Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008041.1 Hibiscus syriacus cultivar Beakdansim tig00110528_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: 4970990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 21
Found at i:2861962 original size:44 final size:44
Alignment explanation
Indices: 2861911--2862184 Score: 318
Period size: 44 Copynumber: 6.4 Consensus size: 44
2861901 GCTCTAAAAC
* *
2861911 AAATGAAAATGAATAACGATGTATTATTGGCAGAAAGGTGCCAT
1 AAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCCAT
*
2861955 AAATGAAAATGCATAA-TAGTGCATTATTGGCAGAAAGGTGCCAT
1 AAATGAAAATGCATAACGA-TGCATTATTGGCAGAAAGGTGCCAT
* * * *
2861999 AAATGAAAATGCATAATGGTGCATTATTGGCATAAAGGTGGCAT
1 AAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCCAT
* * *
2862043 AAATGAAAATGCATAAC-AGTGCATTATTGGCTGAAAGGTTCTAT
1 AAATGAAAATGCATAACGA-TGCATTATTGGCAGAAAGGTGCCAT
*
2862087 AAATAAAAAATGCAT----A---ATTATTGGCAGAAAGGTGCCAT
1 AAAT-GAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCCAT
* *
2862125 AAATTG-AAATGCAT-ACGGTGCATTATTGGAAGAAAGGTGCCAT
1 AAA-TGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCCAT
2862168 AAATGAAAATGCATAAC
1 AAATGAAAATGCATAAC
2862185 AGTACATCAT
Statistics
Matches: 196, Mismatches: 21, Indels: 26
0.81 0.09 0.11
Matches are distributed among these distances:
37 8 0.04
38 22 0.11
39 1 0.01
42 3 0.02
43 33 0.17
44 120 0.61
45 9 0.05
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.26
Consensus pattern (44 bp):
AAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCCAT
Found at i:2865040 original size:13 final size:13
Alignment explanation
Indices: 2865010--2865052 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
2865000 ACCCAGTCAC
*
2865010 TGAGTCAACTTGAT
1 TGAGTCAAC-TCAT
2865024 TGAGTCAACTCAT
1 TGAGTCAACTCAT
*
2865037 TGAGTCAACTCGT
1 TGAGTCAACTCAT
2865050 TGA
1 TGA
2865053 TCATTGACCG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 18 0.67
14 9 0.33
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (13 bp):
TGAGTCAACTCAT
Found at i:2873081 original size:21 final size:21
Alignment explanation
Indices: 2873056--2873121 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 21
2873046 TTATTTATGG
2873056 CATCATTTCATGTCTTTTATA
1 CATCATTTCATGTCTTTTATA
* * *
2873077 CATCATTATACATTTCATTTATGG
1 CATCATT-T-CATGTCTTTTAT-A
* *
2873101 CATCTTTTCATGCCTTTTATA
1 CATCATTTCATGTCTTTTATA
2873122 AATAATTATA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
21 7 0.21
22 10 0.29
23 11 0.32
24 6 0.18
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.50
Consensus pattern (21 bp):
CATCATTTCATGTCTTTTATA
Found at i:2873089 original size:45 final size:45
Alignment explanation
Indices: 2872985--2873275 Score: 343
Period size: 45 Copynumber: 6.4 Consensus size: 45
2872975 GCTTATAATG
* * * *
2872985 CATCATTGTGCATTTTCATTTATGGCAACCGTTCATGCCTTTT-TA
1 CATCATTATACATTTT-ATTTATGGCATCCTTTCATGCCTTTTATA
* * *
2873030 TATACTATTATACATTTTATTTATGGCATCATTTCATGTCTTTTATA
1 CAT-C-ATTATACATTTTATTTATGGCATCCTTTCATGCCTTTTATA
* *
2873077 CATCATTATACATTTCATTTATGGCATCTTTTCATGCCTTTTATA
1 CATCATTATACATTTTATTTATGGCATCCTTTCATGCCTTTTATA
* * *
2873122 AATAATTATACATTTTATTTATGGTATCCTTTCATGCCTTTTATA
1 CATCATTATACATTTTATTTATGGCATCCTTTCATGCCTTTTATA
* *
2873167 CA-CTATTATACATTTTATATATGTCATCCTTTCATGCCTTTTATA
1 CATC-ATTATACATTTTATTTATGGCATCCTTTCATGCCTTTTATA
* * * *
2873212 CACCATTATAAATTTTATTTATGGCATCCTTCCATGCATTTTATA
1 CATCATTATACATTTTATTTATGGCATCCTTTCATGCCTTTTATA
* *
2873257 CACCATTATAAATTGTTAT
1 CATCATTATACATT-TTAT
2873276 ACATCTAGTC
Statistics
Matches: 214, Mismatches: 26, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
45 171 0.80
46 29 0.14
47 14 0.07
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (45 bp):
CATCATTATACATTTTATTTATGGCATCCTTTCATGCCTTTTATA
Found at i:2873200 original size:135 final size:137
Alignment explanation
Indices: 2872995--2873256 Score: 384
Period size: 135 Copynumber: 1.9 Consensus size: 137
2872985 CATCATTGTG
* *
2872995 CATTTTCATTTATGGCAACCGTTCATGCCTTTTTATATACTATTATACATTTTATTTATGGCATC
1 CATTTTCATTTATGGCAACCGTTCATGCCTTTTTATACACTATTATACATTTTATATATGGCATC
* * * * * *
2873060 ATTTCATGTCTTTTATACATCATTATACATTTCATTTATGGCATCTTTTCATGCCTTTTATAAAT
66 ATTTCATGCCTTTTATACACCATTATAAATTTCATTTATGGCATCCTTCCATGCATTTTATAAAT
2873125 AATTATA
131 AATTATA
* * * *
2873132 CATTTT-ATTTATGGTATCCTTTCATGCC-TTTTATACACTATTATACATTTTATATATGTCATC
1 CATTTTCATTTATGGCAACCGTTCATGCCTTTTTATACACTATTATACATTTTATATATGGCATC
* *
2873195 CTTTCATGCCTTTTATACACCATTATAAATTTTATTTATGGCATCCTTCCATGCATTTTATA
66 ATTTCATGCCTTTTATACACCATTATAAATTTCATTTATGGCATCCTTCCATGCATTTTATA
2873257 CACCATTATA
Statistics
Matches: 111, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
135 86 0.77
136 19 0.17
137 6 0.05
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (137 bp):
CATTTTCATTTATGGCAACCGTTCATGCCTTTTTATACACTATTATACATTTTATATATGGCATC
ATTTCATGCCTTTTATACACCATTATAAATTTCATTTATGGCATCCTTCCATGCATTTTATAAAT
AATTATA
Found at i:2873410 original size:68 final size:68
Alignment explanation
Indices: 2873294--2873832 Score: 826
Period size: 68 Copynumber: 7.9 Consensus size: 68
2873284 TCTTTTACTC
* * * * * * **
2873294 AAGGCATTTAACCTTTCATCTAACTGACATGATTGACACATTTTTGTCAAATGCACAACTAGGCC
1 AAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
2873359 TCA
66 TCA
* * * *
2873362 AAGGCACTTAGCCTTTTATCTAACTGCCATAATTGACACCTTTATGTCAAATGCACAGTTAGACC
1 AAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
2873427 TCA
66 TCA
** * ** *
2873430 AAGATACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAACTAGACC
1 AAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
2873495 TCA
66 TCA
*
2873498 AAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCTCAGTTAGGCC
1 AAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
2873563 TCA
66 TCA
* *
2873566 AAGGCACTTAGTCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAAGCC
1 AAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
*
2873631 CCA
66 TCA
* *
2873634 AAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAGTTAGTCC
1 AAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
2873699 TCA
66 TCA
* * *
2873702 AAGGCACTTAACCTTTCATCTAACTGGCATAATTAACACCTTTTTGTCAAATGCACAGTTAGGCC
1 AAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
2873767 TCA
66 TCA
*
2873770 AAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCATAGTTAGG
1 AAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGG
2873833 TATTTAATCT
Statistics
Matches: 428, Mismatches: 43, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 428 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (68 bp):
AAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
TCA
Found at i:2874267 original size:59 final size:59
Alignment explanation
Indices: 2874199--2874655 Score: 679
Period size: 59 Copynumber: 7.8 Consensus size: 59
2874189 AAATTCATCC
* * * *
2874199 TCATACACTTAGTATGAATTTCTTATCATTTTAGCACAC-AAGGTGCCCTATCTGGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAA-GTGCCCTATATGGAAAT
* *
2874258 TCATACACTTAGTATGAATTCCTTCCCATGTTAGCACACGAAGTACCCTATATGGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
* *
2874317 TCATACACTTATTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCTTATATGGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
2874376 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
*
2874435 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAACTGCCCTATATGGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
* * * *
2874494 TCATACACTTAG---GAATTCCTTCTCAGGTTAGCACAAGAAGTTCCCTATATAGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
** **
2874550 TCATACACTTAACATGAATTCCTTCTCACATTAGCACACGAAGTGCCCTATATGGAAAT
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
* ** * *
2874609 TCATACACTTAGTATGAATTTCTTAACATTTTAGCACATGAAGTGCC
1 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCC
2874656 TTTTTTGTAA
Statistics
Matches: 362, Mismatches: 32, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
56 50 0.14
59 310 0.86
60 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (59 bp):
TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
Found at i:2874609 original size:233 final size:234
Alignment explanation
Indices: 2874199--2874655 Score: 693
Period size: 233 Copynumber: 1.9 Consensus size: 234
2874189 AAATTCATCC
* * * *
2874199 TCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAGGTGCCCTATCTGGAAATTCATAC
1 TCATACACTTAGTATGAATTCCTTATCATGTTAGCACACAAGCTGCCCTATATGGAAATTCATAC
* * * *
2874264 ACTTAGTATGAATTCCTTCCCATGTTAGCACACGAAGTACCCTATATGGAAATTCATACACTTAT
66 ACTTAG--TGAATTCCTTCCCAGGTTAGCACAAGAAGTACCCTATATAGAAATTCATACACTTAA
* ** *
2874329 TATGAATTCCTTCTCATGTTAGCACACGAAGTGCCTTATATGGAAATTCATACACTTAGTATGAA
129 CATGAATTCCTTCTCACATTAGCACACGAAGTGCCCTATATGGAAATTCATACACTTAGTATGAA
**
2874394 TTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAAT
194 TTCCTTAACATGTTAGCACACGAAGTGCCCTATATGGAAAT
*
2874435 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAA-CTGCCCTATATGGAAATTCATA
1 TCATACACTTAGTATGAATTCCTTATCATGTTAGCACAC-AAGCTGCCCTATATGGAAATTCATA
* *
2874499 CACTTAG-GAATTCCTTCTCAGGTTAGCACAAGAAGTTCCCTATATAGAAATTCATACACTTAAC
65 CACTTAGTGAATTCCTTCCCAGGTTAGCACAAGAAGTACCCTATATAGAAATTCATACACTTAAC
2874563 ATGAATTCCTTCTCACATTAGCACACGAAGTGCCCTATATGGAAATTCATACACTTAGTATGAAT
130 ATGAATTCCTTCTCACATTAGCACACGAAGTGCCCTATATGGAAATTCATACACTTAGTATGAAT
* * *
2874628 TTCTTAACATTTTAGCACATGAAGTGCC
195 TCCTTAACATGTTAGCACACGAAGTGCC
2874656 TTTTTTGTAA
Statistics
Matches: 200, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
233 135 0.68
236 63 0.31
237 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (234 bp):
TCATACACTTAGTATGAATTCCTTATCATGTTAGCACACAAGCTGCCCTATATGGAAATTCATAC
ACTTAGTGAATTCCTTCCCAGGTTAGCACAAGAAGTACCCTATATAGAAATTCATACACTTAACA
TGAATTCCTTCTCACATTAGCACACGAAGTGCCCTATATGGAAATTCATACACTTAGTATGAATT
CCTTAACATGTTAGCACACGAAGTGCCCTATATGGAAAT
Found at i:2875157 original size:18 final size:18
Alignment explanation
Indices: 2875114--2875150 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2875104 CCATGCTATG
**
2875114 GTATCGATACCCCTTTTA
1 GTATCGATACCAATTTTA
2875132 GTATCGATACCAATTTTA
1 GTATCGATACCAATTTTA
2875150 G
1 G
2875151 ATTCGATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (18 bp):
GTATCGATACCAATTTTA
Found at i:2875172 original size:94 final size:95
Alignment explanation
Indices: 2875001--2875199 Score: 303
Period size: 94 Copynumber: 2.1 Consensus size: 95
2874991 ACCCTAGTAC
* * * * * *
2875001 CGATACTTCTATGTTATGGTACCGATACCCCTTTTCAGTATCGATACCAATTTTAGGTTTGATGT
1 CGATACTACCATGCTATGGTACCGATACCCCTTTTCAGTATCGATACCAATTTTAGATTCGATGA
*
2875066 TTCCTGGTATCGATA-ACCTTACCATGGTAT
66 TTCATGGTATCGATACA-CTTACCATGGTAT
*
2875096 CGATACTACCATGCTATGGTATCGATACCCCTTTT-AGTATCGATACCAATTTTAGATTCGATGA
1 CGATACTACCATGCTATGGTACCGATACCCCTTTTCAGTATCGATACCAATTTTAGATTCGATGA
2875160 TTCATGGTATCGATACACTTACCATGGTAT
66 TTCATGGTATCGATACACTTACCATGGTAT
2875190 CGATACTACC
1 CGATACTACC
2875200 TCTTCGATAT
Statistics
Matches: 95, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
94 63 0.66
95 32 0.34
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (95 bp):
CGATACTACCATGCTATGGTACCGATACCCCTTTTCAGTATCGATACCAATTTTAGATTCGATGA
TTCATGGTATCGATACACTTACCATGGTAT
Found at i:2880976 original size:12 final size:12
Alignment explanation
Indices: 2880959--2880983 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2880949 CTCATCAAAT
2880959 TATAAATACAAC
1 TATAAATACAAC
2880971 TATAAATACAAC
1 TATAAATACAAC
2880983 T
1 T
2880984 TATGGTATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (12 bp):
TATAAATACAAC
Found at i:2881849 original size:26 final size:26
Alignment explanation
Indices: 2881819--2881868 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2881809 AGAAAACGTC
2881819 TGCATTATTATGCACTAAAAACCCCA
1 TGCATTATTATGCACTAAAAACCCCA
* *
2881845 TGCATTATTTTGCATTAAAAACCC
1 TGCATTATTATGCACTAAAAACCC
2881869 ACTAAAGTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (26 bp):
TGCATTATTATGCACTAAAAACCCCA
Found at i:2884521 original size:19 final size:19
Alignment explanation
Indices: 2884494--2884562 Score: 120
Period size: 19 Copynumber: 3.6 Consensus size: 19
2884484 CAGGGTCTAG
*
2884494 AAGGTTGTTAACAGTAGTT
1 AAGGCTGTTAACAGTAGTT
2884513 AAGGCTGTTAACAGTAGTT
1 AAGGCTGTTAACAGTAGTT
*
2884532 AAGGCTGTTAACAGCAGTT
1 AAGGCTGTTAACAGTAGTT
2884551 AAGGCTGTTAAC
1 AAGGCTGTTAAC
2884563 GATTAGTTAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (19 bp):
AAGGCTGTTAACAGTAGTT
Found at i:2884542 original size:38 final size:39
Alignment explanation
Indices: 2884494--2884571 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 39
2884484 CAGGGTCTAG
* *
2884494 AAGGTTGTTAACAGTAGTTAAGGCTGTTAAC-AGTAGTT
1 AAGGCTGTTAACAGCAGTTAAGGCTGTTAACGAGTAGTT
*
2884532 AAGGCTGTTAACAGCAGTTAAGGCTGTTAACGATTAGTT
1 AAGGCTGTTAACAGCAGTTAAGGCTGTTAACGAGTAGTT
2884571 A
1 A
2884572 CAGAGTCTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 29 0.81
39 7 0.19
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (39 bp):
AAGGCTGTTAACAGCAGTTAAGGCTGTTAACGAGTAGTT
Found at i:2884934 original size:18 final size:18
Alignment explanation
Indices: 2884908--2884954 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2884898 AACCGGCCCA
2884908 ACCCAACCCGAACCGTTC
1 ACCCAACCCGAACCGTTC
* * *
2884926 ACTCAACCCAAACCGTTG
1 ACCCAACCCGAACCGTTC
2884944 ACCCAACCCGA
1 ACCCAACCCGA
2884955 CCCGACCCGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.32, C:0.47, G:0.11, T:0.11
Consensus pattern (18 bp):
ACCCAACCCGAACCGTTC
Found at i:2885833 original size:31 final size:30
Alignment explanation
Indices: 2885798--2885882 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 30
2885788 TAAGGAGAGC
* *
2885798 CTTGGGTAGGCTCTGCGGCCCCGAGATTTTT
1 CTTGGGTAGGCTCT-CGGCCCCGAGAATTGT
* *
2885829 CTTGGTTAAGC-CTCCGTGACCCCGAGAATTGT
1 CTTGGGTAGGCTCT-CG-G-CCCCGAGAATTGT
2885861 CTTGGGTAGGCTCTCAGGCCCC
1 CTTGGGTAGGCTCTC-GGCCCC
2885883 AAGGTACTCC
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
30 4 0.09
31 14 0.33
32 22 0.51
33 3 0.07
ACGTcount: A:0.13, C:0.29, G:0.29, T:0.28
Consensus pattern (30 bp):
CTTGGGTAGGCTCTCGGCCCCGAGAATTGT
Found at i:2894401 original size:19 final size:19
Alignment explanation
Indices: 2894377--2894417 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2894367 TCATACCAAC
2894377 CATTCTAGTTTTATTAGGA
1 CATTCTAGTTTTATTAGGA
2894396 CATTCTAGTTTTATTAGGA
1 CATTCTAGTTTTATTAGGA
2894415 CAT
1 CAT
2894418 GTTTTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (19 bp):
CATTCTAGTTTTATTAGGA
Found at i:2896655 original size:26 final size:25
Alignment explanation
Indices: 2896588--2896657 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
2896578 CTGTTGTTTC
* * *
2896588 AAAAAAAAATTTA-CTATAATTTTT
1 AAAAAAATATTTATTTATAATATTT
*
2896612 AAGAAAATATATTAATTTATATATATTT
1 AA-AAAA-ATATTTATTTATA-ATATTT
2896640 AAAAAAATATTTATTTAT
1 AAAAAAATATTTATTTAT
2896658 TTAGAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
24 2 0.05
25 4 0.11
26 16 0.43
27 8 0.22
28 7 0.19
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (25 bp):
AAAAAAATATTTATTTATAATATTT
Found at i:2896943 original size:15 final size:16
Alignment explanation
Indices: 2896920--2896956 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2896910 AATTATGAAA
*
2896920 ATAATAATTTAAATAT
1 ATAATAATTAAAATAT
2896936 ATAA-AATTAAAATAT
1 ATAATAATTAAAATAT
2896951 A-AATAA
1 ATAATAA
2896957 ACAATGAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 2 0.11
15 13 0.68
16 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATAATTAAAATAT
Found at i:2898309 original size:3 final size:3
Alignment explanation
Indices: 2898277--2898345 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
2898267 AATAATTATT
* *
2898277 TAA TAA AAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TATT TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA
**
2898321 TAA TAA TAA TAA TTT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
2898346 TTAAGTAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
2 6 0.11
3 42 0.79
4 5 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:2898344 original size:21 final size:22
Alignment explanation
Indices: 2898266--2898345 Score: 93
Period size: 21 Copynumber: 3.9 Consensus size: 22
2898256 TTTGGGCTTG
2898266 TAATAATTATTTAAT-A-AA-AA
1 TAATAA-TATTTAATAATAATAA
*
2898286 T-ATAATATAT-ATAAT-ATAA
1 TAATAATATTTAATAATAATAA
2898305 TAATAATATTTAATAATAATAA
1 TAATAATATTTAATAATAATAA
2898327 TAATAAT-TTTAATAATAAT
1 TAATAATATTTAATAATAAT
2898346 TTAAGTAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
17 2 0.04
18 6 0.12
19 7 0.13
20 9 0.17
21 17 0.33
22 11 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATAATATTTAATAATAATAA
Found at i:2898724 original size:75 final size:76
Alignment explanation
Indices: 2898521--2899127 Score: 1123
Period size: 75 Copynumber: 8.0 Consensus size: 76
2898511 ACTGAAGGGT
*
2898521 TTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
2898586 GACCCTAAGGC
66 GACCCGAAGGC
2898597 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
2898662 GACCCTAAGGC
66 GACCCGAAGGC
2898673 TTT-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
2898737 GACCCGAAGG-
66 GACCCGAAGGC
*
2898747 TTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
2898812 GACCCGAAGGC
66 GACCCGAAGGC
2898823 -TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
2898887 GACCCTAAGGC
66 GACCCGAAGGC
2898898 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
2898963 GACCCGAAGGC
66 GACCCGAAGGC
*
2898974 -TTGAAAACATCAAAAAGCTCCCGAAGGATTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
2899038 GACCCTAAGGC
66 GACCCGAAGGC
2899049 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
2899114 GACCCGAAGGC
66 GACCCGAAGGC
2899125 TTT
1 TTT
2899128 TTGGAAACAT
Statistics
Matches: 517, Mismatches: 10, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
74 3 0.01
75 286 0.55
76 228 0.44
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (76 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
GACCCGAAGGC
Found at i:2898974 original size:151 final size:151
Alignment explanation
Indices: 2898522--2899126 Score: 1149
Period size: 151 Copynumber: 4.0 Consensus size: 151
2898512 CTGAAGGGTT
*
2898522 TTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
2898587 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
66 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
*
2898652 ACTTACAGATGACCCTAAGGC
131 ACTTACAGATGACCCGAAGGC
*
2898673 TTTAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
* *
2898738 ACCCGAAGG-TTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
66 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
2898802 ACTTACAGATGACCCGAAGGC
131 ACTTACAGATGACCCGAAGGC
2898823 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
2898888 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
66 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
2898953 ACTTACAGATGACCCGAAGGC
131 ACTTACAGATGACCCGAAGGC
*
2898974 TTGAAAACATCAAAAAGCTCCCGAAGGATTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
2899039 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
66 ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
2899104 ACTTACAGATGACCCGAAGGC
131 ACTTACAGATGACCCGAAGGC
2899125 TT
1 TT
2899127 TTTGGAAACA
Statistics
Matches: 444, Mismatches: 9, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
150 146 0.33
151 298 0.67
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (151 bp):
TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
ACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
ACTTACAGATGACCCGAAGGC
Found at i:2899138 original size:47 final size:47
Alignment explanation
Indices: 2899069--2899161 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
2899059 TCAAAAAGCT
*
2899069 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGA
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
2899116 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
2899162 TGGGAAATAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (47 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:2900032 original size:22 final size:22
Alignment explanation
Indices: 2900004--2900058 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2899994 CATAAAGCTT
2900004 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
2900026 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2900048 TCATCTTTGAA
1 TCATCTTTGAA
2900059 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2900556 original size:54 final size:54
Alignment explanation
Indices: 2900425--2900582 Score: 173
Period size: 54 Copynumber: 3.0 Consensus size: 54
2900415 AGAATAACTG
* * * *
2900425 GTTCGTAAAACATTTGACAACACATGCAT-CATCTCATGTGGTTTCTACTC--A-
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTC-TGTGGTTTCTGCTCAAAT
* * * * *
2900476 GAT-GTAAAACACTTGATAAGATATTCATCCTTTTCTGTGGTTTCTGCTCAAAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAAAT
* *
2900529 GTTCGTAAAGCATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAAAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAAAT
2900583 TTCTCAATCA
Statistics
Matches: 86, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
50 33 0.38
51 6 0.07
52 1 0.01
53 2 0.02
54 44 0.51
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAAAT
Found at i:2901696 original size:35 final size:35
Alignment explanation
Indices: 2901636--2901702 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
2901626 TCTTGTTGAG
2901636 ATGAGCCTCTAAGAATGCCCAAATATTCATATTGTT
1 ATGAGCCTCTAAGAATGCCCAAATATTC-TATTGTT
*
2901672 ATGAGCCT-TCAA-AATGCCCCAATATTCTATT
1 ATGAGCCTCT-AAGAATGCCCAAATATTCTATT
2901703 TCTGGTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 4 0.14
35 15 0.52
36 10 0.34
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (35 bp):
ATGAGCCTCTAAGAATGCCCAAATATTCTATTGTT
Found at i:2902796 original size:110 final size:110
Alignment explanation
Indices: 2902664--2903060 Score: 659
Period size: 110 Copynumber: 3.6 Consensus size: 110
2902654 CGAACCAGAT
* * *
2902664 CAGATAACTCAAAGAACACTTCCAGAAGATACTATTGGGCCTCCTTATTTCTACTATGAGCAAAT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAAT
2902729 TCATCTTTCAAATCTAATGATTAGTTTTTGGGGTTCATACCAAAC
66 TCATCTTTCAAATCTAATGATTAGTTTTTGGGGTTCATACCAAAC
*
2902774 CAGATAACTCAAAGAACACTTCCAGAAGATGCTGTTGGGTCTTCTTATTTCTACTATGAGCAAAT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAAT
*
2902839 TCATCTTTCAAATCTAATGATTGGTTTTTGGGGTTCATACCAAATC
66 TCATCTTTCAAATCTAATGATTAGTTTTTGGGGTTCATACCAAA-C
2902885 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGC
1 ----CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGC
* * *
2902950 ACATTTATCTTTCAAATCTAATGATTAGTTTTTGGGGTTCATATCAAAC
62 AAATTCATCTTTCAAATCTAATGATTAGTTTTTGGGGTTCATACCAAAC
* *
2902999 CAGATAACTCGAAGAACACTTCCAGAAGATGCTATTGGGTATTCTTATTTCTACTATGAGCA
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
2903061 CATGGCACTT
Statistics
Matches: 270, Mismatches: 12, Indels: 10
0.92 0.04 0.03
Matches are distributed among these distances:
110 164 0.61
111 1 0.00
114 1 0.00
115 104 0.39
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (110 bp):
CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAAT
TCATCTTTCAAATCTAATGATTAGTTTTTGGGGTTCATACCAAAC
Found at i:2902980 original size:225 final size:224
Alignment explanation
Indices: 2902614--2903060 Score: 741
Period size: 225 Copynumber: 2.0 Consensus size: 224
2902604 GATCATGCAG
* * * *
2902614 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCATACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
2902679 ACACTTCCAGAAGATACTATTGGGCCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATCT
66 ACACTTCCAGAAGATACTATTGGGCCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATCT
*
2902744 AATGATTAGTTTTTGGGGTTCATACCAAACCAGATAACTCAAAGAACACTTCCAGAAGATGCTGT
131 AATGATTAGTTTTTGGGGTTCATACCAAACCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
2902809 TGGGTCTTCTTATTTCTACTATGAGCAAA
196 TGGGTATTCTTATTTCTACTATGAGCAAA
* * *
2902838 TTCATCTTTCAAATCTAATGATTGGTTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGG-TTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* * * * *
2902903 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATTTATCTTTCAAATC
65 AACACTTCCAGAAGATACTATTGGGCCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATC
* *
2902968 TAATGATTAGTTTTTGGGGTTCATATCAAACCAGATAACTCGAAGAACACTTCCAGAAGATGCTA
130 TAATGATTAGTTTTTGGGGTTCATACCAAACCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
2903033 TTGGGTATTCTTATTTCTACTATGAGCA
195 TTGGGTATTCTTATTTCTACTATGAGCA
2903061 CATGGCACTT
Statistics
Matches: 206, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
224 22 0.11
225 184 0.89
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (224 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATACTATTGGGCCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATCT
AATGATTAGTTTTTGGGGTTCATACCAAACCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
TGGGTATTCTTATTTCTACTATGAGCAAA
Found at i:2905144 original size:26 final size:26
Alignment explanation
Indices: 2905114--2905166 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
2905104 TTTATTTTTC
*
2905114 ATTTTT-TTTCTTCTTTCTTTGCTGG
1 ATTTTTCTTTTTTCTTTCTTTGCTGG
2905139 ATTTTTCTTTTTTCTTTCTTTGCTGG
1 ATTTTTCTTTTTTCTTTCTTTGCTGG
2905165 AT
1 AT
2905167 GAGTATAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.06, C:0.15, G:0.11, T:0.68
Consensus pattern (26 bp):
ATTTTTCTTTTTTCTTTCTTTGCTGG
Found at i:2908012 original size:21 final size:21
Alignment explanation
Indices: 2907999--2908038 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2907989 AAAAGTAAGA
*
2907999 ATACAAAATGAAAATGCATAG
1 ATACAAAATGAAAAAGCATAG
* *
2908020 ATACAAAATGTAAATGCAT
1 ATACAAAATGAAAAAGCAT
2908039 GTATGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
ATACAAAATGAAAAAGCATAG
Found at i:2911020 original size:16 final size:16
Alignment explanation
Indices: 2910967--2911022 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
2910957 ATTTAAACAT
2910967 ATAAAATTAAAATATAA
1 ATAAAATTAAAAT-TAA
2910984 ATAAACAATGAGTAAAA-TAA
1 AT-AA-AAT---TAAAATTAA
2911004 ATAAAATTAAAATTAA
1 ATAAAATTAAAATTAA
2911020 ATA
1 ATA
2911023 TAAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 2 0.06
18 5 0.15
19 5 0.15
20 5 0.15
22 5 0.15
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAATTAA
Found at i:2912378 original size:31 final size:29
Alignment explanation
Indices: 2912307--2912387 Score: 91
Period size: 25 Copynumber: 2.9 Consensus size: 29
2912297 TTTGGGCTTG
2912307 TAATAATTATTTAATAATAATA-TAATATA
1 TAATAATT-TTTAATAATAATATTAATATA
*
2912336 T-ATAA--TATAATAATAATATTAATAATAA
1 TAATAATTTTTAATAATAATATTAAT-AT-A
2912364 TAATAATTTTTAATAATAAT-TTAA
1 TAATAATTTTTAATAATAATATTAA
2912388 GTAAAAACTA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
25 12 0.27
26 4 0.09
27 2 0.05
28 6 0.14
29 5 0.11
30 4 0.09
31 11 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TAATAATTTTTAATAATAATATTAATATA
Found at i:2912379 original size:13 final size:13
Alignment explanation
Indices: 2912361--2912385 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2912351 ATATTAATAA
2912361 TAATAATAATTTT
1 TAATAATAATTTT
2912374 TAATAATAATTT
1 TAATAATAATTT
2912386 AAGTAAAAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATAATAATTTT
Found at i:2912383 original size:3 final size:3
Alignment explanation
Indices: 2912318--2912370 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
2912308 AATAATTATT
*
2912318 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
2912361 TAA TAA TAA T
1 TAA TAA TAA T
2912371 TTTTAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 6 0.14
3 35 0.80
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:2913487 original size:37 final size:38
Alignment explanation
Indices: 2913407--2913487 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 38
2913397 AACAAGATGG
* * *
2913407 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCCT
1 AAAA-ATTTATATATTTTCTTTAAAAAATTGAAAATCAT
*
2913446 -AAAATTTATATAATTTT-TTTACAAAATTGAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTAAAAAATTGAAAATCAT
2913482 AAAAAT
1 AAAAAT
2913488 GTTTAATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
36 1 0.03
37 27 0.75
38 8 0.22
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:2922389 original size:31 final size:31
Alignment explanation
Indices: 2922337--2922456 Score: 93
Period size: 31 Copynumber: 3.9 Consensus size: 31
2922327 CTAATGTGAC
* *
2922337 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGAGGCCCTGAGATCAT
* * * **
2922368 TCTTGGGTAGGCCCTGTGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGAGGCCCTGAGAT-CAT
*
2922400 TCTTAGGTAGGTCCC-GAGGCCCTGA-A-CTT
1 TCTTAGGTAGG-CCCTGAGGCCCTGAGATCAT
* * * *
2922429 TCTTGGGTAGGCTCTCAGGCCCTAAGAT
1 TCTTAGGTAGGCCCTGAGGCCCTGAGAT
2922457 GCTCCCTTAG
Statistics
Matches: 69, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
28 2 0.03
29 19 0.28
30 1 0.01
31 25 0.36
32 19 0.28
33 3 0.04
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGAGGCCCTGAGATCAT
Found at i:2932857 original size:23 final size:24
Alignment explanation
Indices: 2932816--2932864 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
2932806 TTTTATTTTG
2932816 TCTAAAATTTTAAAAAAATTTATAC
1 TCTAAAATTTT-AAAAAATTTATAC
*
2932841 TCTAAAATTTT-ATAAATTTATAC
1 TCTAAAATTTTAAAAAATTTATAC
2932864 T
1 T
2932865 TTATGTCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.52
25 11 0.48
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (24 bp):
TCTAAAATTTTAAAAAATTTATAC
Found at i:2936565 original size:65 final size:64
Alignment explanation
Indices: 2936431--2936573 Score: 166
Period size: 65 Copynumber: 2.2 Consensus size: 64
2936421 AATTCATTTT
* * * *
2936431 GTGTACCGATGCACAGCCATGCATCGATGCACTCTTGAATTTATTGAAACATCGAATGCATTTTA
1 GTGTACCGATGCACAACCATGCATCGATGCACTCCTGAATTTATTGAAACATCAAAT-CATATTA
* **
2936496 -TGTACCGATTCACATACCATGCATCGATGCACTCCTGGCTCTT-TTGAAACATCAAAT-ATAAT
1 GTGTACCGATGCACA-ACCATGCATCGATGCACTCCTGAAT-TTATTGAAACATCAAATCAT-AT
2936558 TA
63 TA
2936560 GTGTACCGATGCAC
1 GTGTACCGATGCAC
2936574 TAAGTCTTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
63 2 0.03
64 16 0.24
65 46 0.70
66 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (64 bp):
GTGTACCGATGCACAACCATGCATCGATGCACTCCTGAATTTATTGAAACATCAAATCATATTA
Found at i:2943782 original size:2 final size:2
Alignment explanation
Indices: 2943775--2943805 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2943765 TCAATCTACA
*
2943775 AT AT AT AT TT 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
2943806 ATTTACGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2943980 original size:13 final size:13
Alignment explanation
Indices: 2943962--2943991 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2943952 AATGACGCGC
2943962 AATGTGTGTCATA
1 AATGTGTGTCATA
*
2943975 AATGTGTTTCATA
1 AATGTGTGTCATA
2943988 AATG
1 AATG
2943992 CGCGTCATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (13 bp):
AATGTGTGTCATA
Found at i:2953577 original size:19 final size:21
Alignment explanation
Indices: 2953546--2953586 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
2953536 CGCAAAGTTT
2953546 CATTTTGCAAAA-GATCGATC
1 CATTTTGCAAAAGGATCGATC
2953566 CATTTT-CAAAAGGATCGATC
1 CATTTTGCAAAAGGATCGATC
2953586 C
1 C
2953587 CCGTGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (21 bp):
CATTTTGCAAAAGGATCGATC
Found at i:2957143 original size:21 final size:21
Alignment explanation
Indices: 2957119--2957161 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2957109 ATCTGTTAAG
2957119 AGTCAAGGAGCATTATTACAA
1 AGTCAAGGAGCATTATTACAA
* *
2957140 AGTCAAGGAGTATTATTGCAA
1 AGTCAAGGAGCATTATTACAA
2957161 A
1 A
2957162 CTCATAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.26
Consensus pattern (21 bp):
AGTCAAGGAGCATTATTACAA
Found at i:2985500 original size:17 final size:17
Alignment explanation
Indices: 2985478--2985531 Score: 99
Period size: 17 Copynumber: 3.2 Consensus size: 17
2985468 CGATTTTGAG
2985478 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
2985495 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
*
2985512 CTCGATTCATGCTCGAA
1 CTCGATTCAAGCTCGAA
2985529 CTC
1 CTC
2985532 AAACTCGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:2985515 original size:23 final size:22
Alignment explanation
Indices: 2985506--2985585 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 22
2985496 TCGATTCAAG
*
2985506 CTCGAACTCGATTCATGCTCGAA
1 CTCGAACTCGATTCAAGCTCG-A
* ** *
2985529 CTCAAACTCGAATTTGAGCTCGG
1 CTCGAACTCG-ATTCAAGCTCGA
* *
2985552 TTCGAACTCGATTCAAGCTCAAA
1 CTCGAACTCGATTCAAGCTC-GA
*
2985575 ATCGAACTCGA
1 CTCGAACTCGA
2985586 ATTTGAAACT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
22 8 0.19
23 27 0.63
24 8 0.19
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (22 bp):
CTCGAACTCGATTCAAGCTCGA
Found at i:2988145 original size:7 final size:7
Alignment explanation
Indices: 2988133--2988202 Score: 99
Period size: 7 Copynumber: 10.3 Consensus size: 7
2988123 ATGTATAAAT
*
2988133 TAAACCA
1 TAAACCC
2988140 TAAACCC
1 TAAACCC
2988147 TAAA-CC
1 TAAACCC
2988153 TAAA-CC
1 TAAACCC
2988159 TAAACCC
1 TAAACCC
2988166 TAAACCC
1 TAAACCC
2988173 TAAACCC
1 TAAACCC
*
2988180 TAAAACC
1 TAAACCC
*
2988187 TAAACCA
1 TAAACCC
2988194 TAAACCC
1 TAAACCC
2988201 TA
1 TA
2988203 TCACATAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
6 12 0.21
7 45 0.79
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:2988150 original size:19 final size:19
Alignment explanation
Indices: 2988133--2988199 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 19
2988123 ATGTATAAAT
2988133 TAAACCATAAACCCTAAACC
1 TAAACC-TAAACCCTAAACC
2988153 TAAACCTAAACCCTAAACCC
1 TAAACCTAAACCCTAAA-CC
*
2988173 TAAACCCTAAAACCTAAACC
1 TAAA-CCTAAACCCTAAACC
2988193 ATAAACC
1 -TAAACC
2988200 CTATCACATA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
19 11 0.26
20 16 0.37
21 16 0.37
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (19 bp):
TAAACCTAAACCCTAAACC
Found at i:2988299 original size:14 final size:14
Alignment explanation
Indices: 2988280--2988309 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2988270 TATAATTATC
*
2988280 AATAATGTATTTTT
1 AATAATGTAATTTT
2988294 AATAATGTAATTTT
1 AATAATGTAATTTT
2988308 AA
1 AA
2988310 AATATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:2989730 original size:16 final size:15
Alignment explanation
Indices: 2989709--2989739 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2989699 TTAATATGTA
2989709 CATATAAATTGAAGCT
1 CATATAAATT-AAGCT
2989725 CATATAAATTAAGCT
1 CATATAAATTAAGCT
2989740 TCGTGGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (15 bp):
CATATAAATTAAGCT
Found at i:2996014 original size:22 final size:22
Alignment explanation
Indices: 2995984--2996040 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
2995974 GGACTGTTAA
*
2995984 GCATTTAGCCTTTTACCCAAAG
1 GCATATAGCCTTTTACCCAAAG
2996006 GCATATAGCCTTTTACCCAAAG
1 GCATATAGCCTTTTACCCAAAG
*
2996028 GTATATAGCCTTT
1 GCATATAGCCTTT
2996041 CATCTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (22 bp):
GCATATAGCCTTTTACCCAAAG
Found at i:2996182 original size:81 final size:81
Alignment explanation
Indices: 2996015--2996748 Score: 1071
Period size: 81 Copynumber: 9.1 Consensus size: 81
2996005 GGCATATAGC
* * * ** * * * * * *
2996015 CTTTTACCCAAAGGTATATAGCCTTTCATCTAA-TTTCATGATTAACACCTTCCTATCCAATACA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
* *
2996079 AAGCTAGGCCATTAAT
66 CAGCTAGGCTATTAAT
* ** *
2996095 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCCTAATTGACATTTTTCTTTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
2996160 CAGCTAGGCTATTAAT
66 CAGCTAGGCTATTAAT
* * *
2996176 CTTTTACTCAAAGGTATTTAACCTTTCATATAACTGGCATAATTGACACCTCTCTGTCATATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
* *
2996241 AAACTAGGCTATTAAT
66 CAGCTAGGCTATTAAT
* *
2996257 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCAAAATTGACACATTT-TGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
*
2996321 CAACTAGGCTATTAAT
66 CAGCTAGGCTATTAAT
* * * *
2996337 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-ACATAAATGACACCTTTCTGTCAAAGGAA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
*
2996401 CAGCTAGGCTACTAAT
66 CAGCTAGGCTATTAAT
* *
2996417 CTTTTACTCAAAGGTATTTAACATTTCATCTAACT-GCATAATTGACACCTTTGTTGTCAAATGC
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTT-CTGTCAAATGC
*
2996481 ACAGCTAGACTATTAAT
65 ACAGCTAGGCTATTAAT
*
2996498 CTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACCTTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
2996563 CAGCTAGGCTATTAAT
66 CAGCTAGGCTATTAAT
* * *
2996579 CTTTTACTCAAAGATATTTAACCTTTCATCTAACTAGCATAATTGACACCTTTCTATCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
*
2996644 CAACTAGGCTATTAAT
66 CAGCTAGGCTATTAAT
* *
2996660 CTTTTACTCAAAGGTGTTTAACCTTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
2996725 CAGCTAGGCTATTAAT
66 CAGCTAGGCTATTAAT
2996741 CTTTTACT
1 CTTTTACT
2996749 TTGGAATAGT
Statistics
Matches: 588, Mismatches: 62, Indels: 7
0.89 0.09 0.01
Matches are distributed among these distances:
79 13 0.02
80 162 0.28
81 396 0.67
82 17 0.03
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.36
Consensus pattern (81 bp):
CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
CAGCTAGGCTATTAAT
Found at i:2996933 original size:53 final size:53
Alignment explanation
Indices: 2996876--2996992 Score: 153
Period size: 55 Copynumber: 2.2 Consensus size: 53
2996866 TTTACGTGGG
* * * *
2996876 TTGCACACATTACTAATACAGAAATTCATAAACTTATTTTGAATTTATTATTT
1 TTGCACACAGTACCAATACAGAAATTCATAAACTTATTATGAATTTATTAGTT
* * *
2996929 TTGCACACAAAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTTTTAGTT
1 TTGCACAC--AGTACCAATACAGAAATTCATAAACTTATTATGAATTTATTAGTT
2996984 TTGCACACA
1 TTGCACACA
2996993 CAGTTCCATT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
53 9 0.16
55 46 0.84
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (53 bp):
TTGCACACAGTACCAATACAGAAATTCATAAACTTATTATGAATTTATTAGTT
Found at i:3000349 original size:90 final size:92
Alignment explanation
Indices: 3000193--3000363 Score: 265
Period size: 90 Copynumber: 1.9 Consensus size: 92
3000183 CCTTTTTTAG
* * *
3000193 CCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTATTTCAAATTAATTAAAGCTATATTTAAT
1 CCAAGTTACCCTAATCATATCAGGG-TATTATTATTATTTCAAATTAATTAAAGCTATATTTAAT
* *
3000258 TAATTGGAATTTAATAATCATTTTATAT
65 TAATTGAAATTAAATAATCATTTTATAT
*
3000286 CCAAGTTACCCTAATCATATCAGGG-ATT-TTATTATTTCAAATTAATTAAATCTATATTTAATT
1 CCAAGTTACCCTAATCATATCAGGGTATTATTATTATTTCAAATTAATTAAAGCTATATTTAATT
3000349 AATTGAAATTAAATA
66 AATTGAAATTAAATA
3000364 TTCGGGATTA
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
90 47 0.65
91 2 0.03
93 23 0.32
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.44
Consensus pattern (92 bp):
CCAAGTTACCCTAATCATATCAGGGTATTATTATTATTTCAAATTAATTAAAGCTATATTTAATT
AATTGAAATTAAATAATCATTTTATAT
Found at i:3003599 original size:81 final size:80
Alignment explanation
Indices: 3003505--3003916 Score: 540
Period size: 81 Copynumber: 5.1 Consensus size: 80
3003495 AGCATTTAGC
* * * * * * *
3003505 CTTTTACCCAAAGGCATATAACCTTTCATCTAATGTGCATGATTGACACATTCCTGTCTAATATA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAATG-GCATAATTGACACATTTCTGTCAAATACA
* *
3003570 CAACTATGCCATTAAT
65 CAACTAGGCTATTAAT
*
3003586 CTTTTACTCAAAGGTATTTAACCTTTTATCTAACT-GCATAATTGACACATTTCTGTCAAA-AGC
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAA-TGGCATAATTGACACATTTCTGTCAAATA-C
* *
3003649 ACATCCAGGCTATTAAT
64 ACAACTAGGCTATTAAT
* *
3003666 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAA-TGGCATAATTGACACATTTCTGTCAAATACA
3003731 CAACTAGGCTATTAAT
65 CAACTAGGCTATTAAT
* * *
3003747 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTAAAATACG
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAA-TGGCATAATTGACACATTTCTGTCAAATACA
* *
3003812 TAGCTAGGCTATTAAT
65 CAACTAGGCTATTAAT
* * * *
3003828 CTTTTACTGAAAGGTATTTAACCTTTCATCTAGCTGGCATAATTGACACATTTATGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTA-ATGGCATAATTGACACATTTCTGTCAAATACA
*
3003893 CACCTAGGCTATTAAT
65 CAACTAGGCTATTAAT
3003909 CTTTTACT
1 CTTTTACT
3003917 TTGGAATAGT
Statistics
Matches: 295, Mismatches: 31, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
79 1 0.00
80 69 0.23
81 224 0.76
82 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (80 bp):
CTTTTACTCAAAGGTATTTAACCTTTCATCTAATGGCATAATTGACACATTTCTGTCAAATACAC
AACTAGGCTATTAAT
Found at i:3004531 original size:22 final size:22
Alignment explanation
Indices: 3004504--3004562 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
3004494 ATACCTCTAG
*
3004504 CATGGTATCGATATTAATATAC
1 CATGGTATCGATACTAATATAC
*
3004526 CATGGTATCGATACTACTATAC
1 CATGGTATCGATACTAATATAC
3004548 CATGGTATCGATACT
1 CATGGTATCGATACT
3004563 CTAACGGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (22 bp):
CATGGTATCGATACTAATATAC
Found at i:3009459 original size:81 final size:81
Alignment explanation
Indices: 3009233--3009805 Score: 799
Period size: 81 Copynumber: 7.1 Consensus size: 81
3009223 AGCATTTAGC
* * * * * * * * * * * *
3009233 CTTTTACCCAAAGGCATATAGCCTTTCATCTAATTTGCATGATTGCCTCCTTCCTGTCCAATACA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
*
3009298 CAACTAGGCCATTAAT
66 CAACTAGGCTATTAAT
* *
3009314 CTTTTACTCAAAGATATTTAACC-TTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
*
3009378 CAACTAGGCTCTTAAT
66 CAACTAGGCTATTAAT
* * *
3009394 CTTTTACTCAAAGGTATTTAACCTTTCATATAACTGGCATAATTGACACCTTTCTATCTAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
* *
3009459 CAGCTAAGCTATTAAT
66 CAACTAGGCTATTAAT
* * * *
3009475 CTTTAACTCAAAGGTATTTAACCTTTCATCTAACTGCCATAATTGAAACCTTTCTGTCAATTGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
3009540 CAACTAGGCTATTAAT
66 CAACTAGGCTATTAAT
* * * *
3009556 ATTTTACTCAAAGGTATTTAACCTTTCATCTAA-TTGCATAATTGACACATTTCTATCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
3009620 CAACTAGGCTATTAAT
66 CAACTAGGCTATTAAT
* * * **
3009636 CTTTTACTCAAAGGTATTTAACCTTTCATCTATCTGGCATAGTTGACACCTTTTTGTCAAATATA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
*
3009701 CAGCTAGGCTATTAAT
66 CAACTAGGCTATTAAT
* *
3009717 CTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
3009782 CAACTAGGCTATTAAT
66 CAACTAGGCTATTAAT
3009798 CTTTTACT
1 CTTTTACT
3009806 TTGGATTAGT
Statistics
Matches: 434, Mismatches: 56, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
80 140 0.32
81 294 0.68
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (81 bp):
CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
CAACTAGGCTATTAAT
Found at i:3009498 original size:161 final size:162
Alignment explanation
Indices: 3009233--3009805 Score: 799
Period size: 161 Copynumber: 3.5 Consensus size: 162
3009223 AGCATTTAGC
* * * * * * * * * * * * *
3009233 CTTTTACCCAAAGGCATATAGCCTTTCATCTAATTTGCATGATTGCCTCCTTCCTGTCCAATACA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
* *
3009298 CAACTAGGCCATTAATCTTTTACTCAAAGATATTTAACC-TTCATCTAACTGGCATAATTGACAC
66 CAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACAC
* *
3009362 CTTTCTATCAAATGCACAACTAGGCTCTTAAT
131 CTTTCTGTCAAATGCACAACTAGGCTATTAAT
* *
3009394 CTTTTACTCAAAGGTATTTAACCTTTCATATAACTGGCATAATTGACACCTTTCTATCTAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
* * * * *
3009459 CAGCTAAGCTATTAATCTTTAACTCAAAGGTATTTAACCTTTCATCTAACTGCCATAATTGAAAC
66 CAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACAC
*
3009524 CTTTCTGTCAATTGCACAACTAGGCTATTAAT
131 CTTTCTGTCAAATGCACAACTAGGCTATTAAT
* * *
3009556 ATTTTACTCAAAGGTATTTAACCTTTCATCTAA-TTGCATAATTGACACATTTCTATCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
* *
3009620 CAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTATCTGGCATAGTTGACAC
66 CAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACAC
* ** *
3009685 CTTTTTGTCAAATATACAGCTAGGCTATTAAT
131 CTTTCTGTCAAATGCACAACTAGGCTATTAAT
* * *
3009717 CTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
3009782 CAACTAGGCTATTAATCTTTTACT
66 CAACTAGGCTATTAATCTTTTACT
3009806 TTGGATTAGT
Statistics
Matches: 363, Mismatches: 47, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
161 229 0.63
162 134 0.37
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (162 bp):
CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
CAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACAC
CTTTCTGTCAAATGCACAACTAGGCTATTAAT
Found at i:3009597 original size:242 final size:242
Alignment explanation
Indices: 3009287--3009805 Score: 815
Period size: 242 Copynumber: 2.1 Consensus size: 242
3009277 GCCTCCTTCC
* * *
3009287 TGTCCAATACACAACTAGGCCATTAATCTTTTACTCAAAGATATTTAACCTTCATCTAACTGGCA
1 TGTCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGATATTTAACCTTCATCTAACTGGCA
* *
3009352 TAATTGACACCTTTCTATCAAATGCACAACTAGGCTCTTAATCTTTTACTCAAAGGTATTTAACC
66 TAATTGACACATTTCTATCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAACC
* *
3009417 TTTCATATAACTGGCATAATTGACACCTTTCTATCTAATGCACAGCTAAGCTATTAATCTTTAAC
131 TTTCATATAACTGGCATAATTGACACCTTTCTATCAAATACACAGCTAAGCTATTAATCTTTAAC
* *
3009482 TCAAAGGTATTTAACCTTTCATCTAACTGCCATAATTGAAACCTTTC
196 TCAAAGGTATTTAACATTTCATCTAACTGCCATAATTGAAACCTTTA
* * * *
3009529 TGTCAATTGCACAACTAGGCTATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAA-TTGC
1 TGTCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGATATTTAACC-TTCATCTAACTGGC
3009593 ATAATTGACACATTTCTATCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAAC
65 ATAATTGACACATTTCTATCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAAC
* * * * * * * *
3009658 CTTTCATCTATCTGGCATAGTTGACACCTTTTTGTCAAATATACAGCTAGGCTATTAATCTTTTA
130 CTTTCATATAACTGGCATAATTGACACCTTTCTATCAAATACACAGCTAAGCTATTAATCTTTAA
* *
3009723 CTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTA
195 CTCAAAGGTATTTAACATTTCATCTAACTGCCATAATTGAAACCTTTA
3009771 TGTCAAATGCACAACTAGGCTATTAATCTTTTACT
1 TGTCAAATGCACAACTAGGCTATTAATCTTTTACT
3009806 TTGGATTAGT
Statistics
Matches: 251, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
242 242 0.96
243 9 0.04
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (242 bp):
TGTCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGATATTTAACCTTCATCTAACTGGCA
TAATTGACACATTTCTATCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAACC
TTTCATATAACTGGCATAATTGACACCTTTCTATCAAATACACAGCTAAGCTATTAATCTTTAAC
TCAAAGGTATTTAACATTTCATCTAACTGCCATAATTGAAACCTTTA
Found at i:3010518 original size:21 final size:21
Alignment explanation
Indices: 3010492--3010546 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
3010482 ATCCTCATAG
*
3010492 TATCGATACTACTTGCGTCAA
1 TATCGATACTACTTGCATCAA
3010513 TATCGATACTACTTGCATCAA
1 TATCGATACTACTTGCATCAA
3010534 TATCGATACTACT
1 TATCGATACTACT
3010547 CAGCTGATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.35
Consensus pattern (21 bp):
TATCGATACTACTTGCATCAA
Found at i:3015208 original size:81 final size:81
Alignment explanation
Indices: 3015071--3015650 Score: 784
Period size: 81 Copynumber: 7.1 Consensus size: 81
3015061 GGCATATAGT
* * * ** * * * * *
3015071 CTTTCATCTAATTTGCATGATTTCCACCTTCCTGTCCAATACACAGCTAGGATATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
3015136 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * *
3015152 GTTTCATCTAACTGGCATAATTGACACCTTTCTTTCAAATGTACAACTAGACTATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
3015217 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * *
3015233 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCTAATTCACAGCTAGGCTATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
3015298 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * * *
3015314 CTTTCATCTAATTGACATAATTGACACCTTTATGTAAAATGCACAGCTAGGCTATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
3015379 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * * * * * *
3015395 ATTTCATCTAATTGGCATAATTGACACCTCTCTGTTAAATGCATAGCTAGGCTATTAATATTTTT
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
*
3015460 CTCAAATGTATTTAAC
66 CTCAAAGGTATTTAAC
* * *
3015476 CTTTCATCTAAATGGCATAATTTACA-CTTGTCTGTCAAATGCTCAACTAGGCTATTAATCTTTT
1 CTTTCATCTAACTGGCATAATTGACACCTT-TCTGTCAAATGCACAACTAGGCTATTAATCTTTT
3015540 ACTCAAAGGTATTTAAC
65 ACTCAAAGGTATTTAAC
* * *
3015557 CTTTCATTTAGCTGGCATAATTGACACCTTTCTTCTCAAATGCACAACTAGGCTATTAATCTTTT
1 CTTTCATCTAACTGGCATAATTGACACCTTTC-TGTCAAATGCACAACTAGGCTATTAATCTTTT
3015622 ACTCAAAGGTATTTAAC
65 ACTCAAAGGTATTTAAC
*
3015639 CTTTCATTTAAC
1 CTTTCATCTAAC
3015651 CTGTCTACCA
Statistics
Matches: 440, Mismatches: 56, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
80 2 0.00
81 377 0.86
82 61 0.14
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.39
Consensus pattern (81 bp):
CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
CTCAAAGGTATTTAAC
Found at i:3019261 original size:38 final size:37
Alignment explanation
Indices: 3019219--3019335 Score: 96
Period size: 39 Copynumber: 3.1 Consensus size: 37
3019209 AAAAGAGAAA
3019219 GAAAAGGAAGAGGGTAAAGGAAAAGGGACACCGCAAAG
1 GAAAAGGAAGAGGG-AAAGGAAAAGGGACACCGCAAAG
3019257 GAAAAAGGAAGAGGAGAAA-GAAGAA-GGACACCG-AAGAG
1 G-AAAAGGAAGAGG-GAAAGGAA-AAGGGACACCGCAA-AG
* * * * * *
3019295 GGAAAGAAAGAAAGAAAAGGAGGAAGGAACACCGCAAAG
1 GAAAAGGAAG-AGGGAAAGGA-AAAGGGACACCGCAAAG
3019334 GA
1 GA
3019336 GGAGGACGAG
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
37 12 0.19
38 21 0.33
39 27 0.43
40 3 0.05
ACGTcount: A:0.54, C:0.09, G:0.36, T:0.01
Consensus pattern (37 bp):
GAAAAGGAAGAGGGAAAGGAAAAGGGACACCGCAAAG
Found at i:3021253 original size:4 final size:4
Alignment explanation
Indices: 3021244--3021322 Score: 95
Period size: 4 Copynumber: 19.8 Consensus size: 4
3021234 TCAATCTACA
* * * * * *
3021244 ATAT ATAT ATAT ATAT TTAT TTAT ATTT ATTT ATAT ATAT ATTT ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
3021292 ATAC ATAT ATAT ATAT ATAT ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
3021323 ATTTTTGAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 67 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (4 bp):
ATAT
Found at i:3021255 original size:6 final size:6
Alignment explanation
Indices: 3021244--3021322 Score: 95
Period size: 6 Copynumber: 13.2 Consensus size: 6
3021234 TCAATCTACA
* * * * * *
3021244 ATATAT ATATAT ATATTT ATTTAT ATTTAT TTATAT ATATAT TTATAC
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
3021292 ATACAT ATATAT ATATAT ATATAT ATATAT A
1 ATATAT ATATAT ATATAT ATATAT ATATAT A
3021323 ATTTTTGAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (6 bp):
ATATAT
Found at i:3021259 original size:10 final size:10
Alignment explanation
Indices: 3021244--3021322 Score: 95
Period size: 10 Copynumber: 7.9 Consensus size: 10
3021234 TCAATCTACA
3021244 ATATATATAT
1 ATATATATAT
*
3021254 ATATATTTAT
1 ATATATATAT
* *
3021264 TTATATTTAT
1 ATATATATAT
*
3021274 TTATATATAT
1 ATATATATAT
* *
3021284 ATTTATACAT
1 ATATATATAT
*
3021294 ACATATATAT
1 ATATATATAT
3021304 ATATATATAT
1 ATATATATAT
3021314 ATATATATA
1 ATATATATA
3021323 ATTTTTGAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 59 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (10 bp):
ATATATATAT
Found at i:3021620 original size:85 final size:85
Alignment explanation
Indices: 3021411--3021604 Score: 352
Period size: 85 Copynumber: 2.3 Consensus size: 85
3021401 TGTCAAGCAG
*
3021411 ATTTATGACAGTGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACG
1 ATTTATGACAGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACG
3021476 CACAAATGTGTGTCATCTTA
66 CACAAATGTGTGTCATCTTA
**
3021496 ATTTATGATGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACG
1 ATTTATGACAGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACG
3021561 CACAAATGTGTGTCATCTTA
66 CACAAATGTGTGTCATCTTA
*
3021581 ATTTATGACAGGGGATTCAATGAC
1 ATTTATGACAGGGGCTTCAATGAC
3021605 ACTCAAAGAA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 103 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (85 bp):
ATTTATGACAGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACG
CACAAATGTGTGTCATCTTA
Found at i:3021633 original size:85 final size:85
Alignment explanation
Indices: 3021411--3021637 Score: 287
Period size: 85 Copynumber: 2.7 Consensus size: 85
3021401 TGTCAAGCAG
* * * * * *
3021411 ATTTATGACAGTGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACG
1 ATTTATGACAGGGGATTCAATGACACGCAAAGTAAGTCATACATGAGCGTCATAAATTTATGACG
3021476 CACAAATGTGTGTCATCTTA
66 CACAAATGTGTGTCATCTTA
** * * * * *
3021496 ATTTATGATGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACG
1 ATTTATGACAGGGGATTCAATGACACGCAAAGTAAGTCATACATGAGCGTCATAAATTTATGACG
3021561 CACAAATGTGTGTCATCTTA
66 CACAAATGTGTGTCATCTTA
* *
3021581 ATTTATGACAGGGGATTCAATGACACTCAAAG-AACGTCATTA-ATTAGCGTCATAAAT
1 ATTTATGACAGGGGATTCAATGACACGCAAAGTAA-GTCA-TACATGAGCGTCATAAAT
3021638 GCGCGTCATA
Statistics
Matches: 128, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
84 2 0.02
85 124 0.97
86 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (85 bp):
ATTTATGACAGGGGATTCAATGACACGCAAAGTAAGTCATACATGAGCGTCATAAATTTATGACG
CACAAATGTGTGTCATCTTA
Found at i:3021643 original size:13 final size:13
Alignment explanation
Indices: 3021627--3021660 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3021617 TCATTAATTA
3021627 GCGTCATAAATGC
1 GCGTCATAAATGC
3021640 GCGTCATAAATGC
1 GCGTCATAAATGC
*
3021653 GTGTCATA
1 GCGTCATA
3021661 GATTTATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (13 bp):
GCGTCATAAATGC
Found at i:3023291 original size:25 final size:25
Alignment explanation
Indices: 3023263--3023319 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
3023253 CGAATTGCCG
3023263 CGTAGAAATATT-TCCCGAAGGACCA
1 CGTAGAAAT-TTGTCCCGAAGGACCA
*
3023288 CGTAG-AATTTGTCCCGAAGGACTA
1 CGTAGAAATTTGTCCCGAAGGACCA
*
3023312 CATAGAAA
1 CGTAGAAA
3023320 AGTTCCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.07
24 19 0.68
25 7 0.25
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (25 bp):
CGTAGAAATTTGTCCCGAAGGACCA
Found at i:3027390 original size:13 final size:13
Alignment explanation
Indices: 3027372--3027397 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3027362 TATGGTTGGC
3027372 ATGATCAACCTCA
1 ATGATCAACCTCA
3027385 ATGATCAACCTCA
1 ATGATCAACCTCA
3027398 TATGGACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
ATGATCAACCTCA
Found at i:3033169 original size:54 final size:54
Alignment explanation
Indices: 3032592--3033160 Score: 775
Period size: 54 Copynumber: 10.5 Consensus size: 54
3032582 GAATTTATAA
* * * * *
3032592 TATGTTGATGAATCACCGTTTTGCCACTAAGTGTGTATTTCAC-AGAATTCATCA
1 TATGTTGATGAATCACCATTTCGGCACTAAGTGTGCATTTCACGA-AATTCATCG
* *
3032646 TATGTTGATGAATCACCATTTCGGCACTAAGTGTGCATTTCACGGAATTCATCA
1 TATGTTGATGAATCACCATTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
* *
3032700 TATGTTGATGAATCACCATTTCGGCACTAAGTATGCATTTCAC-AGAATTCATCA
1 TATGTTGATGAATCACCATTTCGGCACTAAGTGTGCATTTCACGA-AATTCATCG
* * * *
3032754 TATGTTGATGAATCACCGTTTCAGCACTAAGTATGCAATTCACGAAATTCATCG
1 TATGTTGATGAATCACCATTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
** * *
3032808 TATGTTGATGAATCACTGTTTCGGAACTAAGTGTGCAATTCAC-AGAATTCATCG
1 TATGTTGATGAATCACCATTTCGGCACTAAGTGTGCATTTCACGA-AATTCATCG
* * * *
3032862 TATGTTGATGAATCGCCGTTTCAGCACTAAGTGTGCATTTCACAAAATTCATCG
1 TATGTTGATGAATCACCATTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
* *
3032916 TATGTTGATGAATCACCATTTCGGCACTAAGTGCGCATTTCACGGAATTCATCG
1 TATGTTGATGAATCACCATTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
*
3032970 TATGTTGATGAATCACCATTTCGGCACTAAGTGCGCATTTCACGAAATTCATCG
1 TATGTTGATGAATCACCATTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
* *
3033024 TATGTTGATGAATAACCATTTCGGCACTAAGTGTGCATTTCACGAAATTCATCA
1 TATGTTGATGAATCACCATTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
* * * * * *
3033078 TATATTGATGAATCACCGTTTCAGCACTAAGTGTGCAATTCACGAAAGTCATTG
1 TATGTTGATGAATCACCATTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
* **
3033132 TATATTGATGAATCACTGTTTCGGCACTA
1 TATGTTGATGAATCACCATTTCGGCACTA
3033161 TGTATGCAAA
Statistics
Matches: 470, Mismatches: 40, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
53 1 0.00
54 467 0.99
55 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (54 bp):
TATGTTGATGAATCACCATTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
Found at i:3034359 original size:36 final size:36
Alignment explanation
Indices: 3034275--3034496 Score: 231
Period size: 36 Copynumber: 6.3 Consensus size: 36
3034265 ATAGTTTCAT
*
3034275 GTGAGATAAAAAT-TTTTTTAAG-AAAACAATCTCAA
1 GTGAGAT-AAAATCTTCTTTAAGAAAAACAATCTCAA
* * * *
3034310 GTGATATATAATCTTCTTTAAGAAAAATAATTTCAA
1 GTGAGATAAAATCTTCTTTAAGAAAAACAATCTCAA
* ***
3034346 GTGAGAAAAAATCTTGAGT--GAAAAACAATCTCAA
1 GTGAGATAAAATCTTCTTTAAGAAAAACAATCTCAA
* *
3034380 GTGAGATAAAATCTGCTTTAAGAAAAGCAATCTCAA
1 GTGAGATAAAATCTTCTTTAAGAAAAACAATCTCAA
* *
3034416 GTGAGACAAAATCTCCTTTAAGAAAAACAATCTCAA
1 GTGAGATAAAATCTTCTTTAAGAAAAACAATCTCAA
* * *
3034452 GGGAGATAAAAT-TTGTTTTAATAAAAACAATCTCAA
1 GTGAGATAAAATCTT-CTTTAAGAAAAACAATCTCAA
*
3034488 -TGACATAAA
1 GTGAGATAAA
3034497 TTTTGAGTGA
Statistics
Matches: 153, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
34 31 0.20
35 22 0.14
36 100 0.65
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (36 bp):
GTGAGATAAAATCTTCTTTAAGAAAAACAATCTCAA
Found at i:3034381 original size:70 final size:70
Alignment explanation
Indices: 3034297--3034508 Score: 232
Period size: 70 Copynumber: 3.0 Consensus size: 70
3034287 TTTTTTTAAG
* * * * *
3034297 AAAACAATCTCAAGTGATATATAATCTTCTTTAAGAAAAATAATTTCAAGTGAGAAAAAATCTTG
1 AAAACAATCTCAAGTGAGATAAAATCTGCTTTAAGAAAAACAATCTCAAGTGAGAAAAAATCTTG
3034362 AGTGA
66 AGTGA
* *
3034367 AAAACAATCTCAAGTGAGATAAAATCTGCTTTAAGAAAAGCAATCTCAAGTGAGACAAAATCTCC
1 AAAACAATCTCAAGTGAGATAAAATCTGCTTTAAGAAAAACAATCTCAAGTGAGA-AAAA-AT-C
* *
3034432 TTTA-AGA
63 TTGAGTGA
* * * * * * *
3034439 AAAACAATCTCAAGGGAGATAAAATTTGTTTTAATAAAAACAATCTCAA-TGA-CATAAATTTTG
1 AAAACAATCTCAAGTGAGATAAAATCTGCTTTAAGAAAAACAATCTCAAGTGAGAAAAAATCTTG
3034502 AGTGA
66 AGTGA
3034507 AA
1 AA
3034509 TGATATGAGT
Statistics
Matches: 118, Mismatches: 20, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
67 3 0.03
68 5 0.04
69 3 0.03
70 49 0.42
71 7 0.06
72 47 0.40
73 4 0.03
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.27
Consensus pattern (70 bp):
AAAACAATCTCAAGTGAGATAAAATCTGCTTTAAGAAAAACAATCTCAAGTGAGAAAAAATCTTG
AGTGA
Found at i:3034382 original size:17 final size:16
Alignment explanation
Indices: 3034331--3034393 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
3034321 TCTTCTTTAA
*
3034331 GAAAAATAATTTCAAGT
1 GAAAAA-AATCTCAAGT
**
3034348 GAGAAAAAATCTTGAGT
1 GA-AAAAAATCTCAAGT
3034365 GAAAAACAATCTCAAGT
1 GAAAAA-AATCTCAAGT
*
3034382 GAGATAAAATCT
1 GA-AAAAAATCT
3034394 GCTTTAAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.11
17 26 0.70
18 7 0.19
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.24
Consensus pattern (16 bp):
GAAAAAAATCTCAAGT
Found at i:3034430 original size:17 final size:17
Alignment explanation
Indices: 3034342--3034430 Score: 65
Period size: 17 Copynumber: 5.1 Consensus size: 17
3034332 AAAAATAATT
3034342 TCAAGTGAGAAAAAATC
1 TCAAGTGAGAAAAAATC
**
3034359 TTGAGTGA-AAAACAATC
1 TCAAGTGAGAAAA-AATC
*
3034376 TCAAGTGAGATAAAATC
1 TCAAGTGAGAAAAAATC
** *
3034393 TGC-TTTAAGAAAAGCAATC
1 T-CAAGTGAGAAAA--AATC
*
3034412 TCAAGTGAGACAAAATC
1 TCAAGTGAGAAAAAATC
3034429 TC
1 TC
3034431 CTTTAAGAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
16 4 0.08
17 33 0.62
18 5 0.09
19 11 0.21
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (17 bp):
TCAAGTGAGAAAAAATC
Found at i:3036207 original size:11 final size:11
Alignment explanation
Indices: 3036191--3036224 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
3036181 TATCATTTTA
3036191 AAAACACACTT
1 AAAACACACTT
3036202 AAAACACACTTT
1 AAAACACAC-TT
3036214 AAAACACACTT
1 AAAACACACTT
3036225 CTTCCCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAACACACTT
Found at i:3038449 original size:21 final size:21
Alignment explanation
Indices: 3038423--3038462 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3038413 CAGAACCCCA
*
3038423 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
3038444 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
3038463 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:3042353 original size:22 final size:21
Alignment explanation
Indices: 3042311--3042350 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3042301 GAGTTTGTTT
*
3042311 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3042332 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3042351 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3044937 original size:3 final size:3
Alignment explanation
Indices: 3044929--3044954 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3044919 TATGTCCCTT
3044929 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
3044955 GGTTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:3064637 original size:15 final size:17
Alignment explanation
Indices: 3064605--3064637 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3064595 AGCCACATCT
3064605 TTGACTTTCTTCTATAA
1 TTGACTTTCTTCTATAA
3064622 TTGAC-TTCTT-TATAA
1 TTGACTTTCTTCTATAA
3064637 T
1 T
3064638 CGAATTTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.55
Consensus pattern (17 bp):
TTGACTTTCTTCTATAA
Found at i:3078519 original size:244 final size:244
Alignment explanation
Indices: 3078090--3078579 Score: 980
Period size: 244 Copynumber: 2.0 Consensus size: 244
3078080 AATTAAAAAA
3078090 AAGGAAAGGCGGCTGGTAGCTGTTAGAATATTTAGGGCTTGCTTGCACTTGAAGGAGGTCATCCA
1 AAGGAAAGGCGGCTGGTAGCTGTTAGAATATTTAGGGCTTGCTTGCACTTGAAGGAGGTCATCCA
3078155 GCTGGCATGTGACATAGGCGATTTCGTCATATCCGCTTAAGACTTTGTAGAATAACCTTGCTTTG
66 GCTGGCATGTGACATAGGCGATTTCGTCATATCCGCTTAAGACTTTGTAGAATAACCTTGCTTTG
3078220 GTGAGATAAATATGCTTCCCACGTTCTTCTCTGTTCTATTAGCCCTTGCAATTTACGTTGTCGTG
131 GTGAGATAAATATGCTTCCCACGTTCTTCTCTGTTCTATTAGCCCTTGCAATTTACGTTGTCGTG
3078285 ACTGAAATGTTCTTCCTCTATAAGTTTCCTGCATATACAGAATTCACAC
196 ACTGAAATGTTCTTCCTCTATAAGTTTCCTGCATATACAGAATTCACAC
3078334 AAGGAAAGGCGGCTGGTAGCTGTTAGAATATTTAGGGCTTGCTTGCACTTGAAGGAGGTCATCCA
1 AAGGAAAGGCGGCTGGTAGCTGTTAGAATATTTAGGGCTTGCTTGCACTTGAAGGAGGTCATCCA
3078399 GCTGGCATGTGACATAGGCGATTTCGTCATATCCGCTTAAGACTTTGTAGAATAACCTTGCTTTG
66 GCTGGCATGTGACATAGGCGATTTCGTCATATCCGCTTAAGACTTTGTAGAATAACCTTGCTTTG
3078464 GTGAGATAAATATGCTTCCCACGTTCTTCTCTGTTCTATTAGCCCTTGCAATTTACGTTGTCGTG
131 GTGAGATAAATATGCTTCCCACGTTCTTCTCTGTTCTATTAGCCCTTGCAATTTACGTTGTCGTG
3078529 ACTGAAATGTTCTTCCTCTATAAGTTTCCTGCATATACAGAATTCACAC
196 ACTGAAATGTTCTTCCTCTATAAGTTTCCTGCATATACAGAATTCACAC
3078578 AA
1 AA
3078580 ACCCTTTCTC
Statistics
Matches: 246, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
244 246 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (244 bp):
AAGGAAAGGCGGCTGGTAGCTGTTAGAATATTTAGGGCTTGCTTGCACTTGAAGGAGGTCATCCA
GCTGGCATGTGACATAGGCGATTTCGTCATATCCGCTTAAGACTTTGTAGAATAACCTTGCTTTG
GTGAGATAAATATGCTTCCCACGTTCTTCTCTGTTCTATTAGCCCTTGCAATTTACGTTGTCGTG
ACTGAAATGTTCTTCCTCTATAAGTTTCCTGCATATACAGAATTCACAC
Found at i:3079598 original size:14 final size:14
Alignment explanation
Indices: 3079579--3079615 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
3079569 TAATATGCAC
3079579 ATAAAATAGTATAA
1 ATAAAATAGTATAA
3079593 ATAAAAATAGTATAA
1 AT-AAAATAGTATAA
3079608 ATAAAATA
1 ATAAAATA
3079616 AAGTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
ATAAAATAGTATAA
Found at i:3079599 original size:15 final size:15
Alignment explanation
Indices: 3079581--3079613 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3079571 ATATGCACAT
3079581 AAAATAGTATAAATA
1 AAAATAGTATAAATA
3079596 AAAATAGTATAAATA
1 AAAATAGTATAAATA
3079611 AAA
1 AAA
3079614 TAAAGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAATAGTATAAATA
Found at i:3079799 original size:2 final size:2
Alignment explanation
Indices: 3079792--3079835 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
3079782 AATGAATCTC
* *
3079792 AT AT AT AT AT AT AT AT AG AT AT AT AG AT AT AT -T GAT 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
3079834 AT
1 AT
3079836 TATTGATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.94
3 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3088827 original size:49 final size:47
Alignment explanation
Indices: 3088772--3089260 Score: 358
Period size: 49 Copynumber: 10.0 Consensus size: 47
3088762 AACTACTCTA
* *
3088772 TAATGCAAGTTAAATGTATAGCAGTGCACTTTTGGTAAAAAGGTGCCAC
1 TAATGCAAGTTAAATGCATA-CAGTGCA-TTTTGGCAAAAAGGTGCCAC
** * *
3088821 TAATGCAAGTTAAATGCATA-ATGGTGCATTTTTTCTAGAAAGGTGTCAC
1 TAATGCAAGTTAAATGCATACA--GTGCATTTTGGC-AAAAAGGTGCCAC
* ** * * *
3088870 TAATGCAAGTTAAATGCATA-ATGCTACATTTTTTCCAGAAAGGTGTCGC
1 TAATGCAAGTTAAATGCATACA-G-TGCA-TTTTGGCAAAAAGGTGCCAC
* * * * *
3088919 TAATGAAACTTAAAAGCATACAGGTGCATTTTTGGCAGAAAGGTGTCAC
1 TAATGCAAGTTAAATGCATACA-GTGCA-TTTTGGCAAAAAGGTGCCAC
** * *
3088968 TAATGCAAGTTAAATGCATA-ATGGTGCATTTTTTACATAAAGGTGTCAC
1 TAATGCAAGTTAAATGCATACA--GTGCA-TTTTGGCAAAAAGGTGCCAC
** *
3089017 TAACACAAGTTAAATGCATAAAGGTGCATTTTTGGCAAAAAGGTGCCAC
1 TAATGCAAGTTAAATGCATACA-GTGCA-TTTTGGCAAAAAGGTGCCAC
** * ** * *
3089066 TAATGCAAGTTAAATGCATATGGTGTATTTTTTACAGAAATGTGCCAC
1 TAATGCAAGTTAAATGCATACAGTGCA-TTTTGGCAAAAAGGTGCCAC
* * * *
3089114 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGCAGAAATGTGCCAC
1 TAATGCAAGTTAAATGCATACA-GTGCATTTTGGCAAAAAGGTGCCAC
* * * * *
3089162 TAAAGCGAGTTAAATTCATA-ACGATGCATTTTTGGCAGAAAGGTGCAAC
1 TAATGCAAGTTAAATGCATACA-G-TGCA-TTTTGGCAAAAAGGTGCCAC
* *
3089211 TAATG-ACAGTTAAATGTATAACAGTGCATTTCGGCATAAAAGGTGCCAC
1 TAATGCA-AGTTAAATGCAT-ACAGTGCATTTTGGCA-AAAAGGTGCCAC
3089260 T
1 T
3089261 CATGGTGTAA
Statistics
Matches: 368, Mismatches: 57, Indels: 30
0.81 0.13 0.07
Matches are distributed among these distances:
47 3 0.01
48 94 0.26
49 259 0.70
50 11 0.03
51 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.30
Consensus pattern (47 bp):
TAATGCAAGTTAAATGCATACAGTGCATTTTGGCAAAAAGGTGCCAC
Found at i:3089047 original size:147 final size:144
Alignment explanation
Indices: 3088795--3089260 Score: 511
Period size: 147 Copynumber: 3.2 Consensus size: 144
3088785 ATGTATAGCA
* * *
3088795 GTGCACTTTTGGTAAAAAGGTGCCACTAATGCAAGTTAAATGCATAATGGTGCATTTTTTCTAGA
1 GTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCATAATGGTGCATTTTTTC-AGA
* * * * ** * *
3088860 AAGGTGTCACTAATGCAAGTTAAATGCATAATGCTACATTTTTTCCAGAAAGGTGTCGCTAATGA
65 AAGGTGTCACTAA-ACAAGTTAAATGCATAAAGATGCATTTTTGGCAGAAAGGTGCCACTAATGA
3088925 AACTTAAAAGCATACAG
129 AACTTAAAAGCATA-AG
* *
3088942 GTGCATTTTTGGCAGAAAGGTGTCACTAATGCAAGTTAAATGCATAATGGTGCATTTTTTACATA
1 GTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCATAATGGTGCATTTTTT-CAGA
* * *
3089007 AAGGTGTCACTAACACAAGTTAAATGCATAAAGGTGCATTTTTGGCAAAAAGGTGCCACTAATGC
65 AAGGTGTCACTAA-ACAAGTTAAATGCATAAAGATGCATTTTTGGCAGAAAGGTGCCACTAATGA
* * *
3089072 AAGTTAAATGCATATG
129 AACTTAAAAGCATAAG
* ** * * *
3089088 GTGTATTTTTTACAGAAATGTGCCACTAATGCAAGTTAAATGCATAAAGGTGCATTTTTGCAGAA
1 GTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCATAATGGTGCATTTTTTCAGAA
* * * * * * *
3089153 ATGTGCCACTAAAGCGAGTTAAATTCATAACGATGCATTTTTGGCAGAAAGGTGCAACTAATGAC
66 AGGTGTCACTAAA-CAAGTTAAATGCATAAAGATGCATTTTTGGCAGAAAGGTGCCACTAATGAA
* * * *
3089218 AGTTAAATGTATAACA
130 ACTTAAAAGCATAA-G
* *
3089234 GTGCA-TTTCGGCATAAAAGGTGCCACT
1 GTGCATTTTTGGCA-GAAAGGTGCCACT
3089261 CATGGTGTAA
Statistics
Matches: 269, Mismatches: 46, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
144 1 0.00
145 74 0.28
146 69 0.26
147 124 0.46
148 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.30
Consensus pattern (144 bp):
GTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCATAATGGTGCATTTTTTCAGAA
AGGTGTCACTAAACAAGTTAAATGCATAAAGATGCATTTTTGGCAGAAAGGTGCCACTAATGAAA
CTTAAAAGCATAAG
Found at i:3089147 original size:97 final size:98
Alignment explanation
Indices: 3088810--3089260 Score: 536
Period size: 98 Copynumber: 4.6 Consensus size: 98
3088800 CTTTTGGTAA
* * *
3088810 AAAGGTGCCACTAATGCAAGTTAAATGCATAATGGTGCATTTTT-TCTAGAAAGGTGTCACTAAT
1 AAAGGTGCCACTAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGC-AGAAAGGTGCCACTAAT
* * *
3088874 GCAAGTTAAATGCATAATGCTACATTTTTTCCAG
65 GCAAGTTAAATGCATAATGGTGCATTTTTTACAG
* * * * * * *
3088908 AAAGGTGTCGCTAATGAAACTTAAAAGCATACAGGTGCATTTTTGGCAGAAAGGTGTCACTAATG
1 AAAGGTGCCACTAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGCCACTAATG
*
3088973 CAAGTTAAATGCATAATGGTGCATTTTTTACAT
66 CAAGTTAAATGCATAATGGTGCATTTTTTACAG
* ** *
3089006 AAAGGTGTCACTAACACAAGTTAAATGCATAAAGGTGCATTTTTGGCAAAAAGGTGCCACTAATG
1 AAAGGTGCCACTAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGCCACTAATG
*
3089071 CAAGTTAAATGCAT-ATGGTGTATTTTTTACAG
66 CAAGTTAAATGCATAATGGTGCATTTTTTACAG
* * *
3089103 AAATGTGCCACTAATGCAAGTTAAATGCATAAAGGTGCATTTTT-GCAGAAATGTGCCACTAAAG
1 AAAGGTGCCACTAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGCCACTAATG
* * * * **
3089167 CGAGTTAAATTCATAACGATGCATTTTTGGCAG
66 CAAGTTAAATGCATAATGGTGCATTTTTTACAG
* * * *
3089200 AAAGGTGCAACTAATG-ACAGTTAAATGTATAACA-GTGCA-TTTCGGCATAAAAGGTGCCACT
1 AAAGGTGCCACTAATGCA-AGTTAAATGCATAA-AGGTGCATTTTTGGCA-GAAAGGTGCCACT
3089261 CATGGTGTAA
Statistics
Matches: 304, Mismatches: 43, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
96 33 0.11
97 104 0.34
98 166 0.55
99 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (98 bp):
AAAGGTGCCACTAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGCCACTAATG
CAAGTTAAATGCATAATGGTGCATTTTTTACAG
Found at i:3090192 original size:11 final size:12
Alignment explanation
Indices: 3090168--3090192 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3090158 ATTGAATTTA
3090168 TTCAAAGTTTTT
1 TTCAAAGTTTTT
3090180 TTCAAAGTTTTT
1 TTCAAAGTTTTT
3090192 T
1 T
3090193 AAAATAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TTCAAAGTTTTT
Found at i:3093731 original size:47 final size:45
Alignment explanation
Indices: 3093637--3093762 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
3093627 GTAACCATGC
* *
3093637 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTAAGAGCTTACGGAATAAATGGTAAGTATATAGGAA
* * * * *
3093681 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTAAGAGCTTACGGAA--TAAATGGTAAGTATATAGGAA
*
3093728 AAATAAGCTTAAGAGCTTACGGGATAAATGGTAAG
1 AAATAAGCTTAAGAGCTTACGGAATAAATGGTAAG
3093763 AGATTTTAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.16
46 1 0.01
47 36 0.51
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTAAGAGCTTACGGAATAAATGGTAAGTATATAGGAA
Found at i:3095106 original size:3 final size:3
Alignment explanation
Indices: 3095100--3095182 Score: 107
Period size: 3 Copynumber: 28.0 Consensus size: 3
3095090 TTGATGATGA
* * *
3095100 AAG AAG AGG AAG AAG ATG AAG -AG AAG CAA- AAC AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG
*
3095144 AAG AAG AAG AAG AAG AAG AAG AAT AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3095183 GTAGCCATTG
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
2 4 0.06
3 64 0.91
4 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.31, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:3101542 original size:64 final size:62
Alignment explanation
Indices: 3101473--3101631 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 62
3101463 GGACTCCTAC
* * **
3101473 TGCATCAATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AGCCTGGTGCATCGATGCATGGATT
1 TGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG---AGTGCATCGATGCATGGAGA
3101536 G
62 G
* * * *
3101537 TGCATCGATGCATCAAATGCATTCAAAGTTTTAATTAAATCAGAGTGCATCGATGCATGGAGAG
1 TGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATCAGAGTGCATCGATGCATGGAGAG
*
3101601 TGCATCGGTGCATGGAATGCATTCGATGTTT
1 TGCATCGATGCAT-GAATGCATTCGATGTTT
3101632 CAACTTATTC
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
64 70 0.90
65 2 0.03
66 4 0.05
67 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (62 bp):
TGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAGAGTGCATCGATGCATGGAGAG
Found at i:3101602 original size:19 final size:19
Alignment explanation
Indices: 3101578--3101628 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3101568 TAATTAAATC
3101578 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
3101597 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
3101616 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
3101629 TTTCAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:3101666 original size:21 final size:21
Alignment explanation
Indices: 3101642--3101681 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3101632 CAACTTATTC
*
3101642 ATTGATGCATTGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
3101663 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
3101682 CCTTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:3104285 original size:24 final size:23
Alignment explanation
Indices: 3104215--3104294 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 23
3104205 CATGGTCTTG
*
3104215 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
*
3104238 TGCATC-AGTG--CA-TCATGCGGA
1 TGCATCGA-TGCACATTCAAG-GGA
3104259 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
3104283 TGCATCGATGCA
1 TGCATCGATGCA
3104295 TTGGTGCATT
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
20 4 0.09
21 12 0.26
22 2 0.04
23 10 0.21
24 17 0.36
25 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:3110116 original size:18 final size:17
Alignment explanation
Indices: 3110062--3110110 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3110052 TTGGACTCCT
* *
3110062 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
3110080 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
3110098 AGTGCATTCGATG
1 AGTGCA-TCGATG
3110111 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:3110176 original size:45 final size:46
Alignment explanation
Indices: 3110079--3110185 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 46
3110069 CGGTGCACTA
* *
3110079 AGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGTC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAGTC
* * *
3110125 TG-GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAA-A-TC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAA-AAATAGTC
3110169 AGAGTGCATCGATGCAT
1 AGAGTGCATCGATGCAT
3110186 GGAGAGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
44 3 0.06
45 47 0.89
46 3 0.06
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (46 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAGTC
Found at i:3110193 original size:19 final size:19
Alignment explanation
Indices: 3110169--3110219 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3110159 TAATTAAATC
3110169 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
3110188 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
3110207 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
3110220 TTTCAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:3110195 original size:64 final size:66
Alignment explanation
Indices: 3110127--3110271 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 66
3110117 AAATAGTCTG
*
3110127 GTGCATCGATGCATCAAATGCATTCGATGTTTTAA-TTAAATCA-GAGTGCATCGATGCATGG-A
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAACTT-AATCATGA-TGCATCGATGCATGGTA
3110189 -GA
64 TGA
* ** *
3110191 GTGCATCGGTGCATGGAATGCATTCGATGTTTCAACTTATTCATTGATGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAACTTAATCA-TGATGCATCGATGCATGGTA-
3110256 TGA
64 TGA
3110259 -TGCATCGATGCAT
1 GTGCATCGATGCAT
3110272 GCCTTTGAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
64 35 0.51
65 17 0.25
66 3 0.04
67 12 0.17
68 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (66 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAACTTAATCATGATGCATCGATGCATGGTATG
A
Found at i:3110257 original size:21 final size:21
Alignment explanation
Indices: 3110233--3110272 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3110223 CAACTTATTC
3110233 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
3110254 ATTGATGCATCGATGCATG
1 ATTGATGCATCGATGCATG
3110273 CCTTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:3113951 original size:115 final size:115
Alignment explanation
Indices: 3113746--3113962 Score: 353
Period size: 115 Copynumber: 1.9 Consensus size: 115
3113736 TTTTTATGGT
* *
3113746 AAGCAAAACCCTTTATTCTTGAAACCTGAAAGGTCATATTTTACCTATAAACAAACCTCCATTTC
1 AAGCAAAACCCTTTATGCTTGAAACCTGAAAGCTCATATTTTACCTATAAACAAACCTCCATTTC
* **
3113811 ACCTAATTAATTATCTTCTTGATCTTCCTATATTTTTTCTTCAAAAATCA
66 ACCTAATTAATTATCTTCTTAATCTTAATATATTTTTTCTTCAAAAATCA
* * * *
3113861 AAGCAAAACCCTTTCTGCTTGAAATCTGAAAGCTCATATTTTACCTATAAACAAACTTCCATTTT
1 AAGCAAAACCCTTTATGCTTGAAACCTGAAAGCTCATATTTTACCTATAAACAAACCTCCATTTC
3113926 ACCTAATTAATTATCTTCTTAATCTTAATATATTTTT
66 ACCTAATTAATTATCTTCTTAATCTTAATATATTTTT
3113963 GGGTAAAATA
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
115 93 1.00
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (115 bp):
AAGCAAAACCCTTTATGCTTGAAACCTGAAAGCTCATATTTTACCTATAAACAAACCTCCATTTC
ACCTAATTAATTATCTTCTTAATCTTAATATATTTTTTCTTCAAAAATCA
Found at i:3114551 original size:27 final size:27
Alignment explanation
Indices: 3114515--3114582 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
3114505 TTAACTGTTA
*
3114515 GGACTCAACAAAACTTTTAACAATAAT
1 GGACTCAACAAAACTTTTAACAATAAG
* *
3114542 GGACTAAACAAAACTTTTAACAATCAG
1 GGACTCAACAAAACTTTTAACAATAAG
3114569 GGACTCAACAAAAC
1 GGACTCAACAAAAC
3114583 AACCTCTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.21
Consensus pattern (27 bp):
GGACTCAACAAAACTTTTAACAATAAG
Found at i:3115800 original size:47 final size:47
Alignment explanation
Indices: 3115746--3115837 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 47
3115736 AATTGGGTTC
* *
3115746 TTTTTAATAAAAACCCTCTTTTATTTGCTTTTGCATTGTTTTTCTTA
1 TTTTTAATAAAAACCCTCTTTTATTTGCCTTTACATTGTTTTTCTTA
* * *
3115793 TTTTTAATAAAAATCCTCTTTTGTTTGCCTTTACCTTGTTTTTCT
1 TTTTTAATAAAAACCCTCTTTTATTTGCCTTTACATTGTTTTTCT
3115838 CCTACTTATC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.20, C:0.16, G:0.07, T:0.58
Consensus pattern (47 bp):
TTTTTAATAAAAACCCTCTTTTATTTGCCTTTACATTGTTTTTCTTA
Found at i:3116386 original size:42 final size:41
Alignment explanation
Indices: 3116277--3116386 Score: 157
Period size: 41 Copynumber: 2.7 Consensus size: 41
3116267 CTCCGAATTC
*
3116277 CCGTGTTTGTTTCACGTAATTTATTTTCAGGAAAACGTTTT
1 CCGTGTTTGTTTCACGTAATTCATTTTCAGGAAAACGTTTT
* * *
3116318 CCGTATTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTT
1 CCGTGTTTGTTTCACGTAATTCATTTTCAGGAAAACGTTTT
* *
3116359 CCAGTGTTTGTTTCACATAATTGATTTT
1 CC-GTGTTTGTTTCACGTAATTCATTTT
3116387 TCATAACGTA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
41 39 0.64
42 22 0.36
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.47
Consensus pattern (41 bp):
CCGTGTTTGTTTCACGTAATTCATTTTCAGGAAAACGTTTT
Found at i:3116601 original size:17 final size:17
Alignment explanation
Indices: 3116581--3116616 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3116571 ATTTATTTAT
3116581 TAATATTTATAATAATA
1 TAATATTTATAATAATA
*
3116598 TAATATTTATAATATTA
1 TAATATTTATAATAATA
3116615 TA
1 TA
3116617 TAAAATAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATATTTATAATAATA
Found at i:3116763 original size:23 final size:23
Alignment explanation
Indices: 3116737--3116781 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3116727 AATAATATTT
3116737 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * * *
3116760 TAATTAATATTTTTATAATATA
1 TAATAAAGATATTTAAAATATA
3116782 ATATAACACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:3116914 original size:20 final size:21
Alignment explanation
Indices: 3116889--3116944 Score: 105
Period size: 20 Copynumber: 2.7 Consensus size: 21
3116879 TAAAATACTA
3116889 TTTAATAATAAATAAATTA-T
1 TTTAATAATAAATAAATTATT
3116909 TTTAATAATAAATAAATTATT
1 TTTAATAATAAATAAATTATT
3116930 TTTAATAATAAATAA
1 TTTAATAATAAATAA
3116945 GTTTTATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAATAATAAATAAATTATT
Found at i:3116940 original size:37 final size:39
Alignment explanation
Indices: 3116894--3116968 Score: 102
Period size: 37 Copynumber: 2.0 Consensus size: 39
3116884 TACTATTTAA
*
3116894 TAATAAATAAATTA-TTTTAATAATAAATAA-ATTATTTT
1 TAATAAATAAATAAGTTTT-ATAATAAATAATATTATTTT
*
3116932 TAAT-AATAAATAAGTTTTATGATAAATAATATTATTT
1 TAATAAATAAATAAGTTTTATAATAAATAATATTATTT
3116969 ATTGTATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 18 0.55
38 15 0.45
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (39 bp):
TAATAAATAAATAAGTTTTATAATAAATAATATTATTTT
Found at i:3117176 original size:29 final size:30
Alignment explanation
Indices: 3117134--3117206 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
3117124 TTCCGGAAAT
3117134 GTAATTCATTTTCCAG-AATTCAAATTACA
1 GTAATTCATTTTCCAGTAATTCAAATTACA
*
3117163 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTACA
*
3117193 GTGATTCATTTTCC
1 GTAATTCATTTTCC
3117207 GAAAAACCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 16 0.39
30 25 0.61
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTACA
Found at i:3117206 original size:15 final size:15
Alignment explanation
Indices: 3117134--3117206 Score: 85
Period size: 15 Copynumber: 4.9 Consensus size: 15
3117124 TTCCGGAAAT
3117134 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
** *
3117149 G-AATTCAAATTACA
1 GTAATTCATTTTCCA
3117163 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
3117178 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
*
3117193 GTGATTCATTTTCC
1 GTAATTCATTTTCC
3117207 GAAAAACCAA
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
14 11 0.24
15 35 0.76
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:3130099 original size:252 final size:252
Alignment explanation
Indices: 3129654--3130160 Score: 852
Period size: 252 Copynumber: 2.0 Consensus size: 252
3129644 AGAAGCTTCC
*
3129654 ATGGCTGAAAACCAGATACTTATCAATAAAAATAGCACTGTAATAGCTGAGCTTCAGGACTGCAA
1 ATGGCTGAAAACCAGATACTTATCAATAAAAATAGCACTGTAATAGCTGAGCTTCAGGACTACAA
* * *
3129719 AAGTAAGATAAAAAAGATAGAGTTCGCTTACTTTGAGGATAATCATCAGCATGCACTTGAAGTTG
66 AAGTAAGATAAAAAAGATAGAGTTCGCTTACTCTCAGGATAACCATCAGCATGCACTTGAAGTTG
*
3129784 AAAGGCTGAAGCACTTACTTGGCTGCTCACGAGAAGAGATTGATAATCTGATGGTATTGAAGGAA
131 AAAGGCTGAAGCACTTACTTGGCTGCTCACAAGAAGAGATTGATAATCTGATGGTATTGAAGGAA
** * *
3129849 GAACTGGAATTCTCTGTCCTAGTACTTAAAGCTAAATTGGATGAACAGAGCACTCAG
196 GAACTGGAATTCAATGTCCTAGTACTCAAAGCTAAATTGGATGAACAGACCACTCAG
*
3129906 ATGGCTGAAAACCAGATACTTATCAATAAAAATAGCTCTGTAATAGCTGAGCTTCAGGACTACAA
1 ATGGCTGAAAACCAGATACTTATCAATAAAAATAGCACTGTAATAGCTGAGCTTCAGGACTACAA
*** * *
3129971 AAGTAAGATCGGAAAGATTGAGTTCGCTTACTCTCAGGATAACCATCAGCATGCTCTTGAAGTTG
66 AAGTAAGATAAAAAAGATAGAGTTCGCTTACTCTCAGGATAACCATCAGCATGCACTTGAAGTTG
*
3130036 AAAGGCTGAAGCACTTACTTGGCTGCTCCCAAGAAGAGATTGATAATCTGATGGTATTGAAGGAA
131 AAAGGCTGAAGCACTTACTTGGCTGCTCACAAGAAGAGATTGATAATCTGATGGTATTGAAGGAA
* *
3130101 GAACTGGAATTCAATGTCTTAGTACTCAAAGGTAAATTGGATGAACAGACCACTCAG
196 GAACTGGAATTCAATGTCCTAGTACTCAAAGCTAAATTGGATGAACAGACCACTCAG
3130158 ATG
1 ATG
3130161 ATCTTACTGG
Statistics
Matches: 237, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
252 237 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (252 bp):
ATGGCTGAAAACCAGATACTTATCAATAAAAATAGCACTGTAATAGCTGAGCTTCAGGACTACAA
AAGTAAGATAAAAAAGATAGAGTTCGCTTACTCTCAGGATAACCATCAGCATGCACTTGAAGTTG
AAAGGCTGAAGCACTTACTTGGCTGCTCACAAGAAGAGATTGATAATCTGATGGTATTGAAGGAA
GAACTGGAATTCAATGTCCTAGTACTCAAAGCTAAATTGGATGAACAGACCACTCAG
Found at i:3130739 original size:42 final size:42
Alignment explanation
Indices: 3130680--3130814 Score: 189
Period size: 42 Copynumber: 3.2 Consensus size: 42
3130670 ATTCTGCATG
*
3130680 GAAGAAAAACAGAAACTTGAAGCATATTTGCAAGAATGTAAT
1 GAAGAAAAACAGAAACTTGAAGCATCTTTGCAAGAATGTAAT
* *
3130722 GAAGAAAAACAGAAACTTGAAGCATCTTTGCAAGAATGCAAC
1 GAAGAAAAACAGAAACTTGAAGCATCTTTGCAAGAATGTAAT
** * * *
3130764 GCGGAAAAACAGAAACTTGAGGCGTCTTTGCTAGAATGTAAT
1 GAAGAAAAACAGAAACTTGAAGCATCTTTGCAAGAATGTAAT
*
3130806 GAGGAAAAA
1 GAAGAAAAA
3130815 TCTAGACTCT
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.19
Consensus pattern (42 bp):
GAAGAAAAACAGAAACTTGAAGCATCTTTGCAAGAATGTAAT
Found at i:3141795 original size:19 final size:18
Alignment explanation
Indices: 3141732--3141804 Score: 119
Period size: 18 Copynumber: 4.0 Consensus size: 18
3141722 ATTTGAATAA
3141732 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
*
3141750 TTGAATCAAATATAAAAT
1 TTGAATCGAATATAAAAT
3141768 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
*
3141786 TTGAAATCGAATAGAAAAT
1 TTG-AATCGAATATAAAAT
3141805 CTTAAATTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
18 37 0.73
19 14 0.27
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.32
Consensus pattern (18 bp):
TTGAATCGAATATAAAAT
Found at i:3142282 original size:250 final size:238
Alignment explanation
Indices: 3141830--3142308 Score: 809
Period size: 250 Copynumber: 2.0 Consensus size: 238
3141820 ACTTTATTGT
3141830 TATCGAAATTTTTCAACAATCTCCCCTTTTTGATATAACAAACCTTTAGAATTTAGGATTTTTTT
1 TATCGAAATTTTTCAACAATCTCCCCTTTTTGATATAACAAACCTTTAGAATTTAGGATTTTTTT
3141895 GAAAATAATTTTGAAAAAAAAAATACCCCCTTACTAAGATTTCTCCCCCTTTTTGTTAAATAAAA
66 GAAAATAATTTTGAAAAAAAAAATACCCCCTTACTAAGATTTCTCCCCCTTTTTGTTAAATAAAA
3141960 GGTCTCTATAAATTTTAAACAATAGCCAATTGATATATATATATATAGCTGCTAAGATCAAGCCA
131 GGTCTCTATAAATTTTAAACAATAGCCAATTGATATATATATATATAGCTGCTAAGATCAAGCCA
3142025 AGAAAAATA-TAGCCATTAGTACACATAATCAATTATTTGTTA
196 AGAAAAATATTAGCCATTAGTACACATAATCAATTATTTGTTA
3142067 TATCGAAATATTTTCAACAATCTCCCCCTTTTTGATATAACAAAACCTTTTAGAAATTTTAGGAT
1 TATCGAAAT-TTTTCAACAATCT-CCCCTTTTTGATATAAC-AAACC-TTTAG-AA-TTTAGGA-
*
3142132 TTTTTTTTGAAAATAATTTTGAAAAAAAATACT-CCCCCTTACTATAAGATTTCTCCCCCTTTTT
59 -TTTTTTTGAAAATAATTTTGAAAAAAAA-AATACCCCCTTAC--TAAGATTTCTCCCCCTTTTT
3142196 GTTAAATAAAAAGGTCTCTATAAATTTTAAACAATATAGCCAATTGATATATATATATATAGCTG
120 GTTAAAT-AAAAGGTCTCTATAAATTTTAAAC-A-ATAGCCAATTGATATATATATATATAGCTG
3142261 CTAAGATCAAGCCAAGAAAAATATTAGCCATTAGTACACATAATCAAT
182 CTAAGATCAAGCCAAGAAAAATATTAGCCATTAGTACACATAATCAAT
3142309 ATTCATAACA
Statistics
Matches: 226, Mismatches: 1, Indels: 16
0.93 0.00 0.07
Matches are distributed among these distances:
237 9 0.04
238 13 0.06
239 17 0.08
240 5 0.02
241 5 0.02
242 2 0.01
243 7 0.03
245 37 0.16
246 2 0.01
247 27 0.12
248 24 0.11
249 1 0.00
250 53 0.23
251 24 0.11
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (238 bp):
TATCGAAATTTTTCAACAATCTCCCCTTTTTGATATAACAAACCTTTAGAATTTAGGATTTTTTT
GAAAATAATTTTGAAAAAAAAAATACCCCCTTACTAAGATTTCTCCCCCTTTTTGTTAAATAAAA
GGTCTCTATAAATTTTAAACAATAGCCAATTGATATATATATATATAGCTGCTAAGATCAAGCCA
AGAAAAATATTAGCCATTAGTACACATAATCAATTATTTGTTA
Found at i:3150365 original size:18 final size:18
Alignment explanation
Indices: 3150342--3150377 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3150332 ATTCAAATAA
3150342 TTGAATCGAAAATAAAAT
1 TTGAATCGAAAATAAAAT
*
3150360 TTGAATCGAATATAAAAT
1 TTGAATCGAAAATAAAAT
3150378 CTTAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.31
Consensus pattern (18 bp):
TTGAATCGAAAATAAAAT
Found at i:3154670 original size:4 final size:4
Alignment explanation
Indices: 3154617--3154651 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
3154607 ATTAGTCAAA
*
3154617 AAAT CAAAT AAAT AAAT GAAT AAAT AAAT AAAT AA
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
3154652 TTTATTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3159071 original size:18 final size:18
Alignment explanation
Indices: 3159034--3159068 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3159024 ATGTACTATG
*
3159034 ATATATGTGATATTCTTT
1 ATATATGTGATATGCTTT
3159052 ATATAT-TGATATGCTTT
1 ATATATGTGATATGCTTT
3159069 TATTTAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (18 bp):
ATATATGTGATATGCTTT
Found at i:3159264 original size:2 final size:2
Alignment explanation
Indices: 3159259--3159303 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
3159249 TATATATATA
* * *
3159259 TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG CG CG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3159301 TG T
1 TG T
3159304 TAATGATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.07, G:0.49, T:0.44
Consensus pattern (2 bp):
TG
Found at i:3159276 original size:12 final size:12
Alignment explanation
Indices: 3159259--3159302 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
3159249 TATATATATA
3159259 TGTGTGTGCGTG
1 TGTGTGTGCGTG
*
3159271 TGTGTGTGTGTG
1 TGTGTGTGCGTG
*
3159283 TGTGTGTGCGCG
1 TGTGTGTGCGTG
3159295 TGTGTGTG
1 TGTGTGTG
3159303 TTAATGATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.00, C:0.07, G:0.50, T:0.43
Consensus pattern (12 bp):
TGTGTGTGCGTG
Found at i:3159808 original size:38 final size:38
Alignment explanation
Indices: 3159757--3159830 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
3159747 TTAAACCAAG
*
3159757 CATGTTTTGAATTGAAAAGTGTATACATACCACTAGAT
1 CATGTTTTGAATTGAAAAGTGTATACATACAACTAGAT
* *
3159795 CATGTTTTGAATTGAAAATTTTATACATACAACTAG
1 CATGTTTTGAATTGAAAAGTGTATACATACAACTAG
3159831 GATATCATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (38 bp):
CATGTTTTGAATTGAAAAGTGTATACATACAACTAGAT
Found at i:3172180 original size:155 final size:159
Alignment explanation
Indices: 3171980--3172294 Score: 577
Period size: 157 Copynumber: 2.0 Consensus size: 159
3171970 GTCTCCAGTG
3171980 GGTAGTGGGTGTGGGGATGGATTTGAGAATGTACACGCGTGGGCGGGTG-GG-TTTGAAAATTTT
1 GGTAGTGGGTGTGGGGATGGATTTGAGAATGTACACGCGTGGGCGGGTGTGGATTTGAAAATTTT
3172043 TACCCATTATGGATGGTGGGCGGGGGTGTGGATTGAAAAATATTAGG-GGATATGGGGATGGGGG
66 TACCCATTATGGATGGTGGGCGGGGG-GTGGATTGAAAAATATTAGGTGGATATGGGGATGGGGG
3172107 AGGGGGTATCCGCA-CCGACCCGCCCGTTT
130 AGGGGGTATCCGCACCCGACCCGCCCGTTT
3172136 GGTAG-GGGTGTGGGGATGGATTTGAGAATGTACACGCGTGGGCGGGTGTGGATTTGAAAATTTT
1 GGTAGTGGGTGTGGGGATGGATTTGAGAATGTACACGCGTGGGCGGGTGTGGATTTGAAAATTTT
*
3172200 TACCCATTATGGATGGTGGGCGGGTGGTGGATTGAAAAATATTAGGTGGATATGGGGATGGGGGA
66 TACCCATTATGGATGGTGGGCGGGGGGTGGATTGAAAAATATTAGGTGGATATGGGGATGGGGGA
3172265 GGGGGTATCCGCACCCGACCCGCCCGTTT
131 GGGGGTATCCGCACCCGACCCGCCCGTTT
3172294 G
1 G
3172295 CCATCCCTAG
Statistics
Matches: 154, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
155 43 0.28
156 27 0.18
157 68 0.44
158 16 0.10
ACGTcount: A:0.20, C:0.12, G:0.42, T:0.26
Consensus pattern (159 bp):
GGTAGTGGGTGTGGGGATGGATTTGAGAATGTACACGCGTGGGCGGGTGTGGATTTGAAAATTTT
TACCCATTATGGATGGTGGGCGGGGGGTGGATTGAAAAATATTAGGTGGATATGGGGATGGGGGA
GGGGGTATCCGCACCCGACCCGCCCGTTT
Found at i:3174554 original size:17 final size:18
Alignment explanation
Indices: 3174532--3174566 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3174522 AGAATTGTAA
3174532 CAAACCG-AAAAATAATT
1 CAAACCGAAAAAATAATT
3174549 CAAACCGAAAAAATAATT
1 CAAACCGAAAAAATAATT
3174567 TAATTAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.60, C:0.17, G:0.06, T:0.17
Consensus pattern (18 bp):
CAAACCGAAAAAATAATT
Done.