Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008532.1 Hibiscus syriacus cultivar Beakdansim tig00111410_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 857509
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:784764 original size:20 final size:17
Alignment explanation
Indices: 784741--784784 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 17
784731 ATTAAATTGC
784741 AAAATATAAAAATGAATAGT
1 AAAATATAAAAAT-AAT--T
*
784761 AAAAAATAAAAATAATT
1 AAAATATAAAAATAATT
784778 AAAATAT
1 AAAATAT
784785 CAGTGATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 7 0.32
19 3 0.14
20 12 0.55
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (17 bp):
AAAATATAAAAATAATT
Found at i:785787 original size:3 final size:3
Alignment explanation
Indices: 785774--785884 Score: 161
Period size: 3 Copynumber: 36.3 Consensus size: 3
785764 AATATTTATT
* *
785774 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
785822 TATA TATA TAA TAA TAA AAA TAA TAA TAA TAA GT-A TAA TAA TAA TAA
1 TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
785869 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
785885 TTAAAACGGA
Statistics
Matches: 99, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
2 1 0.01
3 90 0.91
4 8 0.08
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:797071 original size:46 final size:45
Alignment explanation
Indices: 797021--797116 Score: 104
Period size: 46 Copynumber: 2.1 Consensus size: 45
797011 AGAGCCTCCA
** * *
797021 TTCATACTTACAATGCA-CCATTATGTATTTTCATATATGACATTCT
1 TTCATACCAACAATGCACCCA-TATGCATTTT-ATATATGACATCCT
* * *
797067 TTCATGCCAATAATGCACCCATATGCATTTTATTTATGACATCCT
1 TTCATACCAACAATGCACCCATATGCATTTTATATATGACATCCT
797112 TTCAT
1 TTCAT
797117 GCCCTTTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
45 17 0.40
46 22 0.52
47 3 0.07
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (45 bp):
TTCATACCAACAATGCACCCATATGCATTTTATATATGACATCCT
Found at i:797117 original size:45 final size:46
Alignment explanation
Indices: 797032--797119 Score: 126
Period size: 45 Copynumber: 1.9 Consensus size: 46
797022 TCATACTTAC
* *
797032 AATGCACCATTATGTATTTTCATATATGACATTCTTTCATGCCAAT
1 AATGCACCATTATGCATTTTCATATATGACATCCTTTCATGCCAAT
*
797078 AATGCACCCA-TATGCATTTT-ATTTATGACATCCTTTCATGCC
1 AATGCA-CCATTATGCATTTTCATATATGACATCCTTTCATGCC
797120 CTTTTATAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 20 0.53
46 15 0.39
47 3 0.08
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (46 bp):
AATGCACCATTATGCATTTTCATATATGACATCCTTTCATGCCAAT
Found at i:797160 original size:46 final size:46
Alignment explanation
Indices: 797092--797205 Score: 183
Period size: 46 Copynumber: 2.5 Consensus size: 46
797082 CACCCATATG
* *
797092 CATTTTATTTATGACATCCTTTCATGCCCTTTTATAAGCTATTATA
1 CATTTCATTTATGGCATCCTTTCATGCCCTTTTATAAGCTATTATA
* *
797138 CATTTCATTTATGGCATTCTTTCATGCCCTTTTATACGCTATTATA
1 CATTTCATTTATGGCATCCTTTCATGCCCTTTTATAAGCTATTATA
*
797184 CCTTTCATTTATGGCATCCTTT
1 CATTTCATTTATGGCATCCTTT
797206 ACAACGTTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.48
Consensus pattern (46 bp):
CATTTCATTTATGGCATCCTTTCATGCCCTTTTATAAGCTATTATA
Found at i:797677 original size:55 final size:55
Alignment explanation
Indices: 797458--798071 Score: 798
Period size: 55 Copynumber: 11.2 Consensus size: 55
797448 TTTATTAAGA
* * * *
797458 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAA-TTCTTTCGG--T
1 TGCACACATAGTGCATGTACGGTTA-TTCATCAACTCATGATGAATTTC-GT-GGATT
* * * *
797512 TACACACATCGT--ATGTACGGTTATTTATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
* * * *
797565 CGCACACATAGTGCTTGTACGGTTATTCAAACAACTCATGATGAATTTCATGGATT
1 TGCACACATAGTGCATGTACGGTTATTC-ATCAACTCATGATGAATTTCGTGGATT
*
797621 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCATGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
* * * *
797676 TGCACACATAGTGCATGTACGGTTATACATTAACTCATGATGAATTCCATGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
797731 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
** *
797786 TGCACACATAGTGTTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
* * * *
797841 TGCACACATAATGCCT-TACGGTTATTCATCAACTCATGATGAATTCCGTGTATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
* ** * *
797895 TACACGTATAGTGCATGTACGATTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
* *
797950 TGCACACATAGTGCTTGTACGGTTATTCAATCAACTCATGATGAA-TTCTGTGTATT
1 TGCACACATAGTGCATGTACGGTTATTC-ATCAACTCATGATGAATTTC-GTGGATT
* * *
798006 TGCACACGTAGTGCTTGTACGGTTATTCAT-AACTCATGATGAATTT-GTAGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
798059 TGCACACATAGTG
1 TGCACACATAGTG
798072 TCGAAACGGT
Statistics
Matches: 498, Mismatches: 51, Indels: 23
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.00
52 25 0.05
53 31 0.06
54 70 0.14
55 271 0.54
56 99 0.20
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (55 bp):
TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
Found at i:797940 original size:219 final size:219
Alignment explanation
Indices: 797483--798068 Score: 826
Period size: 219 Copynumber: 2.7 Consensus size: 219
797473 TATACGGTAG
** * * *
797483 TTCATCAACTCATGATGAATTCTTTCGG--TTACACACATCGT--ATGTACGGTTATTTATCAAC
1 TTCATCAACTCATGATGAATTCCAT-GGATTTGCACACATAGTGCATGTACGGTTATTCATCAAC
* * *
797544 TCATGATGAATTCCGTGGATTCGCACACATAGTGCTTGTACGGTTATTCAAACAACTCATGATGA
65 TCATGATGAATTTCGTGGATTTGCACACATAGTGCTTGTACGGTTATTC-ATCAACTCATGATGA
* * *
797609 ATTTCATGGATTTGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCATGGA
129 A-TTCGTGGATTTGCACACATAATGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGA
* *
797674 TTTGCACACATAGTGCATGTACGGTTA
193 TTTACACACATAGTGCATGTACGATTA
* *
797701 TACATTAACTCATGATGAATTCCATGGATTTGCACACATAGTGCATGTACGGTTATTCATCAACT
1 TTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCATGTACGGTTATTCATCAACT
*
797766 CATGATGAATTTCGTGGATTTGCACACATAGTGTTTGTACGGTTATTCATCAACTCATGATGAAT
66 CATGATGAATTTCGTGGATTTGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAAT
* * *
797831 TCCGTGGATTTGCACACATAATGCCT-TACGGTTATTCATCAACTCATGATGAATTCCGTGTATT
131 T-CGTGGATTTGCACACATAATGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
**
797895 TACACGTATAGTGCATGTACGATTA
195 TACACACATAGTGCATGTACGATTA
* *
797920 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTGTACGGTTATTCAATCAAC
1 TTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCATGTACGGTTATTC-ATCAAC
* *
797985 TCATGATGAA-TTCTGTGTATTTGCACACGTAGTGCTTGTACGGTTATTCAT-AACTCATGATGA
65 TCATGATGAATTTC-GTGGATTTGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGA
* *
798048 ATTTGTAGATTTGCACACATA
129 ATTCGTGGATTTGCACACATA
798069 GTGTCGAAAC
Statistics
Matches: 331, Mismatches: 30, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
217 2 0.01
218 37 0.11
219 141 0.43
220 86 0.26
221 65 0.20
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (219 bp):
TTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCATGTACGGTTATTCATCAACT
CATGATGAATTTCGTGGATTTGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAAT
TCGTGGATTTGCACACATAATGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGATTT
ACACACATAGTGCATGTACGATTA
Found at i:798101 original size:54 final size:54
Alignment explanation
Indices: 797458--798305 Score: 717
Period size: 55 Copynumber: 15.6 Consensus size: 54
797448 TTTATTAAGA
* * ** *
797458 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTCTTTCG-GT
1 TGCACACATAGTGCCGATACGGTTA-TTCATCAACTCATGATGAATTCCGT-GATT
* * ** *
797512 TACACACATCGT-ATG-TACGGTTATTTATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCGATACGGTTATTCATCAACTCATGATGAATTCCGT-GATT
* * * * *
797565 CGCACACATAGTGCTTG-TACGGTTATTCAAACAACTCATGATGAATTTCATGGATT
1 TGCACACATAGTGC-CGATACGGTTATTC-ATCAACTCATGATGAATTCCGT-GATT
* * *
797621 TGCACACATAGTGCATG-TACGGTTATTCATCAACTCATGATGAATTTCATGGATT
1 TGCACACATAGTGC-CGATACGGTTATTCATCAACTCATGATGAATTCCGT-GATT
* * * *
797676 TGCACACATAGTGCATG-TACGGTTATACATTAACTCATGATGAATTCCATGGATT
1 TGCACACATAGTGC-CGATACGGTTATTCATCAACTCATGATGAATTCCGT-GATT
* *
797731 TGCACACATAGTGCATG-TACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
1 TGCACACATAGTGC-CGATACGGTTATTCATCAACTCATGATGAATTCCGT-GATT
**
797786 TGCACACATAGTGTTTG-TACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTG-CCGATACGGTTATTCATCAACTCATGATGAATTCCGT-GATT
* *
797841 TGCACACATAATGCC-TTACGGTTATTCATCAACTCATGATGAATTCCGTGTATT
1 TGCACACATAGTGCCGATACGGTTATTCATCAACTCATGATGAATTCCGTG-ATT
* ** * *
797895 TACACGTATAGTGCATG-TACGATTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGC-CGATACGGTTATTCATCAACTCATGATGAATTCCGT-GATT
* *
797950 TGCACACATAGTGCTTG-TACGGTTATTCAATCAACTCATGATGAATTCTGTGTATT
1 TGCACACATAGTGC-CGATACGGTTATTC-ATCAACTCATGATGAATTCCGTG-ATT
* * *
798006 TGCACACGTAGTGCTTG-TACGGTTATTCAT-AACTCATGATGAATT-TGTAGATT
1 TGCACACATAGTGC-CGATACGGTTATTCATCAACTCATGATGAATTCCGT-GATT
* * * * * **
798059 TGCACACATAGTGTCGAAACGGTTATTCATCCACGT-AGGATGAATTCCTTGAAA
1 TGCACACATAGTGCCGATACGGTTATTCATCAAC-TCATGATGAATTCCGTGATT
* * * * * **
798113 TGCACACTTAGTGCCGAAACGATTATTTATCCACGT-ATGATGAATTCCGTGAAA
1 TGCACACATAGTGCCGATACGGTTATTCATCAAC-TCATGATGAATTCCGTGATT
* * * * **
798167 TGCACACTTAGTGCCGAAACGATTATTCATCCACGT-ATGATGAATTCCGTGAAA
1 TGCACACATAGTGCCGATACGGTTATTCATCAAC-TCATGATGAATTCCGTGATT
* * * * * * **
798221 TGCACACTTATTGCCGAAACGGTTATTCATCCACGT-AGGATGAATTCTGTGAAA
1 TGCACACATAGTGCCGATACGGTTATTCATCAAC-TCATGATGAATTCCGTGATT
* *
798275 TGCACACTTAGTGCCGAAACGGTTATTCATC
1 TGCACACATAGTGCCGATACGGTTATTCATC
798306 CACGTAGGAT
Statistics
Matches: 707, Mismatches: 69, Indels: 36
0.87 0.08 0.04
Matches are distributed among these distances:
52 29 0.04
53 43 0.06
54 265 0.37
55 268 0.38
56 102 0.14
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (54 bp):
TGCACACATAGTGCCGATACGGTTATTCATCAACTCATGATGAATTCCGTGATT
Found at i:798306 original size:54 final size:54
Alignment explanation
Indices: 798059--798343 Score: 453
Period size: 54 Copynumber: 5.3 Consensus size: 54
798049 TTTGTAGATT
* * *
798059 TGCACACATAGTGTCGAAACGGTTATTCATCCACGTAGGATGAATTCCTTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACGTAGGATGAATTCCGTGAAA
* * *
798113 TGCACACTTAGTGCCGAAACGATTATTTATCCACGTATGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACGTAGGATGAATTCCGTGAAA
* *
798167 TGCACACTTAGTGCCGAAACGATTATTCATCCACGTATGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACGTAGGATGAATTCCGTGAAA
* *
798221 TGCACACTTATTGCCGAAACGGTTATTCATCCACGTAGGATGAATTCTGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACGTAGGATGAATTCCGTGAAA
* *
798275 TGCACACTTAGTGCCGAAACGGTTATTCATCCACGTAGGATAAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACGTAGGATGAATTCCGTGAAA
*
798329 TGTACACTTAGTGCC
1 TGCACACTTAGTGCC
798344 TAATTGGTAA
Statistics
Matches: 215, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 215 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACGTAGGATGAATTCCGTGAAA
Found at i:798710 original size:22 final size:21
Alignment explanation
Indices: 798668--798721 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
798658 TGGCTCCTCA
798668 GTATCGATACT-CATACCATG
1 GTATCGATACTACATACCATG
*
798688 GTATCGATACTACCATACTATG
1 GTATCGATACTA-CATACCATG
*
798710 GTACCGATACTA
1 GTATCGATACTA
798722 TGCTATGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 11 0.37
22 19 0.63
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (21 bp):
GTATCGATACTACATACCATG
Found at i:800437 original size:18 final size:18
Alignment explanation
Indices: 800405--800452 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
800395 TCGGGTCAAA
* *
800405 GTCAACGGTTTGGGTCGG
1 GTCAACAGTTCGGGTCGG
* *
800423 TTCAATAGTTCGGGTCGG
1 GTCAACAGTTCGGGTCGG
800441 GTCAACAGTTCG
1 GTCAACAGTTCG
800453 TCGGGCAGAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (18 bp):
GTCAACAGTTCGGGTCGG
Found at i:801470 original size:45 final size:44
Alignment explanation
Indices: 801410--801497 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 44
801400 AAATAAGATT
*
801410 TTAGGTAGCGCCCAATATTAACATTTCCGGTAGAAAAAATAATGC
1 TTAGATAGCGCCCAATATTAACA-TTCCGGTAGAAAAAATAATGC
* * *
801455 TTAGATAGTGCCCAATATTAACATTCTGGTAGAACAAATAATG
1 TTAGATAGCGCCCAATATTAACATTCCGGTAGAAAAAATAATG
801498 TTTTAGGTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (44 bp):
TTAGATAGCGCCCAATATTAACATTCCGGTAGAAAAAATAATGC
Found at i:803582 original size:11 final size:11
Alignment explanation
Indices: 803568--803596 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
803558 CGTTAAGAAC
803568 TCGAGTTTAGG
1 TCGAGTTTAGG
803579 TCGAGTTTAGG
1 TCGAGTTTAGG
803590 TCGAGTT
1 TCGAGTT
803597 GAGATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.34, T:0.38
Consensus pattern (11 bp):
TCGAGTTTAGG
Found at i:806222 original size:37 final size:37
Alignment explanation
Indices: 806180--806255 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
806170 TATTAACCAC
806180 TGACATTTATTTATTGTTGATATTTGATTCGACCTTG
1 TGACATTTATTTATTGTTGATATTTGATTCGACCTTG
* *
806217 TGACATTTATTTATTGTTGATATTTTATTCGTCCTTG
1 TGACATTTATTTATTGTTGATATTTGATTCGACCTTG
806254 TG
1 TG
806256 GTGACTCGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.20, C:0.11, G:0.16, T:0.54
Consensus pattern (37 bp):
TGACATTTATTTATTGTTGATATTTGATTCGACCTTG
Found at i:808485 original size:13 final size:13
Alignment explanation
Indices: 808469--808538 Score: 68
Period size: 13 Copynumber: 5.2 Consensus size: 13
808459 GAATAAAGAC
*
808469 AATAAGTAAATAA
1 AATAAATAAATAA
*
808482 AATAAAAAAATAA
1 AATAAATAAATAA
* *
808495 AATAAACAAAGAA
1 AATAAATAAATAA
*
808508 AAAAAATAAATAAAA
1 AATAAATAAAT--AA
808523 AATGAAATAAATAA
1 AAT-AAATAAATAA
808537 AA
1 AA
808539 AAACATAGGA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
13 30 0.65
14 4 0.09
15 4 0.09
16 8 0.17
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (13 bp):
AATAAATAAATAA
Found at i:808495 original size:17 final size:17
Alignment explanation
Indices: 808476--808541 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
808466 GACAATAAGT
808476 AAATAAAATAAAAAAATA
1 AAAT-AAATAAAAAAATA
*
808494 AAATAAACAAAGAAAA-A
1 AAATAAATAAA-AAAATA
*
808511 AAATAAAT-AAAAAATG
1 AAATAAATAAAAAAATA
808527 AAATAAATAAAAAAA
1 AAATAAATAAAAAAA
808542 CATAGGAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
15 4 0.10
16 10 0.24
17 20 0.48
18 8 0.19
ACGTcount: A:0.82, C:0.02, G:0.03, T:0.14
Consensus pattern (17 bp):
AAATAAATAAAAAAATA
Found at i:808509 original size:21 final size:22
Alignment explanation
Indices: 808481--808543 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
808471 TAAGTAAATA
808481 AAAT-AAAAAAATAAAATAAAC
1 AAATGAAAAAAATAAAATAAAC
808502 AAA-GAAAAAAA-ATAAATAAA-
1 AAATGAAAAAAATA-AAATAAAC
*
808522 AAATGAAATAAATAAAA-AAAC
1 AAATGAAAAAAATAAAATAAAC
808543 A
1 A
808544 TAGGAAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
20 7 0.19
21 28 0.78
22 1 0.03
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.13
Consensus pattern (22 bp):
AAATGAAAAAAATAAAATAAAC
Found at i:808518 original size:4 final size:4
Alignment explanation
Indices: 808469--808537 Score: 50
Period size: 4 Copynumber: 16.5 Consensus size: 4
808459 GAATAAAGAC
* * * * *
808469 AATA AGTA AATAA AATA AAAA AATAA AATA AACA AAGAA AAAA AATA AATA
1 AATA AATA AAT-A AATA AATA AAT-A AATA AATA AA-TA AATA AATA AATA
808520 AA-A AATGA AATA AATA AA
1 AATA AAT-A AATA AATA AA
808538 AAAACATAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
3 3 0.06
4 35 0.66
5 15 0.28
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.16
Consensus pattern (4 bp):
AATA
Found at i:808556 original size:21 final size:20
Alignment explanation
Indices: 808485--808556 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 20
808475 TAAATAAAAT
*
808485 AAAAAAATAAAATAAACAAAGA
1 AAAAAAATAAAA-AAAC-AAGG
*
808507 AAAAAAATAAATAAAA-AATG
1 AAAAAAATAAA-AAAACAAGG
*
808527 AAATAAATAAAAAAACATAGG
1 AAAAAAATAAAAAAACA-AGG
*
808548 AAAATAATA
1 AAAAAAATA
808557 GTGAAAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
19 4 0.10
20 13 0.32
21 9 0.22
22 14 0.34
23 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.14
Consensus pattern (20 bp):
AAAAAAATAAAAAAACAAGG
Found at i:808627 original size:2 final size:2
Alignment explanation
Indices: 808620--808688 Score: 115
Period size: 2 Copynumber: 35.5 Consensus size: 2
808610 CAATAAAATA
*
808620 AT AT AT AT AT AT AT AT AT AT A- AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
808661 AT AT AT AT AT AT AT AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
808689 ATAAAATAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
1 2 0.03
2 62 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:808759 original size:23 final size:21
Alignment explanation
Indices: 808718--808759 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
808708 AAAGGAAAAT
808718 AATAATAATAAATAATAATTA
1 AATAATAATAAATAATAATTA
*
808739 AATATATATATAAATACTAAT
1 AATA-ATA-ATAAATAATAAT
808760 GAAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 3 0.17
23 11 0.61
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AATAATAATAAATAATAATTA
Found at i:810874 original size:208 final size:204
Alignment explanation
Indices: 810513--810886 Score: 508
Period size: 208 Copynumber: 1.8 Consensus size: 204
810503 TCCTTCGCCG
*
810513 TGAAGTTGATCTTTAAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAATGGATGCTTCTTGTG
1 TGAAGTTGATCTTGAAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAATGGATGCTTCTTGTG
*
810578 GGCACGATATCATTCGTCGCGAAGCTGAAATCGTGGATGGTCCCTTCGTCGTGAAGTTGAGCCTT
66 GGCACGATATCATTCGCCGCGAAGCTGAAATCGTGGATGGTCCCTTCGTCGTGAAGTTGAGCCTT
* *
810643 GAATTGGATATCCTTTGTCGTGAAGTTGAAATCCAACCTAAAGATGAATGTTGTCGGCATGATAT
131 GAATTGGAGATCCTTCGTCGTGAAGTTGAAATCCAACCTAAAGATGAATGTTGTCGGCATGATAT
810708 CCTTCGTTT
196 CCTTCGTTT
* * *
810717 TGAAGTTGAGTCTTGAA-TTGGATATCCTTCATCGTGAAGTTGAAATCTAA-GTATTG-TATGTT
1 TGAAGTTGA-TCTTGAAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAATGGA-TGCT-TCTT
* * * *
810779 GCTGGTGAACACGATATCCA-TCGCCGTGAAGTTGAAATTGTGGAT-GTCCCCTTCGTTGTGAAG
63 G-TGG-G--CACGATAT-CATTCGCCGCGAAGCTGAAATCGTGGATGGT-CCCTTCGTCGTGAAG
*
810842 TTGAGCC-TGAAATTTGAGATCCTTCGTCGTGAAGTTGAAATCCAA
122 TTGAGCCTTG-AATTGGAGATCCTTCGTCGTGAAGTTGAAATCCAA
810887 GTATTGTTTG
Statistics
Matches: 148, Mismatches: 12, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
203 3 0.02
204 47 0.32
205 9 0.06
206 1 0.01
207 4 0.03
208 82 0.55
209 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (204 bp):
TGAAGTTGATCTTGAAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAATGGATGCTTCTTGTG
GGCACGATATCATTCGCCGCGAAGCTGAAATCGTGGATGGTCCCTTCGTCGTGAAGTTGAGCCTT
GAATTGGAGATCCTTCGTCGTGAAGTTGAAATCCAACCTAAAGATGAATGTTGTCGGCATGATAT
CCTTCGTTT
Found at i:811779 original size:8 final size:8
Alignment explanation
Indices: 811766--811793 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
811756 CTTCTTTTTC
811766 TTTTCTCT
1 TTTTCTCT
811774 TTTTCTCT
1 TTTTCTCT
811782 TTTTCTCT
1 TTTTCTCT
811790 TTTT
1 TTTT
811794 TCCTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTCTCT
Found at i:811799 original size:8 final size:8
Alignment explanation
Indices: 811781--811819 Score: 60
Period size: 8 Copynumber: 4.6 Consensus size: 8
811771 TCTTTTTCTC
811781 TTTTTCTCT
1 TTTTTC-CT
811790 TTTTTCCTT
1 TTTTTCC-T
811799 TTTTTCCT
1 TTTTTCCT
811807 TTTTTCCT
1 TTTTTCCT
811815 TTTTT
1 TTTTT
811820 TTCAATTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 15 0.52
9 14 0.48
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTCCT
Found at i:811819 original size:17 final size:18
Alignment explanation
Indices: 811766--811820 Score: 80
Period size: 17 Copynumber: 3.2 Consensus size: 18
811756 CTTCTTTTTC
*
811766 TTTTCTC-TTTTT-CTCT
1 TTTTCTCTTTTTTCCTTT
811782 TTTTCTCTTTTTTCCTTT
1 TTTTCTCTTTTTTCCTTT
811800 TTTTC-CTTTTTTCCTTT
1 TTTTCTCTTTTTTCCTTT
811817 TTTT
1 TTTT
811821 TCAATTTAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
16 7 0.19
17 21 0.58
18 8 0.22
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTCTTTTTTCCTTT
Found at i:811820 original size:9 final size:9
Alignment explanation
Indices: 811789--811820 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
811779 TCTTTTTCTC
811789 TTTTTTCCT
1 TTTTTTCCT
811798 TTTTTTCC-
1 TTTTTTCCT
811806 TTTTTTCCT
1 TTTTTTCCT
811815 TTTTTT
1 TTTTTT
811821 TCAATTTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:811888 original size:21 final size:21
Alignment explanation
Indices: 811861--811910 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
811851 CCTAAACATT
811861 TTTTCTTTTTCTTTTTGT-TTT
1 TTTTCTTTTTCTTTTT-TCTTT
*
811882 TGTTC-TTTTCTTTTTTCTTT
1 TTTTCTTTTTCTTTTTTCTTT
811902 TTCTTCTTT
1 TT-TTCTTT
811911 GACTTAGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 14 0.58
21 7 0.29
22 2 0.08
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (21 bp):
TTTTCTTTTTCTTTTTTCTTT
Found at i:811890 original size:20 final size:21
Alignment explanation
Indices: 811867--811910 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
811857 CATTTTTTCT
* *
811867 TTTTC-TTTTTGTTTTTGTTC
1 TTTTCTTTTTTCTTTTTCTTC
811887 TTTTCTTTTTTCTTTTTCTTC
1 TTTTCTTTTTTCTTTTTCTTC
811908 TTT
1 TTT
811911 GACTTAGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.82
Consensus pattern (21 bp):
TTTTCTTTTTTCTTTTTCTTC
Found at i:820964 original size:5 final size:5
Alignment explanation
Indices: 820954--821044 Score: 63
Period size: 5 Copynumber: 19.6 Consensus size: 5
820944 GACAATAAGT
* ** *
820954 AAATA AAATA AACT- AAATA AAATA AAATA AACA-A AACGA AAAGA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AA-ATA AAATA AAATA AAATA
* *
821003 AAAGA AAAT- AAAT- AAAT- AAAT- AAAT- AAATG AAAT- AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
821045 ACATAGGAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
4 27 0.36
5 46 0.62
6 1 0.01
ACGTcount: A:0.76, C:0.03, G:0.04, T:0.16
Consensus pattern (5 bp):
AAATA
Found at i:820965 original size:9 final size:9
Alignment explanation
Indices: 820953--821044 Score: 73
Period size: 9 Copynumber: 10.0 Consensus size: 9
820943 AGACAATAAG
820953 TAAATAAAA
1 TAAATAAAA
820962 TAAACT-AAA
1 TAAA-TAAAA
820971 TAAAATAAAA
1 T-AAATAAAA
*
820981 TAAACAAAA
1 TAAATAAAA
* *
820990 CGAAAAGAAAA
1 --TAAATAAAA
*
821001 TAAAAGAAAA
1 T-AAATAAAA
821011 TAAAT-AAA
1 TAAATAAAA
821019 TAAAT-AAA
1 TAAATAAAA
*
821027 TAAATGAAA
1 TAAATAAAA
821036 TAAATAAAA
1 TAAATAAAA
821045 ACATAGGAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
8 16 0.23
9 30 0.43
10 17 0.24
11 7 0.10
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.17
Consensus pattern (9 bp):
TAAATAAAA
Found at i:820986 original size:59 final size:58
Alignment explanation
Indices: 820869--821043 Score: 171
Period size: 59 Copynumber: 3.0 Consensus size: 58
820859 AAGATAAAGA
* * * * *
820869 AAAGAATAC-AAATAAAGATAACAAGTAAATAACATAAACAAAATGAAAATAAAGAAAC
1 AAAGAATACGAAATAAAGAAAATAAGTAAATAAAATAAACTAAAT-AAAATAAATAAAC
*
820927 -AAGAATACGAGAATAAAGACAATAAGTAAATAAAATAAACTAAATAAAATAAAATAAAC
1 AAAGAATACGA-AATAAAGAAAATAAGTAAATAAAATAAACTAAATAAAAT-AAATAAAC
* * *
820986 AAAACGAA-AAGAAAATAAAAGAAAATAAATAAAT-AAATAAA-TAAATGAAATAAATAAA
1 -AAA-GAATACG-AAAT-AAAGAAAATAAGTAAATAAAATAAACTAAATAAAATAAATAAA
821044 AACATAGGAA
Statistics
Matches: 100, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
57 8 0.08
58 6 0.06
59 44 0.44
60 9 0.09
61 14 0.14
62 19 0.19
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.15
Consensus pattern (58 bp):
AAAGAATACGAAATAAAGAAAATAAGTAAATAAAATAAACTAAATAAAATAAATAAAC
Found at i:821017 original size:4 final size:4
Alignment explanation
Indices: 821008--821043 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
820998 AAATAAAAGA
821008 AAAT AAAT AAAT AAAT AAAT AAAT GAAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAA
821044 AACATAGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:821025 original size:12 final size:13
Alignment explanation
Indices: 820998--821043 Score: 67
Period size: 12 Copynumber: 3.5 Consensus size: 13
820988 AACGAAAAGA
*
820998 AAATAAAAGAAAAT
1 AAATAAATG-AAAT
821012 AAATAAAT-AAAT
1 AAATAAATGAAAT
821024 AAATAAATGAAAT
1 AAATAAATGAAAT
821037 AAATAAA
1 AAATAAA
821044 AACATAGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 12 0.40
13 11 0.37
14 7 0.23
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (13 bp):
AAATAAATGAAAT
Found at i:821132 original size:2 final size:2
Alignment explanation
Indices: 821125--821159 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
821115 AATAAAAATA
* *
821125 AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
821160 CAAAATAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:821190 original size:17 final size:17
Alignment explanation
Indices: 821129--821194 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
821119 AAAATAATAT
* *
821129 ATATATATATATACATAC
1 ATATATATATATA-AAAA
*
821147 ATATATATATATACAAA
1 ATATATATATATAAAAA
821164 ATA-ATGATATA-AAAGAA
1 ATATAT-ATATATAAA-AA
821181 ATATATATATATAA
1 ATATATATATATAA
821195 TAGAATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 4 0.10
17 19 0.47
18 17 0.43
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.35
Consensus pattern (17 bp):
ATATATATATATAAAAA
Found at i:822445 original size:2 final size:2
Alignment explanation
Indices: 822438--822472 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
822428 AATGAAATGA
822438 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
822473 GTTTGTAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:824474 original size:31 final size:26
Alignment explanation
Indices: 824408--824459 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
824398 AGGAAAAAAA
824408 GAGTATT-TATATATATATAGAATAG
1 GAGTATTATATATATATATAGAATAG
824433 GAGTATTTATATATATATATAGAATAG
1 GAGTA-TTATATATATATATAGAATAG
824460 TCTGGAGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 5 0.20
26 2 0.08
27 18 0.72
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.40
Consensus pattern (26 bp):
GAGTATTATATATATATATAGAATAG
Found at i:827250 original size:26 final size:25
Alignment explanation
Indices: 827187--827250 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
827177 TTATTATATT
* *
827187 TTTTATTTAAAA-ATATTAAAAATA
1 TTTTATTTAAAATAAATTAAAAAAA
* *
827211 TTTTAAATTGAAATAAATTAAAATAAA
1 TTTT-ATTTAAAATAAATTAAAA-AAA
827238 TTTTATTTAAAAT
1 TTTTATTTAAAAT
827251 TTTAGGCCAG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
24 4 0.13
25 6 0.19
26 15 0.48
27 6 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTTATTTAAAATAAATTAAAAAAA
Found at i:827699 original size:10 final size:10
Alignment explanation
Indices: 827644--827703 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
827634 TAATAATTTC
827644 TTATTTTTAA
1 TTATTTTTAA
*
827654 GTT-TTTTTTA
1 -TTATTTTTAA
*
827664 TTAATTTTGAA
1 TT-ATTTTTAA
*
827675 TATAATTTTTTA
1 T-T-ATTTTTAA
827687 TTATTTTTAA
1 TTATTTTTAA
827697 TTATTTT
1 TTATTTT
827704 GAAATTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
9 2 0.05
10 20 0.50
11 9 0.22
12 9 0.22
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (10 bp):
TTATTTTTAA
Found at i:827710 original size:18 final size:18
Alignment explanation
Indices: 827698--827739 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
827688 TATTTTTAAT
*
827698 TATTTTGAAATTTTAAAA
1 TATTTTAAAATTTTAAAA
827716 TATTTTAAAATTTTAATAA
1 TATTTTAAAATTTTAA-AA
827735 TATTT
1 TATTT
827740 AATTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TATTTTAAAATTTTAAAA
Found at i:827749 original size:20 final size:18
Alignment explanation
Indices: 827691--827741 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
827681 TTTTTATTAT
* *
827691 TTTTAATTAT-TTTGAAA
1 TTTTAATAATATTTAAAA
827708 TTTTAA-AATATTTTAAAA
1 TTTTAATAATA-TTTAAAA
827726 TTTTAATAATATTTAA
1 TTTTAATAATATTTAA
827742 TTAATTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 2 0.07
17 6 0.21
18 17 0.59
19 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTTAATAATATTTAAAA
Found at i:828137 original size:7 final size:7
Alignment explanation
Indices: 828125--828149 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
828115 GATTTTTTTT
828125 GTTTGGG
1 GTTTGGG
828132 GTTTGGG
1 GTTTGGG
828139 GTTTGGG
1 GTTTGGG
828146 GTTT
1 GTTT
828150 CATTTCTTTG
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (7 bp):
GTTTGGG
Found at i:840953 original size:19 final size:20
Alignment explanation
Indices: 840915--840954 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
840905 TATGTGCACA
*
840915 TTTTAAACTTTATTGCTTGC
1 TTTTAAACTTTATGGCTTGC
*
840935 TTTTAAA-TTTATGGGTTGC
1 TTTTAAACTTTATGGCTTGC
840954 T
1 T
840955 ACTATACGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.55
Consensus pattern (20 bp):
TTTTAAACTTTATGGCTTGC
Found at i:844665 original size:21 final size:21
Alignment explanation
Indices: 844641--844686 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
844631 GGAATGTATC
844641 GATCTCCTTCGAAAGCCGCTG
1 GATCTCCTTCGAAAGCCGCTG
844662 GATCTCCTTCGAAAGCCGCTG
1 GATCTCCTTCGAAAGCCGCTG
844683 GATC
1 GATC
844687 ATCTCAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.33, G:0.24, T:0.24
Consensus pattern (21 bp):
GATCTCCTTCGAAAGCCGCTG
Found at i:852704 original size:19 final size:20
Alignment explanation
Indices: 852656--852711 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
852646 TCCGTGTGAT
* *
852656 ATATTTAA-AAAAAAATTAA
1 ATATTTAATATAAAAATAAA
* *
852675 ATTTTTAATATTAAAATAAA
1 ATATTTAATATAAAAATAAA
852695 ATATTT-ATATAAAAATA
1 ATATTTAATATAAAAATA
852712 TAAAAAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATTTAATATAAAAATAAA
Found at i:856195 original size:2 final size:2
Alignment explanation
Indices: 856190--856238 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
856180 AAAAATTAGA
*
856190 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
856232 AG AT AT A
1 AT AT AT A
856239 GATCTATAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:856849 original size:14 final size:14
Alignment explanation
Indices: 856830--856864 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
856820 TATCACCCAT
856830 AATTCATATA-TTC
1 AATTCATATATTTC
856843 AAATTCATATATTTC
1 -AATTCATATATTTC
856858 AATTCAT
1 AATTCAT
856865 CTTTTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTCATATATTTC
Done.