Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010025.1 Corchorus capsularis cultivar CVL-1 contig10046, 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: 64902
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33


Found at i:420 original size:13 final size:13

Alignment explanation

Indices: 404--433 Score: 60 Period size: 13 Copynumber: 2.3 Consensus size: 13 394 AATACAATAC 404 AAAATAAATAAAA 1 AAAATAAATAAAA 417 AAAATAAATAAAA 1 AAAATAAATAAAA 430 AAAA 1 AAAA 434 GGGGGAAGTC Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 17 1.00 ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13 Consensus pattern (13 bp): AAAATAAATAAAA Found at i:3200 original size:35 final size:35 Alignment explanation

Indices: 3161--3500 Score: 424 Period size: 35 Copynumber: 9.7 Consensus size: 35 3151 AGTAATAAGT * * 3161 AACTTAATTCGGGGTAATTAAGTAATTCAATAATC 1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC 3196 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC 1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC * * 3231 AACTTAATTCAGGGTAATTAAATGATTCAGTAATC 1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC 3266 AACTTAATTCAGGGTAATTAAGTGAA-TCAGTAATAAGC 1 AACTTAATTCAGGGTAATTAAGT-AATTCAGTAAT---C 3304 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC 1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC * * * * * 3339 AACTTAATTCAGGGTTATTAAGTGAGTCAGCAGT- 1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC 3373 AACTTAATTCAGGGTAATTAAGTAATTCAGTAAGT- 1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAA-TC * * 3408 AACTTAATTCAGGGTAATTAAGTGAGTT-AATAATC 1 AACTTAATTCAGGGTAATTAAGT-AATTCAGTAATC * * 3443 AACTTAATTTAGGG-AAGTTAAGTAGTTC-GATAAAT- 1 AACTTAATTCAGGGTAA-TTAAGTAATTCAG-T-AATC * 3478 AACTTAATTCAGGGAAATTAAGT 1 AACTTAATTCAGGGTAATTAAGT 3501 TTAGTAAGAA Statistics Matches: 271, Mismatches: 21, Indels: 26 0.85 0.07 0.08 Matches are distributed among these distances: 34 35 0.13 35 193 0.71 36 9 0.03 37 2 0.01 38 32 0.12 ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33 Consensus pattern (35 bp): AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC Found at i:3205 original size:17 final size:17 Alignment explanation

Indices: 3183--3350 Score: 110 Period size: 19 Copynumber: 9.5 Consensus size: 17 3173 GGTAATTAAG * 3183 TAATTCAATAATCAACT 1 TAATTCAGTAATCAACT * * 3200 TAATTCAGGGTAATTAA-G 1 TAATTCA--GTAATCAACT 3218 TAATTCAGTAATCAACT 1 TAATTCAGTAATCAACT * * 3235 TAATTCAGGGTAATTAA-A 1 TAATTCA--GTAATCAACT * 3253 TGATTCAGTAATCAACT 1 TAATTCAGTAATCAACT * * 3270 TAATTCAGGGTAATTAAGT 1 TAATTCA--GTAATCAACT * 3289 GAA-TCAGTAATAAGCAACT 1 TAATTCAGTAAT---CAACT * * 3308 TAATTCAGGGTAATTAA-G 1 TAATTCA--GTAATCAACT 3326 TAATTCAGTAATCAACT 1 TAATTCAGTAATCAACT 3343 TAATTCAG 1 TAATTCAG 3351 GGTTATTAAG Statistics Matches: 115, Mismatches: 21, Indels: 30 0.69 0.13 0.18 Matches are distributed among these distances: 16 26 0.23 17 28 0.24 18 23 0.20 19 30 0.26 20 3 0.03 22 5 0.04 ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33 Consensus pattern (17 bp): TAATTCAGTAATCAACT Found at i:11238 original size:86 final size:84 Alignment explanation

Indices: 11072--11241 Score: 198 Period size: 86 Copynumber: 2.0 Consensus size: 84 11062 AATATTCAAG * * * ** 11072 TTCTTTCTCTTCCTCCATGTACTCGAATAATCCAATGGTATGCTTTAAACCCTAAACCCTAAATC 1 TTCTTTCTCTTCCTCCATGTACTCCAATAATCCAATGGTATGCCTCAAACCCTAAACCAGAAATC * 11137 ACATTCCTTAATTAAACAA 66 AAATTCCTTAATTAAACAA ** ** 11156 TTCTTTCTCTTCC-CCATGTACTCCAATTAATCCAATTTTTTATGCCTCAAACCCTAAACCAGGG 1 TTCTTTCTCTTCCTCCATGTACTCCAA-TAATCCAA--TGGTATGCCTCAAACCCTAAACCAGAA * * 11220 ATCAAATTTCTTATTTAAACAA 63 ATCAAATTCCTTAATTAAACAA 11242 AATAAGTCAC Statistics Matches: 71, Mismatches: 12, Indels: 4 0.82 0.14 0.05 Matches are distributed among these distances: 83 12 0.17 84 21 0.30 86 38 0.54 ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36 Consensus pattern (84 bp): TTCTTTCTCTTCCTCCATGTACTCCAATAATCCAATGGTATGCCTCAAACCCTAAACCAGAAATC AAATTCCTTAATTAAACAA Found at i:14087 original size:31 final size:32 Alignment explanation

Indices: 14016--14094 Score: 92 Period size: 31 Copynumber: 2.5 Consensus size: 32 14006 CAGAGGACCT 14016 AGATTAAATTAAGATTTCTTTTCAAATTCAAA 1 AGATTAAATTAAGATTTCTTTTCAAATTCAAA * *** 14048 AGGA--AAATTAATATTTCTTTTTTTATT-AAA 1 A-GATTAAATTAAGATTTCTTTTCAAATTCAAA 14078 AGATTAAATTAAGATTT 1 AGATTAAATTAAGATTT 14095 ATCACTATTA Statistics Matches: 39, Mismatches: 5, Indels: 7 0.76 0.10 0.14 Matches are distributed among these distances: 29 2 0.05 30 4 0.10 31 30 0.77 32 1 0.03 33 2 0.05 ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44 Consensus pattern (32 bp): AGATTAAATTAAGATTTCTTTTCAAATTCAAA Found at i:14684 original size:25 final size:25 Alignment explanation

Indices: 14633--14684 Score: 68 Period size: 25 Copynumber: 2.1 Consensus size: 25 14623 GAGAGGATTA * ** 14633 AAGGGTTTAGGGTTTATAAGTAATT 1 AAGGGTTTAGGGTTTAGAAACAATT * 14658 AAGGGTTTAGGGTTTAGAAACAGTT 1 AAGGGTTTAGGGTTTAGAAACAATT 14683 AA 1 AA 14685 TTAAAAGACT Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 25 23 1.00 ACGTcount: A:0.35, C:0.02, G:0.29, T:0.35 Consensus pattern (25 bp): AAGGGTTTAGGGTTTAGAAACAATT Found at i:17063 original size:102 final size:101 Alignment explanation

Indices: 16859--17163 Score: 398 Period size: 102 Copynumber: 3.0 Consensus size: 101 16849 CGGATTTTTC * * * * 16859 TGTAGTAATTTCCGTTGGAACAAATT-TTTTTGGCGCAAAATATTTGGGCTAGCGGGAATTCGAA 1 TGTAGTAATTTCCGTTGCAA-AAATTAATTTTGGCGCAAAATATTTAGG--AGCGGGAATTCAAA * * * 16923 TTTTAATTTGTCAAGAAAGTTAAAATCGTTGCAAAATTT 63 TTTTAATTTGTCACGAAAATTAAATTCGTTGCAAAATTT * 16962 TGTAGTAATTTCCGTTGCAAAAATTAATTTTGGCGCAAAATATTTAAGGAGCGGGAATTCAAAAT 1 TGTAGTAATTTCCGTTGCAAAAATTAATTTTGGCGCAAAATATTT-AGGAGCGGGAATTCAAATT * * 17027 TTAATTTGTTACGAAAACTAAATTCGTTGCAAAATTT 65 TTAATTTGTCACGAAAATTAAATTCGTTGCAAAATTT * * * 17064 CGTAATAATTT-CGTTGCAAAAATTAATTTTGGCGCAAAATTTTTGAGCGAGCGGGAATTCAAAT 1 TGTAGTAATTTCCGTTGCAAAAATTAATTTTGGCGCAAAATATTT-AG-GAGCGGGAATTCAAAT * * * 17128 TTTAATTTGCCACGAAAATTAATTTCGTGGCAAAAT 64 TTTAATTTGTCACGAAAATTAAATTCGTTGCAAAAT 17164 CTGTAGCAAA Statistics Matches: 179, Mismatches: 20, Indels: 7 0.87 0.10 0.03 Matches are distributed among these distances: 101 34 0.19 102 106 0.59 103 37 0.21 104 2 0.01 ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35 Consensus pattern (101 bp): TGTAGTAATTTCCGTTGCAAAAATTAATTTTGGCGCAAAATATTTAGGAGCGGGAATTCAAATTT TAATTTGTCACGAAAATTAAATTCGTTGCAAAATTT Found at i:19347 original size:31 final size:31 Alignment explanation

Indices: 19289--19347 Score: 82 Period size: 31 Copynumber: 1.9 Consensus size: 31 19279 CATGGCGTGG * *** 19289 CAACTCGCACGAGTGCTCCCTTGAGCACGTT 1 CAACTCGCACGAGTACTCCCCCAAGCACGTT 19320 CAACTCGCACGAGTACTCCCCCAAGCAC 1 CAACTCGCACGAGTACTCCCCCAAGCAC 19348 ATGACCAACG Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 31 24 1.00 ACGTcount: A:0.24, C:0.41, G:0.19, T:0.17 Consensus pattern (31 bp): CAACTCGCACGAGTACTCCCCCAAGCACGTT Found at i:19408 original size:28 final size:28 Alignment explanation

Indices: 19368--19422 Score: 110 Period size: 28 Copynumber: 2.0 Consensus size: 28 19358 AACCTCTATA 19368 AATACCTCTATATCTTCCATTCTCGAGT 1 AATACCTCTATATCTTCCATTCTCGAGT 19396 AATACCTCTATATCTTCCATTCTCGAG 1 AATACCTCTATATCTTCCATTCTCGAG 19423 GTATGATAAT Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 27 1.00 ACGTcount: A:0.25, C:0.29, G:0.07, T:0.38 Consensus pattern (28 bp): AATACCTCTATATCTTCCATTCTCGAGT Found at i:31213 original size:1 final size:1 Alignment explanation

Indices: 31207--31231 Score: 50 Period size: 1 Copynumber: 25.0 Consensus size: 1 31197 ATACTAAAGC 31207 AAAAAAAAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAA 31232 GAACTCTAAT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 24 1.00 ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:46357 original size:34 final size:37 Alignment explanation

Indices: 46305--46375 Score: 94 Period size: 35 Copynumber: 2.0 Consensus size: 37 46295 TTTTTATTTA 46305 ATATGTAAAATATTTTA-TTAAATA-AGAATATATAT 1 ATATGTAAAATATTTTATTTAAATATAGAATATATAT * * * 46340 ATATGTAAGA-ATTTTATTTTAATATATAATATATAT 1 ATATGTAAAATATTTTATTTAAATATAGAATATATAT 46376 TATTAATATG Statistics Matches: 31, Mismatches: 3, Indels: 3 0.84 0.08 0.08 Matches are distributed among these distances: 34 6 0.19 35 15 0.48 36 10 0.32 ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46 Consensus pattern (37 bp): ATATGTAAAATATTTTATTTAAATATAGAATATATAT Found at i:46383 original size:20 final size:19 Alignment explanation

Indices: 46354--46395 Score: 66 Period size: 20 Copynumber: 2.2 Consensus size: 19 46344 GTAAGAATTT 46354 TATTTTAATATATAATATA 1 TATTTTAATATATAATATA * 46373 TATTATTAATATGTAATATA 1 TATT-TTAATATATAATATA 46393 TAT 1 TAT 46396 ATATATATAT Statistics Matches: 21, Mismatches: 1, Indels: 1 0.91 0.04 0.04 Matches are distributed among these distances: 19 4 0.19 20 17 0.81 ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52 Consensus pattern (19 bp): TATTTTAATATATAATATA Found at i:46384 original size:13 final size:14 Alignment explanation

Indices: 46362--46406 Score: 51 Period size: 13 Copynumber: 3.4 Consensus size: 14 46352 TTTATTTTAA 46362 TATATAATATATAT 1 TATATAATATATAT * * 46376 TAT-TAATATGTAA 1 TATATAATATATAT 46389 TATAT-ATATATA- 1 TATATAATATATAT 46401 TATATA 1 TATATA 46407 TGTGTGTGTG Statistics Matches: 26, Mismatches: 3, Indels: 5 0.76 0.09 0.15 Matches are distributed among these distances: 12 5 0.19 13 17 0.65 14 4 0.15 ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49 Consensus pattern (14 bp): TATATAATATATAT Found at i:46426 original size:2 final size:2 Alignment explanation

Indices: 46361--46407 Score: 50 Period size: 2 Copynumber: 26.0 Consensus size: 2 46351 TTTTATTTTA * 46361 AT AT AT A- AT AT AT AT -T AT -T A- AT AT GT A- 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 46398 AT AT AT AT AT 1 AT AT AT AT AT 46408 GTGTGTGTGT Statistics Matches: 38, Mismatches: 2, Indels: 10 0.76 0.04 0.20 Matches are distributed among these distances: 1 5 0.13 2 33 0.87 ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49 Consensus pattern (2 bp): AT Found at i:48623 original size:109 final size:109 Alignment explanation

Indices: 48427--48723 Score: 461 Period size: 109 Copynumber: 2.7 Consensus size: 109 48417 ACTATTATAG * * * 48427 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT 1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTATTT 48492 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA 61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA 48541 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTATTTTATTT 1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTATTTTATTT 48606 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA 66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA * * 48650 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA 1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTATTTT- 48714 ATTTTTACCA 62 ATTTTTACCA 48724 TTTTAATTTA Statistics Matches: 174, Mismatches: 5, Indels: 10 0.92 0.03 0.05 Matches are distributed among these distances: 108 1 0.01 109 126 0.72 110 8 0.05 111 8 0.05 112 10 0.06 114 21 0.12 ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50 Consensus pattern (109 bp): TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTATTTTATTT TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA Found at i:51007 original size:16 final size:16 Alignment explanation

Indices: 50982--51013 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 50972 TTTCTGGTTC 50982 TGAATAAAAAATTCAG 1 TGAATAAAAAATTCAG * 50998 TGAATTAAAAATTCAG 1 TGAATAAAAAATTCAG 51014 AATTGGAGGC 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:0.53, C:0.06, G:0.12, T:0.28 Consensus pattern (16 bp): TGAATAAAAAATTCAG Found at i:55271 original size:25 final size:27 Alignment explanation

Indices: 55219--55271 Score: 74 Period size: 27 Copynumber: 2.0 Consensus size: 27 55209 TTACTCAACT ** 55219 AAAAACTCTATTTTTATTTTTCTGTAA 1 AAAAACTCTATTTTTATTTTAATGTAA 55246 AAAAACTCTATTTTTA-TTTAAT-TAA 1 AAAAACTCTATTTTTATTTTAATGTAA 55271 A 1 A 55272 TCTAATATCC Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 25 4 0.17 26 4 0.17 27 16 0.67 ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49 Consensus pattern (27 bp): AAAAACTCTATTTTTATTTTAATGTAA Found at i:56688 original size:2 final size:2 Alignment explanation

Indices: 56681--56706 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 56671 CGGCTGAAAG 56681 AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT 56707 GTGAACTAAA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:57619 original size:58 final size:58 Alignment explanation

Indices: 57524--57640 Score: 207 Period size: 58 Copynumber: 2.0 Consensus size: 58 57514 TTTAATCAGA * 57524 TATTTTACATTTAAGAAGCATTGAACTCTTTCTAGTTAACTAAATAGATAATGCTTGG 1 TATTTTACATTTAAGAAGCATTGAACTCTTTCCAGTTAACTAAATAGATAATGCTTGG * * 57582 TATTTTATATTTAAGAAGCATTGAACTCTTTCCAGTTAACTAAATAGATGATGCTTGG 1 TATTTTACATTTAAGAAGCATTGAACTCTTTCCAGTTAACTAAATAGATAATGCTTGG 57640 T 1 T 57641 GTATTGGATA Statistics Matches: 56, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 58 56 1.00 ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40 Consensus pattern (58 bp): TATTTTACATTTAAGAAGCATTGAACTCTTTCCAGTTAACTAAATAGATAATGCTTGG Found at i:59065 original size:14 final size:14 Alignment explanation

Indices: 59046--59074 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 59036 ATCATAGTCG 59046 TACACAAATGTTCA 1 TACACAAATGTTCA 59060 TACACAAATGTTCA 1 TACACAAATGTTCA 59074 T 1 T 59075 GGTTATACTA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31 Consensus pattern (14 bp): TACACAAATGTTCA Found at i:62294 original size:2 final size:2 Alignment explanation

Indices: 62287--62321 Score: 70 Period size: 2 Copynumber: 17.5 Consensus size: 2 62277 GATGTGAACC 62287 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 62322 TTAAAGAAAA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 33 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (2 bp): TA Found at i:63873 original size:29 final size:28 Alignment explanation

Indices: 63797--63879 Score: 87 Period size: 29 Copynumber: 2.8 Consensus size: 28 63787 ACGGCTAAAT 63797 GCTCAATTTGGTCCTAAACC-TTTCACG 1 GCTCAATTTGGTCCTAAACCTTTTCACG * * * 63824 GTCTACTCGATTTGGTTCTAAACCTTTTGACCG 1 G----CTCAATTTGGTCCTAAACCTTTTCA-CG 63857 GCTCAATTTGGTCCTAAACCTTT 1 GCTCAATTTGGTCCTAAACCTTT 63880 CAATTTCTTA Statistics Matches: 45, Mismatches: 5, Indels: 10 0.75 0.08 0.17 Matches are distributed among these distances: 27 1 0.02 29 20 0.44 31 17 0.38 32 4 0.09 33 3 0.07 ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37 Consensus pattern (28 bp): GCTCAATTTGGTCCTAAACCTTTTCACG Found at i:64859 original size:18 final size:15 Alignment explanation

Indices: 64822--64854 Score: 66 Period size: 15 Copynumber: 2.2 Consensus size: 15 64812 AAAGAGACAA 64822 ATAATCTTGATTATT 1 ATAATCTTGATTATT 64837 ATAATCTTGATTATT 1 ATAATCTTGATTATT 64852 ATA 1 ATA 64855 GTAATTCAAA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52 Consensus pattern (15 bp): ATAATCTTGATTATT Done.