 AAAAT-AAATTTGGAAAAAC
1 AAAATGAAATTT-GAAAAAC
1058656 AAAATGAAATTTGAAAAA
1 AAAATGAAATTTGAAAAA
1058674 TGAGTTAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.65, C:0.03, G:0.11, T:0.22
Consensus pattern (19 bp):
AAAATGAAATTTGAAAAAC
Found at i:1058832 original size:117 final size:116
Alignment explanation
Indices: 1058622--1058837 Score: 274
Period size: 117 Copynumber: 1.9 Consensus size: 116
1058612 TAAAAATGAT
* *
1058622 CTTATTTTGAAAGCTAAAATAAATTTGGAAAAACAAAATGAAATTTGAAAAATGAGTTAGAGCTT
1 CTTATTTAGAAAGCTAAAATAAATTTGGAAAAACAAAATGAAATTTGAAAAAGGAGTTAGAGCTT
* *
1058687 TCAAAAATGAAATCTGAAAACTTTGAAAAAGAAATTTTCAAATTAAACAAA
66 TCAAAAATAAAATCTGAAAACTTGGAAAAAGAAATTTTCAAATTAAACAAA
** * * * **
1058738 CTTATTCTAGAAA-CTAAAATGGATTTTGAAAATCAAAATGAAATATTGAAGAAGGCTTTAGAGC
1 CTTATT-TAGAAAGCTAAAATAAATTTGGAAAAACAAAATGAAAT-TTGAAAAAGGAGTTAGAGC
* *
1058802 TTTCAAAAATAAAATTTG-AAAGTATGGAAAAAGAAA
64 TTTCAAAAATAAAATCTGAAAACT-TGGAAAAAGAAA
1058838 ATCTTGATTT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
116 37 0.44
117 47 0.56
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.28
Consensus pattern (116 bp):
CTTATTTAGAAAGCTAAAATAAATTTGGAAAAACAAAATGAAATTTGAAAAAGGAGTTAGAGCTT
TCAAAAATAAAATCTGAAAACTTGGAAAAAGAAATTTTCAAATTAAACAAA
Found at i:1062740 original size:14 final size:14
Alignment explanation
Indices: 1062721--1062747 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1062711 GTGCATATAG
1062721 TGTATCGATACATA
1 TGTATCGATACATA
1062735 TGTATCGATACAT
1 TGTATCGATACAT
1062748 CCTCGTTATG
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:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (14 bp):
TGTATCGATACATA
Found at i:1063062 original size:94 final size:94
Alignment explanation
Indices: 1062901--1063091 Score: 382
Period size: 94 Copynumber: 2.0 Consensus size: 94
1062891 TCTCTCAAAT
1062901 CAACCAAATTCTCCTTTTGCTCATTTTCAACGCTTTCAAGTCAAAATCTCTTTGTTCTTTAACTC
1 CAACCAAATTCTCCTTTTGCTCATTTTCAACGCTTTCAAGTCAAAATCTCTTTGTTCTTTAACTC
1062966 CAAATCTTACTACGATCAATAAAATCGTG
66 CAAATCTTACTACGATCAATAAAATCGTG
1062995 CAACCAAATTCTCCTTTTGCTCATTTTCAACGCTTTCAAGTCAAAATCTCTTTGTTCTTTAACTC
1 CAACCAAATTCTCCTTTTGCTCATTTTCAACGCTTTCAAGTCAAAATCTCTTTGTTCTTTAACTC
1063060 CAAATCTTACTACGATCAATAAAATCGTG
66 CAAATCTTACTACGATCAATAAAATCGTG
1063089 CAA
1 CAA
1063092 ACATCACTAC
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 97 1.00
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (94 bp):
CAACCAAATTCTCCTTTTGCTCATTTTCAACGCTTTCAAGTCAAAATCTCTTTGTTCTTTAACTC
CAAATCTTACTACGATCAATAAAATCGTG
Found at i:1071651 original size:41 final size:40
Alignment explanation
Indices: 1071606--1072118 Score: 176
Period size: 41 Copynumber: 12.5 Consensus size: 40
1071596 ATTGTGGTGT
*
1071606 TTTTTCAATAAACGCCGCAACAGATTAATACTATAGCAGCG
1 TTTTT-AATAAACGCCGCAACAGATTAATACTATAGCGGCG
* * ** * * * **
1071647 TTTTTATACAAACGCCGCAATAGATCCAT-TTGTAGTGGTA
1 TTTTTA-ATAAACGCCGCAACAGATTAATACTATAGCGGCG
* * * *
1071687 TTTTTCAATAAACGCCGCAACAGATTAGTTCTTTAGCGGTG
1 TTTTT-AATAAACGCCGCAACAGATTAATACTATAGCGGCG
* ** * * * * *
1071728 TTTTTATACAAACGCCATAATAG-TGTCA-CCTATAGTGGCA
1 TTTTTA-ATAAACGCCGCAACAGAT-TAATACTATAGCGGCG
* * * ***
1071768 TTTTTAGTAAACGCCGTAACAGATTAGA-ACTTTAGCAATG
1 TTTTTAATAAACGCCGCAACAGATTA-ATACTATAGCGGCG
* * * **
1071808 TTTTTATATAAACGTCGCAATAGTATT--TACCTATAGTGGTAT
1 TTTTTA-ATAAACGCCGCAACAG-ATTAATA-CTATAGCGG-CG
* *
1071850 TTTTTCAATAAACACCGCAACAGATTAGA-ACTTTAGCGGCG
1 TTTTT-AATAAACGCCGCAACAGATTA-ATACTATAGCGGCG
* * * ** *
1071891 TTTTTATACAAATGCCGCAATAG-TTTTTACCTATAGTGGCG
1 TTTTTA-ATAAACGCCGCAACAGATTAATA-CTATAGCGGCG
*
1071932 TTTTTTCAATAAACGCTGCAACAGATT-ATAAC-ATTAGCGGCG
1 -TTTTT-AATAAACGCCGCAACAGATTAAT-ACTA-TAGCGGCG
* * * *
1071974 TTTTTATACAAACACCGCAATAGTATT--TACCTATAGTGGCG
1 TTTTTA-ATAAACGCCGCAACAG-ATTAATA-CTATAGCGGCG
*
1072015 TTTTTTCAATAAACGCTGCAACAGATT-ATAAC-ATTAGCGGCG
1 -TTTTT-AATAAACGCCGCAACAGATTAAT-ACTA-TAGCGGCG
* * * * *
1072057 TTTTTATACAAACACCGTAATAGTATT--TACTTATAGTGGCG
1 TTTTTA-ATAAACGCCGCAACAG-ATTAATAC-TATAGCGGCG
1072098 TTTTTAAAATAAACGCCGCAA
1 TTTTT--AATAAACGCCGCAA
1072119 TTGTTTGAAC
Statistics
Matches: 341, Mismatches: 92, Indels: 77
0.67 0.18 0.15
Matches are distributed among these distances:
39 13 0.04
40 66 0.19
41 155 0.45
42 98 0.29
43 9 0.03
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (40 bp):
TTTTTAATAAACGCCGCAACAGATTAATACTATAGCGGCG
Found at i:1071883 original size:83 final size:83
Alignment explanation
Indices: 1071594--1072118 Score: 614
Period size: 83 Copynumber: 6.4 Consensus size: 83
1071584 ATAGGTCCAT
* * * *
1071594 CTATTGTGGTGTTTTTTCAATAAACGCCGCAACAGATTA-ATACTATAGCAGCGTTTTTATACAA
1 CTATAGTGGCGTTTTTTCAATAAACGCCGCAACAGATTAGA-ACTTTAGCGGCGTTTTTATACAA
** *
1071658 ACGCCGCAATAG-ATCCAT
65 ACGCCGCAATAGTATTTAC
* * ** *
1071676 TTGTAGT-G-GTATTTTTCAATAAACGCCGCAACAGATTAGTTCTTTAGCGGTGTTTTTATACAA
1 CTATAGTGGCGT-TTTTTCAATAAACGCCGCAACAGATTAGAACTTTAGCGGCGTTTTTATACAA
** * *
1071739 ACGCCATAATAGT-GTCAC
65 ACGCCGCAATAGTATTTAC
* * * *** *
1071757 CTATAGTGGC-ATTTTT-AGTAAACGCCGTAACAGATTAGAACTTTAGCAATGTTTTTATATAAA
1 CTATAGTGGCGTTTTTTCAATAAACGCCGCAACAGATTAGAACTTTAGCGGCGTTTTTATACAAA
*
1071820 CGTCGCAATAGTATTTAC
66 CGCCGCAATAGTATTTAC
** *
1071838 CTATAGTGGTATTTTTTCAATAAACACCGCAACAGATTAGAACTTTAGCGGCGTTTTTATACAAA
1 CTATAGTGGCGTTTTTTCAATAAACGCCGCAACAGATTAGAACTTTAGCGGCGTTTTTATACAAA
* *
1071903 TGCCGCAATAGTTTTTAC
66 CGCCGCAATAGTATTTAC
* * *
1071921 CTATAGTGGCGTTTTTTCAATAAACGCTGCAACAGATTATAACATTAGCGGCGTTTTTATACAAA
1 CTATAGTGGCGTTTTTTCAATAAACGCCGCAACAGATTAGAACTTTAGCGGCGTTTTTATACAAA
*
1071986 CACCGCAATAGTATTTAC
66 CGCCGCAATAGTATTTAC
* * *
1072004 CTATAGTGGCGTTTTTTCAATAAACGCTGCAACAGATTATAACATTAGCGGCGTTTTTATACAAA
1 CTATAGTGGCGTTTTTTCAATAAACGCCGCAACAGATTAGAACTTTAGCGGCGTTTTTATACAAA
* *
1072069 CACCGTAATAGTATTTAC
66 CGCCGCAATAGTATTTAC
* **
1072087 TTATAGTGGCGTTTTTAAAATAAACGCCGCAA
1 CTATAGTGGCGTTTTTTCAATAAACGCCGCAA
1072119 TTGTTTGAAC
Statistics
Matches: 381, Mismatches: 54, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
80 51 0.13
81 81 0.21
82 10 0.03
83 239 0.63
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (83 bp):
CTATAGTGGCGTTTTTTCAATAAACGCCGCAACAGATTAGAACTTTAGCGGCGTTTTTATACAAA
CGCCGCAATAGTATTTAC
Found at i:1072057 original size:42 final size:42
Alignment explanation
Indices: 1071849--1072061 Score: 179
Period size: 42 Copynumber: 5.1 Consensus size: 42
1071839 TATAGTGGTA
* * *
1071849 TTTTTTCAATAAACACCGCAACAGATTAGAACTTTAGCGGCG
1 TTTTTTCAATAAACGCCGCAACAGATTATAACATTAGCGGCG
* * * * * * *
1071891 -TTTTT-ATACAAATGCCGCAATAG-TTTTTACCTATAGTGGCG
1 TTTTTTCA-ATAAACGCCGCAACAGATTATAACAT-TAGCGGCG
*
1071932 TTTTTTCAATAAACGCTGCAACAGATTATAACATTAGCGGCG
1 TTTTTTCAATAAACGCCGCAACAGATTATAACATTAGCGGCG
* * * * *
1071974 -TTTTT-ATACAAACACCGCAATAGTATT-T-ACCTATAGTGGCG
1 TTTTTTCA-ATAAACGCCGCAACAG-ATTATAACAT-TAGCGGCG
*
1072015 TTTTTTCAATAAACGCTGCAACAGATTATAACATTAGCGGCG
1 TTTTTTCAATAAACGCCGCAACAGATTATAACATTAGCGGCG
1072057 TTTTT
1 TTTTT
1072062 ATACAAACAC
Statistics
Matches: 130, Mismatches: 29, Indels: 24
0.71 0.16 0.13
Matches are distributed among these distances:
40 10 0.08
41 52 0.40
42 57 0.44
43 11 0.08
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (42 bp):
TTTTTTCAATAAACGCCGCAACAGATTATAACATTAGCGGCG
Found at i:1072238 original size:22 final size:22
Alignment explanation
Indices: 1072211--1072255 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1072201 CCCTCTTCTC
1072211 TCACTTTTATCGTATATAGGGT
1 TCACTTTTATCGTATATAGGGT
*
1072233 TCACTTTTATCGTATCTAGGGT
1 TCACTTTTATCGTATATAGGGT
1072255 T
1 T
1072256 TTAGAATCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.47
Consensus pattern (22 bp):
TCACTTTTATCGTATATAGGGT
Found at i:1072495 original size:17 final size:17
Alignment explanation
Indices: 1072473--1072510 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1072463 GGGTAGTTAT
1072473 GTTCGGATTTTGCTTAA
1 GTTCGGATTTTGCTTAA
1072490 GTTCGGATTTTGCTTAA
1 GTTCGGATTTTGCTTAA
1072507 GTTC
1 GTTC
1072511 TTTCATGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.16, C:0.13, G:0.24, T:0.47
Consensus pattern (17 bp):
GTTCGGATTTTGCTTAA
Found at i:1082750 original size:42 final size:43
Alignment explanation
Indices: 1082638--1082982 Score: 333
Period size: 42 Copynumber: 8.1 Consensus size: 43
1082628 AATTAGTGAT
* * * * * * *
1082638 GTTTGT-TTCAAAAATACCGCTACATATATGACATTTTACGGC
1 GTTTGTATCCAAAAATGCCGCTATAGATCTGACTTTTTGCGGC
* * *
1082680 GTTTGTATCCAAAAATGCCACTATAGATCTGACTTTTTACGAC
1 GTTTGTATCCAAAAATGCCGCTATAGATCTGACTTTTTGCGGC
* * *
1082723 GTTTGT-TCCAAAAATGCCGCTACAGATCTGACCTTTCGCGGC
1 GTTTGTATCCAAAAATGCCGCTATAGATCTGACTTTTTGCGGC
* * * *
1082765 ATTTGTAT-AAAAAATGCCGCTATAGATATGACTTTTTGCGTC
1 GTTTGTATCCAAAAATGCCGCTATAGATCTGACTTTTTGCGGC
* * * *
1082807 GTTTGT-TCAAAAAATGCCGCTATAGATCTTACATTTTGCGGT
1 GTTTGTATCCAAAAATGCCGCTATAGATCTGACTTTTTGCGGC
* *
1082849 GTTTGTATCCAAAAATGCCGCTATAGATCTCAACCTTTTGCGGC
1 GTTTGTATCCAAAAATGCCGCTATAGATCT-GACTTTTTGCGGC
* ** *
1082893 GTTTGTATACAAAAACACCGCTATAGATCTGAAC-TTTTGGGGC
1 GTTTGTATCCAAAAATGCCGCTATAGATCTG-ACTTTTTGCGGC
* ** * *
1082936 GTTTGT-TTCAAAAACACCGCTATATATCTTGACTTTTTTCGGC
1 GTTTGTATCCAAAAATGCCGCTATAGATC-TGACTTTTTGCGGC
1082979 GTTT
1 GTTT
1082983 TTATTTCACA
Statistics
Matches: 255, Mismatches: 40, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.00
42 131 0.51
43 84 0.33
44 39 0.15
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (43 bp):
GTTTGTATCCAAAAATGCCGCTATAGATCTGACTTTTTGCGGC
Found at i:1085280 original size:17 final size:18
Alignment explanation
Indices: 1085258--1085296 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1085248 GAAAATATTA
*
1085258 AAATAA-TAAAAGCGATT
1 AAATAAGTAAAAGCAATT
1085275 AAATAAGTAAAAGCAATT
1 AAATAAGTAAAAGCAATT
1085293 AAAT
1 AAAT
1085297 TAAAAATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (18 bp):
AAATAAGTAAAAGCAATT
Found at i:1088710 original size:6 final size:6
Alignment explanation
Indices: 1088699--1088741 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
1088689 TGTTTGAATG
*
1088699 AATAAA AAT-AA AAT-AA AATAAA AAGTAAA GATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA-TAAA AATAAA AATAAA AA
1088742 ATGTAACGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 10 0.30
6 18 0.55
7 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:1091604 original size:18 final size:19
Alignment explanation
Indices: 1091581--1091622 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1091571 GTAAGAAAAT
*
1091581 ATTAAAATAA-TAAAAGCG
1 ATTAAAATAAGTAAAAGCA
1091599 ATT-AAATAAGTAAAAGCA
1 ATTAAAATAAGTAAAAGCA
1091617 ATTAAA
1 ATTAAA
1091623 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
ATTAAAATAAGTAAAAGCA
Found at i:1101096 original size:12 final size:13
Alignment explanation
Indices: 1101064--1101105 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1101054 TGTGATTGGT
1101064 AGTAGGAAAGAGA
1 AGTAGGAAAGAGA
*
1101077 AGCGAGGAAAGA-A
1 AG-TAGGAAAGAGA
1101090 AGTAGGAAAGATGA
1 AGTAGGAAAGA-GA
1101104 AG
1 AG
1101106 ATTTTCCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 8 0.33
13 5 0.21
14 11 0.46
ACGTcount: A:0.52, C:0.02, G:0.38, T:0.07
Consensus pattern (13 bp):
AGTAGGAAAGAGA
Found at i:1105592 original size:17 final size:17
Alignment explanation
Indices: 1105570--1105602 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1105560 AGTTTAGGGA
1105570 TCAAAATAGTAATTTTC
1 TCAAAATAGTAATTTTC
*
1105587 TCAAAATAGTTATTTT
1 TCAAAATAGTAATTTT
1105603 TATCCCATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
TCAAAATAGTAATTTTC
Done.