Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 91 of 204
Found at i:28427115 original size:18 final size:18
Alignment explanation
Indices: 28427096--28427136 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
28427086 TTAAGTAATA
28427096 AAAACT-AAATTTATTTT
1 AAAACTGAAATTTATTTT
*
28427113 AAATCTGAAATTTATTTTT
1 AAAACTGAAATTTA-TTTT
28427132 AAAAC
1 AAAAC
28427137 ATTTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 7 0.35
19 8 0.40
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (18 bp):
AAAACTGAAATTTATTTT
Found at i:28427383 original size:20 final size:21
Alignment explanation
Indices: 28427338--28427393 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
28427328 AAAACATAAA
* *
28427338 ATTTTATAAAATATATTATAT
1 ATTTTTTAAAATATACTATAT
*
28427359 ATTTTTTAAAATATACTGT-T
1 ATTTTTTAAAATATACTATAT
*
28427379 ATTTTTTAAATTATA
1 ATTTTTTAAAATATA
28427394 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTTTTAAAATATACTATAT
Found at i:28429593 original size:22 final size:25
Alignment explanation
Indices: 28429543--28429620 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
28429533 CGTAACTTAA
28429543 ATCATTCATTTTCAAACACATGCAT
1 ATCATTCATTTTCAAACACATGCAT
*
28429568 ATCATTCATTTTCATA-A-AT-CAT
1 ATCATTCATTTTCAAACACATGCAT
28429590 ATCATAACTCA--TTCAAACACATGCAT
1 ATCAT---TCATTTTCAAACACATGCAT
28429616 ATCAT
1 ATCAT
28429621 CCTTTATTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
22 8 0.18
23 7 0.16
24 2 0.04
25 20 0.44
26 8 0.18
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (25 bp):
ATCATTCATTTTCAAACACATGCAT
Found at i:28430972 original size:20 final size:20
Alignment explanation
Indices: 28430944--28431000 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
28430934 TAAACTATGA
* *
28430944 ACCACTCCATTTACTTTCTT
1 ACCATTCCATTTACTTACTT
28430964 ACCATTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
* *
28430984 TCCATTTCATTTACTTA
1 ACCATTCCATTTACTTA
28431001 GCATAAGCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (20 bp):
ACCATTCCATTTACTTACTT
Found at i:28431739 original size:35 final size:35
Alignment explanation
Indices: 28431693--28431833 Score: 201
Period size: 35 Copynumber: 4.0 Consensus size: 35
28431683 AACACATCAG
* *
28431693 ATGCTCATAAGAGCCAATCCAACTGTAACATGCCA
1 ATGCTCATAAGAGCTAATCCAACTGTAACACGCCA
* * *
28431728 ATGCTCATAAGAGTTAATCCAACTGTAGCACGTCA
1 ATGCTCATAAGAGCTAATCCAACTGTAACACGCCA
* *
28431763 ATTCTCATAAGAGCTAATCCAACTGAAACACGCCA
1 ATGCTCATAAGAGCTAATCCAACTGTAACACGCCA
* *
28431798 ATGCTCATAAGAGCTAATCCAACCGAAACACGCCA
1 ATGCTCATAAGAGCTAATCCAACTGTAACACGCCA
28431833 A
1 A
28431834 ATAGAGAGTA
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 94 1.00
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (35 bp):
ATGCTCATAAGAGCTAATCCAACTGTAACACGCCA
Found at i:28441048 original size:20 final size:20
Alignment explanation
Indices: 28441017--28441074 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
28441007 AGAGCATCGA
*
28441017 AGTGCA-AATAGGTCACCAG
1 AGTGCATAATAGGGCACCAG
**
28441036 AGTGCATAATAGGGCATTAG
1 AGTGCATAATAGGGCACCAG
*
28441056 AGTGCATTATAGGGGCACC
1 AGTGCATAATA-GGGCACC
28441075 GTAGTTCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 6 0.19
20 20 0.65
21 5 0.16
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (20 bp):
AGTGCATAATAGGGCACCAG
Found at i:28442666 original size:17 final size:17
Alignment explanation
Indices: 28442644--28442677 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28442634 CAGCTAACCC
28442644 GTACCTCTATTTTTGAA
1 GTACCTCTATTTTTGAA
28442661 GTACCTCTATTTTTGAA
1 GTACCTCTATTTTTGAA
28442678 ACTGTTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.47
Consensus pattern (17 bp):
GTACCTCTATTTTTGAA
Found at i:28446297 original size:29 final size:29
Alignment explanation
Indices: 28446265--28446425 Score: 173
Period size: 29 Copynumber: 5.6 Consensus size: 29
28446255 AGCTATCGAT
28446265 TATGAAAAGGGATGGTGACGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
* *
28446294 TATGGAAAGGGATGGTCACGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
* *
28446323 TATGAAAAGGGATGGTAACGACCAT-AGAA
1 TATGAAAAGGGATGGTGACGACCATCA-AC
* ** * * *
28446352 TAAGAAAAGGGATGGCTTTCG-CTATCGAT
1 TATGAAAAGGGATGG-TGACGACCATCAAC
** *
28446381 TATGAAAAAAGATGATGACGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
28446410 TATGAAAAGGGATGGT
1 TATGAAAAGGGATGGT
28446426 TTCAACCGTT
Statistics
Matches: 105, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
28 4 0.04
29 98 0.93
30 3 0.03
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (29 bp):
TATGAAAAGGGATGGTGACGACCATCAAC
Found at i:28446440 original size:58 final size:57
Alignment explanation
Indices: 28446259--28446464 Score: 198
Period size: 58 Copynumber: 3.5 Consensus size: 57
28446249 AACATCAGCT
* **
28446259 ATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGGAAAGGGATGGTCACGACC
1 ATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTTTC-ACC
* * * * * * *
28446317 ATCAACTATGAAAAGGGATGGTAACGACCAT-AGAATAAGAAAAGGGATGGCTTTCGCT
1 ATCGATTATGAAAAGGGATGGTGACGACCATCA-ACTATGAAAAGGGATGG-TTTCACC
** *
28446375 ATCGATTATGAAAAAAGATGATGACGACCATCAACTATGAAAAGGGATGGTTTCAACC
1 ATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTTTC-ACC
* * * * *
28446433 GTTGATTAAAGAAAAGGGATGGTTACAACCAT
1 ATCGATT-ATGAAAAGGGATGGTGACGACCAT
28446465 ATTTTAGCAC
Statistics
Matches: 115, Mismatches: 28, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
57 5 0.04
58 89 0.77
59 21 0.18
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (57 bp):
ATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTTTCACC
Found at i:28456455 original size:34 final size:34
Alignment explanation
Indices: 28456396--28456485 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 34
28456386 AATGATCAGC
* * * ** *
28456396 TGTCCGTTGAGGTGCCCGAACAGCCTTGTTGGTA
1 TGTCCTTTGATGTGCACGAACAGCCTTGAAGATA
28456430 TGT-CTCTTGATGTGCACGAACAGCCTTGAAGATA
1 TGTCCT-TTGATGTGCACGAACAGCCTTGAAGATA
*
28456464 TGTCCTTTCATGTGCACGAACA
1 TGTCCTTTGATGTGCACGAACA
28456486 AGTTTTGATG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
33 1 0.02
34 44 0.94
35 2 0.04
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (34 bp):
TGTCCTTTGATGTGCACGAACAGCCTTGAAGATA
Found at i:28458822 original size:18 final size:18
Alignment explanation
Indices: 28458799--28458834 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28458789 TAGCATGTCA
28458799 CTTAGTCAACTTGTGCTG
1 CTTAGTCAACTTGTGCTG
28458817 CTTAGTCAACTTGTGCTG
1 CTTAGTCAACTTGTGCTG
28458835 TCCCTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (18 bp):
CTTAGTCAACTTGTGCTG
Found at i:28460318 original size:18 final size:19
Alignment explanation
Indices: 28460297--28460337 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
28460287 TTATGAACTC
*
28460297 TTTTCT-TTTTCTTTTTCA
1 TTTTCTCTTTTCTTGTTCA
28460315 TTTT-TCTTTTCTTGTTCA
1 TTTTCTCTTTTCTTGTTCA
28460333 TTTTC
1 TTTTC
28460338 ACTCGACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTCTCTTTTCTTGTTCA
Found at i:28463177 original size:34 final size:33
Alignment explanation
Indices: 28463122--28463207 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 33
28463112 ATTAGCTATC
* * ** *
28463122 CATTGAGGTGCCCGAACAGCCTTGTTGGTATGT
1 CATTGATGTGCACGAACAGCCTTGAAGATATGT
*
28463155 CTATTGATGTGCACGAATAGCCTTGAAGATATGT
1 C-ATTGATGTGCACGAACAGCCTTGAAGATATGT
28463189 CATTTGATGTGCACGAACA
1 CA-TTGATGTGCACGAACA
28463208 ACTTTTGATG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 2 0.05
34 42 0.95
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (33 bp):
CATTGATGTGCACGAACAGCCTTGAAGATATGT
Found at i:28465402 original size:34 final size:34
Alignment explanation
Indices: 28465341--28465431 Score: 101
Period size: 34 Copynumber: 2.7 Consensus size: 34
28465331 AATGATCAGC
* * * ** *
28465341 TGTCCGTTGAGGTGCCCGAACAACCTTGTTGGTA
1 TGTCCTTTGATGTGCACGAACAACCTTGAAGATA
* * *
28465375 TGTCTTTTGATGTGCATGAACAGCCTTGAAGATA
1 TGTCCTTTGATGTGCACGAACAACCTTGAAGATA
28465409 TGTCCTTTGATGTGCACGAACAA
1 TGTCCTTTGATGTGCACGAACAA
28465432 GTTTTGATGG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (34 bp):
TGTCCTTTGATGTGCACGAACAACCTTGAAGATA
Found at i:28467716 original size:18 final size:18
Alignment explanation
Indices: 28467693--28467728 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28467683 TAGCATGTCA
28467693 CTTAGTCAACTTGTGCTG
1 CTTAGTCAACTTGTGCTG
28467711 CTTAGTCAACTTGTGCTG
1 CTTAGTCAACTTGTGCTG
28467729 TCCCTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (18 bp):
CTTAGTCAACTTGTGCTG
Found at i:28469212 original size:5 final size:6
Alignment explanation
Indices: 28469193--28469238 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
28469183 TCTGAACTCC
* *
28469193 TTTCTT TTTCTT TTTCTT TTTCATT TTT-AT TTTCTT TTTCAT TTTC
1 TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT TTTCTT TTTCTT TTTC
28469239 ACTCGACTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 4 0.11
6 26 0.74
7 5 0.14
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:28469214 original size:18 final size:18
Alignment explanation
Indices: 28469193--28469238 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
28469183 TCTGAACTCC
*
28469193 TTTCTTTTTCTTTTTCTT
1 TTTCATTTTCTTTTTCTT
28469211 TTTCATTTT-TATTTTCTT
1 TTTCATTTTCT-TTTTCTT
28469229 TTTCATTTTC
1 TTTCATTTTC
28469239 ACTCGACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTCATTTTCTTTTTCTT
Found at i:28472088 original size:34 final size:34
Alignment explanation
Indices: 28472050--28472123 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
28472040 TTGAGGTGCC
** *
28472050 CGAACAGCCTTGTTGGTATGTC-TATTGATGTACA
1 CGAACAGCCTTGAAGATATGTCAT-TTGATGTACA
*
28472084 CGAACAGCCTTGAAGATATGTCATTTGATGTGCA
1 CGAACAGCCTTGAAGATATGTCATTTGATGTACA
28472118 CGAACA
1 CGAACA
28472124 ACTTTTGATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 34 0.97
35 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (34 bp):
CGAACAGCCTTGAAGATATGTCATTTGATGTACA
Found at i:28491657 original size:22 final size:21
Alignment explanation
Indices: 28491632--28491675 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
28491622 TGATAAAATT
28491632 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
28491654 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
28491675 T
1 T
28491676 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:28495435 original size:25 final size:24
Alignment explanation
Indices: 28495406--28495489 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 24
28495396 GACATTGTCT
*
28495406 CAATCTAAAGTTTCTATCCTTTTCA
1 CAATCTAAAGTTTCTAT-ATTTTCA
* * *
28495431 CAATCTATAGTCTCTTATAGTTTCA
1 CAATCTAAAGTTTC-TATATTTTCA
* * *
28495456 AAATCTATAGTTTCTATTATTTTTA
1 CAATCTAAAGTTTCTA-TATTTTCA
28495481 C-ATCTAAAG
1 CAATCTAAAG
28495490 ATCACCTAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
24 9 0.19
25 35 0.74
26 3 0.06
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.45
Consensus pattern (24 bp):
CAATCTAAAGTTTCTATATTTTCA
Found at i:28506170 original size:29 final size:29
Alignment explanation
Indices: 28506136--28506195 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
28506126 CTGATTTTCA
28506136 GATAAACTACCACTAATAACACTGATGTG
1 GATAAACTACCACTAATAACACTGATGTG
28506165 GATAAACTACCACTAATAACACTGATGTG
1 GATAAACTACCACTAATAACACTGATGTG
28506194 GA
1 GA
28506196 CAAGTCAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (29 bp):
GATAAACTACCACTAATAACACTGATGTG
Found at i:28511498 original size:18 final size:17
Alignment explanation
Indices: 28511471--28511504 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28511461 ACGAATAATT
28511471 AATAAATACAAATAAGC
1 AATAAATACAAATAAGC
*
28511488 AATACAATACACATAAG
1 AATA-AATACAAATAAG
28511505 AGCAATAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (17 bp):
AATAAATACAAATAAGC
Found at i:28512011 original size:20 final size:20
Alignment explanation
Indices: 28511986--28512023 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28511976 TCATATATGT
28511986 ATGTATGT-ATAATATAAATC
1 ATGTATGTAAT-ATATAAATC
28512006 ATGTATGTAATATATAAA
1 ATGTATGTAATATATAAA
28512024 ATAGTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATGTAATATATAAATC
Found at i:28512274 original size:3 final size:3
Alignment explanation
Indices: 28512266--28512314 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
28512256 ATAGAAAAAT
* * * *
28512266 ATA ATA ATA ATA CTA ACA ATA ATA ATA ATG ATA ATA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28512314 A
1 A
28512315 ATTAATATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:28517989 original size:21 final size:20
Alignment explanation
Indices: 28517944--28517989 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
28517934 TTGTTGGAAT
28517944 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
28517963 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
28517984 GGTTGA
1 GGTTGA
28517990 TTGCATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:28519407 original size:20 final size:20
Alignment explanation
Indices: 28519382--28519420 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
28519372 TACTTTCTTC
28519382 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
28519402 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
28519421 AAATGACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:28519845 original size:56 final size:50
Alignment explanation
Indices: 28519676--28519863 Score: 153
Period size: 50 Copynumber: 3.6 Consensus size: 50
28519666 CTGTACTACA
* * * * ** * ** *
28519676 AATGCCATATCCTAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAATACC
* * *
28519726 CATGCCATGTCCCAGACATGGTCTTA-TTGGGGACCTCTCATCTCGATACC
1 AATGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATCTCAATACC
* * *
28519776 AAAGCCATGTCCCAGACATGGTATTACATGGGACCTCTCATAACCTCAATAATGTC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT---CTCAAT-A--CC
*
28519832 AATGCCATGTCCCAGATATGGTCTTACATGGG
1 AATGCCATGTCCCAGACATGGTCTTACATGGG
28519864 GTCTCATTCC
Statistics
Matches: 110, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
49 1 0.01
50 72 0.65
51 1 0.01
53 5 0.05
54 1 0.01
56 30 0.27
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (50 bp):
AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAATACC
Found at i:28527383 original size:44 final size:44
Alignment explanation
Indices: 28527324--28527425 Score: 141
Period size: 44 Copynumber: 2.3 Consensus size: 44
28527314 AGAAGGGTAA
* ** *
28527324 TGCTCACACAAGCTGACAAAGGGTCATTAATTGATACACGATGC
1 TGCTCACACAAGCTGACAAAGGGACATTAATCAATACACGATAC
* * *
28527368 TGCTCACCCGAGCTGACAAAGGGACATTAATCAATACATGATAC
1 TGCTCACACAAGCTGACAAAGGGACATTAATCAATACACGATAC
28527412 TGCTCACACAAGCT
1 TGCTCACACAAGCT
28527426 TCAGAGAATC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (44 bp):
TGCTCACACAAGCTGACAAAGGGACATTAATCAATACACGATAC
Found at i:28527530 original size:29 final size:28
Alignment explanation
Indices: 28527489--28527554 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
28527479 ACCAATACAT
* *
28527489 AGTACCTTAAACTATAATCACCGGCACAG
1 AGTACCTGAAACTATAA-CACCGGCACAA
* * *
28527518 AGTACCTGGAACTGTAACACCGGTACAA
1 AGTACCTGAAACTATAACACCGGCACAA
*
28527546 AGTAACTGA
1 AGTACCTGA
28527555 TCTGTAATCA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (28 bp):
AGTACCTGAAACTATAACACCGGCACAA
Found at i:28527549 original size:28 final size:29
Alignment explanation
Indices: 28527484--28527554 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 29
28527474 CCATCACCAA
* *
28527484 TACATAGTACCTTAAACTATAATCACCGG
1 TACAAAGTACCTGAAACTATAATCACCGG
* * * *
28527513 CACAGAGTACCTGGAACTGTAA-CACCGG
1 TACAAAGTACCTGAAACTATAATCACCGG
*
28527541 TACAAAGTAACTGA
1 TACAAAGTACCTGA
28527555 TCTGTAATCA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
28 16 0.48
29 17 0.52
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (29 bp):
TACAAAGTACCTGAAACTATAATCACCGG
Found at i:28528512 original size:22 final size:22
Alignment explanation
Indices: 28528487--28528533 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
28528477 GTCTGACTTA
28528487 AAACATGTATTAATACTGTACG
1 AAACATGTATTAATACTGTACG
**
28528509 AAACATGTATTAATGTTGTACG
1 AAACATGTATTAATACTGTACG
28528531 AAA
1 AAA
28528534 TAGGACATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (22 bp):
AAACATGTATTAATACTGTACG
Found at i:28544586 original size:40 final size:40
Alignment explanation
Indices: 28544503--28544805 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
28544493 TTGAATGCTG
* * * * * *
28544503 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
28544543 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
28544583 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
28544623 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
28544663 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
28544703 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
28544743 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
28544782 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28544806 TGAACGAGGA
Statistics
Matches: 239, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
39 35 0.15
40 196 0.82
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:28550525 original size:16 final size:16
Alignment explanation
Indices: 28550504--28550559 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
28550494 TTTTCAATTC
28550504 TTTTTTTCCTTTCTTT
1 TTTTTTTCCTTTCTTT
**
28550520 TTTTTTTGATTT-TTT
1 TTTTTTTCCTTTCTTT
*
28550535 TTCTTTTT-CTTTCTCAT
1 TT-TTTTTCCTTTCT-TT
28550552 TTTTTTTC
1 TTTTTTTC
28550560 TCTTGATCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
15 8 0.25
16 21 0.66
17 3 0.09
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTTTTTCCTTTCTTT
Found at i:28550542 original size:22 final size:22
Alignment explanation
Indices: 28550513--28550560 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
28550503 CTTTTTTTCC
* *
28550513 TTTCTTTTT-TTTTTGATTTTT
1 TTTCTTTTTCTTTCTCATTTTT
28550534 TTTCTTTTTCTTTCTCATTTTT
1 TTTCTTTTTCTTTCTCATTTTT
28550556 TTTCT
1 TTTCT
28550561 CTTGATCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTCTTTTTCTTTCTCATTTTT
Found at i:28552687 original size:58 final size:60
Alignment explanation
Indices: 28552593--28552725 Score: 193
Period size: 58 Copynumber: 2.3 Consensus size: 60
28552583 CCAGAATTTA
* * *
28552593 AAATAAATA-ATATA-CTAGAAATTGAAATAACCAAAATAGATAATAGATAATTTGAAAG
1 AAATAAATATATATATATAGAAATTGAAATAACCAAAATAAAAAATAGATAATTTGAAAG
**
28552651 AAATAAATATATATATATAGAAA-T-AAATAAGTAAAATAAAAAATAGATAATTTGAAAG
1 AAATAAATATATATATATAGAAATTGAAATAACCAAAATAAAAAATAGATAATTTGAAAG
28552709 AAATAAATATATATATA
1 AAATAAATATATATATA
28552726 GAAAATTAAG
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
58 56 0.82
59 6 0.09
60 6 0.09
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (60 bp):
AAATAAATATATATATATAGAAATTGAAATAACCAAAATAAAAAATAGATAATTTGAAAG
Found at i:28554887 original size:50 final size:50
Alignment explanation
Indices: 28554833--28554972 Score: 163
Period size: 50 Copynumber: 2.8 Consensus size: 50
28554823 CACCGATGTG
* * *
28554833 GCTTTAATCTGTTCCACTGCACCGCCAGAGAAGTAAGATTCCCTGTTGTA
1 GCTTTAATCTATTCCACTGCAACGCCAGGGAAGTAAGATTCCCTGTTGTA
* ** * * * * *
28554883 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTGTG
1 GCTTTAATCTATTCCACTGCAACGCCAGGGAAGTAAGATTCCCTGTTGTA
* *
28554933 GCTTTAATCTATTCCACTGCATCGCCTGGGAAGTAAGATT
1 GCTTTAATCTATTCCACTGCAACGCCAGGGAAGTAAGATT
28554973 TGAAATTCTT
Statistics
Matches: 72, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (50 bp):
GCTTTAATCTATTCCACTGCAACGCCAGGGAAGTAAGATTCCCTGTTGTA
Found at i:28554915 original size:100 final size:99
Alignment explanation
Indices: 28554733--28554972 Score: 275
Period size: 100 Copynumber: 2.4 Consensus size: 99
28554723 TGCTATTGTA
* * * * * * * *
28554733 GCTTCAATTTGTTCCACTACACCACTAGGGAAGTGAGATTTGCCGTTGTGGCTTTAATCTTTTTA
1 GCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGA-TTCCCGTTGTAGCTTTAATCTTTTTA
* **
28554798 ACTGCAATGTTGAGGAAGCGGGATACACCGATGTG
65 ACTGCAATGTAGAGGAAGCAAGATACACCGATGTG
*
28554833 GCTTTAATCTGTTCCACTGCACCGCCAGAGAAGTAAGATTCCCTGTTGTAGCTTTAATCTTTTTA
1 GCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCCC-GTTGTAGCTTTAATCTTTTTA
* * * *
28554898 ACTGCAATGTCAG-GGAAGCAAGATTCGCTGTTGTG
65 ACTGCAATGT-AGAGGAAGCAAGATACACCGATGTG
* * *
28554933 GCTTTAATCTATTCCACTGCATCGCCTGGGAAGTAAGATT
1 GCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATT
28554973 TGAAATTCTT
Statistics
Matches: 118, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
99 4 0.03
100 113 0.96
101 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (99 bp):
GCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCCCGTTGTAGCTTTAATCTTTTTAA
CTGCAATGTAGAGGAAGCAAGATACACCGATGTG
Found at i:28555122 original size:44 final size:44
Alignment explanation
Indices: 28554995--28556022 Score: 500
Period size: 44 Copynumber: 23.5 Consensus size: 44
28554985 GTCTATTCCC
* * * * *
28554995 CTGTAATCTCAAGGAGATAAGA--CCTGA-TGCGATCTACTCTA
1 CTGTAATCTCAGGGAGATAAGATTCCTGACTTCAATCTGCTCCA
* * * * * * * *
28555036 CTGTAATTTCCGAGAGATAAG-TTCATTTATTTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTC-CTGACTTCAATCTGCTCCA
* * * *
28555080 CTGTAATCTCAGGGAAATAGGATTACTGACTTCAATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATTCCTGACTTCAATCTGCTCCA
* ** *
28555124 CTGTAATCTCAAGGAGATAAGATTTTTGGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTCCTGACTTCAATCTGCTCCA
* * * * ** ** *
28555168 CTATAACCTTAGGGAGATGAGATT--TGAAATTCTTCGGTCTATTCCC
1 CTGTAATCTCAGGGAGATAAGATTCCTG--A--CTTCAATCTGCTCCA
* * * * * * *
28555214 CTATAATCTCAAGGAGATAAGA--CCT-AATGCGATCTACTCTA
1 CTGTAATCTCAGGGAGATAAGATTCCTGACTTCAATCTGCTCCA
* * * * * * *
28555255 CTGTAATTTCAGAGAGATAA-AATCCTTTATTTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTCC-TGACTTCAATCTGCTCCA
* * * * * *
28555299 CTATAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGCTTCA
1 CTGTAATCTCAGGGAGATAAGATTCCTGACTTCAATCTGCTCCA
* * *
28555343 CTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTACTCCA
1 CTGTAATCTCAGGGAGATAAGATTCCTGACTTCAATCTGCTCCA
* * ** ** *
28555387 CTGTAACCTCAGGGAGATGAGATT--TGAAATTCTTCGGTCTATTCCC
1 CTGTAATCTCAGGGAGATAAGATTCCTG--A--CTTCAATCTGCTCCA
* * * *
28555433 CTGTAATCTCAGGGAGATAAGA--CCTGA-TGCGATCTACTCTA
1 CTGTAATCTCAGGGAGATAAGATTCCTGACTTCAATCTGCTCCA
* * * * * *
28555474 CTGTAATTTCAGAGAGATAAGA-TCCTTTATTTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTCC-TGACTTCAATCTGCTCCA
* * *
28555518 CTGTAATCTCAGGGAAATAAGATTACT-AGCTTCAATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATTCCTGA-CTTCAATCTGCTCCA
* *
28555562 CTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTCCTGACTTCAATCTGCTCCA
* * ** ** *
28555606 CTGTAACCTCAGGGAGATGAGATT--TGAAATTCTTCGGTCTATTCCC
1 CTGTAATCTCAGGGAGATAAGATTCCTG--A--CTTCAATCTGCTCCA
* * * *
28555652 CTGTAATCTCAGGGAGATAAGA--CCTGA-TGCGATCTACTCTA
1 CTGTAATCTCAGGGAGATAAGATTCCTGACTTCAATCTGCTCCA
* * * * *
28555693 CTGTAATTTCAGAGAGATAAGA-TCCTTTATTTTAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTCC-TGACTTCAATCTGCTCCA
* * * *
28555737 CTGTAATCTCAGGGAAATAAGATTACTCG-CTTCAATCTACTCCG
1 CTGTAATCTCAGGGAGATAAGATTCCT-GACTTCAATCTGCTCCA
** ** *
28555781 CTGTAATCTCAGGGAGATAAGATT--TGAAATTCTTCGTTCTATTCCC
1 CTGTAATCTCAGGGAGATAAGATTCCTG--A--CTTCAATCTGCTCCA
* * * * *
28555827 CTGTAATCTCAGAGAGATAAGA--CCTGA-TGCGATCTACTCTA
1 CTGTAATCTCAGGGAGATAAGATTCCTGACTTCAATCTGCTCCA
* * * * * * *
28555868 TTGTAATTTCAGAGAGATAAGA-TCCTTTATTTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTCC-TGACTTCAATCTGCTCCA
* * * * *
28555912 CTGTAATCTCAGGCAGATAAGATTCTTTG-TTTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTC-CTGACTTCAATCTGCTCCA
* * * * *
28555956 CTATAATCTCAGGGAGATAGGATTACT-AGCTTCAATCTACTCCG
1 CTGTAATCTCAGGGAGATAAGATTCCTGA-CTTCAATCTGCTCCA
*
28556000 CTGTAATCTCAGAGAGATAAGAT
1 CTGTAATCTCAGGGAGATAAGAT
28556023 CTAAAATTCT
Statistics
Matches: 746, Mismatches: 188, Indels: 103
0.72 0.18 0.10
Matches are distributed among these distances:
40 1 0.00
41 130 0.17
42 16 0.02
43 12 0.02
44 447 0.60
45 12 0.02
46 128 0.17
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
CTGTAATCTCAGGGAGATAAGATTCCTGACTTCAATCTGCTCCA
Found at i:28555349 original size:219 final size:219
Alignment explanation
Indices: 28554968--28555805 Score: 1469
Period size: 219 Copynumber: 3.8 Consensus size: 219
28554958 CTGGGAAGTA
28554968 AGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACT
1 AGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACT
* * *
28555033 CTACTGTAATTTCCGAGAGATAAGTTCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAAT
66 CTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAAT
* * * *
28555098 AGGATTACTGACTTCAATCTGCTCCGCTGTAATCTCAAGGAGATAAGATTTTTGGCTTCAATCTG
131 AAGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTG
* *
28555163 CTCCACTATAACCTTAGGGAGATG
196 CTCCACTGTAACCTCAGGGAGATG
* *
28555187 AGATTTGAAATTCTTCGGTCTATTCCCCTATAATCTCAAGGAGATAAGACCTAATGCGATCTACT
1 AGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACT
* *
28555252 CTACTGTAATTTCAGAGAGATAAAATCCTTTATTTTAATCCGCTCCACTATAATCTCAGGGAAAT
66 CTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAAT
* * * *
28555317 AGGATTACTGGCTTCAATCTGCTTCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTA
131 AAGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTG
28555382 CTCCACTGTAACCTCAGGGAGATG
196 CTCCACTGTAACCTCAGGGAGATG
*
28555406 AGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACT
1 AGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACT
28555471 CTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAAT
66 CTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAAT
*
28555536 AAGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTG
131 AAGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTG
28555601 CTCCACTGTAACCTCAGGGAGATG
196 CTCCACTGTAACCTCAGGGAGATG
*
28555625 AGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACT
1 AGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACT
*
28555690 CTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAAAT
66 CTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAAT
* *
28555755 AAGATTACTCGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTT
131 AAGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
28555806 GAAATTCTTC
Statistics
Matches: 591, Mismatches: 28, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
219 591 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (219 bp):
AGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACT
CTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAAT
AAGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTG
CTCCACTGTAACCTCAGGGAGATG
Found at i:28555698 original size:175 final size:174
Alignment explanation
Indices: 28555551--28556021 Score: 653
Period size: 175 Copynumber: 2.7 Consensus size: 174
28555541 TACTAGCTTC
* * *
28555551 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTCGCTTCAATCTGCTCCACTGTAATCTC
* *
28555616 AGGGAGATGAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATG
66 AGGGAGATAAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGAGAGATAAGACCTGATG
28555681 CGATCTACTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTT
131 CGATCTACTCTACTGTAATTTCAGAGAGATAAGAT-CTTTATTTT
* * * *
28555726 AATCTGCTCCACTGTAATCTCAGGGAAATAAGATTACTCGCTTCAATCTACTCCGCTGTAATCTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTCGCTTCAATCTGCTCCACTGTAATCTC
*
28555791 AGGGAGATAAGATTTGAAATTCTTCGTTCTATTCCCCTGTAATCTCAGAGAGATAAGACCTGATG
66 AGGGAGATAAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGAGAGATAAGACCTGATG
*
28555856 CGATCTACTCTATTGTAATTTCAGAGAGATAAGATCCTTTATTTT
131 CGATCTACTCTACTGTAATTTCAGAGAGATAAGAT-CTTTATTTT
* * * * * * *
28555901 AATCCGCTCCACTGTAATCTCAGGCAGATAAGA-TTCTTTGTTTTAATCCGCTCCACTATAATCT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTC-TCGCTTCAATCTGCTCCACTGTAATCT
* * * ** * *
28555965 CAGGGAGATAGGA-TT--ACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAGATAAGA
65 CAGGGAGATAAGATTTGAAAT-TCTTCGGTCTATTCCCCTGTAATCTCAGAGAGATAAGA
28556022 TCTAAAATTC
Statistics
Matches: 265, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
172 2 0.01
173 33 0.12
174 4 0.02
175 226 0.85
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (174 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTCGCTTCAATCTGCTCCACTGTAATCTC
AGGGAGATAAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGAGAGATAAGACCTGATG
CGATCTACTCTACTGTAATTTCAGAGAGATAAGATCTTTATTTT
Found at i:28555763 original size:438 final size:438
Alignment explanation
Indices: 28554966--28556022 Score: 1509
Period size: 438 Copynumber: 2.4 Consensus size: 438
28554956 GCCTGGGAAG
*
28554966 TAAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAAGGAGATAAGACCTGATGCGATCTA
1 TAAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
* * *
28555031 CTCTACTGTAATTTCCGAGAGATAAGTTCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAA
66 CTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAA
* *
28555096 ATAGGATTACT-GACTTCAATCTGCTCCGCTGTAATCTCAAGGAGATAAGATTTTTGGCTTCAAT
131 ATAGGATTACTAG-CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAAT
*
28555160 CTGCTCCACTATAACCTTAGGGAGATGAGATTTGAAATTCTTCGGTCTATTCCCCTATAATCTCA
195 CTGCTCCACTATAACCTCAGGGAGATGAGATTTGAAATTCTTCGGTCTATTCCCCTATAATCTCA
28555225 AGGAGATAAGACCTAATGCGATCTACTCTACTGTAATTTCAGAGAGATAAAATCCTTTATTTTAA
260 AGGAGATAAGACCTAATGCGATCTACTCTACTGTAATTTCAGAGAGATAAAATCCTTTATTTTAA
* * * *
28555290 TCCGCTCCACTATAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGCTTCACTGTAATCTCAG
325 TCCGCTCCACTATAATCTCAGGGAAATAAGATTACTCGCTTCAATCTACTCCACTGTAATCTCAG
* *
28555355 GGAGATAAGATTT-CTGGCTTCAATCTACTCCACTGTAACCTCAGGGAGA
390 GGAGATAAGATTTAAT-GCTTCAATCTACTCCACTGTAACCTCAGAGAGA
*
28555404 TGAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
1 TAAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
28555469 CTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAA
66 CTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAA
*
28555534 ATAAGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATC
131 ATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATC
* * *
28555599 TGCTCCACTGTAACCTCAGGGAGATGAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAG
196 TGCTCCACTATAACCTCAGGGAGATGAGATTTGAAATTCTTCGGTCTATTCCCCTATAATCTCAA
* *
28555664 GGAGATAAGACCTGATGCGATCTACTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAAT
261 GGAGATAAGACCTAATGCGATCTACTCTACTGTAATTTCAGAGAGATAAAATCCTTTATTTTAAT
* * *
28555729 CTGCTCCACTGTAATCTCAGGGAAATAAGATTACTCGCTTCAATCTACTCCGCTGTAATCTCAGG
326 CCGCTCCACTATAATCTCAGGGAAATAAGATTACTCGCTTCAATCTACTCCACTGTAATCTCAGG
* ** * * *
28555794 GAGATAAGATTTGAAATTCTTCGTTCTATTCCCCTGTAATCTCAGAGAGA
391 GAGATAAGATTT--AATGCTTCAATCTACTCCACTGTAACCTCAGAGAGA
** * * * *** * * * ***
28555844 TAAGACCTG--A---TGCGATCTACTCTATTGTAATTTCAGAGAGATAAGATCCTTTATTTTAAT
1 TAAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGA-CC-TGA-TGCGAT
** * * * * *
28555904 CCGCTCCACTGTAATCTCAG-GCAGATAAGATTCTTTGTTTTAATCCGCTCCACTATAATCTCAG
63 CTACTCTACTGTAATTTCAGAG-AGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAG
* * *
28555968 GGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAGATAAGAT
127 GGAAATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
28556023 CTAAAATTCT
Statistics
Matches: 556, Mismatches: 55, Indels: 16
0.89 0.09 0.03
Matches are distributed among these distances:
435 28 0.05
436 2 0.00
437 3 0.01
438 489 0.88
439 1 0.00
440 32 0.06
441 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (438 bp):
TAAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
CTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAA
ATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATC
TGCTCCACTATAACCTCAGGGAGATGAGATTTGAAATTCTTCGGTCTATTCCCCTATAATCTCAA
GGAGATAAGACCTAATGCGATCTACTCTACTGTAATTTCAGAGAGATAAAATCCTTTATTTTAAT
CCGCTCCACTATAATCTCAGGGAAATAAGATTACTCGCTTCAATCTACTCCACTGTAATCTCAGG
GAGATAAGATTTAATGCTTCAATCTACTCCACTGTAACCTCAGAGAGA
Found at i:28555807 original size:394 final size:394
Alignment explanation
Indices: 28555332--28556064 Score: 1180
Period size: 394 Copynumber: 1.9 Consensus size: 394
28555322 TACTGGCTTC
* * * *
28555332 AATCTGCTTCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTACTCCACTGTAACCTC
1 AATCTGCTCCACTGTAATCTCAGGGAAATAAGATTACTCGCTTCAATCTACTCCACTGTAACCTC
* *
28555397 AGGGAGATGAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATG
66 AGGGAGATAAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGAGAGATAAGACCTGATG
28555462 CGATCTACTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
131 CGATCTACTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
* * * * * *
28555527 CAGGGAAATAAGATTAC-TAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGG
196 CAGGCAAATAAGATT-CTTAGCTTCAATCCGCTCCACTATAATCTCAGGGAGATAAGATTACTAG
* * * * * *
28555591 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATGAGATTTGAAATTCTTCGGTCTATTCCCCTGT
260 CTTCAATCTACTCCACTGTAACCTCAGAGAGATAAGATCTAAAATTCTTCGGTCTATTCCACTGT
28555656 AATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAATTTCAGAGAGATAAGATCCTTT
325 AATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAATTTCAGAGAGATAAGATCCTTT
28555721 ATTTT
390 ATTTT
* *
28555726 AATCTGCTCCACTGTAATCTCAGGGAAATAAGATTACTCGCTTCAATCTACTCCGCTGTAATCTC
1 AATCTGCTCCACTGTAATCTCAGGGAAATAAGATTACTCGCTTCAATCTACTCCACTGTAACCTC
*
28555791 AGGGAGATAAGATTTGAAATTCTTCGTTCTATTCCCCTGTAATCTCAGAGAGATAAGACCTGATG
66 AGGGAGATAAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGAGAGATAAGACCTGATG
*
28555856 CGATCTACTCTATTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
131 CGATCTACTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
* * * * *
28555921 CAGGCAGATAAGATTCTTTGTTTTAATCCGCTCCACTATAATCTCAGGGAGATAGGATTACTAGC
196 CAGGCAAATAAGATTCTTAGCTTCAATCCGCTCCACTATAATCTCAGGGAGATAAGATTACTAGC
* * *
28555986 TTCAATCTACTCCGCTGTAATCTCAGAGAGATAAGATCTAAAATTCTTCGGTCTATTGCACTGTA
261 TTCAATCTACTCCACTGTAACCTCAGAGAGATAAGATCTAAAATTCTTCGGTCTATTCCACTGTA
28556051 ATCTCAGGGAGATA
326 ATCTCAGGGAGATA
28556065 GGATTATCGG
Statistics
Matches: 308, Mismatches: 30, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
393 1 0.00
394 307 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (394 bp):
AATCTGCTCCACTGTAATCTCAGGGAAATAAGATTACTCGCTTCAATCTACTCCACTGTAACCTC
AGGGAGATAAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGAGAGATAAGACCTGATG
CGATCTACTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
CAGGCAAATAAGATTCTTAGCTTCAATCCGCTCCACTATAATCTCAGGGAGATAAGATTACTAGC
TTCAATCTACTCCACTGTAACCTCAGAGAGATAAGATCTAAAATTCTTCGGTCTATTCCACTGTA
ATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAATTTCAGAGAGATAAGATCCTTTA
TTTT
Found at i:28555917 original size:219 final size:216
Alignment explanation
Indices: 28554966--28556022 Score: 1341
Period size: 219 Copynumber: 4.8 Consensus size: 216
28554956 GCCTGGGAAG
*
28554966 TAAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAAGGAGATAAGACCTGATGCGATCTA
1 TAAGATTTG-AA-T-TTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
* * * *
28555031 CTCTACTGTAATTTCCGAGAGATAAGTTCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAA
63 CTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATCTCAGGGAA
* * * *
28555096 ATAGGATTACT-GACTTCAATCTGCTCCGCTGTAATCTCAAGGAGATAAGATTTTTGGCTTCAAT
128 ATAAGATTACTAG-CTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTATGGCTTCAAT
* * *
28555160 CTGCTCCACTATAACCTTAGGGAGA
192 CTACTCCACTGTAACCTCAGGGAGA
* * * *
28555185 TGAGATTTGAAATTCTTCGGTCTATTCCCCTATAATCTCAAGGAGATAAGACCTAATGCGATCTA
1 TAAGATTTG-AA-T-TTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
*
28555250 CTCTACTGTAATTTCAGAGAGATAAAATCCTTTATTTTAATCCGCTCCACTATAATCTCAGGGAA
63 CTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATCTCAGGGAA
* * * * * *
28555315 ATAGGATTACTGGCTTCAATCTGCTTCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATC
128 ATAAGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTATGGCTTCAATC
28555380 TACTCCACTGTAACCTCAGGGAGA
193 TACTCCACTGTAACCTCAGGGAGA
*
28555404 TGAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
1 TAAGATTTG-AA-T-TTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
*
28555469 CTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAA
63 CTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATCTCAGGGAA
* *
28555534 ATAAGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATC
128 ATAAGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTATGGCTTCAATC
*
28555599 TGCTCCACTGTAACCTCAGGGAGA
193 TACTCCACTGTAACCTCAGGGAGA
*
28555623 TGAGATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
1 TAAGATTTG-AA-T-TTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTA
* *
28555688 CTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAA
63 CTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATCTCAGGGAA
* * *
28555753 ATAAGATTACTCGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTGAAAT-TCTTCG
128 ATAAGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTT---ATGGCTTCA
* * * * *
28555817 TTCTATTCCCCTGTAATCTCAGAGAGA
190 ATCTACTCCACTGTAACCTCAGGGAGA
** * * * *** * * * *** **
28555844 TAAGACCTG-A-TGCGATCTACTCTATTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 TAAGATTTGAATTTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGA-CC-TGA-TGCGATCTA
* * * *
28555907 CTCCACTGTAATCTCAG-GCAGATAAGATTCTTTGTTTTAATCCGCTCCACTATAATCTCAGGGA
63 CTCTACTGTAATTTCAGAG-AGATAAGATCCTTTATTTTAATCCGCTCCACTATAATCTCAGGGA
* * *
28555971 GATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAGATAAGAT
127 AATAAGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGAT
28556023 CTAAAATTCT
Statistics
Matches: 766, Mismatches: 64, Indels: 16
0.91 0.08 0.02
Matches are distributed among these distances:
216 28 0.04
217 2 0.00
218 3 0.00
219 700 0.91
220 1 0.00
221 31 0.04
222 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (216 bp):
TAAGATTTGAATTTCGGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTC
TACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATCTCAGGGAAATA
AGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTATGGCTTCAATCTAC
TCCACTGTAACCTCAGGGAGA
Found at i:28556318 original size:129 final size:129
Alignment explanation
Indices: 28556086--28556329 Score: 427
Period size: 129 Copynumber: 1.9 Consensus size: 129
28556076 TTCAATCTAC
28556086 TTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAG
1 TTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAG
*
28556151 ATCTGTAATTTCCCAACCTATTCCACTGCTGACTAGGGATATAGGACTTGTGGCTTAAAATTGT
66 ATCTGTAATTTCCCAACCTATTCCACTGCTGACTAGGGAGATAGGACTTGTGGCTTAAAATTGT
**
28556215 TTCCTTACACTTGAAGATAAGATTCGTTGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAG
1 TTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAG
* *
28556280 ATCTGTAATTTCCCAACCTATTCCACTGCTG-GTCAGGGAGCTAGGACTTG
66 ATCTGTAATTTCCCAACCTATTCCACTGCTGACT-AGGGAGATAGGACTTG
28556330 CAATCTTAAA
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
128 1 0.01
129 108 0.99
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (129 bp):
TTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAG
ATCTGTAATTTCCCAACCTATTCCACTGCTGACTAGGGAGATAGGACTTGTGGCTTAAAATTGT
Found at i:28562174 original size:54 final size:58
Alignment explanation
Indices: 28562025--28562157 Score: 180
Period size: 58 Copynumber: 2.3 Consensus size: 58
28562015 CCAGAATTTA
* ** * *
28562025 AAATAAATA-ATATA-CTAGAAATTGAAATAACCAAAATAGATAATAGATAATTTGAAAG
1 AAATAAATATATATATATAGAAA-T-AAATAAGTAAAATAAAAAATAGATAATTTGAAAG
*
28562083 AAATAAATATATATATATAGAAATAAATACGTAAAATAAAAAATAGATAATTTGAAAG
1 AAATAAATATATATATATAGAAATAAATAAGTAAAATAAAAAATAGATAATTTGAAAG
28562141 AAATAAATATATATATA
1 AAATAAATATATATATA
28562158 GAAAATTAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
58 55 0.82
59 6 0.09
60 6 0.09
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (58 bp):
AAATAAATATATATATATAGAAATAAATAAGTAAAATAAAAAATAGATAATTTGAAAG
Found at i:28569224 original size:50 final size:50
Alignment explanation
Indices: 28569122--28569314 Score: 208
Period size: 50 Copynumber: 3.7 Consensus size: 50
28569112 GGGAATGAGA
* *
28569122 TCCCATGTAAGACCATGTCTGGAACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
* * *
28569178 TCCCATGTAAAACCATGTTTGGGACATGGCATTGGCACCGAGATGAGAGT
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * *
28569228 TCCCATGTAAGACCATGTCTGGGACATGGTGTTGGAAACGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * *
28569278 TCTCC-CGTAAGACCATATCTGGGATATGGCATTGGCA
1 TC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28569315 GTACAGAAAA
Statistics
Matches: 118, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
50 78 0.66
51 2 0.02
53 3 0.03
55 1 0.01
56 34 0.29
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:28569580 original size:12 final size:12
Alignment explanation
Indices: 28569563--28569601 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28569553 ATGAGTTATT
28569563 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
28569575 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
28569587 TAAGTGAGTAAG
1 TAAGTAAGCAAG
28569599 TAA
1 TAA
28569602 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:28576410 original size:55 final size:52
Alignment explanation
Indices: 28576314--28576561 Score: 197
Period size: 50 Copynumber: 4.8 Consensus size: 52
28576304 CATTAAGGGA
* ** * *
28576314 ATGAGA-TCCCATGTAAGACCATGTCTGGGACATAGATTTGGCATCATTGAGATT
1 ATGAGAGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCA---AGATG
*
28576368 ATGAGAGTCCCGTGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 ATGAGAGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
* * *
28576420 AT-AG-GTCCCATGTAGGACCATTTCTGGGACATGGCGTTGGCACCGAGATG
1 ATGAGAGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
** * ** ** * * *
28576470 A-GAG-GTCCCCCGTAGGACCATGTCTAAGACATCACATGGGCATC--GAT-
1 ATGAGAGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
* * * *
28576517 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 ATGAG-AGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
28576562 GTACCGAAAA
Statistics
Matches: 158, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
47 1 0.01
48 6 0.04
50 102 0.65
51 2 0.01
52 6 0.04
54 6 0.04
55 35 0.22
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (52 bp):
ATGAGAGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
Found at i:28577002 original size:107 final size:107
Alignment explanation
Indices: 28576863--28577079 Score: 407
Period size: 107 Copynumber: 2.0 Consensus size: 107
28576853 GCGAGTAAAG
* *
28576863 ATTCTAATGTTTGATGAACTTTATGAGTATGATTATTTATGATAAATGTTGTTATTTATTTACTT
1 ATTCTAATGTTTGATGAAATCTATGAGTATGATTATTTATGATAAATGTTGTTATTTATTTACTT
28576928 GTAAATATACTAAGCTTTATGCTTACTTTCTTTATCTTCCTT
66 GTAAATATACTAAGCTTTATGCTTACTTTCTTTATCTTCCTT
28576970 ATTCTAATGTTTGATGAAATCTATGAGTATGATTATTTATGATAAATGTTGTTATTTATTTACTT
1 ATTCTAATGTTTGATGAAATCTATGAGTATGATTATTTATGATAAATGTTGTTATTTATTTACTT
*
28577035 GTAAATATACTAAGCTTTATGCTTACTTTCTTTATCTTTCTT
66 GTAAATATACTAAGCTTTATGCTTACTTTCTTTATCTTCCTT
28577077 ATT
1 ATT
28577080 TTTATAGTAT
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.28, C:0.10, G:0.11, T:0.52
Consensus pattern (107 bp):
ATTCTAATGTTTGATGAAATCTATGAGTATGATTATTTATGATAAATGTTGTTATTTATTTACTT
GTAAATATACTAAGCTTTATGCTTACTTTCTTTATCTTCCTT
Found at i:28581986 original size:102 final size:101
Alignment explanation
Indices: 28581802--28581986 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
28581792 AAAGTGATGG
* * *
28581802 TCACTTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGGATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGGATAATAGGTCACATGTGTAGTAC
28581867 TATGTGCAGGCTACTATGCGTATCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTATCGGATAGCTTCGA
* * *
28581903 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATC-GGATAATGATGGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGGATAAT-A-GGTCACATGTGTAGT
28581967 ACTATGTGCAGGCTACTATG
64 ACTATGTGCAGGCTACTATG
28581987 TGAACCAGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 6 0.08
101 36 0.47
102 34 0.45
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGGATAATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTATCGGATAGCTTCGA
Found at i:28581987 original size:51 final size:50
Alignment explanation
Indices: 28581796--28581988 Score: 239
Period size: 51 Copynumber: 3.8 Consensus size: 50
28581786 AAAGTGAAAG
* * * *
28581796 TGATGGTCACTTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGG--A
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTATC-GGATA
* *
28581845 TGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATA
1 TGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATA
* * *
28581896 -GCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATAA
1 TG-AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGAT-A
28581948 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
28581989 AACCAGTATC
Statistics
Matches: 123, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
49 6 0.05
50 36 0.29
51 78 0.63
52 2 0.02
53 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (50 bp):
TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATA
Found at i:28582233 original size:16 final size:16
Alignment explanation
Indices: 28582212--28582243 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28582202 TGATTGAAAG
*
28582212 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
28582228 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
28582244 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:28585805 original size:34 final size:34
Alignment explanation
Indices: 28585762--28585864 Score: 197
Period size: 34 Copynumber: 3.0 Consensus size: 34
28585752 GTTGGTTGGG
*
28585762 CAAAAAAGTATTTGCTAGTAAAAATAGAGTTATA
1 CAAAAAAGTATTTGCTAGTAAAAGTAGAGTTATA
28585796 CAAAAAAGTATTTGCTAGTAAAAGTAGAGTTATA
1 CAAAAAAGTATTTGCTAGTAAAAGTAGAGTTATA
28585830 CAAAAAAGTATTTGCTAGTAAAAGTAGAGTTATA
1 CAAAAAAGTATTTGCTAGTAAAAGTAGAGTTATA
28585864 C
1 C
28585865 TTAAATTAGA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.29
Consensus pattern (34 bp):
CAAAAAAGTATTTGCTAGTAAAAGTAGAGTTATA
Found at i:28585818 original size:18 final size:18
Alignment explanation
Indices: 28585763--28585852 Score: 57
Period size: 18 Copynumber: 5.2 Consensus size: 18
28585753 TTGGTTGGGC
28585763 AAAAAAGTATTTGCTAGT
1 AAAAAAGTATTTGCTAGT
* * *
28585781 AAAAATAG-AGTT-ATA-C
1 AAAAA-AGTATTTGCTAGT
28585797 AAAAAAGTATTTGCTAGT
1 AAAAAAGTATTTGCTAGT
* * * *
28585815 AAAAGTAG-AGTT-ATA-C
1 AAAA-AAGTATTTGCTAGT
28585831 AAAAAAGTATTTGCTAGT
1 AAAAAAGTATTTGCTAGT
28585849 AAAA
1 AAAA
28585853 GTAGAGTTAT
Statistics
Matches: 50, Mismatches: 14, Indels: 16
0.62 0.17 0.20
Matches are distributed among these distances:
15 4 0.08
16 15 0.30
17 8 0.16
18 19 0.38
19 4 0.08
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.29
Consensus pattern (18 bp):
AAAAAAGTATTTGCTAGT
Found at i:28587216 original size:57 final size:59
Alignment explanation
Indices: 28587064--28587243 Score: 197
Period size: 57 Copynumber: 3.0 Consensus size: 59
28587054 TTGTTTTTTA
*
28587064 AAAATTTTTGCACAAAGTTGATCATCTTTTCCCATGCAAAACTGTCCACTTTAATGCATGT
1 AAAATTATTGCACAAAGTTGATCATCTTTTCCCATGCAAAACTGT-C-CTTTAATGCATGT
** ** * ** *
28587125 AACTCTTATT-TTCAAA-TTGATCATCTTTTACCATGCAAAACTGTCC-TT-ATTTATTT
1 AA-AATTATTGCACAAAGTTGATCATCTTTTCCCATGCAAAACTGTCCTTTAATGCATGT
*
28587181 AAAATTATTGCACAAAGTTGATCATCTTTTCCCATGCAAAACTGTCCACTCTAATGCATGT
1 AAAATTATTGCACAAAGTTGATCATCTTTTCCCATGCAAAACTGT-C-CTTTAATGCATGT
28587242 AA
1 AA
28587244 CTCTTATTTT
Statistics
Matches: 94, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
55 5 0.05
56 11 0.12
57 29 0.31
58 2 0.02
59 2 0.02
60 28 0.30
61 13 0.14
62 4 0.04
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (59 bp):
AAAATTATTGCACAAAGTTGATCATCTTTTCCCATGCAAAACTGTCCTTTAATGCATGT
Found at i:28610817 original size:28 final size:28
Alignment explanation
Indices: 28610785--28610842 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
28610775 AATTGGTCAC
*
28610785 ACAACCGTTATATGACAACAGGAGACTA
1 ACAACCATTATATGACAACAGGAGACTA
*
28610813 ACAACCATTATATGGCAACAGGAGACTA
1 ACAACCATTATATGACAACAGGAGACTA
28610841 AC
1 AC
28610843 CGTGCATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.17
Consensus pattern (28 bp):
ACAACCATTATATGACAACAGGAGACTA
Found at i:28623450 original size:13 final size:14
Alignment explanation
Indices: 28623428--28623456 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28623418 AACTAAAACA
28623428 AAAACAAAAAAAGT
1 AAAACAAAAAAAGT
28623442 AAAAC-AAAAAAGT
1 AAAACAAAAAAAGT
28623455 AA
1 AA
28623457 TAATTTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (14 bp):
AAAACAAAAAAAGT
Found at i:28628993 original size:22 final size:22
Alignment explanation
Indices: 28628967--28629010 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28628957 TTCTATGTTA
28628967 TTTTAAGGATTGAGTATTGGAT
1 TTTTAAGGATTGAGTATTGGAT
28628989 TTTTAAGGATTGAGTATTGGAT
1 TTTTAAGGATTGAGTATTGGAT
28629011 ATTTCTATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (22 bp):
TTTTAAGGATTGAGTATTGGAT
Found at i:28631505 original size:4 final size:4
Alignment explanation
Indices: 28631498--28631526 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
28631488 TATATATCAT
28631498 AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
28631527 GATGGATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:28639069 original size:29 final size:29
Alignment explanation
Indices: 28639037--28639125 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 29
28639027 GTTGTACTTA
28639037 AAATTTTAAATATTAAAAGTATAAAGACT
1 AAATTTTAAATATTAAAAGTATAAAGACT
* * * * *
28639066 AAATTCTTAAA-AATAAAAATTTAAAAATT
1 AAATT-TTAAATATTAAAAGTATAAAGACT
* * *
28639095 AAATTTAAAATGTATAAAATGTATAGAGACT
1 AAATTTTAAATAT-TAAAA-GTATAAAGACT
28639126 CAAAGCATAT
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
28 4 0.09
29 23 0.53
30 10 0.23
31 6 0.14
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (29 bp):
AAATTTTAAATATTAAAAGTATAAAGACT
Found at i:28639098 original size:13 final size:14
Alignment explanation
Indices: 28639072--28639104 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28639062 GACTAAATTC
28639072 TTAAAAATAAAAAT
1 TTAAAAATAAAAAT
*
28639086 TTAAAAAT-TAAAT
1 TTAAAAATAAAAAT
28639099 TTAAAA
1 TTAAAA
28639105 TGTATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAAATAAAAAT
Found at i:28640153 original size:42 final size:42
Alignment explanation
Indices: 28640107--28640190 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
28640097 AGTGTAGGGA
28640107 AATTTAGTGAGATATACAATTTATATTTAATTTGTGTAATTT
1 AATTTAGTGAGATATACAATTTATATTTAATTTGTGTAATTT
28640149 AATTTAGTGAGATATACAATTTATATTTAATTTGTGTAATTT
1 AATTTAGTGAGATATACAATTTATATTTAATTTGTGTAATTT
28640191 TTCCCTTGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (42 bp):
AATTTAGTGAGATATACAATTTATATTTAATTTGTGTAATTT
Found at i:28641215 original size:19 final size:19
Alignment explanation
Indices: 28641186--28641237 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
28641176 TTGAATCGAT
28641186 TTTATAATTTTTAA-TATA
1 TTTATAATTTTTAATTATA
* *
28641204 TTTCTAATTTTTAATTATT
1 TTTATAATTTTTAATTATA
28641223 TTTATAATTTTTAAT
1 TTTATAATTTTTAAT
28641238 GAATTTTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 13 0.43
19 17 0.57
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATAATTTTTAATTATA
Found at i:28641225 original size:10 final size:10
Alignment explanation
Indices: 28641185--28641245 Score: 58
Period size: 9 Copynumber: 6.4 Consensus size: 10
28641175 GTTGAATCGA
28641185 TTTT-ATAAT
1 TTTTAATAAT
28641194 TTTTAAT-AT
1 TTTTAATAAT
* *
28641203 ATTT-CTAAT
1 TTTTAATAAT
*
28641212 TTTTAATTAT
1 TTTTAATAAT
28641222 TTTT-ATAAT
1 TTTTAATAAT
28641231 TTTTAATGAAT
1 TTTTAAT-AAT
28641242 TTTT
1 TTTT
28641246 CAATTATTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
8 1 0.02
9 22 0.54
10 11 0.27
11 7 0.17
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:28641244 original size:19 final size:18
Alignment explanation
Indices: 28641184--28641244 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
28641174 AGTTGAATCG
28641184 ATTTTATAATTTTTAAT-
1 ATTTTATAATTTTTAATA
*
28641201 ATATTTCTAATTTTTAATTA
1 AT-TTTATAATTTTTAA-TA
*
28641221 TTTTTATAATTTTTAATGA
1 ATTTTATAATTTTTAAT-A
28641240 ATTTT
1 ATTTT
28641245 TCAATTATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 2 0.06
18 14 0.39
19 19 0.53
20 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
ATTTTATAATTTTTAATA
Found at i:28642298 original size:82 final size:83
Alignment explanation
Indices: 28642162--28642328 Score: 327
Period size: 82 Copynumber: 2.0 Consensus size: 83
28642152 CGAAGTTCTT
28642162 AAGCATCAAACATTGCCTTTAAAAAAATCAGGATAACAAAATATCACATCCAGTAAGTTAGGATG
1 AAGCATCAAACATTGCCTTTAAAAAAATCAGGATAACAAAATATCACATCCAGTAAGTTAGGATG
28642227 CGACATTTTGAAATTATA
66 CGACATTTTGAAATTATA
28642245 AAGCATCAAACATTGCC-TTAAAAAAATCAGGATAACAAAATATCACATCCAGTAAGTTAGGATG
1 AAGCATCAAACATTGCCTTTAAAAAAATCAGGATAACAAAATATCACATCCAGTAAGTTAGGATG
28642309 CGACATTTTGAAATTATA
66 CGACATTTTGAAATTATA
28642327 AA
1 AA
28642329 TGTTTAGTTT
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 67 0.80
83 17 0.20
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.26
Consensus pattern (83 bp):
AAGCATCAAACATTGCCTTTAAAAAAATCAGGATAACAAAATATCACATCCAGTAAGTTAGGATG
CGACATTTTGAAATTATA
Found at i:28642719 original size:10 final size:10
Alignment explanation
Indices: 28642694--28642728 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
28642684 AATACAAATA
*
28642694 AAATAATAAT
1 AAATAACAAT
28642704 -AATAACAAT
1 AAATAACAAT
28642713 AAATAACAAT
1 AAATAACAAT
28642723 AAATAA
1 AAATAA
28642729 TATGAACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (10 bp):
AAATAACAAT
Found at i:28648276 original size:24 final size:24
Alignment explanation
Indices: 28648203--28648282 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
28648193 TTAGGAAAAC
* *
28648203 TTTATTTCTA-TTAATTTATCCATT
1 TTTATTT-TATTTAATTTTTACATT
* *
28648227 TTTATTTTATTTCATTTTTA-TTT
1 TTTATTTTATTTAATTTTTACATT
*
28648250 TTTTTTTTAATTTAATTTTTACATT
1 TTTATTTT-ATTTAATTTTTACATT
*
28648275 TTAATTTT
1 TTTATTTT
28648283 TCTTTTGTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
23 11 0.25
24 25 0.57
25 8 0.18
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTATTTTATTTAATTTTTACATT
Found at i:28654692 original size:3 final size:3
Alignment explanation
Indices: 28654684--28654734 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
28654674 GCCCCTCCCC
*
28654684 TAT TAT TAT T-T TAT T-T TATT TAT TATT TAT TATT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT TA-T TAT TAT TAT TAT
28654730 TAT TA
1 TAT TA
28654735 CTGTTATTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 4 0.10
3 28 0.68
4 9 0.22
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:28654711 original size:7 final size:7
Alignment explanation
Indices: 28654699--28654734 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
28654689 TTATTTTATT
28654699 TTATTTA
1 TTATTTA
28654706 TTATTTA
1 TTATTTA
28654713 TTATTTA
1 TTATTTA
28654720 TTATTT-
1 TTATTTA
28654726 TTA-TTA
1 TTATTTA
28654732 TTA
1 TTA
28654735 CTGTTATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 2 0.07
6 6 0.21
7 20 0.71
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATTTA
Found at i:28654719 original size:23 final size:24
Alignment explanation
Indices: 28654686--28654733 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
28654676 CCCTCCCCTA
28654686 TTATTATTTTATT-TTATTTATTAT
1 TTATTATTTTATTATT-TTTATTAT
28654710 TTATTA-TTTATTATTTTTATTAT
1 TTATTATTTTATTATTTTTATTAT
28654733 T
1 T
28654734 ACTGTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (24 bp):
TTATTATTTTATTATTTTTATTAT
Found at i:28657567 original size:3 final size:3
Alignment explanation
Indices: 28657495--28657548 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
28657485 AACTAGTTTG
*
28657495 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28657543 TTA TTA
1 TTA TTA
28657549 GGTTTCATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:28659071 original size:6 final size:6
Alignment explanation
Indices: 28659060--28659107 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
28659050 TTCTTTTCAG
*
28659060 TTTTAT TTTTAT TTTTA- TTTTGT TTTTAGTT GTTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA--T -TTTTAT TTTTAT TTTT
28659108 TAGACTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
5 4 0.11
6 25 0.69
7 1 0.03
8 1 0.03
9 5 0.14
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:28659086 original size:12 final size:12
Alignment explanation
Indices: 28659060--28659107 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 12
28659050 TTCTTTTCAG
28659060 TTTTATTTTTAT
1 TTTTATTTTTAT
*
28659072 TTTTA-TTTTGT
1 TTTTATTTTTAT
28659083 TTTTAGTTGTTTTAT
1 TTTTA--T-TTTTAT
28659098 TTTTATTTTT
1 TTTTATTTTT
28659108 TAGACTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
11 10 0.33
12 9 0.30
13 1 0.03
15 10 0.33
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:28666736 original size:5 final size:5
Alignment explanation
Indices: 28666726--28666754 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28666716 AAACAAAATA
28666726 ATTAG ATTAG ATTAG ATTAG ATTAG ATTA
1 ATTAG ATTAG ATTAG ATTAG ATTAG ATTA
28666755 TAAATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (5 bp):
ATTAG
Found at i:28669157 original size:14 final size:14
Alignment explanation
Indices: 28669138--28669190 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
28669128 ACATGTATAC
*
28669138 AAAAATAACAAAAT
1 AAAAATAAAAAAAT
28669152 AAAAATAAAAAAAAT
1 AAAAAT-AAAAAAAT
* * *
28669167 AAAATTTATAAAAT
1 AAAAATAAAAAAAT
28669181 AAAAATAAAA
1 AAAAATAAAA
28669191 TTATAAACAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:28669165 original size:23 final size:23
Alignment explanation
Indices: 28669138--28669185 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28669128 ACATGTATAC
28669138 AAAAATAACAAAATA-AAAATAAA
1 AAAAATAA-AAAATATAAAATAAA
**
28669161 AAAAATAAAATTTATAAAATAAA
1 AAAAATAAAAAATATAAAATAAA
28669184 AA
1 AA
28669186 TAAAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (23 bp):
AAAAATAAAAAATATAAAATAAA
Found at i:28669186 original size:20 final size:20
Alignment explanation
Indices: 28669161--28669202 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
28669151 TAAAAATAAA
28669161 AAAAATAAAATTTATAAA-AT
1 AAAAATAAAA-TTATAAACAT
28669181 AAAAATAAAATTATAAACAT
1 AAAAATAAAATTATAAACAT
28669201 AA
1 AA
28669203 TATACTAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATAAAATTATAAACAT
Found at i:28669533 original size:11 final size:11
Alignment explanation
Indices: 28669502--28669545 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
28669492 GCGGTAAGTA
*
28669502 TAATAATAAAAA
1 TAATAAT-AAAC
28669514 TATATAATAAAC
1 TA-ATAATAAAC
28669526 TAATAATAAAC
1 TAATAATAAAC
28669537 TAATAATAA
1 TAATAATAA
28669546 TTCAGTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 18 0.60
12 7 0.23
13 5 0.17
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (11 bp):
TAATAATAAAC
Found at i:28671470 original size:24 final size:24
Alignment explanation
Indices: 28671442--28671493 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
28671432 TTTCTAGAAG
* *
28671442 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
28671466 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
28671490 ATTT
1 ATTT
28671494 GACCTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:28679130 original size:31 final size:31
Alignment explanation
Indices: 28679087--28679148 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
28679077 GGGTAACACA
28679087 CTTACGACAAGGTCGTTGGACAAGCACTGAT
1 CTTACGACAAGGTCGTTGGACAAGCACTGAT
* *
28679118 CTTATGACAAGGTCGTTGGACAATCACTGAT
1 CTTACGACAAGGTCGTTGGACAAGCACTGAT
28679149 TAAGTTACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (31 bp):
CTTACGACAAGGTCGTTGGACAAGCACTGAT
Found at i:28682618 original size:27 final size:27
Alignment explanation
Indices: 28682580--28682636 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
28682570 CAATTGTTTA
* *
28682580 TACACAAACTCGCCAGACCTTTTGGTG
1 TACACAAACTCGCCAAACCTATTGGTG
*
28682607 TACACGAACTCGCCAAACCTATTGGTG
1 TACACAAACTCGCCAAACCTATTGGTG
28682634 TAC
1 TAC
28682637 GCTAGCTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (27 bp):
TACACAAACTCGCCAAACCTATTGGTG
Found at i:28693259 original size:46 final size:46
Alignment explanation
Indices: 28693203--28693296 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
28693193 AAGTAACAAA
* *
28693203 AAGAAAATCAACATTCTAGAGAAGTATATATACCACACTCTTAAAC
1 AAGAAAATCAACATTCTAGAGAAGTATATACAACACACTCTTAAAC
* *
28693249 AAGAAAATCAACATTCTAGAGCAGTATATACAATACACTCTTAAAC
1 AAGAAAATCAACATTCTAGAGAAGTATATACAACACACTCTTAAAC
28693295 AA
1 AA
28693297 CAGTAACCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.49, C:0.19, G:0.09, T:0.23
Consensus pattern (46 bp):
AAGAAAATCAACATTCTAGAGAAGTATATACAACACACTCTTAAAC
Found at i:28693638 original size:3 final size:3
Alignment explanation
Indices: 28693610--28693653 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
28693600 TTCAAATCCC
* * * *
28693610 TCT TCT TGT TCT TGT TCT TGT TCT TCT TCA TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
28693654 GACTATTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.02, C:0.27, G:0.07, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:28698920 original size:50 final size:50
Alignment explanation
Indices: 28698843--28699088 Score: 305
Period size: 50 Copynumber: 4.9 Consensus size: 50
28698833 TCCTGTACTA
* * * ** * *
28698843 CCAATGCCATATCCCAGATATGATCTTACATGGGAGTTCTCATATCGATG
1 CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * ** * ** *
28698893 CCCATGCCATGCCCCAAACATGGTCTTACGGGGGACCTCTCATCTTGGTG
1 CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* *
28698943 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTG
1 CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* *
28698993 CAAACGCCATATCCCAGACATGGTCCTACATGGGACCTCTCATCTCGGTG
1 CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
28699043 CCAATGCCATATCCCAGACAT-GTCTTACATGGGACCTCTCATCTCG
1 CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
28699089 TGTTGACATG
Statistics
Matches: 170, Mismatches: 26, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 24 0.14
50 146 0.86
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.26
Consensus pattern (50 bp):
CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
Found at i:28699170 original size:44 final size:44
Alignment explanation
Indices: 28699106--28699201 Score: 165
Period size: 44 Copynumber: 2.2 Consensus size: 44
28699096 ATGGATCAAC
*
28699106 CATGGTACTTTTCCGTCAATTCTTTATTAATTGCCATGTTATAAA
1 CATGG-ACTTTTCCGTCAATTCTTCATTAATTGCCATGTTATAAA
*
28699151 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
1 CATGGACTTTTCCGTCAATTCTTCATTAATTGCCATGTTATAAA
28699195 CATGGAC
1 CATGGAC
28699202 CTTGAGATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 44 0.90
45 5 0.10
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (44 bp):
CATGGACTTTTCCGTCAATTCTTCATTAATTGCCATGTTATAAA
Found at i:28707799 original size:41 final size:42
Alignment explanation
Indices: 28707754--28707835 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 42
28707744 TATCACAAAA
* * *
28707754 CTCACAAAAGCCCATGCTCTC-GAGGAGCACGCAGAGTGAGG
1 CTCACAAAAGCCCATGCTCTCAAAGGAACACGCAAAGTGAGG
* *
28707795 CTCACAAAAGCTCATGTTCTCAAAGGAACACGCAAAGTGAG
1 CTCACAAAAGCCCATGCTCTCAAAGGAACACGCAAAGTGAG
28707836 ACTTAACATG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 19 0.54
42 16 0.46
ACGTcount: A:0.34, C:0.27, G:0.24, T:0.15
Consensus pattern (42 bp):
CTCACAAAAGCCCATGCTCTCAAAGGAACACGCAAAGTGAGG
Found at i:28708712 original size:25 final size:25
Alignment explanation
Indices: 28708684--28708731 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
28708674 TTGACCAGCG
* *
28708684 AACCCTGTTCGCACCTTGACTGGCA
1 AACCCAGTTCGCAACTTGACTGGCA
* *
28708709 AACCCAGTTGGCAACTTGCCTGG
1 AACCCAGTTCGCAACTTGACTGG
28708732 TGAACACAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.23
Consensus pattern (25 bp):
AACCCAGTTCGCAACTTGACTGGCA
Found at i:28721137 original size:7 final size:7
Alignment explanation
Indices: 28721127--28721152 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28721117 TTGGGGTAGA
28721127 TGGGAGG
1 TGGGAGG
28721134 TGGGAGG
1 TGGGAGG
28721141 TGGGAGG
1 TGGGAGG
28721148 TGGGA
1 TGGGA
28721153 TGGGAAGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.69, T:0.15
Consensus pattern (7 bp):
TGGGAGG
Found at i:28721192 original size:30 final size:31
Alignment explanation
Indices: 28721153--28721212 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
28721143 GGAGGTGGGA
* *
28721153 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
* *
28721184 TGGG-AGGGAGTAAAAATTTTTGGGAAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAA
28721213 TAAAAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.37, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:28729027 original size:14 final size:15
Alignment explanation
Indices: 28729001--28729043 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
28728991 ATTATCTTAA
28729001 ATTATGAATATGTGT
1 ATTATGAATATGTGT
28729016 ATTATG-ATATGTGT
1 ATTATGAATATGTGT
*
28729030 TTATATGAA-ATGTG
1 AT-TATGAATATGTG
28729044 ACCATTATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 9 0.36
15 15 0.60
16 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.47
Consensus pattern (15 bp):
ATTATGAATATGTGT
Found at i:28729122 original size:39 final size:39
Alignment explanation
Indices: 28729079--28729216 Score: 224
Period size: 39 Copynumber: 3.5 Consensus size: 39
28729069 ATGTTTTTGT
*
28729079 GTATTGTGATATATGCTTGAATGTTATGTGATTATATGA
1 GTATTGTGATATATGCTTAAATGTTATGTGATTATATGA
28729118 GTATTGTGATATATGCTTAAATGTTATGTGATTATATGA
1 GTATTGTGATATATGCTTAAATGTTATGTGATTATATGA
* *
28729157 GTATTGTGATATATGATTAAATGTTATATGATTATAT-A
1 GTATTGTGATATATGCTTAAATGTTATGTGATTATATGA
*
28729195 TGTAATGTGATATATGCTTAAA
1 -GTATTGTGATATATGCTTAAA
28729217 AGTGAATATG
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
38 1 0.01
39 92 0.99
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.46
Consensus pattern (39 bp):
GTATTGTGATATATGCTTAAATGTTATGTGATTATATGA
Found at i:28729193 original size:8 final size:8
Alignment explanation
Indices: 28729102--28729193 Score: 57
Period size: 8 Copynumber: 11.8 Consensus size: 8
28729092 TGCTTGAATG
*
28729102 TTATGTGA
1 TTATATGA
28729110 TTATATGA
1 TTATATGA
* *
28729118 GTATTGTGA
1 TTA-TATGA
*
28729127 -TATATGC
1 TTATATGA
*
28729134 TTAAATG-
1 TTATATGA
*
28729141 TTATGTGA
1 TTATATGA
28729149 TTATATGA
1 TTATATGA
* *
28729157 GTATTGTGA
1 TTA-TATGA
28729166 -TATATGA
1 TTATATGA
*
28729173 TTAAATG-
1 TTATATGA
28729180 TTATATGA
1 TTATATGA
28729188 TTATAT
1 TTATAT
28729194 ATGTAATGTG
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
7 18 0.28
8 38 0.59
9 8 0.12
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (8 bp):
TTATATGA
Found at i:28732201 original size:30 final size:28
Alignment explanation
Indices: 28732165--28732237 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 28
28732155 ACCGTCAGAC
28732165 TTAAATTTAAAAATATAAAAATTAAAAAAA
1 TTAAATTTAAAAATA-AAAAA-TAAAAAAA
* *
28732195 TTAAATTCTTGAAAATAAAAAATATAAAAA
1 TTAAA-T-TTAAAAATAAAAAATAAAAAAA
*
28732225 TTAAATTTCAAAA
1 TTAAATTTAAAAA
28732238 GAGTGCAGCG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 6 0.16
29 1 0.03
30 17 0.45
31 6 0.16
32 8 0.21
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (28 bp):
TTAAATTTAAAAATAAAAAATAAAAAAA
Found at i:28732562 original size:20 final size:20
Alignment explanation
Indices: 28732516--28732562 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28732506 TGAATTAATC
*
28732516 AAGGTGCAATGCGGATATCT
1 AAGGTGTAATGCGGATATCT
*
28732536 AAGGTGTAATGTGGATA-CT
1 AAGGTGTAATGCGGATATCT
28732555 AGAGGTGT
1 A-AGGTGT
28732563 TTATGGGCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.30, C:0.09, G:0.34, T:0.28
Consensus pattern (20 bp):
AAGGTGTAATGCGGATATCT
Found at i:28732737 original size:15 final size:16
Alignment explanation
Indices: 28732713--28732745 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
28732703 CCCGTATTAA
*
28732713 TTTTATTATAT-TATT
1 TTTTAATATATATATT
28732728 TTTTAATATATATATT
1 TTTTAATATATATATT
28732744 TT
1 TT
28732746 AAAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTAATATATATATT
Found at i:28732746 original size:14 final size:15
Alignment explanation
Indices: 28732707--28732747 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
28732697 GGCTCGCCCG
*
28732707 TATTA-ATTTTATTA
1 TATTATATTTTAATA
*
28732721 TATTATTTTTTAATA
1 TATTATATTTTAATA
28732736 TA-TATATTTTAA
1 TATTATATTTTAA
28732748 AAATATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTATATTTTAATA
Found at i:28732752 original size:17 final size:18
Alignment explanation
Indices: 28732732--28732770 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28732722 ATTATTTTTT
* *
28732732 AATATAT-ATATTTTAAA
1 AATATATAATATATCAAA
28732749 AATATATAATATATCAAA
1 AATATATAATATATCAAA
28732767 AATA
1 AATA
28732771 CTAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AATATATAATATATCAAA
Found at i:28733029 original size:24 final size:24
Alignment explanation
Indices: 28732997--28733045 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
28732987 CAACAACAAG
* *
28732997 AAAATAGCAAGAAAACAGTAAAAA
1 AAAAGAGCAAGAAAACAGCAAAAA
28733021 AAAAGAGCAAGAAAACAGCAAAAA
1 AAAAGAGCAAGAAAACAGCAAAAA
28733045 A
1 A
28733046 GACAATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.71, C:0.10, G:0.14, T:0.04
Consensus pattern (24 bp):
AAAAGAGCAAGAAAACAGCAAAAA
Found at i:28733408 original size:18 final size:18
Alignment explanation
Indices: 28733374--28733408 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28733364 ACCTATTTTC
*
28733374 AAAATCTAAACTGAAAAA
1 AAAATCTAAACTCAAAAA
*
28733392 AAAATCTAAATTCAAAA
1 AAAATCTAAACTCAAAA
28733409 CACGAAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (18 bp):
AAAATCTAAACTCAAAAA
Found at i:28734017 original size:15 final size:16
Alignment explanation
Indices: 28733988--28734033 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
28733978 CGACCCGACC
*
28733988 CAAAT-TATATATTAA
1 CAAATATATATTTTAA
*
28734003 -ATATATATATTTTAA
1 CAAATATATATTTTAA
28734018 TCAAATATATATTTTA
1 -CAAATATATATTTTA
28734034 TTTTTAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 3 0.12
15 9 0.36
17 13 0.52
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (16 bp):
CAAATATATATTTTAA
Found at i:28734025 original size:19 final size:19
Alignment explanation
Indices: 28734001--28734072 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 19
28733991 ATTATATATT
28734001 AAATATATATATTTTAATC
1 AAATATATATATTTTAATC
28734020 AAATATATATTTTATTTTTAATC
1 AAATATATA---TA-TTTTAATC
* *
28734043 AAATATAT-TTTTTATATATT
1 AAATATATATATTT-TA-ATC
28734063 AAATATATAT
1 AAATATATAT
28734073 TTAATATGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
18 3 0.07
19 12 0.27
20 10 0.23
21 1 0.02
22 2 0.05
23 16 0.36
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATATATATATTTTAATC
Found at i:28734029 original size:21 final size:23
Alignment explanation
Indices: 28734003--28734050 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
28733993 TATATATTAA
28734003 ATATA-TATA-TTTTAATCAAAT
1 ATATATTATATTTTTAATCAAAT
*
28734024 ATATATTTTATTTTTAATCAAAT
1 ATATATTATATTTTTAATCAAAT
28734047 ATAT
1 ATAT
28734051 TTTTTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.21
22 3 0.12
23 16 0.67
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATATTATATTTTTAATCAAAT
Found at i:28734051 original size:21 final size:23
Alignment explanation
Indices: 28734012--28734057 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
28734002 AATATATATA
28734012 TTTTAATCAAATATATATTTTAT
1 TTTTAATCAAATATATATTTTAT
*
28734035 TTTTAATCAAATATATTTTTTAT
1 TTTTAATCAAATATATATTTTAT
28734058 ATATTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTAATCAAATATATATTTTAT
Found at i:28734471 original size:17 final size:17
Alignment explanation
Indices: 28734449--28734483 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28734439 AATATAGAAA
*
28734449 GTAATCTTAGAAGATTT
1 GTAATCTGAGAAGATTT
*
28734466 GTAATCTGATAAGATTT
1 GTAATCTGAGAAGATTT
28734483 G
1 G
28734484 ATTTTATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (17 bp):
GTAATCTGAGAAGATTT
Found at i:28750403 original size:18 final size:19
Alignment explanation
Indices: 28750369--28750404 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28750359 TTGAGCAGAT
28750369 ATTCTTTTAAGATTCTTTC
1 ATTCTTTTAAGATTCTTTC
*
28750388 ATTCTTTTGA-ATTCTTT
1 ATTCTTTTAAGATTCTTT
28750405 GTCAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.19, C:0.14, G:0.06, T:0.61
Consensus pattern (19 bp):
ATTCTTTTAAGATTCTTTC
Found at i:28751775 original size:3 final size:3
Alignment explanation
Indices: 28751769--28751822 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
28751759 TACTACTACC
* *
28751769 ATT ATT ATC ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28751817 ATT ATT
1 ATT ATT
28751823 TTTAATGTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:28758233 original size:44 final size:44
Alignment explanation
Indices: 28758162--28758470 Score: 113
Period size: 44 Copynumber: 6.9 Consensus size: 44
28758152 AGAAGATGGC
* * **
28758162 AAATCTTATTTCCCTGAAGTTGTAGTGGAGCAAATTAAAGCCAA
1 AAATCCTATCTCCCTGAAGTTAAAGTGGAGCAAATTAAAGCCAA
* ** ** *
28758206 AAATCCTATCTCCCTGAGGTTAAAGTGGAGCGGATTAAAGTTAT
1 AAATCCTATCTCCCTGAAGTTAAAGTGGAGCAAATTAAAGCCAA
* * * * * * ** *
28758250 AAGTCTTATCTCCCTGAAGTTGCAA-TGGAGTAGACTAAAGATAGC
1 AAATCCTATCTCCCTGAAGTT-AAAGTGGAGCAAATTAAAGCCA-A
* * * * ** * *
28758295 GAATCTTATTTCCCTAAAGTTGTAGTGGAACAAATTAAAGCTATAAA
1 AAATCCTATCTCCCTGAAGTTAAAGTGGAGCAAATTAAAGC---CAA
* ** ** * * * *
28758342 TCACAGATCTTATCTCTTTGAAGTTGTAGTAGAGCAAA-TCATGGC--
1 --A-A-ATCCTATCTCCCTGAAGTTAAAGTGGAGCAAATTAAAGCCAA
* ** *
28758387 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
1 AAATCCTATCTCCCTGAAGTTAAAGTGGAGCAAATTAAAGCCAA
* ** *
28758431 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAG
1 AAATCCTATCTCCCTGAAGTTAAAGTGGAGCAAATTAAAG
28758471 TTACAAGTCT
Statistics
Matches: 197, Mismatches: 55, Indels: 26
0.71 0.20 0.09
Matches are distributed among these distances:
41 27 0.14
42 5 0.03
43 1 0.01
44 103 0.52
45 30 0.15
48 1 0.01
50 4 0.02
51 26 0.13
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (44 bp):
AAATCCTATCTCCCTGAAGTTAAAGTGGAGCAAATTAAAGCCAA
Found at i:28758796 original size:44 final size:44
Alignment explanation
Indices: 28758748--28758952 Score: 159
Period size: 44 Copynumber: 4.7 Consensus size: 44
28758738 AAGTTACAAG
28758748 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
* * * * ** * *** *
28758792 TCTTATTTCTCTGAAATTACAGTAAAGTAGA-TCGCATCA-GG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
* ***
28758833 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGAA--ACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-AATGATGGA
* * * *
28758877 TCCTATCTCCCTAAAGTTGCAATGGAGCAAATTAAAATGATGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
* * *
28758921 TCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
28758953 CGCATCAGAC
Statistics
Matches: 115, Mismatches: 39, Indels: 14
0.68 0.23 0.08
Matches are distributed among these distances:
41 23 0.20
42 6 0.05
43 6 0.05
44 80 0.70
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
Found at i:28759013 original size:129 final size:129
Alignment explanation
Indices: 28758742--28759024 Score: 363
Period size: 129 Copynumber: 2.2 Consensus size: 129
28758732 GGATTAAAGT
* * * *
28758742 TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGATCTTATTTCTCTGAA
1 TACAAGTCTTATCTCCCTAAAGTTGCAATGGAGCAAATTAAAATGATGGATCTTATCTCTCTGAA
** * * * * *
28758807 ATTACAGTAAAGTAGATCGCATCAGGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGA
66 ATTACAGTAAAGTAGATCGCATCAGACCTTATCTCCTTGAAATTACAGTGAAGAAGATGGAAGA
* *
28758871 AACCAA-TCCTATCTCCCTAAAGTTGCAATGGAGCAAATTAAAATGATGGATCTTATCTCTCTGA
1 TA-CAAGTCTTATCTCCCTAAAGTTGCAATGGAGCAAATTAAAATGATGGATCTTATCTCTCTGA
* * * * *
28758935 AGTTGCAGTAGAGTAGATCGCATCAGACCTTATTTCCTTGAAATTACAGTGAAATAAG-TGGAAG
65 AATTACAGTAAAGTAGATCGCATCAGACCTTATCTCCTTGAAATTACAGTG-AAGAAGATGGAAG
*
28758999 C
129 A
28759000 TACAAGTCTTATCTCCCTAAAGTTG
1 TACAAGTCTTATCTCCCTAAAGTTG
28759025 TGTGGAGAAA
Statistics
Matches: 130, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
128 3 0.02
129 121 0.93
130 6 0.05
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (129 bp):
TACAAGTCTTATCTCCCTAAAGTTGCAATGGAGCAAATTAAAATGATGGATCTTATCTCTCTGAA
ATTACAGTAAAGTAGATCGCATCAGACCTTATCTCCTTGAAATTACAGTGAAGAAGATGGAAGA
Found at i:28772989 original size:18 final size:18
Alignment explanation
Indices: 28772966--28773006 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
28772956 CACTCAACCC
28772966 TATCATAAGCTTTGCTCA
1 TATCATAAGCTTTGCTCA
28772984 TATCATAAGCTTTGCTCA
1 TATCATAAGCTTTGCTCA
28773002 TATCA
1 TATCA
28773007 ATTCCCACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (18 bp):
TATCATAAGCTTTGCTCA
Found at i:28774113 original size:307 final size:307
Alignment explanation
Indices: 28773523--28774143 Score: 1084
Period size: 307 Copynumber: 2.0 Consensus size: 307
28773513 ACGCTACTTC
*
28773523 ATTAATCTCACTCTCTCAATAGCTGCTCCTCCTTCAACTTTCTCCAACTTGGAAATTATATTTAT
1 ATTAATCTCACTCTCTCAATAGCTGCTCCTCC-TCAACTTTCTCCAACTCGGAAATTATATTTAT
28773588 ACGTCTACGGTATGTAGCAAATCTATGAAAAAGGCTGAATTCTTATCCCCTGCTTGAAGCCAGTT
65 ACGTCTACGGTATGTAGCAAATCTATGAAAAAGGCTGAATTCTTATCCCCTGCTTGAAGCCAGTT
*
28773653 CGCCCTTGCCCTTTGTTCCCAATAAATTTAATCTTTAACAATTTCCATATTCAGGTGAATCTTGG
130 CGCCCTTGCCCTTTGTTCCCAATAAATTTAATCTTTAACAATTTCCAAATTCAGGTGAATCTTGG
**
28773718 TGTCAATGATTTCTGCCAACGTATTATCATTCCTATCCTCTCCCAGTAATTTATCATGCTGCTCT
195 TGTCAATGATTTCTGCCAACGTATTATCATTCCTATCCTCTCCCAGTAATGAATCATGCTGCTCT
*
28773783 AATAATTTCTTTTTTAGTCCTCTATCCTTCCTGATTGTTTTTGCCCAA
260 AATAATTTCTTTTTTAGTCCTCTATCCTTCCTAATTGTTTTTGCCCAA
*
28773831 ATTAATCTCACTCTCCTCAATAGCTGCTCCT-C-CAGCTTTCTCCAACTCGGAAATTATATTTAT
1 ATTAATCTCACTCT-CTCAATAGCTGCTCCTCCTCAACTTTCTCCAACTCGGAAATTATATTTAT
* *
28773894 ATGTCTACGGTATGTAGCAAATCTATGAAAAAAGGCTGAATTCTTATCCCCTGCTTGAAGCTAGT
65 ACGTCTACGGTATGTAGCAAATCTATG-AAAAAGGCTGAATTCTTATCCCCTGCTTGAAGCCAGT
* ** *
28773959 TCGCCCTTGCCCTTTGTTCCCAATAAATTTCATCTTTATGAATTTCCAAATTCAGGTGAATTTTG
129 TCGCCCTTGCCCTTTGTTCCCAATAAATTTAATCTTTAACAATTTCCAAATTCAGGTGAATCTTG
*
28774024 GTGTCAATGATTTCTGCCAACGTATTATCATTCCTATCCTCTCCCTGTAATGAATCATGCTGCTC
194 GTGTCAATGATTTCTGCCAACGTATTATCATTCCTATCCTCTCCCAGTAATGAATCATGCTGCTC
28774089 TAATAATTTCTTTTTTAGTCCTCTATCCTTCCTAATTGTTTTTGCCCAA
259 TAATAATTTCTTTTTTAGTCCTCTATCCTTCCTAATTGTTTTTGCCCAA
28774138 ATTAAT
1 ATTAAT
28774144 AATTCAGCCT
Statistics
Matches: 298, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
306 55 0.18
307 212 0.71
308 15 0.05
309 16 0.05
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (307 bp):
ATTAATCTCACTCTCTCAATAGCTGCTCCTCCTCAACTTTCTCCAACTCGGAAATTATATTTATA
CGTCTACGGTATGTAGCAAATCTATGAAAAAGGCTGAATTCTTATCCCCTGCTTGAAGCCAGTTC
GCCCTTGCCCTTTGTTCCCAATAAATTTAATCTTTAACAATTTCCAAATTCAGGTGAATCTTGGT
GTCAATGATTTCTGCCAACGTATTATCATTCCTATCCTCTCCCAGTAATGAATCATGCTGCTCTA
ATAATTTCTTTTTTAGTCCTCTATCCTTCCTAATTGTTTTTGCCCAA
Found at i:28775014 original size:36 final size:36
Alignment explanation
Indices: 28774967--28775038 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
28774957 TGAACATTCC
*
28774967 AACTTACAATTTTCTTTGCGTCCGGTCAGCTTGCCT
1 AACTTACAATTTTCATTGCGTCCGGTCAGCTTGCCT
28775003 AACTTACAATTTTCATTGCGTCCGGTCAGCTTGCCT
1 AACTTACAATTTTCATTGCGTCCGGTCAGCTTGCCT
28775039 CATGGCAGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.38
Consensus pattern (36 bp):
AACTTACAATTTTCATTGCGTCCGGTCAGCTTGCCT
Found at i:28779311 original size:16 final size:15
Alignment explanation
Indices: 28779285--28779315 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
28779275 TTTTAGAAAC
28779285 ACTTTGTATATGATA
1 ACTTTGTATATGATA
28779300 ACTTTAGTATATGATA
1 ACTTT-GTATATGATA
28779316 TGACATTTTG
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:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (15 bp):
ACTTTGTATATGATA
Found at i:28779360 original size:7 final size:7
Alignment explanation
Indices: 28779348--28779372 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28779338 AAGAAAATGT
28779348 GTTTAAA
1 GTTTAAA
28779355 GTTTAAA
1 GTTTAAA
28779362 GTTTAAA
1 GTTTAAA
28779369 GTTT
1 GTTT
28779373 GTATATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (7 bp):
GTTTAAA
Found at i:28779424 original size:12 final size:12
Alignment explanation
Indices: 28779407--28779431 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28779397 CACGTGAGTG
28779407 GCATCTAGCAAT
1 GCATCTAGCAAT
28779419 GCATCTAGCAAT
1 GCATCTAGCAAT
28779431 G
1 G
28779432 AGTGGCATCT
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:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (12 bp):
GCATCTAGCAAT
Found at i:28779441 original size:17 final size:17
Alignment explanation
Indices: 28779401--28779448 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
28779391 TCGAAACACG
28779401 TGAGTGGCATCTAGC-A
1 TGAGTGGCATCTAGCAA
28779417 --A-T-GCATCTAGCAA
1 TGAGTGGCATCTAGCAA
28779430 TGAGTGGCATCTAGCAA
1 TGAGTGGCATCTAGCAA
28779447 TG
1 TG
28779449 CATCATTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 1 0.04
15 1 0.04
16 1 0.04
17 13 0.48
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (17 bp):
TGAGTGGCATCTAGCAA
Found at i:28797131 original size:37 final size:37
Alignment explanation
Indices: 28797063--28797146 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
28797053 TGCCACATAT
* * *
28797063 TGGTTTGATTAGATGGATGGACTCTATTAGTCCAATA
1 TGGTGTGATTAGATGGATCGACTATATTAGTCCAATA
28797100 TGGTGTGATTAGATGGATCGACTAT-TGTAGTCCAATA
1 TGGTGTGATTAGATGGATCGACTATAT-TAGTCCAATA
28797137 TGGTGTGATT
1 TGGTGTGATT
28797147 GGTTGGACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 1 0.02
37 42 0.98
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (37 bp):
TGGTGTGATTAGATGGATCGACTATATTAGTCCAATA
Found at i:28802467 original size:53 final size:55
Alignment explanation
Indices: 28802344--28802473 Score: 149
Period size: 53 Copynumber: 2.4 Consensus size: 55
28802334 ATTCAAAAAG
* * *
28802344 AAAATCAAAAATCAAAATAAAATGATAGAAAAAAGAAGAAGAAAAAAGAAAAATCA
1 AAAATC-AAGATCAAAATAAAATGAGAGAAAAAAGAAGAAGAAAAAAGAAAAAACA
* * * *
28802400 AAAATCAAGGTCAAAATGAAAATGAGAG-AAAAAG-A-AAGAAGAATGAAAAAAGA
1 AAAATCAAGATCAAAAT-AAAATGAGAGAAAAAAGAAGAAGAAAAAAGAAAAAACA
*
28802453 AAAATCTAGATCAAAATAAAA
1 AAAATCAAGATCAAAATAAAA
28802474 AATGACAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
52 4 0.06
53 29 0.45
54 1 0.02
55 15 0.23
56 15 0.23
ACGTcount: A:0.69, C:0.05, G:0.14, T:0.12
Consensus pattern (55 bp):
AAAATCAAGATCAAAATAAAATGAGAGAAAAAAGAAGAAGAAAAAAGAAAAAACA
Found at i:28804754 original size:87 final size:87
Alignment explanation
Indices: 28804604--28805189 Score: 897
Period size: 87 Copynumber: 6.7 Consensus size: 87
28804594 CAGATCAGTG
* * *
28804604 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGTAGATCGAAAAAAAAGCCTTACCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
28804669 TCGGTTGCAGTGGAGCTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
*
28804691 AAGATAGCAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
28804756 TCGGTTGCAATGGAGCTAGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
* *
28804778 AAGATGGCAGATCTTGCCTTCCTGCATTGACAGCGAAACAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
28804843 TCGGTTGCAGTGGAGCTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
* * * * *
28804865 AAGATGGCAGATATTGTCTTCTTGCATTGACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
*
28804930 TCAGTTGCAGTGGA-CTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
*
28804951 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
28805016 TCGGTTGTAGTGGAGCTGGTCA
66 TCGGTTGCAGTGGAGCTGGTTA
* * * *
28805038 AAGATGGCAGATCTTGCCTTCCTACATTGATAGCGAAGCAGATCGAAAACAAAACCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
* *
28805103 TCGGTTGCAGTAGAGCAGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
* * * *
28805125 AAGATAGCAGATCTTGCCTTCCAGCACTGACAGCGAAGCAAATCGAAGATAC-CAGCCTTGCCTC
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTC
28805189 C
64 C
28805190 CAAGTAGTGC
Statistics
Matches: 453, Mismatches: 43, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
86 78 0.17
87 361 0.80
88 12 0.03
89 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.23
Consensus pattern (87 bp):
AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
TCGGTTGCAGTGGAGCTGGTTA
Done.